ICSB 2022: THE 21ST INTERNATIONAL CONFERENCE ON SYSTEMS BIOLOGY (ICSB 2022)

This page contains an index consisting of author-provided keywords.

(
(Bio)Chemical Reaction Systems	Quasi-Entropy Closure: A Fast and Reliable Approach to Close the Moment Equations of the Chemical Master Equation
(bio)medical data	MeDaX - our vision for bioMedical Data eXploration
1
13C Metabolic Flux Analysis	Integrating 13C labeling and thermodynamic data for thermodynamically consistent Bayesian Metabolic Flux Analysis (T13C-MFA)
13CFLUX2	Integrating 13C labeling and thermodynamic data for thermodynamically consistent Bayesian Metabolic Flux Analysis (T13C-MFA)
16S rRNA gene	Effect of dispersal by inundation on soil bacterial communities depends on soil developmental stage
3
3D reconstruction	3D reconstruction and mathematical modelling of whole slide images to elucidate resistance to the targeted therapy in melanoma
A
ABC	FitMultiCell: Simulating and parameterizating computational models of multi-cellular processes
Abiotic stress	Metabolome-wise analysis of plants exposed to abiotic stress conditions to identify potential metabolites inducers of cross-tolerance to biotic stressors
ABM	Control of COVID-19 Outbreaks under Stochastic Community Dynamics, Bimodality, or Limited Vaccination
Absolute quantification	Development of a mass-spectrometry based clinical proteomics pipeline allows absolute quantification of pathway components and provides insights in pathway activation
Abstract interpretation	A generic framework to coarse-grain stochastic reaction networks by Abstract Interpretation
academia	From Academic Research to Pharmaceutical R&D and Back Become an ICSB - an Interdisciplinary Champion of Systems & Biology From bench to scientific publishing
acetylation	Decrypting drug actions and protein modifications by dose- and time-resolved proteomics
Acinetobacter baumannii	Manually curated genome-scale metabolic reconstructions of the multi-drug resistant Gram-negative pathogens A. baumannii and K. pneumoniae
ACLF	A graph-based approach to analyze signal transduction involving cytokines and the JAK-STAT pathway in hepatocytes using Petri nets
actin	On multistability and constitutive relations of cell motion on Fibronectin lanes
actin cytoskeleton	Directed cell migration by cortical actin and ER-PM contact site-mediated restriction of receptor signaling to the front
adaptive immune response	Modeling the adaptive immune response of a lymph node as Petri net
Adaptive Model Predictive Control (MPC)	Model Predictive Control of Cancer Cellular Dynamics: A New Strategy For Therapy Design
adipocytes	A comprehensive mechanistic model of adipocyte signaling with layers of confidence
adipogenesis	A dynamic HIF1α-PPARγ circuit controls a paradoxical adipocyte regulatory landscape
ADPKD	Improving Our Understanding of ADPKD: Computational Analysis of Metabolome Data
adverse drug reactions	Hypergraph for predicting adverse drug reactions
AEE	Web-based analysis of indirect calorimetric data arising from metabolic phenotyping systems
affinity	Decrypting drug actions and protein modifications by dose- and time-resolved proteomics
Ageing	A Systems Biology Approach To Study The Spatiotemporal Dynamics Of Senescent Cells In Wound Healing And Tissue Repair
Agent-based modeling	Agent-based modeling of spatiotemporal organization of bacteria in the human gut Computational analysis of cambium activity during plant radial growth Robust oscillations against spatial-temporal noise in intra-inter cellular kinetics
aging	Machine learning-based prediction of frailty in elderly people - Data from the Berlin Aging Study-II (BASE-II)
ai	Artificial Intelligence in Digital Pathology Research - Where do we come from and where do we go?
AI / ML	Pitching for AI / ML modeling
AI based risk mitigation strategy in chemotherapy induced anemia	Personalized Treatment of Anemia in Lung Carcinoma
akaike information criterion	Efficient brute-force model selection by iterative elimination of less useful model subspaces
Algae	In silico analysis of metabolic capabilities in a synthetic community of phycosphere bacteria
AlphaFold	Identification of a SARS-CoV-2 inhibitor by combining binary protein-protein interaction mapping, structure prediction and virtual screening
alternative splicing	Harnessing cancer heterogeneity for the systematic discovery of treatable cancer-driver exons with spotter Using multi-omics data and machine learning to unravel alternative splicing regulation
Alzheimer´s disease	Formatting Biological Big Data to Enable Systems Pharmacology
Alzheimer’s Disease	Impact of Amyloid-Beta Induced Disruption on Ca2+ Homeostasis in a Simple model of Neuronal Activity
Amino acid metabolism	Amino acid metabolism of Chinese Hamster Ovary cells: Comparison of growth and production phases in a fed-batch
Amyloid formation kinetics	A generic approach to decipher the mechanistic pathway of heterogeneous protein aggregation kinetics
Amyloid-Beta	Impact of Amyloid-Beta Induced Disruption on Ca2+ Homeostasis in a Simple model of Neuronal Activity
Analysis of genetic systems	SynBioSuite: Web-based modeling and analysis of biological systems
analysis of interactions	The insidious trappings of gene set enrichments
Analysis Workflows	Benchmarking of analysis strategies for data-independent acquisition proteomics data
ancient genomics	What we can learn from ancient genomics? Human history, ecosystem change, infectious disease, and disease susceptibility. (EXCEPTION - ZOOM)
animal behaviour	Quantitative Impacts of Bumble Bee Ecology on Foraging Behaviour: An Economic Model
ANN Simplification	Phylogeny and artificial neural networks
Annotation	Genome-wide analysis of genetic variants affecting metabolomic abundance in pigs divergent for feed efficiency
anoxia	Implementation of multiplexed single cell proteomics for the investigation of cellular heterogeneity in mammalian cell lines
anthranilic acid	The role of the kynurenine metabolism in chronic graft-versus-host-disease: Insights from computational modeling and patient data
Antibiotic discovery	Microbial compound bioactivity descriptors enable large-scale prediction of small molecule impact on microbiota species and pathogens
antibiotic resistance	Manually curated genome-scale metabolic reconstructions of the multi-drug resistant Gram-negative pathogens A. baumannii and K. pneumoniae
Antibiotic tolerance	A model of RNA repair to study antibiotic tolerance
Antibiotics	An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness
Antimicrobial resistance	Towards rational design of antibiotic combination therapies
Antiretrovirals	A framework for predicting the effect of multiple factors on HIV protection from heterosexual transmission through truvada-based pre-exposure prophylaxis (PrEP) in women
Antivenoms	Defining Design Rules for Next-Generation Snakebite Antivenoms
antiviral targets	New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
anxiety	Using graph theory and recurrent neural network models to investigate the anxiety circuit
Apoptosis	Modelling mutations in B-cell malignancies reveals how mutations synergise to contribute to aggressive disease. Cell-to-cell variability in JAK2/STAT5 pathway components and cytoplasmic volumes defines survival threshold in erythroid progenitor cells Boolean dynamic modeling of TNFR1 signaling predicts a nested feedback loop regulating the apoptotic response at single-cell level (EXCEPTION - ZOOM) Computational modeling of DLBCL predicts response to BH3-mimetics
aptamer sensors	A new platform for deep multiplexed metabolomics with a DNA barcode readout
Arabidopsis	Metabolome-wise analysis of plants exposed to abiotic stress conditions to identify potential metabolites inducers of cross-tolerance to biotic stressors Computational analysis of cambium activity during plant radial growth Topological properties accurately predict cell division events and organization of Arabidopsis thaliana’s shoot apical meristem
Arabidopsis thaliana	A modular concept for modeling of plant lipid metabolism
Artificial Intelligence	3D reconstruction and mathematical modelling of whole slide images to elucidate resistance to the targeted therapy in melanoma GEARS: Predicting transcriptional outcomes of novel multi-gene perturbations
Artificial Neural Networks	Phylogeny and artificial neural networks
ASD	Neural Circuits Underlying Autism Spectrum Disorders
Aspergillus fumigatus	Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection
assay	Decrypting drug actions and protein modifications by dose- and time-resolved proteomics
Assertions	Jinkō Knowledge: An integrated knowledge management tool prior to in silico multiscale model development
audience	Q&A
Augmented Kalman Smoother	Non-parametric model-based estimation of the effective reproduction number for SARS-CoV-2
Autism	Inference of a causal synaptic molecular network from multiplexed imaging and its perturbations in autism and schizophrenia
Autism spectrum disorders	Neural Circuits Underlying Autism Spectrum Disorders
autoencoder	A disease network-based deep learning approach for characterizing melanoma
Autoencoders	Biological-informed multi-modality integration of unmatched single-cell-omics datasets to provide a multi-dimensional view New data-driven gene representations using deep autoencoders at multiple omics to identify candidate disease genes and robust classifiers
Automated reconstruction pipeline	Computationally Modeling the Human Microbiome of the Respiratory Tract
Automation	Automated improvement of genome-scale models using a first-order logical model of metabolism
auxin	Cell Type view into tomato stem elongation in Shade avoidance response
aversive contextual processing	Using graph theory and recurrent neural network models to investigate the anxiety circuit
B
B-cells	Multi-scale modeling of B-cell fate decisions required for antibody generation
bacteria	Candida expansion in the human gut is associated with an ecological signature that supports growth under dysbiotic conditions Quantification of bacterial resource allocation in changining environments on the single-cell level Agent-based modeling of spatiotemporal organization of bacteria in the human gut How do single bacterial cells make decisions?
bacterial adaptation	Quantification of bacterial resource allocation in changining environments on the single-cell level
Bacterial growth law	An optimal RNA growth law and its relationship with genome organization in bacteria
bacterial growth laws	The limit on dry mass density is an organizing principle for cellular physiology
Bacterial growth physiology	Towards rational design of antibiotic combination therapies
bacteriome	Candida expansion in the human gut is associated with an ecological signature that supports growth under dysbiotic conditions
bacteriophage	Towards identification of new life cycle-associated regions in phage genomes using deep learning
Balanced cellular growth	The Economy and Control of Balanced Cellular Growth
barrier island	Effect of dispersal by inundation on soil bacterial communities depends on soil developmental stage
BASE-II	Machine learning-based prediction of frailty in elderly people - Data from the Berlin Aging Study-II (BASE-II)
Bayesian	Continuous-time models under uncertainty
Bayesian Flux Inference	Integrating 13C labeling and thermodynamic data for thermodynamically consistent Bayesian Metabolic Flux Analysis (T13C-MFA)
Bayesian inference	Scalable and flexible inference framework for stochastic dynamic single-cell models Latent variable models of fungal growth considering the data measurement process Posterior marginalization accelerates Bayesian inference for dynamical systems Unified Tumor Growth Mechanisms from Multimodel Inference and Dataset Integration Systematic inference identifies a major source of heterogeneity in non-Markovian cell signaling dynamics: the rate-limiting step number
bayesian information criterion	Efficient brute-force model selection by iterative elimination of less useful model subspaces
bayesian methods	Fast and scalable machine learning approach for dynamic metabolic engineering
Bayesian Network Inference	Inference of a causal synaptic molecular network from multiplexed imaging and its perturbations in autism and schizophrenia
Bayesian Topic modelling	Latent Dirichlet Allocation for Double Clustering (LDA-DC): Discovering patients phenotypes and cell populations within a single Bayesian framework
Benchmarking	Benchmarking of analysis strategies for data-independent acquisition proteomics data Benchmarking Phage-Host Prediction Tools using Real Metagenomics Data
BH3-Mimetics	Computational modeling of DLBCL predicts response to BH3-mimetics
Bifurcation	Initial source of heterogeneity in a model for cell fate decision in the early mammalian embryo
bifurcation analysis	Computational modeling of the Hes1 oscillator for the self-renewal of muscle stem cells Impact of Amyloid-Beta Induced Disruption on Ca2+ Homeostasis in a Simple model of Neuronal Activity
Bifurcation theory	Unraveling the role of network motifs to decipher the origin of robust decision-making in biological systems
bile acids	A physiology-based model of bile acid metabolism in mice
Bimodality	Control of COVID-19 Outbreaks under Stochastic Community Dynamics, Bimodality, or Limited Vaccination
Binary Data	A training strategy for hybrid models to break the curse of dimensionality: An application in mortality estimation for cohorts of COVID-19 patients
Bioactivity descriptors	Formatting Biological Big Data to Enable Systems Pharmacology
Biochemical network	Theory of biochemical information processing with transients
Biofuel production	In silico analysis of metabolic capabilities in a synthetic community of phycosphere bacteria
bioinformatics	Candida expansion in the human gut is associated with an ecological signature that supports growth under dysbiotic conditions GuaCAMOLE: fragment GC bias-aware abundance estimation from metagenomic data increases accuracy and comparability Systems Approaches to Deciphering Kinase Signaling and the Phosphoproteome: A Focus on Cancer, Inflammation, and DNA Damage
biological and biomedical systems	BioModels: an open repository of mathematical models of the biological and biomedical processes
Biological embeddings	Formatting Biological Big Data to Enable Systems Pharmacology
Biological Network	COVRECON: Combining Genome-scale Metabolic Network Reconstruction and Data-driven Inverse Modeling to Reveal Causal Biochemical Regulations
Biological networks	Mutually Antagonistic Protein Pairs of Cancer
biological oscillators	Combined multiple transcriptional repression mechanisms generate ultrasensitivity and oscillations
biologically informed deep learning	DeepCellRegMap: An interpretable deep learning framework for mapping genetic effects at cell subtype resolution using large-scale single-cell sequencing data
biomarker	COVIDpro: Database for mining protein dysregulation in patients with COVID-19 Dimethyl fumarate shifts CSF protein profile in relapsing remitting MS: a proteomics approach for biomarker discovery
biomarker and target gene	Exploring the “dark proteome” in hepatocellular carcinoma
Biomarker discovery	New data-driven gene representations using deep autoencoders at multiple omics to identify candidate disease genes and robust classifiers
biomarkers	Machine learning-based prediction of frailty in elderly people - Data from the Berlin Aging Study-II (BASE-II) Proteomics profiling revealed a combination of protein biomarkers for predicting disease trajectory of multiple sclerosis
biomass composition	Analyzing Optimal and Non-Optimal Resource Allocations in Whole-Cell Models
Biomedical imaging	Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide images
Biomedical research	Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide images
biomedical signals	Nonstationary Biomedical Signal Feature Extraction
BioModels	BioModels: an open repository of mathematical models of the biological and biomedical processes
BioNetGen	Virtual Cell Modeling and Simulation Software
Biophysics	Optimal prediction of a noisy signal
bioreactor	Implementation of multiplexed single cell proteomics for the investigation of cellular heterogeneity in mammalian cell lines
biosensor design	Fast and scalable machine learning approach for dynamic metabolic engineering
Biotic stress	Metabolome-wise analysis of plants exposed to abiotic stress conditions to identify potential metabolites inducers of cross-tolerance to biotic stressors
bistability	Information Processing by Homo-Oligomeric Proteins: From First Principles to Cardiac Disease
bitter taste receptor	Elucidating the role of TAS2R43 in HGT-1 cells – an integrated omics approach
BLAST	Temporal Proteomics and Transcriptomics Unravels the Host-Pathogen Interaction Network of Macrophages and Corynebacterium diphtheriae.
Blood Oxygen Level Dependent signal	Connecting the Neurovascular coupling and Electrophysiological signaling – a modeling approach
blood pressure	Insights on hemodynamic changes in hypertension and T2D through non-invasive cardiovascular modeling
BOLD-fMRI	An interconnected multi-level mechanistic model of the human brain
Bombus terrestris	Quantitative Impacts of Bumble Bee Ecology on Foraging Behaviour: An Economic Model
Bone metastases	Hybrid cellular automaton representation of the influence of mechanical stimulation on the development of bone metastases
Boolean dynamic modeling	Boolean dynamic modeling of TNFR1 signaling predicts a nested feedback loop regulating the apoptotic response at single-cell level (EXCEPTION - ZOOM)
Boolean modeling	A Boolean Modeling Framework for Drug Synergy Prediction in Breast Cancer
Boolean modelling	Cohort-specific Boolean models highlight different regulatory modules during disease progression
Brain Development	Investigating brain development using tissue and single-cell gene expression data
Brain Organogenesis	Investigating brain development using tissue and single-cell gene expression data
breast cancer	Mechanistic modeling of patient-specific response to hormone therapy and CDK inhibitors in breast cancer Disentangling Proliferation Signaling in Breast Cancer Subtypes based on an integrative modeling approach
breast cancer cell lines	A Boolean Modeling Framework for Drug Synergy Prediction in Breast Cancer
budding yeast	A Novel and Robust Molecular Switch Actuating the Quantitative Model of Eukaryotic Cell Cycle Control When cells decide to give up on repairing DNA damage
bumble bees	Quantitative Impacts of Bumble Bee Ecology on Foraging Behaviour: An Economic Model
C
C. albicans	Human host and pathogenic fungi: modeling and deciphering nested metabolic defense strategies
Ca2+	Impact of Amyloid-Beta Induced Disruption on Ca2+ Homeostasis in a Simple model of Neuronal Activity
Ca2+ signalling	Foundations for a theory of IP3 induced Ca2+ signalling - re-inventing a classic.
calcium cycling	Information Processing by Homo-Oligomeric Proteins: From First Principles to Cardiac Disease
calcium imaging	Using graph theory and recurrent neural network models to investigate the anxiety circuit
Cambium	Computational analysis of cambium activity during plant radial growth
cancer	Disentangling the internal composition of tumour activities through a hierarchical factorization model Identification of personalised driver gene panels in Melanoma Alterations in hepatocyte growth factor induced signal transduction in fatty liver disease foster cancer development Stochastic Model of Intra-Tumor Heterogeneity (SMITH) Multi-platform model training reduces bias in translational drug sensitivity models for cancer patients Modelling mutations in B-cell malignancies reveals how mutations synergise to contribute to aggressive disease. Decrypting drug actions and protein modifications by dose- and time-resolved proteomics Digital Twin models for the precision diagnosis and therapy of cancer Analyzing single-cell trajectories with augmented machine learning methods predicts cancer drugs response in live-cell microscopy assays Learning synthetic cell classifier designs with genetic algorithms and logic programming Expanding the disease network of Glioblastoma Multiforme via topological analysis Model ensembling as a tool to form interpretable multi-omic predictors of cancer pharmacosensitivity A Mechanistic model of EGFR and ERK signaling reveals how allostery and rewiring contribute to drug resistance Harnessing cancer heterogeneity for the systematic discovery of treatable cancer-driver exons with spotter Reconstructing a quantitative measure of disease dynamics for discovery and clinical benefit System Pathology of Cancer Modelling of Pharmacokinetics and Pharmacodynamics for first-in-man dose selection of targeted alpha therapy Mechanisms of Pro- and Anti-Oncogenic Signaling Downstream of Dual Tyrosine Protein Kinases
Cancer cell fate decision	Cancer cell fate decisions
cancer cell line	Elucidating the role of TAS2R43 in HGT-1 cells – an integrated omics approach
cancer cell-lines	Reconstruction of a catalogue of enzyme constrained models of metabolism using GECKO 2.0 and its applications to eukaryote metabolism
cancer genome analysis	Discovery of Latent Drivers from Double Mutations in Pan-Cancer Data
Cancer Metabolism	Cancer cells depend on environmental lipids for proliferation when electron acceptors are limited
cancer modelling	Flow Cytometry Combined with Systems Biology Modelling Reveals Heterogeneous “NFkB Fingerprints” in DLBCL
cancer patients	Machine learning-based sepsis risk prediction modeling using electronic health records of cancer patients
cancer signaling pathways	A Boolean Modeling Framework for Drug Synergy Prediction in Breast Cancer
Cancer Sub-typing	MultiOmics Network Embedding for SubType Analysis
cancer system biology	Exploring the “dark proteome” in hepatocellular carcinoma
cancer systems biology	Mutually Antagonistic Protein Pairs of Cancer Flow Cytometry Combined with Systems Biology Modelling Reveals Heterogeneous “NFkB Fingerprints” in DLBCL Cancer cells depend on environmental lipids for proliferation when electron acceptors are limited
Cancer treatment outcome	Cancer cell fate decisions
Cancerous genomic alterations	Patient-specific modeling of the TP53 pathway in endometrial carcinoma patients
candida	Candida expansion in the human gut is associated with an ecological signature that supports growth under dysbiotic conditions
candidiasis	Lactobacillus rhamnosus colonisation antagonizes Candida albicans by forcing metabolic adaptations that compromise pathogenicity
cardiac arrhythmias	Information Processing by Homo-Oligomeric Proteins: From First Principles to Cardiac Disease
cardiac fibroblast	Characterization of cardiac fibroblast remodeling dynamics after myocardial infarction
Cardiac Myocytes	Multiscale Modeling of Dyadic Structure-Function Relation in Ventricular Cardiac Myocytes
cardiac potentials	Nonstationary Biomedical Signal Feature Extraction
cardiac signal transduction	Information Processing by Homo-Oligomeric Proteins: From First Principles to Cardiac Disease
cardiomyocytes	Information Processing by Homo-Oligomeric Proteins: From First Principles to Cardiac Disease
cardiomyopathies	Predicting pathogenicity of TPM1 variants using multi-scale models
cardiovascular	Insights on hemodynamic changes in hypertension and T2D through non-invasive cardiovascular modeling
career	Thinking of a career in big pharma? Here is what you need to know. How to find good problems with collaborators! Become an ICSB - an Interdisciplinary Champion of Systems & Biology Q&A and Open Discussion
career decision	From Academic Research to Pharmaceutical R&D and Back
Causal Inference	Identification of causal genes at GWAS loci with pleiotropic gene regulatory effects using instrumental variable sets
causality	Deciphering transcriptional drivers of stem cell differentiation using causal inference
cell biology	PolarityJaM: An image analysis toolbox for cell polarity, junction and morphology quantification
Cell culture	Amino acid metabolism of Chinese Hamster Ovary cells: Comparison of growth and production phases in a fed-batch
Cell cycle	Modelling mutations in B-cell malignancies reveals how mutations synergise to contribute to aggressive disease. The transcriptome dynamics of single cells during the cell cycle A low-granularity model integrating metabolism, growth and cell cycle: towards multi-level whole cell modeling of budding yeast Improving our Mechanistic Understanding of Cell Cycle Dynamics
cell cycle duration variabilities	Transcriptional fluctuations govern the serum dependent cell cycle duration heterogeneities in Mammalian cells
cell cycle dynamics	A Novel and Robust Molecular Switch Actuating the Quantitative Model of Eukaryotic Cell Cycle Control
cell cycle modeling	Building a synthetic cell: search for the minimal requirements for robust, sustainable, and tunable cell cycles
Cell decision	Avoiding errant activation of mitophagy: dual factor authentication of the Pink1/Parkin circuit
Cell differentiation	Initial source of heterogeneity in a model for cell fate decision in the early mammalian embryo Investigating brain development using tissue and single-cell gene expression data
cell division	Topological properties accurately predict cell division events and organization of Arabidopsis thaliana’s shoot apical meristem
cell dynamics	Dynamic analysis framework to detect cell division and cell death in live-cell imaging, using signal processing and machine learning Unified Tumor Growth Mechanisms from Multimodel Inference and Dataset Integration
cell economy	Rhythmic protein degradation for cost-effective circadian oscillation
cell events detection	Dynamic analysis framework to detect cell division and cell death in live-cell imaging, using signal processing and machine learning
cell fate	Coordination of p53 and MAPK dynamics controls heterogeneous responses to genotoxic agents in single cells Inference and dynamical simulation of the gene-regulatory network in single cells
cell fate decision	Computational modeling for the elucidation of cell fate decisions in early development Cell-to-cell variability in JAK2/STAT5 pathway components and cytoplasmic volumes defines survival threshold in erythroid progenitor cells
Cell fate decisions	Unraveling the role of network motifs to decipher the origin of robust decision-making in biological systems Multi-scale modeling of B-cell fate decisions required for antibody generation
cell fate-decision	Data-driven modeling of cell-cell communication networks
cell growth	Dynamics of growth and ribosome level in batch cultures of S. cerevisiae A low-granularity model integrating metabolism, growth and cell cycle: towards multi-level whole cell modeling of budding yeast
Cell migration	Decoding cellular deformation from pseudo-simultaneously observed RhoGTPase activities Directed cell migration by cortical actin and ER-PM contact site-mediated restriction of receptor signaling to the front Cells use molecular working memory to navigate in changing chemoattractant fields
cell morphology	Development of a geometric blood vessel model to quantify morphological changes of endothelial cells in 3D during vascular remodeling
cell motility	On multistability and constitutive relations of cell motion on Fibronectin lanes
cell polarity	PolarityJaM: An image analysis toolbox for cell polarity, junction and morphology quantification
cell polarization	Directed cell migration by cortical actin and ER-PM contact site-mediated restriction of receptor signaling to the front Cells use molecular working memory to navigate in changing chemoattractant fields
Cell prediction	Optimal prediction of a noisy signal
Cell reprogramming	NETISCE: A dynamical systems and control theory approach to cell reprogramming
cell signaling	Dynamic analysis framework to detect cell division and cell death in live-cell imaging, using signal processing and machine learning
Cell type phenotyping	Tribus reveals the single-cell tumor architecture and effect of chemotherapy in ovarian cancer
Cell-based model	A Systems Biology Approach To Study The Spatiotemporal Dynamics Of Senescent Cells In Wound Healing And Tissue Repair
cell-cell communication	Analysis of Heterogeneity in the Tumor Microenvironment in the 4NQO HNSCC Mouse Model
cell-cell contacts	PolarityJaM: An image analysis toolbox for cell polarity, junction and morphology quantification
cell-cell network	Single cell analysis of a breast pre-cancerous state to explore critical tumor microenvironment interactions
Cell-to-cell heterogeneity	Systematic inference identifies a major source of heterogeneity in non-Markovian cell signaling dynamics: the rate-limiting step number
cell-to-cell variability	Fast parameter estimation for ODE-based models of heterogeneous cell populations
CellML	The COmputational MOdeling in BIology NEtwork in 2022: Evolving needs in standardisation and model reuse
Cellular Biochemical Networks	Cancer cells depend on environmental lipids for proliferation when electron acceptors are limited
cellular biophysics	On multistability and constitutive relations of cell motion on Fibronectin lanes
cellular compartmentalization	Building a synthetic cell: search for the minimal requirements for robust, sustainable, and tunable cell cycles
Cellular compensation	Precision machine-learning identifies a new paradigm for therapeutic discovery in Huntington’s disease: remodeling stress response to re-instate neuronal health and resilience.
cellular dynamics	FLOVELO - Pushing Boundaries of Cell Dynamics Inference with Maximum Flow Networks
Cellular economy	The Economy and Control of Balanced Cellular Growth
Cellular level Signal processing	Mathematical modelling of the regulatory mechanisms of keratinocyte differentiation for epidermal homeostasis
cellular memory	Real-time biochemical computations at criticality
cellular processes	Unified Tumor Growth Mechanisms from Multimodel Inference and Dataset Integration
cellular senescence	A Systems Biology Approach To Study The Spatiotemporal Dynamics Of Senescent Cells In Wound Healing And Tissue Repair Data-driven mathematical modeling of human skin aging and its application for natural compound screening
cellular transitions	Evaluation of methods to compute quasi-potential functions and their use as systems biology models
Cerebral Metabolism	An interconnected multi-level mechanistic model of the human brain
CFU-E cells	Cell-to-cell variability in JAK2/STAT5 pathway components and cytoplasmic volumes defines survival threshold in erythroid progenitor cells
checkpoints	When cells decide to give up on repairing DNA damage
Chemical biology	Improving drug-induced transcriptional descriptors and their biological connectivity
Chemical genetics	Dynamic metabolome profiling uncovers potential TOR signaling genes CRISPRi meets metabolomics: a platform for rapid functional annotation of compound libraries
Chemical Master Equation	Variance of filtered signals: characterization for linear reaction networks and application to neurotransmission dynamics Quasi-Entropy Closure: A Fast and Reliable Approach to Close the Moment Equations of the Chemical Master Equation
chemical reaction networks	Structural reduction of chemical reaction networks based on topology Linking models of biochemical dynamics via mass-constrained neural ordinary differential equations
Chemical systems biology	Gene-essentiality based drug signature helps repurposing non-cancer drugs
Chemical-genetics	Mapping Genetic and Chemical Genetic Interaction Networks in Yeast and Human Cells
Chemoattractants	Cells use molecular working memory to navigate in changing chemoattractant fields
Chemoinformatics	Microbial compound bioactivity descriptors enable large-scale prediction of small molecule impact on microbiota species and pathogens
Chinese Hamster Ovary cells	Amino acid metabolism of Chinese Hamster Ovary cells: Comparison of growth and production phases in a fed-batch
Chromatin	Investigating antagonistic chromatin remodeling by the Swi-Snf and Tup1-Cyc8 (Ssn6) complexes in yeast
chronic graft-versus-host disease	The role of the kynurenine metabolism in chronic graft-versus-host-disease: Insights from computational modeling and patient data
Chronotherapy	Dynamics of the circadian clock in models of cancer and its potential for treatment
CICR	Multiscale Modeling of Dyadic Structure-Function Relation in Ventricular Cardiac Myocytes
Circadian	Circadian and cell cycle control of terminal cell differentiation
Circadian clock	Dynamics of the circadian clock in models of cancer and its potential for treatment Rhythmic protein degradation for cost-effective circadian oscillation
Circadian rhythm	Spatially-Coordinated Collective Protein Behaviors Enable Robust Circadian Timekeeping
Circadian rhythms	Robust oscillations against spatial-temporal noise in intra-inter cellular kinetics
circuit topology	Avoiding errant activation of mitophagy: dual factor authentication of the Pink1/Parkin circuit
circulating markers	Multilevel approach characterizing the progression of fatty liver disease
Classical	Pitching for Classical modeling
classification	Learning synthetic cell classifier designs with genetic algorithms and logic programming
classification models	Topological properties accurately predict cell division events and organization of Arabidopsis thaliana’s shoot apical meristem
Clinical diagnosis	Reconstructing a quantitative measure of disease dynamics for discovery and clinical benefit
Clinical proteomics	Development of a mass-spectrometry based clinical proteomics pipeline allows absolute quantification of pathway components and provides insights in pathway activation
Clinical-Grade AI Algorithms	EMPAIA - Harmonizing Access to Clinical-Grade AI Algorithms in Pathology
Cloud-based application	SynBioSuite: Web-based modeling and analysis of biological systems
Clustering	Resolving Resolution Hindrances in Spatial Transcriptomics Dissecting the Developing Mouse Brain at Spatial Single-Cell Resolution Using PASTA-seq A robust clustering strategy for patient stratification in complex diseases
co-expression network	Co-expression analysis of transcriptome and proteome identifies LRR-VIII-1 kinase and MAPK-kinase (MEK1) regulatory modules associated with P-deficiency adaptation and P use efficiency in maize
co-expression networks	Cell type-specific gene co-expression modules define tumor heterogeneity in melanoma patients
Coarse-grain modelling	Towards rational design of antibiotic combination therapies
coarse-grained	Studying conformational transitions of selected proteins using UNRES coarse-grained replica exchange molecular dynamics simulations with Lorentzian restraints.
Coarse-graining	A generic framework to coarse-grain stochastic reaction networks by Abstract Interpretation
codon optimization	Tissue-specific codon usage: from systems to synthetic biology
codon usage	Tissue-specific codon usage: from systems to synthetic biology
collaboration	How to find good problems with collaborators!
collective protein behavior	Spatially-Coordinated Collective Protein Behaviors Enable Robust Circadian Timekeeping
Collective Variables	Path Integral Stochastic Optimal Control for Sampling Transition Paths
colorectal cancer	Modeling the tumor microenvironment in patient-derived organoid culture NETISCE: A dynamical systems and control theory approach to cell reprogramming Quantification of imaging biomarkers in the extracellular matrix of left and right sided colon cancer tissues
Combination Therapies	Towards rational design of antibiotic combination therapies Model Predictive Control of Cancer Cellular Dynamics: A New Strategy For Therapy Design
Combinatorial stress	Metabolome-wise analysis of plants exposed to abiotic stress conditions to identify potential metabolites inducers of cross-tolerance to biotic stressors
COMBINE	Virtual Cell Modeling and Simulation Software The COmputational MOdeling in BIology NEtwork in 2022: Evolving needs in standardisation and model reuse
COMBINE models	FAIR assessment of biosimulation models - a cross-community project
community effort	The COmputational MOdeling in BIology NEtwork in 2022: Evolving needs in standardisation and model reuse
community modelling	Composing and perturbing large-scale constraint-based metabolic models with COBREXA.jl
community recommendation	FAIR assessment of biosimulation models - a cross-community project
comorbidity	Integrative analysis on comorbid signatures in psychotic disorders using multi-rank non-negative matrix factorization based graph approach
comparative genomics	GO Term-based Comparative Functional Genomics in Plants
competition	Frequency preference in miRNA-mRNA interaction models: competition and cooperativity effects
Computational Approaches	From Plants to Plants and Beyond: How Modeling Strategies from the Engineering Field Could Benefit Systems Biology
computational biology	Modelling mutations in B-cell malignancies reveals how mutations synergise to contribute to aggressive disease. Advanced Modelling of Multicellular Systems in Morpheus Fast and scalable machine learning approach for dynamic metabolic engineering The E. coli Whole-Cell Modeling Project: Vision and Progress Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide images
Computational Lipidomics	LipiDetective: a Deep Learning Model for the Detection of Lipid Species in Mass Spectra
computational medicine	Extracting knowledge from multi-omics and clinical datasets using graph machine learning
Computational modelling	Defining Design Rules for Next-Generation Snakebite Antivenoms Timelapse of Single Cell Lipidomics BioModels: an open repository of mathematical models of the biological and biomedical processes
Computational modelling reproducibility	Bias and reproducibility in a Computational Neurobiology PhD’s journey
computational neuroscience	Using graph theory and recurrent neural network models to investigate the anxiety circuit
Computational Pathology	Computational Pathology of Kidney Disease Quantitative Spatial Profiling Reveals Tumor Microenvironment Heterogeneity and Prognostic Biomarkers Associated with Immune Population Architectures Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide images Rapid parallel model inference and on-the-fly tiling of digital pathology images
computational proteomics	Explainable Machine Learning in Mass Spectrometry-based Proteomics
Computer vision	Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide images
conditional random forest	Using multi-omics data and machine learning to unravel alternative splicing regulation
Cone photoreceptor mosaics	Universality of form: The case of retinal cone photoreceptor mosaics
Confidence Bands	Exact Confidence Regions for Non-Linear Models
Confidence Regions	Exact Confidence Regions for Non-Linear Models
Connectome	Neural Circuits Underlying Autism Spectrum Disorders
Consensus Modeling	Multi-platform model training reduces bias in translational drug sensitivity models for cancer patients
constraint-based metabolic control analysis	Interrogating the effect of enzyme kinetics on metabolism using differentiable constraint-based models
Constraint-based metabolic model	Amino Acid Impact on Protein Secretion in B. subtilis: an RBA Approach
constraint-based model	FROG Analysis - a community standard to foster reproducibility and curation of constraint-based models
constraint-based modeling	Manually curated genome-scale metabolic reconstructions of the multi-drug resistant Gram-negative pathogens A. baumannii and K. pneumoniae
Constraint-based modelling	Geometric programming to Solve Optimal Concentrations of Metabolites and Enzymes in Constraint-based modelling
constraint-based models	Composing and perturbing large-scale constraint-based metabolic models with COBREXA.jl
constraint-based reconstruction and analysis (COBRA)	The metabolic community model of Staphylococcus aureus and four abundant human nasal microbes
Convolutional neural network	Deep convolutional neural networks capture the relationship between genetic variation and gene expression in plants
Cooperativity	Frequency preference in miRNA-mRNA interaction models: competition and cooperativity effects A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation
copy number variants	Single cell pseudo-time inference based on copy number variants for identifying a tumor transition state
Copy number variation	Single cell analysis of colorectal cancers with familial adenomatous polyposis for revealing differential pre-malignant programs
Correlation	Dynamic single cell analysis of a MAPK signaling cascade and its impact on transcriptional output
correlation analysis	Multilevel approach characterizing the progression of fatty liver disease
Correlation metrics	Hierarchical gene function prediction using a novel topology-based threshold and comparing 6 correlation metrics. Study case: Rice
counter-defense	Human host and pathogenic fungi: modeling and deciphering nested metabolic defense strategies
COVID-19	Non-linear mixed effects modeling of the T cell response in individuals infected with SARS-CoV-2 Multi-dimensional immune correlates of early prediction of COVID-19 severe versus asymptomatic disease course New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells FAIR sharing of reproducible COVID-19 models of epidemic and pandemic forecast Preventing & limiting pandemics through vaccination: what have we learned from COVID-19 and MPX?
Covid-19 modeling	INSIDe: Integrative modeling of the spread of serious infectious diseases Control of COVID-19 Outbreaks under Stochastic Community Dynamics, Bimodality, or Limited Vaccination
covid19	A training strategy for hybrid models to break the curse of dimensionality: An application in mortality estimation for cohorts of COVID-19 patients COVIDpro: Database for mining protein dysregulation in patients with COVID-19
crispr	Building a Mind for Cancer
CRISPR interference	Mapping metabolic regulation in E. coli with a metabolism-wide CRISPRi library
Critical illness	An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness
critical transition	Towards a Computational Toolkit for Cell Fate Decision Detection
criticality	Dynamical basis of cellular sensing and responsiveness to spatial-temporal signals
Crops	Metabolome-wise analysis of plants exposed to abiotic stress conditions to identify potential metabolites inducers of cross-tolerance to biotic stressors
cross species analysis	Integrational approaches for cross-species analysis of lung pathologies at single-cell resolution.
cross-correlation	Variance of filtered signals: characterization for linear reaction networks and application to neurotransmission dynamics
Cross-inhibitory feedbacks	Cross-inhibitory feedbacks of nucleocytoplasmic transport give rise to divergent multicellular phenotype in ERBB2-activated breast epithelia
cross-reactivity	A multi-strain model of immunization against influenza A viruses after infection or vaccination
cross-species extrapolation	A physiology-based model of bile acid metabolism in mice
curation	FROG Analysis - a community standard to foster reproducibility and curation of constraint-based models
Curse of Dimensionality	A training strategy for hybrid models to break the curse of dimensionality: An application in mortality estimation for cohorts of COVID-19 patients
Cybergenetics	Model Predictive Control of Cancer Cellular Dynamics: A New Strategy For Therapy Design
CyTOF	Multi-dimensional immune correlates of early prediction of COVID-19 severe versus asymptomatic disease course
cytokine gradients	Spatio-temporal modeling reveals a layer of tunable control circuits for the distribution of cytokines in tissues.
cytokines	A graph-based approach to analyze signal transduction involving cytokines and the JAK-STAT pathway in hepatocytes using Petri nets
Cytoplasmic congestion	Robust oscillations against spatial-temporal noise in intra-inter cellular kinetics
cytoplasmic density	Building a synthetic cell: search for the minimal requirements for robust, sustainable, and tunable cell cycles
D
d3	Deep insight into SABIO-RK data via visualization
Dark proteome	Exploring the “dark proteome” in hepatocellular carcinoma
Data alignment	BlotIt - Optimal alignment of Western blot and qPCR experiments
data analysis tools	MeDaX - our vision for bioMedical Data eXploration
Data imputation	Multi-Omics Regulatory Network Inference in the Presence of Missing Data
data integration	INSIDe: Integrative modeling of the spread of serious infectious diseases Discovery of potential functional paths by integration of phospho-proteomics data in the PPI network using a RWR framework Integrational approaches for cross-species analysis of lung pathologies at single-cell resolution. Integrative analysis on comorbid signatures in psychotic disorders using multi-rank non-negative matrix factorization based graph approach Lipid metabolic reprogramming extends beyond histological tumor demarcations in human operable pancreatic cancer Molecular principles governing substrate specificity of human SUMO E3 Ligases Improving Our Understanding of ADPKD: Computational Analysis of Metabolome Data Leveraging the Molecular Signatures of Cancer for Dynamic Network Modeling Can we trust genome-wide metabolic models? A workflow for the creation of regulatory networks integrating miRNAs and lncRNAs associated with exposure to ionizing radiation using open source data and tools
Data leveraging	Precision machine-learning identifies a new paradigm for therapeutic discovery in Huntington’s disease: remodeling stress response to re-instate neuronal health and resilience.
Data missingness	Multi-Omics Regulatory Network Inference in the Presence of Missing Data
Data pre-processing	BlotIt - Optimal alignment of Western blot and qPCR experiments
data provenance	MeDaX - our vision for bioMedical Data eXploration
data quality	MeDaX - our vision for bioMedical Data eXploration
data visualization	BioSimulations: integrated models, model languages, model repositories, simulation experiments, simulation tools and data visualization
data-driven mathematical mechanistic modeling	Data-driven modeling of mitochondrial metabolism
Data-driven mathematical modeling	A generic approach to decipher the mechanistic pathway of heterogeneous protein aggregation kinetics
data-driven modeling	Hybrid mechanistic and deep learning modeling in systems biology Data-driven modeling of cell-cell communication networks
data-driven prediction	Discovery of Hidden Control Variables and modeling Non-Linear Dynamical Biological Systems
Data-Independent Acquisition	Benchmarking of analysis strategies for data-independent acquisition proteomics data
database	Deep insight into SABIO-RK data via visualization
De novo mutations	Neural Circuits Underlying Autism Spectrum Disorders
Decision-making	Multimodal perception links cellular state to decision making in single cells
decryptM	Decrypting drug actions and protein modifications by dose- and time-resolved proteomics
Deep artificial neural networks	New data-driven gene representations using deep autoencoders at multiple omics to identify candidate disease genes and robust classifiers
deep hidden physics	Continuous-time models under uncertainty
deep learning	Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction A deep learning-based approach for counting ovarian follicles Biological-informed multi-modality integration of unmatched single-cell-omics datasets to provide a multi-dimensional view LipiDetective: a Deep Learning Model for the Detection of Lipid Species in Mass Spectra Towards identification of new life cycle-associated regions in phage genomes using deep learning Deep learning a model of cytotoxic T cell activation in the tumor microenvironment GEARS: Predicting transcriptional outcomes of novel multi-gene perturbations Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide images Multi-Omics Visible Drug Activity prediction, interpreting the biological processes underlying drug sensitivity
degradation	Modelling how mRNA flows through subcellular compartments
degradation control	Rhythmic protein degradation for cost-effective circadian oscillation
delays	Inferring individual interactions in gene regulatory networks with delays from time-series experiments
deletions	Exploring the missing heritability in SPG7 heterozygous carriers with Whole Genome Sequencing
Desensitization and priming	Mechanistic insights into sensitization and desensitization of the Interferon α signal transduction pathway
design	Machine learning for hard biological problems
DFBA	PlantEd - a serious game about plant growth that aims to support metabolic modeling with citizen science
diabetes	Insights on hemodynamic changes in hypertension and T2D through non-invasive cardiovascular modeling
diet intervention	Resistant starch decreases intrahepatic triglycerides in NAFLD patients via the gut microbiome contribution to the branched-chain amino acids pool
differentiable metabolic model	Interrogating the effect of enzyme kinetics on metabolism using differentiable constraint-based models
differential co-expression	Inference of differential gene regulatory networks from gene expression data using boosted differential trees
differential equation model	The role of the kynurenine metabolism in chronic graft-versus-host-disease: Insights from computational modeling and patient data
differential equations	Fast and scalable machine learning approach for dynamic metabolic engineering
differential network	Inference of differential gene regulatory networks from gene expression data using boosted differential trees
differentiation	Computational modeling of the Hes1 oscillator for the self-renewal of muscle stem cells
Diffusion	DUNE-COPASI: Multi-Compartment Diffusion-Reaction solver for Cell Biology
digital	Artificial Intelligence in Digital Pathology Research - Where do we come from and where do we go?
digital pathology	3D reconstruction and mathematical modelling of whole slide images to elucidate resistance to the targeted therapy in melanoma
Digital twin	M4-health: digital twins that follow you throughout your health journey Digital twins and hybrid modelling for simulation of physiological variables and stroke risk Physiologically based pharmacokinetic (PBPK) models for metabolic phenotyping and evaluation of liver function
Digital Twins	From Plants to Plants and Beyond: How Modeling Strategies from the Engineering Field Could Benefit Systems Biology Digital Twin models for the precision diagnosis and therapy of cancer
Dimensionality Reduction	Resolving Resolution Hindrances in Spatial Transcriptomics
dimethyl fumarate	Dimethyl fumarate shifts CSF protein profile in relapsing remitting MS: a proteomics approach for biomarker discovery
diphosphate kinase	New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
discussion	Panel Discussion Q&A and Open Discussion
disease	Combining multi-omics and biological knowledge to understand signaling deregulation in disease Computational Pathology of Kidney Disease Bacterial therapy for pulmonary infectious diseases
Disease mechanisms	Lipid network and moiety analysis for revealing enzymatic dysregulation and mechanistic alterations from lipidomics data
Disease modules	MODalyseR—a novel software for inference of disease module hub regulators identified a putative multiple sclerosis regulator supported by independent eQTL data
disease network	A disease network-based deep learning approach for characterizing melanoma
Disease outcome prediction	Mathematical model of the immunopathological progression of tuberculosis
Disease targets	Precision machine-learning identifies a new paradigm for therapeutic discovery in Huntington’s disease: remodeling stress response to re-instate neuronal health and resilience.
Divalent metal transporter 1	Quantify the role of DMT1 endocytosis, IRPs activity, and FT iron sequestration in duodenal enterocyte iron regulation
Divergent phenotypes	Cross-inhibitory feedbacks of nucleocytoplasmic transport give rise to divergent multicellular phenotype in ERBB2-activated breast epithelia
DLBCL	Patient- and cell line-specific modeling of diffuse large B-cell lymphoma Computational Models of Heterogeneous Mutations in Diffuse Large B-cell Lymphoma.
DNA barcodes	A new platform for deep multiplexed metabolomics with a DNA barcode readout
DNA Damage	Coordination of p53 and MAPK dynamics controls heterogeneous responses to genotoxic agents in single cells Systems Approaches to Deciphering Kinase Signaling and the Phosphoproteome: A Focus on Cancer, Inflammation, and DNA Damage
DNA damage response	A workflow for the creation of regulatory networks integrating miRNAs and lncRNAs associated with exposure to ionizing radiation using open source data and tools
DNA methylation	The pharmaco-epigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity Using multi-omics data and machine learning to unravel alternative splicing regulation
dose-response	Decrypting drug actions and protein modifications by dose- and time-resolved proteomics
Double Clustering	Latent Dirichlet Allocation for Double Clustering (LDA-DC): Discovering patients phenotypes and cell populations within a single Bayesian framework
Double Pendulum	On data-driven learning of an effective energy landscape from trajectories of nonlinear dynamical biological systems
DREAM networks	Inferring individual interactions in gene regulatory networks with delays from time-series experiments
Driver mutation	Identification of personalised driver gene panels in Melanoma
drug	Decrypting drug actions and protein modifications by dose- and time-resolved proteomics
drug combinations	Comparative analysis of molecular fingerprints in prediction of drug combination effects
Drug discovery	CRISPRi meets metabolomics: a platform for rapid functional annotation of compound libraries DecryptM: decrypting drug actions and protein modification by dose- and time-resolved proteomics
Drug inhalation	A physiologically-structured population model for pharmacokinetics of orally inhaled drugs
Drug mechanism of action	DecryptM: decrypting drug actions and protein modification by dose- and time-resolved proteomics
drug perturbation	Network-based Stratification of Cancer Drugs
Drug repositioning	Improving drug-induced transcriptional descriptors and their biological connectivity Gene-essentiality based drug signature helps repurposing non-cancer drugs
drug resistance	Leveraging the Molecular Signatures of Cancer for Dynamic Network Modeling A novel drug response network analysis on supercomputers uncovered gastric cancer drug sensitivity mechanism
drug sensitivity	Multi-platform model training reduces bias in translational drug sensitivity models for cancer patients A Mechanistic model of EGFR and ERK signaling reveals how allostery and rewiring contribute to drug resistance
drug synergy	Comparative analysis of molecular fingerprints in prediction of drug combination effects
drug synergy prediction	A Boolean Modeling Framework for Drug Synergy Prediction in Breast Cancer
drug virtual screening	Multi-Omics Visible Drug Activity prediction, interpreting the biological processes underlying drug sensitivity
Drug-tolerant persisters	Analyzing single-cell trajectories with augmented machine learning methods predicts cancer drugs response in live-cell microscopy assays
drugcell	Building a Mind for Cancer
drugs	Multiple-omics based metabolic modelling reveals effects of drug-induced liver toxicity Decrypting drug actions and protein modifications by dose- and time-resolved proteomics Modelling of Pharmacokinetics and Pharmacodynamics for first-in-man dose selection of targeted alpha therapy
dual tyrosine kinases	Mechanisms of Pro- and Anti-Oncogenic Signaling Downstream of Dual Tyrosine Protein Kinases
dynamic conditions	Quantification of bacterial resource allocation in changining environments on the single-cell level
Dynamic Modeling	Seroepidemiology And Modeling Of SARS-CoV-2 In Ethiopia: Longitudinal Cohort Study Among Front-line Health-care Workers And Community
Dynamic modelling	Scalable and flexible inference framework for stochastic dynamic single-cell models
dynamic optimization	Human host and pathogenic fungi: modeling and deciphering nested metabolic defense strategies
dynamic systems theory	Towards a Computational Toolkit for Cell Fate Decision Detection
Dynamical ghost	Cells use molecular working memory to navigate in changing chemoattractant fields
dynamical modeling	More BANG for the buck: how to distribute measurements to optimize information gain for mathematical models Stress Knowledge Map: A knowledge resource for modeling of plant stress responses
dynamical systems	Macroecological Laws Naturally Arise from Complex Chaotic Dynamics of Gut Microbiota Fast parameter estimation for ODE-based models of heterogeneous cell populations Posterior marginalization accelerates Bayesian inference for dynamical systems Information Processing by Homo-Oligomeric Proteins: From First Principles to Cardiac Disease Discovery of Hidden Control Variables and modeling Non-Linear Dynamical Biological Systems NETISCE: A dynamical systems and control theory approach to cell reprogramming On data-driven learning of an effective energy landscape from trajectories of nonlinear dynamical biological systems Quantitative Impacts of Bumble Bee Ecology on Foraging Behaviour: An Economic Model Linking models of biochemical dynamics via mass-constrained neural ordinary differential equations
Dynamics	Coordination of p53 and MAPK dynamics controls heterogeneous responses to genotoxic agents in single cells A powerful modelling approach tailored to cellular signalling Dynamic fluctuations in a bacterial metabolic network
E
E. Coli	Towards rational design of antibiotic combination therapies Quantification of bacterial resource allocation in changining environments on the single-cell level Dynamic fluctuations in a bacterial metabolic network
E3 ligases	Analyzing human E3 ligome for efficient design of PROTACs
early Drosophila development	Mitotic Memory as Spontaneous Symmetry Breaking in the Cell
ecm	Morphometric analysis of macrophage populations in response to animal-derived extracellular matrices
Ecmtool	Characterizing all feasible metabolic conversions of individual cells and microbial communities with elementary conversion modes.
eco-systems	Molecular eco-systems biology of microbiomes for human and planetary health Tara Oceans: Eco-Systems Biology at Planetary Scale
economic modelling	Quantitative Impacts of Bumble Bee Ecology on Foraging Behaviour: An Economic Model
ecosystems	What we can learn from ancient genomics? Human history, ecosystem change, infectious disease, and disease susceptibility. (EXCEPTION - ZOOM)
Effective reproduction number	Non-parametric model-based estimation of the effective reproduction number for SARS-CoV-2
efficient computation	Rapid parallel model inference and on-the-fly tiling of digital pathology images
EGF	Periodic Forcing of the ERK pathway
EGFR	The abundance and cross-talk of EGFR and MET receptors in lung cancer cell lines is critical for the efficacy of tyrosine kinase inhibitors Improving Our Understanding of ADPKD: Computational Analysis of Metabolome Data Cells use molecular working memory to navigate in changing chemoattractant fields
elastic net	Using multi-omics data and machine learning to unravel alternative splicing regulation
electrograms	Nonstationary Biomedical Signal Feature Extraction
electronic health records	Machine learning-based sepsis risk prediction modeling using electronic health records of cancer patients
Elementary conversion modes (ECMs)	Characterizing all feasible metabolic conversions of individual cells and microbial communities with elementary conversion modes.
elementary growth modes	Analyzing Optimal and Non-Optimal Resource Allocations in Whole-Cell Models
Embedding	MultiOmics Network Embedding for SubType Analysis
Embryogenesis	Initial source of heterogeneity in a model for cell fate decision in the early mammalian embryo
Embryonic Stem Cells	Unraveling the role of network motifs to decipher the origin of robust decision-making in biological systems A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation
emergent properties	A low-granularity model integrating metabolism, growth and cell cycle: towards multi-level whole cell modeling of budding yeast
Encoding and decoding of biochemical information	Theory of biochemical information processing with transients
endocrinology	A mechanistic model for endocrine profiles of female puberty maturation
endothelial cells	Development of a geometric blood vessel model to quantify morphological changes of endothelial cells in 3D during vascular remodeling
Endothelial dysfunction	Molecular regulators of catecholamine response in human pulmonary microvascular endothelial cells
Energy Landscape	Construction and Decomposition of Cellular Energy Landscapes using Hopfield Neural Networks
enhancers	Exploring the missing heritability in SPG7 heterozygous carriers with Whole Genome Sequencing
ensemble learning	Inference of differential gene regulatory networks from gene expression data using boosted differential trees
ensembles	Advantages of Ensemble CNN’s in Computational Pathology.
Enterocytes	Quantify the role of DMT1 endocytosis, IRPs activity, and FT iron sequestration in duodenal enterocyte iron regulation
enteroviruses	Individualized modules and models of enterovirus infection in host cells
enzyme activity	Proteomes in 3D: Structural proteome snapshots as a new functional ‘omics readout
enzyme constrained flux balance analysis	Interrogating the effect of enzyme kinetics on metabolism using differentiable constraint-based models
enzyme constraints	Reconstruction of a catalogue of enzyme constrained models of metabolism using GECKO 2.0 and its applications to eukaryote metabolism
enzyme cost	Statistical estimation of enzyme kinetics and pathway cost predicts overflow metabolism
enzyme kinetics	Statistical estimation of enzyme kinetics and pathway cost predicts overflow metabolism Prediction of enzyme kinetic parameters and substrate scopes using artificial intelligence Metabolic Atlas - extending metabolic networks for model organisms with enzyme turnover predictions with GotEnzymes
Enzyme-Substrate networks	Molecular principles governing substrate specificity of human SUMO E3 Ligases
Enzyme-substrate pairs	Prediction of enzyme kinetic parameters and substrate scopes using artificial intelligence
Enzymes	The limit on dry mass density is an organizing principle for cellular physiology Prediction of enzyme kinetic parameters and substrate scopes using artificial intelligence
enzymes optimization	Optimization of functional efficiency in key tissues constrains protein rate of evolution in multicellular species
Epidemiology	INSIDe: Integrative modeling of the spread of serious infectious diseases FAIR sharing of reproducible COVID-19 models of epidemic and pandemic forecast Control of COVID-19 Outbreaks under Stochastic Community Dynamics, Bimodality, or Limited Vaccination
Epidemology	Seroepidemiology And Modeling Of SARS-CoV-2 In Ethiopia: Longitudinal Cohort Study Among Front-line Health-care Workers And Community
Epidermal growth factor receptor	Cells use molecular working memory to navigate in changing chemoattractant fields
epigenetic landscape	Evaluation of methods to compute quasi-potential functions and their use as systems biology models
epigenetic memory system	Model-based design of a synthetic oscillator based on an epigenetic memory system
epigenetics	The pharmaco-epigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity Using multi-omics data and machine learning to unravel alternative splicing regulation
epigenomics	The pharmaco-epigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity
Epithelial	XAI × Fugaku uncovered EMT mechanisms via cancer characteristic specific gene network analysis
Epo	Cell-to-cell variability in JAK2/STAT5 pathway components and cytoplasmic volumes defines survival threshold in erythroid progenitor cells
eQTLs	DeepCellRegMap: An interpretable deep learning framework for mapping genetic effects at cell subtype resolution using large-scale single-cell sequencing data
ERBB signaling	Disentangling Proliferation Signaling in Breast Cancer Subtypes based on an integrative modeling approach
ERK pathway	Periodic Forcing of the ERK pathway
Estimation of time-dependent parameters	Non-parametric model-based estimation of the effective reproduction number for SARS-CoV-2
Ethical Science	Bias and reproducibility in a Computational Neurobiology PhD’s journey
Ethiopia	Seroepidemiology And Modeling Of SARS-CoV-2 In Ethiopia: Longitudinal Cohort Study Among Front-line Health-care Workers And Community
evolution	Stochastic Model of Intra-Tumor Heterogeneity (SMITH)
evolutionary optima	When cells decide to give up on repairing DNA damage
evolutionary simulations	Being noisy in a crowd: differential selective pressure on gene expression noise in model gene regulatory networks
exon	Harnessing cancer heterogeneity for the systematic discovery of treatable cancer-driver exons with spotter
Experimental design	More BANG for the buck: how to distribute measurements to optimize information gain for mathematical models
explainability	Explainable Machine Learning in Mass Spectrometry-based Proteomics
Explainable AI	XAI × Fugaku uncovered EMT mechanisms via cancer characteristic specific gene network analysis Metabolic profile predictions using efficient and interpretable data descriptors generated with relational learning
Explainable AI (XAI)	Multi-Omics Visible Drug Activity prediction, interpreting the biological processes underlying drug sensitivity
export	Modelling how mRNA flows through subcellular compartments
expression noise	Being noisy in a crowd: differential selective pressure on gene expression noise in model gene regulatory networks
External Feedback Control	Model Predictive Control of Cancer Cellular Dynamics: A New Strategy For Therapy Design
Extrapolation	A training strategy for hybrid models to break the curse of dimensionality: An application in mortality estimation for cohorts of COVID-19 patients
F
FAIR	FAIR sharing of reproducible COVID-19 models of epidemic and pandemic forecast A Reproducibility Scorecard for Self-checking of Systems Biology Models
FAIR RDA indicators	FAIR assessment of biosimulation models - a cross-community project
far-red light	Cell Type view into tomato stem elongation in Shade avoidance response
fear	Using graph theory and recurrent neural network models to investigate the anxiety circuit
feature analysis	Nonstationary Biomedical Signal Feature Extraction
Federated Learning	Federated mathematical modelling and machine learning for a multi-national cohort of COVID-19 patients
Feedback	Dynamic fluctuations in a bacterial metabolic network
Feedback abundance	Mechanistic insights into sensitization and desensitization of the Interferon α signal transduction pathway
Feedback loops	Combinatorial effects of ligands are predicted by a genome-scale model of signaling based on artificial neural networks
Feedback Vertex Set	NETISCE: A dynamical systems and control theory approach to cell reprogramming
Ferritin	Quantify the role of DMT1 endocytosis, IRPs activity, and FT iron sequestration in duodenal enterocyte iron regulation
FGFR	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
fibroblast	Characterization of cardiac fibroblast remodeling dynamics after myocardial infarction
fibrosis	The role of the kynurenine metabolism in chronic graft-versus-host-disease: Insights from computational modeling and patient data
final	Final remarks
Finite Element Method	DUNE-COPASI: Multi-Compartment Diffusion-Reaction solver for Cell Biology
First-order Logic	Automated improvement of genome-scale models using a first-order logical model of metabolism
FISH	FISHing for Correlation
flint germplasm	Co-expression analysis of transcriptome and proteome identifies LRR-VIII-1 kinase and MAPK-kinase (MEK1) regulatory modules associated with P-deficiency adaptation and P use efficiency in maize
flow cytometry	Flow Cytometry Combined with Systems Biology Modelling Reveals Heterogeneous “NFkB Fingerprints” in DLBCL
fluid shear stress	Development of a geometric blood vessel model to quantify morphological changes of endothelial cells in 3D during vascular remodeling
Flux Balance Analysis	New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells Can we trust genome-wide metabolic models? Automated improvement of genome-scale models using a first-order logical model of metabolism
flux variability analysis	New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
folding	The workings and impact of AlphaFold
Follicles	A deep learning-based approach for counting ovarian follicles
forum	Introduction How to find good problems with collaborators!
frailty	Machine learning-based prediction of frailty in elderly people - Data from the Berlin Aging Study-II (BASE-II)
free-form learning	Continuous-time models under uncertainty
frequency domain	Periodic Forcing of the ERK pathway
frequency preference	Frequency preference in miRNA-mRNA interaction models: competition and cooperativity effects
FRET	Dynamic fluctuations in a bacterial metabolic network
functional analysis	The insidious trappings of gene set enrichments
Functional Genomics	GEARS: Predicting transcriptional outcomes of novel multi-gene perturbations Patterns of differentially essential genetic interactions characterize functional modules across cancer types GO Term-based Comparative Functional Genomics in Plants
Fungal growth	Latent variable models of fungal growth considering the data measurement process
fungal metabolism	Lactobacillus rhamnosus colonisation antagonizes Candida albicans by forcing metabolic adaptations that compromise pathogenicity
fungi	Candida expansion in the human gut is associated with an ecological signature that supports growth under dysbiotic conditions
G
Game	PlantEd - a serious game about plant growth that aims to support metabolic modeling with citizen science
Gamification	PlantEd - a serious game about plant growth that aims to support metabolic modeling with citizen science
Gastric cancer	A novel drug response network analysis on supercomputers uncovered gastric cancer drug sensitivity mechanism
Gene circuit	Construction and Decomposition of Cellular Energy Landscapes using Hopfield Neural Networks
Gene co-expression network	Hierarchical gene function prediction using a novel topology-based threshold and comparing 6 correlation metrics. Study case: Rice
Gene co-expression networks	Inferring Gene Networks Rewiring of Naive and Primed Human Embryonic Stem Cells During Cellular Reprogramming Using Single-Cell RNA-seq Data
gene dependency	Harnessing cancer heterogeneity for the systematic discovery of treatable cancer-driver exons with spotter
Gene expression	Neural Circuits Underlying Autism Spectrum Disorders Deep convolutional neural networks capture the relationship between genetic variation and gene expression in plants Improving drug-induced transcriptional descriptors and their biological connectivity Dissecting the principles underlying transcriptional heterogeneity An optimal RNA growth law and its relationship with genome organization in bacteria GEARS: Predicting transcriptional outcomes of novel multi-gene perturbations Dissecting the Developing Mouse Brain at Spatial Single-Cell Resolution Using PASTA-seq
Gene expression data analysis	Are metastatic triple negative breast cancers closer to their parental tumors or primary tumors of their destination tissues?
gene function	GO Term-based Comparative Functional Genomics in Plants
gene function annotation	The metabolic and proteomic landscape of genome-scale genetic perturbation
Gene function prediction	Hierarchical gene function prediction using a novel topology-based threshold and comparing 6 correlation metrics. Study case: Rice
gene network	XAI × Fugaku uncovered EMT mechanisms via cancer characteristic specific gene network analysis
Gene Networks	Inferring Gene Networks Rewiring of Naive and Primed Human Embryonic Stem Cells During Cellular Reprogramming Using Single-Cell RNA-seq Data
Gene position	An optimal RNA growth law and its relationship with genome organization in bacteria
Gene prioritization	Precision machine-learning identifies a new paradigm for therapeutic discovery in Huntington’s disease: remodeling stress response to re-instate neuronal health and resilience.
gene regulation	The pharmaco-epigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity Computational modeling for the elucidation of cell fate decisions in early development How do single bacterial cells make decisions? Reconstruction of regulatory networks driving patterned expression in the Drosophila embryo based on spatially resolved single-cell sequencing data​
Gene regulatory network	A quantum circuit model for inferring gene regulatory networks with application to single-cell transcriptomic data A novel drug response network analysis on supercomputers uncovered gastric cancer drug sensitivity mechanism
gene regulatory network inference	Inference and dynamical simulation of the gene-regulatory network in single cells
Gene Regulatory Networks	Initial source of heterogeneity in a model for cell fate decision in the early mammalian embryo Being noisy in a crowd: differential selective pressure on gene expression noise in model gene regulatory networks GEARS: Predicting transcriptional outcomes of novel multi-gene perturbations Deciphering transcriptional drivers of stem cell differentiation using causal inference A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation
gene set enrichment	The insidious trappings of gene set enrichments
genetic algorithms	Learning synthetic cell classifier designs with genetic algorithms and logic programming
genetic diseases	Predicting pathogenicity of TPM1 variants using multi-scale models
Genetic Essentiality	Patterns of differentially essential genetic interactions characterize functional modules across cancer types
Genetic Interaction	GEARS: Predicting transcriptional outcomes of novel multi-gene perturbations
Genetic Interactions	Patterns of differentially essential genetic interactions characterize functional modules across cancer types
Genetic Networks	Mapping Genetic and Chemical Genetic Interaction Networks in Yeast and Human Cells
Genetic screening	Gene-essentiality based drug signature helps repurposing non-cancer drugs
Genetic sub clones	Ionizing radiation triggers differential signaling dynamics of p-p53 and p-ERK1/2 in sensitive and resistant HNSCC cell clones
Genome organization	An optimal RNA growth law and its relationship with genome organization in bacteria
genome scale metabolic model	Metabolic Atlas - extending metabolic networks for model organisms with enzyme turnover predictions with GotEnzymes
genome-scale metabolic model	Manually curated genome-scale metabolic reconstructions of the multi-drug resistant Gram-negative pathogens A. baumannii and K. pneumoniae
genome-scale metabolic modeling	Lactobacillus rhamnosus colonisation antagonizes Candida albicans by forcing metabolic adaptations that compromise pathogenicity
genome-scale metabolic models	From genome sequencing to the first draft of the genome scale metabolic model of the symbiont fungus Leucoagaricus gongylophorus LEU18496. Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction Reconstruction of a catalogue of enzyme constrained models of metabolism using GECKO 2.0 and its applications to eukaryote metabolism FROG Analysis - a community standard to foster reproducibility and curation of constraint-based models
Genome-scale metabolic network	Predicting plasticity of rosette growth and metabolic fluxes in Arabidopsis thaliana
Genome-scale metabolic network reconstructions	The metabolic community model of Staphylococcus aureus and four abundant human nasal microbes
Genome-wide metabolic networks	Can we trust genome-wide metabolic models?
genomic annotation	From genome sequencing to the first draft of the genome scale metabolic model of the symbiont fungus Leucoagaricus gongylophorus LEU18496.
Genomic diversity	Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection
Genomic Engineering	GEARS: Predicting transcriptional outcomes of novel multi-gene perturbations
Genomic prediction	Predicting plasticity of rosette growth and metabolic fluxes in Arabidopsis thaliana
genomic variability	Disentangling the internal composition of tumour activities through a hierarchical factorization model
genomics	A disease network-based deep learning approach for characterizing melanoma
Genotype-by-environment interaction	Predicting plasticity of rosette growth and metabolic fluxes in Arabidopsis thaliana
Geometric programming	Geometric programming to Solve Optimal Concentrations of Metabolites and Enzymes in Constraint-based modelling
ghost of a saddle node bifurcation	Real-time biochemical computations at criticality
Gibbs energies	Integrating 13C labeling and thermodynamic data for thermodynamically consistent Bayesian Metabolic Flux Analysis (T13C-MFA)
Gillespie algorithm	Universally valid reduction of multiscale stochastic biochemical systems with simple non-elementary propensities
Glioblastoma	Vasculogenic mimicry induced by multicellular interaction in a 3D glioblastoma model-on-a-chip
globular domains	What are the functions of the short open reading frame-encoded peptides in monocytes? An interactomic approach.
Glycolysis	Analysis of the impact of MYCN on the energy metabolism in neuroblastoma using metabolomics data and mathematical modeling Dynamic fluctuations in a bacterial metabolic network
Glycolytic metabolon	Structural proteomics evidence for a predicted glycolytic metabolon
Glycolytic oscillations	Dynamic fluctuations in a bacterial metabolic network
GNU R	Web-based analysis of indirect calorimetric data arising from metabolic phenotyping systems
Good-Turing estimation	Accounting for low transcript sampling rates in scRNA-seq using the Good-Turing estimator
Gradient-based local optimization	Efficient parameter estimation for ODE models with semi-quantitative data using spline approximation
graph autoencoder	Extracting knowledge from multi-omics and clinical datasets using graph machine learning
graph databases	MeDaX - our vision for bioMedical Data eXploration
graph machine learning	Extracting knowledge from multi-omics and clinical datasets using graph machine learning
graph theory	Using graph theory and recurrent neural network models to investigate the anxiety circuit
graph-based cellular automata	Leveraging the Molecular Signatures of Cancer for Dynamic Network Modeling
Graphical models	A probabilistic graphical model for taxonomic profiling of viral and microbiome proteome samples
Growth control	The Economy and Control of Balanced Cellular Growth
growth laws	Quantification of bacterial resource allocation in changining environments on the single-cell level
GSEA	Temporal Proteomics and Transcriptomics Unravels the Host-Pathogen Interaction Network of Macrophages and Corynebacterium diphtheriae.
Gut Microbiota	Discovery of Robust and Highly Specific Microbiome Signatures for Non-Alcoholic Fatty Liver Disease Resistant starch decreases intrahepatic triglycerides in NAFLD patients via the gut microbiome contribution to the branched-chain amino acids pool An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness
GWAS	Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection Identification of causal genes at GWAS loci with pleiotropic gene regulatory effects using instrumental variable sets
H
Harmonisation	BioCypher: an ontology-driven framework for flexible harmonisation of large-scale biomedical knowledge graphs
Harmonizing Access	EMPAIA - Harmonizing Access to Clinical-Grade AI Algorithms in Pathology
HDAC	Decrypting drug actions and protein modifications by dose- and time-resolved proteomics
Head and neck cancer	Ionizing radiation triggers differential signaling dynamics of p-p53 and p-ERK1/2 in sensitive and resistant HNSCC cell clones
Head and Neck Squamous Cell Carcinoma	Analysis of Heterogeneity in the Tumor Microenvironment in the 4NQO HNSCC Mouse Model
health	Molecular eco-systems biology of microbiomes for human and planetary health
Health journey	M4-health: digital twins that follow you throughout your health journey
healthcareworkers	Seroepidemiology And Modeling Of SARS-CoV-2 In Ethiopia: Longitudinal Cohort Study Among Front-line Health-care Workers And Community
heart disease	Information Processing by Homo-Oligomeric Proteins: From First Principles to Cardiac Disease
HEK293	Implementation of multiplexed single cell proteomics for the investigation of cellular heterogeneity in mammalian cell lines
hemodynamics	Insights on hemodynamic changes in hypertension and T2D through non-invasive cardiovascular modeling
Hepatocellular Carcinoma	Alterations in hepatocyte growth factor induced signal transduction in fatty liver disease foster cancer development
Hes1	Computational modeling of the Hes1 oscillator for the self-renewal of muscle stem cells
heterogeneity	Cell-to-cell variability in JAK2/STAT5 pathway components and cytoplasmic volumes defines survival threshold in erythroid progenitor cells Quantification of bacterial resource allocation in changining environments on the single-cell level Gene expression heterogeneity arises from signaling networks Multi-scale modeling of B-cell fate decisions required for antibody generation
hidden variables	Discovery of Hidden Control Variables and modeling Non-Linear Dynamical Biological Systems
Hierarchical model composition	Computationally Modeling the Human Microbiome of the Respiratory Tract
Hierarchical multi-label classification	Hierarchical gene function prediction using a novel topology-based threshold and comparing 6 correlation metrics. Study case: Rice
Hierarchical optimization	Efficient parameter estimation for ODE models with semi-quantitative data using spline approximation
high resolution lung CT	The potential of PBI for high resolution lung imaging in patients
High-dimensional	Analysis of multivariate longitudinal metabolomics data from meal challenges using RM-ASCA+
high-resolution images	Rapid parallel model inference and on-the-fly tiling of digital pathology images
high-throughput drug screen	The pharmaco-epigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity
High-throughput screening	GEARS: Predicting transcriptional outcomes of novel multi-gene perturbations
Highly-multiplexed-imaging	Single-cell spatial atlas of high-grade serous ovarian cancer
histology	A deep learning-based approach for counting ovarian follicles
histone marks	Using multi-omics data and machine learning to unravel alternative splicing regulation
histopathological	Advantages of Ensemble CNN’s in Computational Pathology.
HIV	A framework for predicting the effect of multiple factors on HIV protection from heterosexual transmission through truvada-based pre-exposure prophylaxis (PrEP) in women Numerical approaches for the rapid analysis of prophylactic efficacy against HIV
Hofield Network	Construction and Decomposition of Cellular Energy Landscapes using Hopfield Neural Networks
Hog1	Dynamic single cell analysis of a MAPK signaling cascade and its impact on transcriptional output
Homeostasis	Reinforcement learning and Monte-Carlo tree search in gene expression enable the entire gene regulation in a cell
host-derived enforcement	New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
Host-Pathogen Interactions	Temporal Proteomics and Transcriptomics Unravels the Host-Pathogen Interaction Network of Macrophages and Corynebacterium diphtheriae.
host-virus interactions	New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
human	Molecular eco-systems biology of microbiomes for human and planetary health
Human Embryonic Stem Cell	Inferring Gene Networks Rewiring of Naive and Primed Human Embryonic Stem Cells During Cellular Reprogramming Using Single-Cell RNA-seq Data
human evolution	What we can learn from ancient genomics? Human history, ecosystem change, infectious disease, and disease susceptibility. (EXCEPTION - ZOOM)
human gut	Candida expansion in the human gut is associated with an ecological signature that supports growth under dysbiotic conditions
human health	Individualized modules and models of enterovirus infection in host cells
Human Monocytes	Mathematical modeling of cytokine interplay in human monocytes during LPS stimulation
Human respiratory tract	Computationally Modeling the Human Microbiome of the Respiratory Tract
Hurst law	Macroecological Laws Naturally Arise from Complex Chaotic Dynamics of Gut Microbiota
Hybrid	Pitching for hybrid/data-driven modeling
hybrid approach	How can we unleash the potentials of whole-cell modelling?
Hybrid cellular automaton	Hybrid cellular automaton representation of the influence of mechanical stimulation on the development of bone metastases
hybrid model	Digital twins and hybrid modelling for simulation of physiological variables and stroke risk
hybrid modeling	Hybrid mechanistic and deep learning modeling in systems biology A training strategy for hybrid models to break the curse of dimensionality: An application in mortality estimation for cohorts of COVID-19 patients Combining machine learning and ODE’s to build multiscale models for estimation of metabolic trajectories
Hybrid models	Hybrid models for cellular signaling: meso-scale pathway identification
hypergraph	Hypergraph for predicting adverse drug reactions
hypertension	Insights on hemodynamic changes in hypertension and T2D through non-invasive cardiovascular modeling
hypothesis exploration	Unified Tumor Growth Mechanisms from Multimodel Inference and Dataset Integration
hypoxia	Cancer cells depend on environmental lipids for proliferation when electron acceptors are limited Implementation of multiplexed single cell proteomics for the investigation of cellular heterogeneity in mammalian cell lines
hypoxic signaling	A dynamic HIF1α-PPARγ circuit controls a paradoxical adipocyte regulatory landscape
I
IFNα signaling pathway	Mechanistic insights into sensitization and desensitization of the Interferon α signal transduction pathway
IL-18	The role of the kynurenine metabolism in chronic graft-versus-host-disease: Insights from computational modeling and patient data
IL-2 and IL-7 receptor kinetics	Spatio-temporal modeling reveals a layer of tunable control circuits for the distribution of cytokines in tissues.
image analysis	Combining single-cell imaging techniques to probe surface-adhesion-dependent morphological features of disease state Dynamic analysis framework to detect cell division and cell death in live-cell imaging, using signal processing and machine learning PolarityJaM: An image analysis toolbox for cell polarity, junction and morphology quantification
ImageJ	Virtual Cell Modeling and Simulation Software
Imaging	Inference of a causal synaptic molecular network from multiplexed imaging and its perturbations in autism and schizophrenia The Systems of Size and Shape Control
Imaging biomarkers	Quantification of imaging biomarkers in the extracellular matrix of left and right sided colon cancer tissues
Imaging flow cytometry	Combining single-cell imaging techniques to probe surface-adhesion-dependent morphological features of disease state
immune response	Data-driven modeling of cell-cell communication networks
immunization	A multi-strain model of immunization against influenza A viruses after infection or vaccination
Immuno-oncology	Quantitative Spatial Profiling Reveals Tumor Microenvironment Heterogeneity and Prognostic Biomarkers Associated with Immune Population Architectures
Immunofluorescence	Improving our Mechanistic Understanding of Cell Cycle Dynamics
Immunology	Reconstructing a quantitative measure of disease dynamics for discovery and clinical benefit
immunotherapy	Deep learning a model of cytotoxic T cell activation in the tumor microenvironment
Impact Evaluation	Federated mathematical modelling and machine learning for a multi-national cohort of COVID-19 patients
In Silico Metabolites	Discovery of Robust and Highly Specific Microbiome Signatures for Non-Alcoholic Fatty Liver Disease
In silico models	Jinkō Knowledge: An integrated knowledge management tool prior to in silico multiscale model development
in silico RNA isoform screening	Harnessing cancer heterogeneity for the systematic discovery of treatable cancer-driver exons with spotter
In Silico Trials	Personalized medicine for Multiple Sclerosis treatment strategies at the individual and population level
indirect calorimetry	Web-based analysis of indirect calorimetric data arising from metabolic phenotyping systems
indoleamine-dioxygenase	The role of the kynurenine metabolism in chronic graft-versus-host-disease: Insights from computational modeling and patient data
Induced Pluripotent Stem Cells Reprogramming	NETISCE: A dynamical systems and control theory approach to cell reprogramming
Inductive Logic Programming	Metabolic profile predictions using efficient and interpretable data descriptors generated with relational learning
industry	Thinking of a career in big pharma? Here is what you need to know.
infection	Bacterial therapy for pulmonary infectious diseases
infectious disease modeling	Non-linear mixed effects modeling of the T cell response in individuals infected with SARS-CoV-2
Inflammation	Mathematical modeling of cytokine interplay in human monocytes during LPS stimulation Combinatorial effects of ligands are predicted by a genome-scale model of signaling based on artificial neural networks
Inflammatory Cytokines	Multi-dimensional immune correlates of early prediction of COVID-19 severe versus asymptomatic disease course
Influenza	A multi-strain model of immunization against influenza A viruses after infection or vaccination
Information bottleneck	Optimal prediction of a noisy signal
Information theory	Optimal prediction of a noisy signal Towards a Computational Toolkit for Cell Fate Decision Detection
inhibitor	Decrypting drug actions and protein modifications by dose- and time-resolved proteomics
Instrument Variables	Identification of causal genes at GWAS loci with pleiotropic gene regulatory effects using instrumental variable sets
integrated framework	BioSimulations: integrated models, model languages, model repositories, simulation experiments, simulation tools and data visualization
integration	Biological-informed multi-modality integration of unmatched single-cell-omics datasets to provide a multi-dimensional view
integrative analysis	Integrative analysis on comorbid signatures in psychotic disorders using multi-rank non-negative matrix factorization based graph approach
integrative modeling	Integrating cellular and physiologically-based pharmacokinetic (PBPK) modelling
Integrative systems biology	Molecular regulators of catecholamine response in human pulmonary microvascular endothelial cells
Intensive care unit	An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness
Interdisciplinary Modeling	From Plants to Plants and Beyond: How Modeling Strategies from the Engineering Field Could Benefit Systems Biology
interleukin	A graph-based approach to analyze signal transduction involving cytokines and the JAK-STAT pathway in hepatocytes using Petri nets
interpretability	Learning synthetic cell classifier designs with genetic algorithms and logic programming Towards identification of new life cycle-associated regions in phage genomes using deep learning
interpretable deep learning	DeepCellRegMap: An interpretable deep learning framework for mapping genetic effects at cell subtype resolution using large-scale single-cell sequencing data
intracellular localization	Modelling how mRNA flows through subcellular compartments
Intrinsic and extrinsic noise	Scalable and flexible inference framework for stochastic dynamic single-cell models
intrinsically disordered regions	Proteome-scale mapping of binding sites in the intrinsically disordered regions of human and viral proteomes
Invariant analysis	Manatee invariants entailing signal transduction pathways in Petri nets of signaling networks
Inverse Jacobian	COVRECON: Combining Genome-scale Metabolic Network Reconstruction and Data-driven Inverse Modeling to Reveal Causal Biochemical Regulations
Ion regulation	Non-monotonic Na+ dynamics in the malaria parasite Plasmodium falciparum
ionizing radiation	A workflow for the creation of regulatory networks integrating miRNAs and lncRNAs associated with exposure to ionizing radiation using open source data and tools
iron physiology	Regulation of Mammalian Iron Physiology Across Scales
Iron regulatory proteins	Quantify the role of DMT1 endocytosis, IRPs activity, and FT iron sequestration in duodenal enterocyte iron regulation
ITS2	An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness
J
JAK/STAT	Cell-to-cell variability in JAK2/STAT5 pathway components and cytoplasmic volumes defines survival threshold in erythroid progenitor cells Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
JAK/STAT pathway	A graph-based approach to analyze signal transduction involving cytokines and the JAK-STAT pathway in hepatocytes using Petri nets
JCVI-syn3.0 minimal cell	Characterizing all feasible metabolic conversions of individual cells and microbial communities with elementary conversion modes.
Jinkō Knowledge	Jinkō Knowledge: An integrated knowledge management tool prior to in silico multiscale model development
joint embeddings	Explainable Machine Learning in Mass Spectrometry-based Proteomics
Julia	Modelling mutations in B-cell malignancies reveals how mutations synergise to contribute to aggressive disease.
junction regulation	PolarityJaM: An image analysis toolbox for cell polarity, junction and morphology quantification
K
k-means clustering	Transcription start site signal profiling improves transposable element RNA expression analysis at locus-level
kcat	Prediction of enzyme kinetic parameters and substrate scopes using artificial intelligence
Kidney	Computational Pathology of Kidney Disease
kinase	Decrypting drug actions and protein modifications by dose- and time-resolved proteomics Inferring kinase activity of a tumor from phosphoproteomic data
Kinase inhibitors	DecryptM: decrypting drug actions and protein modification by dose- and time-resolved proteomics
kinases/phosphatases	Information Processing by Homo-Oligomeric Proteins: From First Principles to Cardiac Disease
kinetic constraints	Geometric programming to Solve Optimal Concentrations of Metabolites and Enzymes in Constraint-based modelling
kinetic modeling	A Novel and Robust Molecular Switch Actuating the Quantitative Model of Eukaryotic Cell Cycle Control Integrating cellular and physiologically-based pharmacokinetic (PBPK) modelling
kinetic parameter	Deep insight into SABIO-RK data via visualization
Klebsiella pneumoniae	Manually curated genome-scale metabolic reconstructions of the multi-drug resistant Gram-negative pathogens A. baumannii and K. pneumoniae
KM	Prediction of enzyme kinetic parameters and substrate scopes using artificial intelligence
Knowledge based models	Jinkō Knowledge: An integrated knowledge management tool prior to in silico multiscale model development
Knowledge graph	BioCypher: an ontology-driven framework for flexible harmonisation of large-scale biomedical knowledge graphs
Knowledge modeling	Jinkō Knowledge: An integrated knowledge management tool prior to in silico multiscale model development
kynurenic acid	The role of the kynurenine metabolism in chronic graft-versus-host-disease: Insights from computational modeling and patient data
kynurenine	The role of the kynurenine metabolism in chronic graft-versus-host-disease: Insights from computational modeling and patient data
L
L1 regularization	Uncovering cell-type specific mechanisms across an arbitrary number of cell-types by adapting the clustered LASSO to differential equation models
labeling data	Integrating 13C labeling and thermodynamic data for thermodynamically consistent Bayesian Metabolic Flux Analysis (T13C-MFA)
Lagrangian	On data-driven learning of an effective energy landscape from trajectories of nonlinear dynamical biological systems
large intestine	Agent-based modeling of spatiotemporal organization of bacteria in the human gut
large-scale	Decrypting drug actions and protein modifications by dose- and time-resolved proteomics A comprehensive mechanistic model of adipocyte signaling with layers of confidence
Large-scale data analysis	XAI × Fugaku uncovered EMT mechanisms via cancer characteristic specific gene network analysis
laser-capture microdissection	Lipid metabolic reprogramming extends beyond histological tumor demarcations in human operable pancreatic cancer
Lasso model	Multi-Omics Regulatory Network Inference in the Presence of Missing Data
Latent Dirichlet Allocation	Latent Dirichlet Allocation for Double Clustering (LDA-DC): Discovering patients phenotypes and cell populations within a single Bayesian framework
latent drivers	Discovery of Latent Drivers from Double Mutations in Pan-Cancer Data
LCMS	Decrypting drug actions and protein modifications by dose- and time-resolved proteomics
Leucoagaricus gongylophorus	From genome sequencing to the first draft of the genome scale metabolic model of the symbiont fungus Leucoagaricus gongylophorus LEU18496.
LGD LoF	Neural Circuits Underlying Autism Spectrum Disorders
Lineage plasticity	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
linear reaction networks	Variance of filtered signals: characterization for linear reaction networks and application to neurotransmission dynamics
Lipid Fragmentation	LipiDetective: a Deep Learning Model for the Detection of Lipid Species in Mass Spectra
Lipid metabolic networks	Lipid network and moiety analysis for revealing enzymatic dysregulation and mechanistic alterations from lipidomics data
Lipid metabolism	Lipid metabolic reprogramming extends beyond histological tumor demarcations in human operable pancreatic cancer Timelapse of Single Cell Lipidomics Cancer cells depend on environmental lipids for proliferation when electron acceptors are limited A modular concept for modeling of plant lipid metabolism
lipid transport	Lipid metabolic reprogramming extends beyond histological tumor demarcations in human operable pancreatic cancer
Lipidomics	Lipid network and moiety analysis for revealing enzymatic dysregulation and mechanistic alterations from lipidomics data Molecular regulators of catecholamine response in human pulmonary microvascular endothelial cells
live-cell	Dynamic analysis framework to detect cell division and cell death in live-cell imaging, using signal processing and machine learning
live-cell imaging	Transcriptional fluctuations govern the serum dependent cell cycle duration heterogeneities in Mammalian cells
Liver	Alterations in hepatocyte growth factor induced signal transduction in fatty liver disease foster cancer development Physiologically based pharmacokinetic (PBPK) models for metabolic phenotyping and evaluation of liver function
liver cancer	Exploring the “dark proteome” in hepatocellular carcinoma
liver cirrhosis	A systems pharmacology approach reveals robust drug metabolism and altered glucuronide disposition in a mouse model of liver cirrhosis
liver toxicity	Multiple-omics based metabolic modelling reveals effects of drug-induced liver toxicity
lncRNA	A workflow for the creation of regulatory networks integrating miRNAs and lncRNAs associated with exposure to ionizing radiation using open source data and tools
Logical modeling	Logical modeling of signaling mechanisms in early development A generic framework to coarse-grain stochastic reaction networks by Abstract Interpretation
Logical Modelling	Learning synthetic cell classifier designs with genetic algorithms and logic programming Automated improvement of genome-scale models using a first-order logical model of metabolism
Long Branch Attraction	Phylogeny and artificial neural networks
Long Branch Repulsion	Phylogeny and artificial neural networks
Longitudinal analysis	Reconstructing a quantitative measure of disease dynamics for discovery and clinical benefit
Longitudinal data analysis	Analysis of multivariate longitudinal metabolomics data from meal challenges using RM-ASCA+
longitudinal dynamics	Combining machine learning and ODE’s to build multiscale models for estimation of metabolic trajectories
longitudinal seroprevalence study	Seroepidemiology And Modeling Of SARS-CoV-2 In Ethiopia: Longitudinal Cohort Study Among Front-line Health-care Workers And Community
LRR-VIII-1 kinase	Co-expression analysis of transcriptome and proteome identifies LRR-VIII-1 kinase and MAPK-kinase (MEK1) regulatory modules associated with P-deficiency adaptation and P use efficiency in maize
lung	Bacterial therapy for pulmonary infectious diseases
lung biology	Integrational approaches for cross-species analysis of lung pathologies at single-cell resolution.
lung cancer	The abundance and cross-talk of EGFR and MET receptors in lung cancer cell lines is critical for the efficacy of tyrosine kinase inhibitors
lung disease detection	The potential of PBI for high resolution lung imaging in patients
lymph node	Modeling the adaptive immune response of a lymph node as Petri net
lymphoma	Computational Models of Heterogeneous Mutations in Diffuse Large B-cell Lymphoma. Modelling mutations in B-cell malignancies reveals how mutations synergise to contribute to aggressive disease. Flow Cytometry Combined with Systems Biology Modelling Reveals Heterogeneous “NFkB Fingerprints” in DLBCL Computational modeling of DLBCL predicts response to BH3-mimetics
M
machine learning	Precision machine-learning identifies a new paradigm for therapeutic discovery in Huntington’s disease: remodeling stress response to re-instate neuronal health and resilience. Discovery of Robust and Highly Specific Microbiome Signatures for Non-Alcoholic Fatty Liver Disease Machine learning-based prediction of frailty in elderly people - Data from the Berlin Aging Study-II (BASE-II) Machine learning based pathway deregulation analysis of metabolomics data for Parkinson's Disease Combining single-cell imaging techniques to probe surface-adhesion-dependent morphological features of disease state Phylogeny and artificial neural networks Dynamic analysis framework to detect cell division and cell death in live-cell imaging, using signal processing and machine learning Multi-platform model training reduces bias in translational drug sensitivity models for cancer patients Federated mathematical modelling and machine learning for a multi-national cohort of COVID-19 patients Accelerating whole-cell modelling with surrogate machine learning models A training strategy for hybrid models to break the curse of dimensionality: An application in mortality estimation for cohorts of COVID-19 patients Candida expansion in the human gut is associated with an ecological signature that supports growth under dysbiotic conditions Machine learning-based sepsis risk prediction modeling using electronic health records of cancer patients Analyzing single-cell trajectories with augmented machine learning methods predicts cancer drugs response in live-cell microscopy assays Inference and dynamical simulation of the gene-regulatory network in single cells Predicting metabolite accumulation in cancerous metabolic network Learning synthetic cell classifier designs with genetic algorithms and logic programming Digital twins and hybrid modelling for simulation of physiological variables and stroke risk Microbial compound bioactivity descriptors enable large-scale prediction of small molecule impact on microbiota species and pathogens Fast and scalable machine learning approach for dynamic metabolic engineering Prediction of enzyme kinetic parameters and substrate scopes using artificial intelligence GEARS: Predicting transcriptional outcomes of novel multi-gene perturbations Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide images Metabolic profile predictions using efficient and interpretable data descriptors generated with relational learning Comparative analysis of molecular fingerprints in prediction of drug combination effects Identification of a SARS-CoV-2 inhibitor by combining binary protein-protein interaction mapping, structure prediction and virtual screening Linking models of biochemical dynamics via mass-constrained neural ordinary differential equations New data-driven gene representations using deep autoencoders at multiple omics to identify candidate disease genes and robust classifiers Automated improvement of genome-scale models using a first-order logical model of metabolism
Machine learning for health	Latent Dirichlet Allocation for Double Clustering (LDA-DC): Discovering patients phenotypes and cell populations within a single Bayesian framework
Machine Learning Methods	NETISCE: A dynamical systems and control theory approach to cell reprogramming
machine-learning	Model ensembling as a tool to form interpretable multi-omic predictors of cancer pharmacosensitivity
Macrophage polarization	Combinatorial effects of ligands are predicted by a genome-scale model of signaling based on artificial neural networks
maize	Co-expression analysis of transcriptome and proteome identifies LRR-VIII-1 kinase and MAPK-kinase (MEK1) regulatory modules associated with P-deficiency adaptation and P use efficiency in maize
Malaria	Non-monotonic Na+ dynamics in the malaria parasite Plasmodium falciparum
Manatee invariant	Manatee invariants entailing signal transduction pathways in Petri nets of signaling networks
MAPK	Dynamic single cell analysis of a MAPK signaling cascade and its impact on transcriptional output
MAPK-kinase	Co-expression analysis of transcriptome and proteome identifies LRR-VIII-1 kinase and MAPK-kinase (MEK1) regulatory modules associated with P-deficiency adaptation and P use efficiency in maize
Mass spectrometry	Development of a mass-spectrometry based clinical proteomics pipeline allows absolute quantification of pathway components and provides insights in pathway activation Benchmarking of analysis strategies for data-independent acquisition proteomics data Targeted Proteomics-Driven Computational Modeling of the Mouse Macrophage Toll-like Receptor Signaling Pathway DecryptM: decrypting drug actions and protein modification by dose- and time-resolved proteomics
mass spectrometry proteomics	Lipid metabolic reprogramming extends beyond histological tumor demarcations in human operable pancreatic cancer
mathematical and computational modelling	Transcriptional fluctuations govern the serum dependent cell cycle duration heterogeneities in Mammalian cells
mathematical ecology	Macroecological Laws Naturally Arise from Complex Chaotic Dynamics of Gut Microbiota
mathematical model	The role of the kynurenine metabolism in chronic graft-versus-host-disease: Insights from computational modeling and patient data A model of RNA repair to study antibiotic tolerance Data-driven mathematical modeling of human skin aging and its application for natural compound screening
Mathematical model of immune system	Mathematical model of the immunopathological progression of tuberculosis
mathematical modeling	Mathematical modeling of cytokine interplay in human monocytes during LPS stimulation Quantify the role of DMT1 endocytosis, IRPs activity, and FT iron sequestration in duodenal enterocyte iron regulation Cell-to-cell variability in JAK2/STAT5 pathway components and cytoplasmic volumes defines survival threshold in erythroid progenitor cells A Mechanistic model of EGFR and ERK signaling reveals how allostery and rewiring contribute to drug resistance Disentangling Proliferation Signaling in Breast Cancer Subtypes based on an integrative modeling approach Spatially-Coordinated Collective Protein Behaviors Enable Robust Circadian Timekeeping Avoiding errant activation of mitophagy: dual factor authentication of the Pink1/Parkin circuit
Mathematical modeling of cancer	Patient-specific modeling of the TP53 pathway in endometrial carcinoma patients
Mathematical modelling	Initial source of heterogeneity in a model for cell fate decision in the early mammalian embryo Deciphering dysregulation in Erythroleukemia to design intervention strategies Modelling mutations in B-cell malignancies reveals how mutations synergise to contribute to aggressive disease. Uncovering cell-type specific mechanisms across an arbitrary number of cell-types by adapting the clustered LASSO to differential equation models A framework for predicting the effect of multiple factors on HIV protection from heterosexual transmission through truvada-based pre-exposure prophylaxis (PrEP) in women Computational modeling for the elucidation of cell fate decisions in early development On the relation between input and output distributions of scRNA-seq experiments Numerical approaches for the rapid analysis of prophylactic efficacy against HIV The transcriptome dynamics of single cells during the cell cycle
mathematical models	BioModels: an open repository of mathematical models of the biological and biomedical processes
mathematicaloncology	Computational Models of Heterogeneous Mutations in Diffuse Large B-cell Lymphoma.
matrix factorization	Disentangling the internal composition of tumour activities through a hierarchical factorization model
MDA-MB-231 cells	On multistability and constitutive relations of cell motion on Fibronectin lanes
Meal challenge	Analysis of multivariate longitudinal metabolomics data from meal challenges using RM-ASCA+
Measurement process	Latent variable models of fungal growth considering the data measurement process
mechanism inference	Unified Tumor Growth Mechanisms from Multimodel Inference and Dataset Integration
mechanism of action	Harnessing cancer heterogeneity for the systematic discovery of treatable cancer-driver exons with spotter
Mechanistic	M4-health: digital twins that follow you throughout your health journey A comprehensive mechanistic model of adipocyte signaling with layers of confidence
mechanistic model	The role of the kynurenine metabolism in chronic graft-versus-host-disease: Insights from computational modeling and patient data
Mechanistic model of cell differentiation	Mathematical modelling of the regulatory mechanisms of keratinocyte differentiation for epidermal homeostasis
mechanistic modeling	Mechanistic modeling of patient-specific response to hormone therapy and CDK inhibitors in breast cancer A multi-strain model of immunization against influenza A viruses after infection or vaccination A Mechanistic model of EGFR and ERK signaling reveals how allostery and rewiring contribute to drug resistance
mechanistic modelling	A mechanistic model for endocrine profiles of female puberty maturation Towards rational design of antibiotic combination therapies Digital twins and hybrid modelling for simulation of physiological variables and stroke risk An interconnected multi-level mechanistic model of the human brain
Mechanistic Models	Building the knowledge base to understand cellular signal transduction in different inflammatory phenotypes The Mixed Meal Model; quantifying metabolic resilience in overweight and obesity
Mechanoregulation	Hybrid cellular automaton representation of the influence of mechanical stimulation on the development of bone metastases
Media design	Amino Acid Impact on Protein Secretion in B. subtilis: an RBA Approach
Meiotic maturation	Stochasticity of Meiotic Entry in Xenopus Oocytes
melanoma	3D reconstruction and mathematical modelling of whole slide images to elucidate resistance to the targeted therapy in melanoma A disease network-based deep learning approach for characterizing melanoma
membrane receptor abundance	The abundance and cross-talk of EGFR and MET receptors in lung cancer cell lines is critical for the efficacy of tyrosine kinase inhibitors
Mendelian Randomization	Identification of causal genes at GWAS loci with pleiotropic gene regulatory effects using instrumental variable sets
MET	The abundance and cross-talk of EGFR and MET receptors in lung cancer cell lines is critical for the efficacy of tyrosine kinase inhibitors
Meta-Analysis	Discovery of Robust and Highly Specific Microbiome Signatures for Non-Alcoholic Fatty Liver Disease
metabolic engineering	Reconstruction of a catalogue of enzyme constrained models of metabolism using GECKO 2.0 and its applications to eukaryote metabolism Fast and scalable machine learning approach for dynamic metabolic engineering
Metabolic flexibility	Analysis of multivariate longitudinal metabolomics data from meal challenges using RM-ASCA+
Metabolic flux	Predicting plasticity of rosette growth and metabolic fluxes in Arabidopsis thaliana
Metabolic Flux Analysis	Simulation Based Metabolic Flux Inference Amino acid metabolism of Chinese Hamster Ovary cells: Comparison of growth and production phases in a fed-batch
metabolic model	Predicting metabolite accumulation in cancerous metabolic network
metabolic modeling	New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells Human host and pathogenic fungi: modeling and deciphering nested metabolic defense strategies
Metabolic modeling framework	A modular concept for modeling of plant lipid metabolism
Metabolic Modelling	Multiple-omics based metabolic modelling reveals effects of drug-induced liver toxicity Metabolic profile predictions using efficient and interpretable data descriptors generated with relational learning Automated improvement of genome-scale models using a first-order logical model of metabolism
Metabolic module	A modular concept for modeling of plant lipid metabolism
Metabolic network analysis	Are metastatic triple negative breast cancers closer to their parental tumors or primary tumors of their destination tissues?
Metabolic network reconstruction	A modular concept for modeling of plant lipid metabolism
Metabolic networks	Mapping metabolic regulation in E. coli with a metabolism-wide CRISPRi library Manually curated genome-scale metabolic reconstructions of the multi-drug resistant Gram-negative pathogens A. baumannii and K. pneumoniae
metabolic pathways	Structural reduction of chemical reaction networks based on topology
metabolic phenotyping	Web-based analysis of indirect calorimetric data arising from metabolic phenotyping systems Physiologically based pharmacokinetic (PBPK) models for metabolic phenotyping and evaluation of liver function
Metabolic resilience	The Mixed Meal Model; quantifying metabolic resilience in overweight and obesity
metabolism	The role of the kynurenine metabolism in chronic graft-versus-host-disease: Insights from computational modeling and patient data The limit on dry mass density is an organizing principle for cellular physiology Dynamic fluctuations in a bacterial metabolic network The metabolic and proteomic landscape of genome-scale genetic perturbation Combining machine learning and ODE’s to build multiscale models for estimation of metabolic trajectories A low-granularity model integrating metabolism, growth and cell cycle: towards multi-level whole cell modeling of budding yeast Composing and perturbing large-scale constraint-based metabolic models with COBREXA.jl
Metabolite GWAS	Genome-wide analysis of genetic variants affecting metabolomic abundance in pigs divergent for feed efficiency
Metabolomics	Machine learning based pathway deregulation analysis of metabolomics data for Parkinson's Disease Analysis of the impact of MYCN on the energy metabolism in neuroblastoma using metabolomics data and mathematical modeling COVRECON: Combining Genome-scale Metabolic Network Reconstruction and Data-driven Inverse Modeling to Reveal Causal Biochemical Regulations Improving Our Understanding of ADPKD: Computational Analysis of Metabolome Data An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness Mapping metabolic regulation in E. coli with a metabolism-wide CRISPRi library Dynamic metabolome profiling uncovers potential TOR signaling genes CRISPRi meets metabolomics: a platform for rapid functional annotation of compound libraries Metabolic profile predictions using efficient and interpretable data descriptors generated with relational learning Molecular regulators of catecholamine response in human pulmonary microvascular endothelial cells Analysis of multivariate longitudinal metabolomics data from meal challenges using RM-ASCA+
Metagenomics	Discovery of Robust and Highly Specific Microbiome Signatures for Non-Alcoholic Fatty Liver Disease Candida expansion in the human gut is associated with an ecological signature that supports growth under dysbiotic conditions An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness GuaCAMOLE: fragment GC bias-aware abundance estimation from metagenomic data increases accuracy and comparability Benchmarking Phage-Host Prediction Tools using Real Metagenomics Data
Metastable states	Cells use molecular working memory to navigate in changing chemoattractant fields
Metastasis	Are metastatic triple negative breast cancers closer to their parental tumors or primary tumors of their destination tissues?
metaviromics	Towards identification of new life cycle-associated regions in phage genomes using deep learning
Method of Moments	Quasi-Entropy Closure: A Fast and Reliable Approach to Close the Moment Equations of the Chemical Master Equation
Methylation	New data-driven gene representations using deep autoencoders at multiple omics to identify candidate disease genes and robust classifiers
Metric learning	Analyzing human E3 ligome for efficient design of PROTACs
Michaelis constant	Prediction of enzyme kinetic parameters and substrate scopes using artificial intelligence
Microbial communities	Characterizing all feasible metabolic conversions of individual cells and microbial communities with elementary conversion modes.
Microbial interactions	In silico analysis of metabolic capabilities in a synthetic community of phycosphere bacteria
Microbial Pathogens	Microbial compound bioactivity descriptors enable large-scale prediction of small molecule impact on microbiota species and pathogens
microbial physiology	Quantification of bacterial resource allocation in changining environments on the single-cell level
microbiology	The E. coli Whole-Cell Modeling Project: Vision and Progress
microbiome	GuaCAMOLE: fragment GC bias-aware abundance estimation from metagenomic data increases accuracy and comparability Computationally Modeling the Human Microbiome of the Respiratory Tract Microbial compound bioactivity descriptors enable large-scale prediction of small molecule impact on microbiota species and pathogens Agent-based modeling of spatiotemporal organization of bacteria in the human gut
microbiomes	Molecular eco-systems biology of microbiomes for human and planetary health
microbiota	Macroecological Laws Naturally Arise from Complex Chaotic Dynamics of Gut Microbiota
microfluidics	Quantification of bacterial resource allocation in changining environments on the single-cell level
microplate reader	Dynamics of growth and ribosome level in batch cultures of S. cerevisiae
Microscopy	Combining single-cell imaging techniques to probe surface-adhesion-dependent morphological features of disease state
minimal genome design	Accelerating whole-cell modelling with surrogate machine learning models
miRNA	A workflow for the creation of regulatory networks integrating miRNAs and lncRNAs associated with exposure to ionizing radiation using open source data and tools
miRNA regulation	Frequency preference in miRNA-mRNA interaction models: competition and cooperativity effects
miRNA-mRNA interaction models	Frequency preference in miRNA-mRNA interaction models: competition and cooperativity effects
mitochondrial metabolism	Data-driven modeling of mitochondrial metabolism
mitophagy	Avoiding errant activation of mitophagy: dual factor authentication of the Pink1/Parkin circuit
mitotic memory	Mitotic Memory as Spontaneous Symmetry Breaking in the Cell
ML	Machine learning for hard biological problems
mode of action	Decrypting drug actions and protein modifications by dose- and time-resolved proteomics
model	Modeling the adaptive immune response of a lymph node as Petri net
model calibration	Moving Horizon Estimation for Patient-Specific Optimal Control of Blood Glucose in Intensive Care Units
model calibration and validation	Regulation of Mammalian Iron Physiology Across Scales
model formats	BioSimulations: integrated models, model languages, model repositories, simulation experiments, simulation tools and data visualization
model integration	Regulation of Mammalian Iron Physiology Across Scales
model reduction	From System Biology to Pharmacology: Identifying what is important Discovery of Hidden Control Variables and modeling Non-Linear Dynamical Biological Systems
model reproducibility	FAIR assessment of biosimulation models - a cross-community project
model reuse	The COmputational MOdeling in BIology NEtwork in 2022: Evolving needs in standardisation and model reuse
Model selection	Mechanistic insights into sensitization and desensitization of the Interferon α signal transduction pathway Efficient brute-force model selection by iterative elimination of less useful model subspaces
Model Simulation	Computationally Modeling the Human Microbiome of the Respiratory Tract
model-based design	Model-based design of a synthetic oscillator based on an epigenetic memory system
Modeling	PlantEd - a serious game about plant growth that aims to support metabolic modeling with citizen science Virtual Cell Modeling and Simulation Software Alterations in hepatocyte growth factor induced signal transduction in fatty liver disease foster cancer development From Plants to Plants and Beyond: How Modeling Strategies from the Engineering Field Could Benefit Systems Biology Deep insight into SABIO-RK data via visualization Integrating 13C labeling and thermodynamic data for thermodynamically consistent Bayesian Metabolic Flux Analysis (T13C-MFA) The metabolic community model of Staphylococcus aureus and four abundant human nasal microbes Dynamic fluctuations in a bacterial metabolic network Pitching for Classical modeling Pitching for AI / ML modeling Pitching for hybrid/data-driven modeling Panel Discussion Become an ICSB - an Interdisciplinary Champion of Systems & Biology
Modeling of genetic systems	SynBioSuite: Web-based modeling and analysis of biological systems
Modeling via splines	Efficient parameter estimation for ODE models with semi-quantitative data using spline approximation
modelling	FitMultiCell: Simulating and parameterizating computational models of multi-cellular processes Delivering Virtual Reality and Gaming Technologies to the Field of Systems Biology Stochastic Model of Intra-Tumor Heterogeneity (SMITH) Advanced Modelling of Multicellular Systems in Morpheus Impact of Amyloid-Beta Induced Disruption on Ca2+ Homeostasis in a Simple model of Neuronal Activity A powerful modelling approach tailored to cellular signalling Combining multi-omics and biological knowledge to understand signaling deregulation in disease Dynamic single cell analysis of a MAPK signaling cascade and its impact on transcriptional output
modelling concepts	Foundations for a theory of IP3 induced Ca2+ signalling - re-inventing a classic.
Modelling disease dynamics	Mathematical model of the immunopathological progression of tuberculosis
modelling experiments	On the relation between input and output distributions of scRNA-seq experiments
Molecular circuits	Mutually Antagonistic Protein Pairs of Cancer
molecular clock	Optimization of functional efficiency in key tissues constrains protein rate of evolution in multicellular species
molecular fingerprints	Comparative analysis of molecular fingerprints in prediction of drug combination effects
Molecular mechanisms	Cohort-specific Boolean models highlight different regulatory modules during disease progression
molecular modeling	Studying conformational transitions of selected proteins using UNRES coarse-grained replica exchange molecular dynamics simulations with Lorentzian restraints.
molecular signatures of cancer	Discovery of Latent Drivers from Double Mutations in Pan-Cancer Data
molecular systems	Path Integral Stochastic Optimal Control for Sampling Transition Paths
Moment Closure Scheme	Quasi-Entropy Closure: A Fast and Reliable Approach to Close the Moment Equations of the Chemical Master Equation
monkeypox	Preventing & limiting pandemics through vaccination: what have we learned from COVID-19 and MPX?
monotone control system	Model-based design of a synthetic oscillator based on an epigenetic memory system
Monte-Carlo tree search	Reinforcement learning and Monte-Carlo tree search in gene expression enable the entire gene regulation in a cell
Morphometric	Morphometric analysis of macrophage populations in response to animal-derived extracellular matrices
motifs	Deep convolutional neural networks capture the relationship between genetic variation and gene expression in plants
moving horizon estimation	Moving Horizon Estimation for Patient-Specific Optimal Control of Blood Glucose in Intensive Care Units
Mplrs	Characterizing all feasible metabolic conversions of individual cells and microbial communities with elementary conversion modes.
MRI	Insights on hemodynamic changes in hypertension and T2D through non-invasive cardiovascular modeling
mRNA	FISHing for Correlation
mRNA dynamics	Modelling how mRNA flows through subcellular compartments
MS2/MCP live imaging	Mitotic Memory as Spontaneous Symmetry Breaking in the Cell
multi omics modeling	TREAT-SGS - a multi-omics approach to treat the rare neuro-developmental disorder Schinzel–Giedion syndrome
Multi-cellular simulations	Computational modeling of DLBCL predicts response to BH3-mimetics
multi-cpu	Rapid parallel model inference and on-the-fly tiling of digital pathology images
multi-dimension parameter tuning in microfluidics	Building a synthetic cell: search for the minimal requirements for robust, sustainable, and tunable cell cycles
multi-drug resistant bacteria	Manually curated genome-scale metabolic reconstructions of the multi-drug resistant Gram-negative pathogens A. baumannii and K. pneumoniae
multi-gpu	Rapid parallel model inference and on-the-fly tiling of digital pathology images
Multi-level	M4-health: digital twins that follow you throughout your health journey
Multi-level data integration	Mathematical model of the immunopathological progression of tuberculosis
multi-modality	Biological-informed multi-modality integration of unmatched single-cell-omics datasets to provide a multi-dimensional view
multi-omics	Transomic network analysis of glucose metabolism and its dysfunction associated with obesity Combining multi-omics and biological knowledge to understand signaling deregulation in disease
multi-omics analysis	Extracting knowledge from multi-omics and clinical datasets using graph machine learning
Multi-omics data	Precision machine-learning identifies a new paradigm for therapeutic discovery in Huntington’s disease: remodeling stress response to re-instate neuronal health and resilience.
Multi-omics data integration	Mapping metabolic regulation in E. coli with a metabolism-wide CRISPRi library
multi-omics integration	Elucidating the role of TAS2R43 in HGT-1 cells – an integrated omics approach The pharmaco-epigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity Multi-Omics Regulatory Network Inference in the Presence of Missing Data
Multi-organ	M4-health: digital twins that follow you throughout your health journey
multi-scale	A multi-strain model of immunization against influenza A viruses after infection or vaccination Circadian and cell cycle control of terminal cell differentiation Individualized modules and models of enterovirus infection in host cells
multi-scale model	A Systems Biology Approach To Study The Spatiotemporal Dynamics Of Senescent Cells In Wound Healing And Tissue Repair Combining machine learning and ODE’s to build multiscale models for estimation of metabolic trajectories A low-granularity model integrating metabolism, growth and cell cycle: towards multi-level whole cell modeling of budding yeast
Multi-scale modeling	Multi-scale modeling of B-cell fate decisions required for antibody generation
Multi-scale modelling	An interconnected multi-level mechanistic model of the human brain
Multi-timescale	M4-health: digital twins that follow you throughout your health journey
multicellular	FitMultiCell: Simulating and parameterizating computational models of multi-cellular processes Advanced Modelling of Multicellular Systems in Morpheus
Multicellular communication	Vasculogenic mimicry induced by multicellular interaction in a 3D glioblastoma model-on-a-chip
multicellular systems	Topological properties accurately predict cell division events and organization of Arabidopsis thaliana’s shoot apical meristem
multidimensional file storage	Rapid parallel model inference and on-the-fly tiling of digital pathology images
multilevel-approach	Multilevel approach characterizing the progression of fatty liver disease
multiome	Reconstruction of regulatory networks driving patterned expression in the Drosophila embryo based on spatially resolved single-cell sequencing data​
Multiomics	Dynamic metabolome profiling uncovers potential TOR signaling genes MultiOmics Network Embedding for SubType Analysis New data-driven gene representations using deep autoencoders at multiple omics to identify candidate disease genes and robust classifiers
Multiple cell-types	Uncovering cell-type specific mechanisms across an arbitrary number of cell-types by adapting the clustered LASSO to differential equation models
Multiple sclerosis	Proteomics profiling revealed a combination of protein biomarkers for predicting disease trajectory of multiple sclerosis MODalyseR—a novel software for inference of disease module hub regulators identified a putative multiple sclerosis regulator supported by independent eQTL data Dimethyl fumarate shifts CSF protein profile in relapsing remitting MS: a proteomics approach for biomarker discovery
multiple timescale models	Fast and scalable machine learning approach for dynamic metabolic engineering
Multiplexed imaging	Multimodal perception links cellular state to decision making in single cells Improving our Mechanistic Understanding of Cell Cycle Dynamics
Multiplexed Immunofluorescence Imaging	Tribus reveals the single-cell tumor architecture and effect of chemotherapy in ovarian cancer
multiscale	FitMultiCell: Simulating and parameterizating computational models of multi-cellular processes Advanced Modelling of Multicellular Systems in Morpheus How can we unleash the potentials of whole-cell modelling?
multiscale biochemical system	Universally valid reduction of multiscale stochastic biochemical systems with simple non-elementary propensities
multiscale model	3D reconstruction and mathematical modelling of whole slide images to elucidate resistance to the targeted therapy in melanoma Digital twins and hybrid modelling for simulation of physiological variables and stroke risk
multiscale model reduction	Universally valid reduction of multiscale stochastic biochemical systems with simple non-elementary propensities
multiscale modeling	A bottom-up investigation of emergence in a self-organizing model of embryonic pattern formation A physiology-based model of bile acid metabolism in mice Predicting pathogenicity of TPM1 variants using multi-scale models Multiscale Modeling of Dyadic Structure-Function Relation in Ventricular Cardiac Myocytes
muscle stem cells	Computational modeling of the Hes1 oscillator for the self-renewal of muscle stem cells
Mushroom and Isola Bifurcation	Unraveling the role of network motifs to decipher the origin of robust decision-making in biological systems
mutation doublets	Discovery of Latent Drivers from Double Mutations in Pan-Cancer Data
mutations	Stochastic Model of Intra-Tumor Heterogeneity (SMITH) Mechanisms of Pro- and Anti-Oncogenic Signaling Downstream of Dual Tyrosine Protein Kinases
Mutual Information	FISHing for Correlation
Mycobacterium tuberculosis	Combinatorial effects of ligands are predicted by a genome-scale model of signaling based on artificial neural networks
mycobiome	Candida expansion in the human gut is associated with an ecological signature that supports growth under dysbiotic conditions
myocardial infarction	Characterization of cardiac fibroblast remodeling dynamics after myocardial infarction
N
N-acetylaspartate	Data-driven modeling of mitochondrial metabolism
NAFLD	Discovery of Robust and Highly Specific Microbiome Signatures for Non-Alcoholic Fatty Liver Disease
NAFLD prevention	Resistant starch decreases intrahepatic triglycerides in NAFLD patients via the gut microbiome contribution to the branched-chain amino acids pool
NAFLD progression	Multilevel approach characterizing the progression of fatty liver disease
Nasal Microbiome Community	The metabolic community model of Staphylococcus aureus and four abundant human nasal microbes
natural genetic variation	DeepCellRegMap: An interpretable deep learning framework for mapping genetic effects at cell subtype resolution using large-scale single-cell sequencing data
navigation in changing environments	Real-time biochemical computations at criticality
negative feedback control	Model-based design of a synthetic oscillator based on an epigenetic memory system
nested defense strategies	Human host and pathogenic fungi: modeling and deciphering nested metabolic defense strategies
network analysis	Lactobacillus rhamnosus colonisation antagonizes Candida albicans by forcing metabolic adaptations that compromise pathogenicity Stress Knowledge Map: A knowledge resource for modeling of plant stress responses In silico analysis of metabolic capabilities in a synthetic community of phycosphere bacteria
Network Biology	Identification of personalised driver gene panels in Melanoma Building the knowledge base to understand cellular signal transduction in different inflammatory phenotypes Temporal Proteomics and Transcriptomics Unravels the Host-Pathogen Interaction Network of Macrophages and Corynebacterium diphtheriae. Being noisy in a crowd: differential selective pressure on gene expression noise in model gene regulatory networks Transomic network analysis of glucose metabolism and its dysfunction associated with obesity Patterns of differentially essential genetic interactions characterize functional modules across cancer types Inferring Gene Networks Rewiring of Naive and Primed Human Embryonic Stem Cells During Cellular Reprogramming Using Single-Cell RNA-seq Data
Network Control	NETISCE: A dynamical systems and control theory approach to cell reprogramming
Network Embedding	MultiOmics Network Embedding for SubType Analysis
Network Enrichment	Lipid network and moiety analysis for revealing enzymatic dysregulation and mechanistic alterations from lipidomics data
Network inference	Inferring individual interactions in gene regulatory networks with delays from time-series experiments Multi-Omics Regulatory Network Inference in the Presence of Missing Data
network medicine	Network-based Stratification of Cancer Drugs
network modeling	Leveraging the Molecular Signatures of Cancer for Dynamic Network Modeling Network-based Stratification of Cancer Drugs
Network motifs	Unraveling the role of network motifs to decipher the origin of robust decision-making in biological systems A Novel and Robust Molecular Switch Actuating the Quantitative Model of Eukaryotic Cell Cycle Control
Network reconstruction	Hybrid models for cellular signaling: meso-scale pathway identification
network topology	Structural reduction of chemical reaction networks based on topology
networks	Expanding the disease network of Glioblastoma Multiforme via topological analysis Topological properties accurately predict cell division events and organization of Arabidopsis thaliana’s shoot apical meristem Inferring kinase activity of a tumor from phosphoproteomic data Combining multi-omics and biological knowledge to understand signaling deregulation in disease Gene expression heterogeneity arises from signaling networks
Neural circuit	Neural Circuits Underlying Autism Spectrum Disorders
neural network	Hypergraph for predicting adverse drug reactions A disease network-based deep learning approach for characterizing melanoma
Neural superposition	A robust model of neural superposition sorting
Neuroblastoma	Analysis of the impact of MYCN on the energy metabolism in neuroblastoma using metabolomics data and mathematical modeling
Neurodegenerative disease	Precision machine-learning identifies a new paradigm for therapeutic discovery in Huntington’s disease: remodeling stress response to re-instate neuronal health and resilience.
Neuroectoderm patterning	Logical modeling of signaling mechanisms in early development
Neurological scales	Modeling disease progression in spinocerebellar ataxias
Neuronal structures	Neural Circuits Underlying Autism Spectrum Disorders
Neuroscience	Neural Circuits Underlying Autism Spectrum Disorders
neurotransmission model	Variance of filtered signals: characterization for linear reaction networks and application to neurotransmission dynamics
Neurovascular coupling	Connecting the Neurovascular coupling and Electrophysiological signaling – a modeling approach An interconnected multi-level mechanistic model of the human brain
NFkB	Computational Models of Heterogeneous Mutations in Diffuse Large B-cell Lymphoma. Flow Cytometry Combined with Systems Biology Modelling Reveals Heterogeneous “NFkB Fingerprints” in DLBCL
noise	How do single bacterial cells make decisions?
Non linear optical microscopy	Quantification of imaging biomarkers in the extracellular matrix of left and right sided colon cancer tissues
Non-autonomous systems	Theory of biochemical information processing with transients
non-coding variants	Exploring the missing heritability in SPG7 heterozygous carriers with Whole Genome Sequencing
non-elementary reaction function	Universally valid reduction of multiscale stochastic biochemical systems with simple non-elementary propensities
non-equilibrium systems	Evaluation of methods to compute quasi-potential functions and their use as systems biology models
Non-linear monotone data	Efficient parameter estimation for ODE models with semi-quantitative data using spline approximation
Non-Markovian stochastic process	Systematic inference identifies a major source of heterogeneity in non-Markovian cell signaling dynamics: the rate-limiting step number
non-negative matrix factorization	Integrative analysis on comorbid signatures in psychotic disorders using multi-rank non-negative matrix factorization based graph approach
Non-Pharmaceutical Intervention	Control of COVID-19 Outbreaks under Stochastic Community Dynamics, Bimodality, or Limited Vaccination
Non-Small Cell Lung Cancer (NSCLC)	Model Predictive Control of Cancer Cellular Dynamics: A New Strategy For Therapy Design
nonlinear dynamics	Spatially-Coordinated Collective Protein Behaviors Enable Robust Circadian Timekeeping
nonlinear manifolds	Discovery of Hidden Control Variables and modeling Non-Linear Dynamical Biological Systems
nonlinear mixed effects modeling	Non-linear mixed effects modeling of the T cell response in individuals infected with SARS-CoV-2
nonlinear mixed-effects models	Fast parameter estimation for ODE-based models of heterogeneous cell populations
Nonlinear Modelling	Exact Confidence Regions for Non-Linear Models
Nonlinear optimization	The Economy and Control of Balanced Cellular Growth
normal forms	Discovery of Hidden Control Variables and modeling Non-Linear Dynamical Biological Systems
Normalizing flows	Simulation Based Metabolic Flux Inference
Notch signalling	Computational modeling of the Hes1 oscillator for the self-renewal of muscle stem cells
Nucleocytoplasmic shuttling	Cross-inhibitory feedbacks of nucleocytoplasmic transport give rise to divergent multicellular phenotype in ERBB2-activated breast epithelia
nucleoside	New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
nucleosome remodelling	Using multi-omics data and machine learning to unravel alternative splicing regulation
numerical analysis	Quantitative Impacts of Bumble Bee Ecology on Foraging Behaviour: An Economic Model
O
obesity	Transomic network analysis of glucose metabolism and its dysfunction associated with obesity
obesity and metabolic syndrome	Combining machine learning and ODE’s to build multiscale models for estimation of metabolic trajectories
oceans	Tara Oceans: Eco-Systems Biology at Planetary Scale
ODE	Data-driven modeling of mitochondrial metabolism
ODE based mechanistic modeling	A generic approach to decipher the mechanistic pathway of heterogeneous protein aggregation kinetics
ODE model	Patient-specific modeling of the TP53 pathway in endometrial carcinoma patients Analysis of the impact of MYCN on the energy metabolism in neuroblastoma using metabolomics data and mathematical modeling Non-monotonic Na+ dynamics in the malaria parasite Plasmodium falciparum
ODE modeling	Mechanistic insights into sensitization and desensitization of the Interferon α signal transduction pathway Regulation of Mammalian Iron Physiology Across Scales
ODE models	Analyzing single-cell trajectories with augmented machine learning methods predicts cancer drugs response in live-cell microscopy assays Information Processing by Homo-Oligomeric Proteins: From First Principles to Cardiac Disease
ODE-model	A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation
Omics	Biological-informed multi-modality integration of unmatched single-cell-omics datasets to provide a multi-dimensional view Model ensembling as a tool to form interpretable multi-omic predictors of cancer pharmacosensitivity
oncogenic mutations	Leveraging the Molecular Signatures of Cancer for Dynamic Network Modeling
ontology	BioCypher: an ontology-driven framework for flexible harmonisation of large-scale biomedical knowledge graphs GO Term-based Comparative Functional Genomics in Plants
open source	A workflow for the creation of regulatory networks integrating miRNAs and lncRNAs associated with exposure to ionizing radiation using open source data and tools
open tooling	Rapid parallel model inference and on-the-fly tiling of digital pathology images
optimal control	Moving Horizon Estimation for Patient-Specific Optimal Control of Blood Glucose in Intensive Care Units
optimisation	Quantitative Impacts of Bumble Bee Ecology on Foraging Behaviour: An Economic Model
Optimization problem	Universality of form: The case of retinal cone photoreceptor mosaics
ordinary differential equation	Data-driven mathematical modeling of human skin aging and its application for natural compound screening
ordinary differential equation model	Patient- and cell line-specific modeling of diffuse large B-cell lymphoma
Ordinary Differential Equations	Mathematical modeling of cytokine interplay in human monocytes during LPS stimulation Non-parametric model-based estimation of the effective reproduction number for SARS-CoV-2 Mechanistic modeling of patient-specific response to hormone therapy and CDK inhibitors in breast cancer Flow Cytometry Combined with Systems Biology Modelling Reveals Heterogeneous “NFkB Fingerprints” in DLBCL A powerful modelling approach tailored to cellular signalling
Organ-on-a-chip	Vasculogenic mimicry induced by multicellular interaction in a 3D glioblastoma model-on-a-chip
organizing principles	The limit on dry mass density is an organizing principle for cellular physiology
Organoids	Modeling the tumor microenvironment in patient-derived organoid culture Understanding Stem Cell Growth Dynamics in Human Cerebral Organoids
oscillations	Computational modeling of the Hes1 oscillator for the self-renewal of muscle stem cells Circadian and cell cycle control of terminal cell differentiation
Oscillatory dynamics	Computational modeling for the elucidation of cell fate decisions in early development
Ovarian cancer	Tribus reveals the single-cell tumor architecture and effect of chemotherapy in ovarian cancer Single-cell spatial atlas of high-grade serous ovarian cancer
overflow metabolism	Statistical estimation of enzyme kinetics and pathway cost predicts overflow metabolism
P
p53	Coordination of p53 and MAPK dynamics controls heterogeneous responses to genotoxic agents in single cells
Pan-genome	Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection
Pancreatic cell fate differentiation	NETISCE: A dynamical systems and control theory approach to cell reprogramming
pancreatic ductal adenocarcinoma	Lipid metabolic reprogramming extends beyond histological tumor demarcations in human operable pancreatic cancer Quantitative Spatial Profiling Reveals Tumor Microenvironment Heterogeneity and Prognostic Biomarkers Associated with Immune Population Architectures
pandemics	FAIR sharing of reproducible COVID-19 models of epidemic and pandemic forecast
panel	Panel Discussion
parallel inference	Rapid parallel model inference and on-the-fly tiling of digital pathology images
parallel processing	Composing and perturbing large-scale constraint-based metabolic models with COBREXA.jl
Parameter estimation	FitMultiCell: Simulating and parameterizating computational models of multi-cellular processes Efficient parameter estimation for ODE models with semi-quantitative data using spline approximation Fast parameter estimation for ODE-based models of heterogeneous cell populations The Mixed Meal Model; quantifying metabolic resilience in overweight and obesity Improving our Mechanistic Understanding of Cell Cycle Dynamics
Parameter Inference	Exact Confidence Regions for Non-Linear Models
Parameter optimisation	Defining Design Rules for Next-Generation Snakebite Antivenoms
Parameterization	Multiscale Modeling of Dyadic Structure-Function Relation in Ventricular Cardiac Myocytes
Parkinson’s disease	Machine learning based pathway deregulation analysis of metabolomics data for Parkinson's Disease Cohort-specific Boolean models highlight different regulatory modules during disease progression
Partial Differential Equations	DUNE-COPASI: Multi-Compartment Diffusion-Reaction solver for Cell Biology Quantitative Impacts of Bumble Bee Ecology on Foraging Behaviour: An Economic Model
passenger mutations	Discovery of Latent Drivers from Double Mutations in Pan-Cancer Data
patch reconstruction	Rapid parallel model inference and on-the-fly tiling of digital pathology images
Pathology	System Pathology of Cancer Artificial Intelligence in Digital Pathology Research - Where do we come from and where do we go? EMPAIA - Harmonizing Access to Clinical-Grade AI Algorithms in Pathology
pathway modeling	Targeted Proteomics-Driven Computational Modeling of the Mouse Macrophage Toll-like Receptor Signaling Pathway
pathways	Machine learning based pathway deregulation analysis of metabolomics data for Parkinson's Disease Building a Mind for Cancer
patient samples	COVIDpro: Database for mining protein dysregulation in patients with COVID-19
patient stratification	Harnessing cancer heterogeneity for the systematic discovery of treatable cancer-driver exons with spotter A robust clustering strategy for patient stratification in complex diseases
Patient-individual antiviral response	Mechanistic insights into sensitization and desensitization of the Interferon α signal transduction pathway
patient-specific	Insights on hemodynamic changes in hypertension and T2D through non-invasive cardiovascular modeling
Patient-specific modeling	Patient- and cell line-specific modeling of diffuse large B-cell lymphoma
pattern formation	Topological properties accurately predict cell division events and organization of Arabidopsis thaliana’s shoot apical meristem
patterning	A bottom-up investigation of emergence in a self-organizing model of embryonic pattern formation
PBPK	A physiology-based model of bile acid metabolism in mice Physiologically based pharmacokinetic (PBPK) models for metabolic phenotyping and evaluation of liver function
PBPK modeling	Integrating cellular and physiologically-based pharmacokinetic (PBPK) modelling
PBPK modelling	A systems pharmacology approach reveals robust drug metabolism and altered glucuronide disposition in a mouse model of liver cirrhosis
PC12 cells	Periodic Forcing of the ERK pathway
Pearson Correlation	FISHing for Correlation
periodic forcing	Periodic Forcing of the ERK pathway
Personalised anemia management	Personalized Treatment of Anemia in Lung Carcinoma
Personalised medicine	Identification of personalised driver gene panels in Melanoma
Personalised Models	The Mixed Meal Model; quantifying metabolic resilience in overweight and obesity
personalized	Insights on hemodynamic changes in hypertension and T2D through non-invasive cardiovascular modeling
personalized medicine	Moving Horizon Estimation for Patient-Specific Optimal Control of Blood Glucose in Intensive Care Units Cell type-specific gene co-expression modules define tumor heterogeneity in melanoma patients Personalized medicine for Multiple Sclerosis treatment strategies at the individual and population level
Perturb-seq	Dissecting the principles underlying transcriptional heterogeneity
PEtab	Moving Horizon Estimation for Patient-Specific Optimal Control of Blood Glucose in Intensive Care Units Improving our Mechanistic Understanding of Cell Cycle Dynamics
Petri net	Manatee invariants entailing signal transduction pathways in Petri nets of signaling networks Modeling the adaptive immune response of a lymph node as Petri net
Petri Nets	A graph-based approach to analyze signal transduction involving cytokines and the JAK-STAT pathway in hepatocytes using Petri nets
phage display	Proteome-scale mapping of binding sites in the intrinsically disordered regions of human and viral proteomes
phage therapy	Towards identification of new life cycle-associated regions in phage genomes using deep learning
Phage-Host Prediction	Benchmarking Phage-Host Prediction Tools using Real Metagenomics Data
pharma	Thinking of a career in big pharma? Here is what you need to know.
pharmaceutical R&D	From Academic Research to Pharmaceutical R&D and Back
pharmaco kinetics	Modelling of Pharmacokinetics and Pharmacodynamics for first-in-man dose selection of targeted alpha therapy
Pharmacodynamics	Analyzing single-cell trajectories with augmented machine learning methods predicts cancer drugs response in live-cell microscopy assays
Pharmacokinetics	A physiologically-structured population model for pharmacokinetics of orally inhaled drugs Physiologically based pharmacokinetic (PBPK) models for metabolic phenotyping and evaluation of liver function
pharmacometrics	Numerical approaches for the rapid analysis of prophylactic efficacy against HIV
phase contrast CT	The potential of PBI for high resolution lung imaging in patients
Phase-space trajectories	Theory of biochemical information processing with transients
Phenotype classes	Theory of biochemical information processing with transients
Phenotypic decision model	Mathematical modelling of the regulatory mechanisms of keratinocyte differentiation for epidermal homeostasis
Phenotypic heterogeneity	Cancer cell fate decisions
Phenotypic plasticity	Predicting plasticity of rosette growth and metabolic fluxes in Arabidopsis thaliana
phospholamban	Information Processing by Homo-Oligomeric Proteins: From First Principles to Cardiac Disease
Phosphoproteomics	Development of a mass-spectrometry based clinical proteomics pipeline allows absolute quantification of pathway components and provides insights in pathway activation Inferring kinase activity of a tumor from phosphoproteomic data Systems Approaches to Deciphering Kinase Signaling and the Phosphoproteome: A Focus on Cancer, Inflammation, and DNA Damage
phosphorus	Co-expression analysis of transcriptome and proteome identifies LRR-VIII-1 kinase and MAPK-kinase (MEK1) regulatory modules associated with P-deficiency adaptation and P use efficiency in maize
phosphorylation	Decrypting drug actions and protein modifications by dose- and time-resolved proteomics DecryptM: decrypting drug actions and protein modification by dose- and time-resolved proteomics A comprehensive mechanistic model of adipocyte signaling with layers of confidence
phycosphere	In silico analysis of metabolic capabilities in a synthetic community of phycosphere bacteria
Phylogeny	Phylogeny and artificial neural networks
Physical modeling	Decoding cellular deformation from pseudo-simultaneously observed RhoGTPase activities
Physics Informed Neural Networks	On data-driven learning of an effective energy landscape from trajectories of nonlinear dynamical biological systems
physics-informed neural networks	Hybrid mechanistic and deep learning modeling in systems biology
physiology	Information Processing by Homo-Oligomeric Proteins: From First Principles to Cardiac Disease
Pigs	Genome-wide analysis of genetic variants affecting metabolomic abundance in pigs divergent for feed efficiency
pitch	Pitching for Classical modeling Pitching for AI / ML modeling Pitching for hybrid/data-driven modeling
pith	Cell Type view into tomato stem elongation in Shade avoidance response
planet	Tara Oceans: Eco-Systems Biology at Planetary Scale
Plant growth	Predicting plasticity of rosette growth and metabolic fluxes in Arabidopsis thaliana
Plant radial growth	Computational analysis of cambium activity during plant radial growth
plants	Stress Knowledge Map: A knowledge resource for modeling of plant stress responses GO Term-based Comparative Functional Genomics in Plants
Plasticity	A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation
plenatary	Molecular eco-systems biology of microbiomes for human and planetary health
pneumology	Integrational approaches for cross-species analysis of lung pathologies at single-cell resolution.
Poincaré−Bendixson theorem	Model-based design of a synthetic oscillator based on an epigenetic memory system
polarization	Real-time biochemical computations at criticality
Post-translational modification	DecryptM: decrypting drug actions and protein modification by dose- and time-resolved proteomics
Potential landscape	Unraveling the role of network motifs to decipher the origin of robust decision-making in biological systems
Potential Landscapes	On data-driven learning of an effective energy landscape from trajectories of nonlinear dynamical biological systems
Pre-cancerous state	Single cell analysis of a breast pre-cancerous state to explore critical tumor microenvironment interactions Single cell analysis of colorectal cancers with familial adenomatous polyposis for revealing differential pre-malignant programs
pre-exposure prophylaxis	Numerical approaches for the rapid analysis of prophylactic efficacy against HIV
Pre-implantation development	A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation
precision medicine	Personalized Treatment of Anemia in Lung Carcinoma The pharmaco-epigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity Learning synthetic cell classifier designs with genetic algorithms and logic programming Latent Dirichlet Allocation for Double Clustering (LDA-DC): Discovering patients phenotypes and cell populations within a single Bayesian framework Inferring kinase activity of a tumor from phosphoproteomic data Comparative analysis of molecular fingerprints in prediction of drug combination effects A robust clustering strategy for patient stratification in complex diseases
Precision nutrition	The Mixed Meal Model; quantifying metabolic resilience in overweight and obesity
precision oncology	The pharmaco-epigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity
preclinical models	A physiology-based model of bile acid metabolism in mice
Predictability	Predicting developmental states in zebrafish using transfer learning
predicting drug-drug interactions	Hypergraph for predicting adverse drug reactions
prediction	Machine learning-based prediction of frailty in elderly people - Data from the Berlin Aging Study-II (BASE-II) Multi-dimensional immune correlates of early prediction of COVID-19 severe versus asymptomatic disease course Optimal prediction of a noisy signal Dimethyl fumarate shifts CSF protein profile in relapsing remitting MS: a proteomics approach for biomarker discovery
Predictions	Proteomics profiling revealed a combination of protein biomarkers for predicting disease trajectory of multiple sclerosis
predictive biomarker	The pharmaco-epigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity
Predictive Modelling	Improving Our Understanding of ADPKD: Computational Analysis of Metabolome Data
prize-collecting Steiner forest	Network-based Stratification of Cancer Drugs
probability distributions	On the relation between input and output distributions of scRNA-seq experiments
Prognosis	Identification of personalised driver gene panels in Melanoma
Prognostic biomarkers	Quantitative Spatial Profiling Reveals Tumor Microenvironment Heterogeneity and Prognostic Biomarkers Associated with Immune Population Architectures
proliferation prediction	Disentangling Proliferation Signaling in Breast Cancer Subtypes based on an integrative modeling approach
prophylactic efficacy	Numerical approaches for the rapid analysis of prophylactic efficacy against HIV
Prostate Cancer	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
protein	Machine learning for hard biological problems The workings and impact of AlphaFold
Protein aggregation	A generic approach to decipher the mechanistic pathway of heterogeneous protein aggregation kinetics
protein evolution	Optimization of functional efficiency in key tissues constrains protein rate of evolution in multicellular species
protein expression	Optimization of functional efficiency in key tissues constrains protein rate of evolution in multicellular species
Protein KInases	Systems Approaches to Deciphering Kinase Signaling and the Phosphoproteome: A Focus on Cancer, Inflammation, and DNA Damage
Protein Network	Inference of a causal synaptic molecular network from multiplexed imaging and its perturbations in autism and schizophrenia Dynamic fluctuations in a bacterial metabolic network
Protein networks	Mutually Antagonistic Protein Pairs of Cancer
Protein Secretion	Amino Acid Impact on Protein Secretion in B. subtilis: an RBA Approach
protein translation	The limit on dry mass density is an organizing principle for cellular physiology
protein-protein interaction networks	Discovery of potential functional paths by integration of phospho-proteomics data in the PPI network using a RWR framework
protein-protein interactions	Proteome-scale mapping of binding sites in the intrinsically disordered regions of human and viral proteomes Information Processing by Homo-Oligomeric Proteins: From First Principles to Cardiac Disease Identification of a SARS-CoV-2 inhibitor by combining binary protein-protein interaction mapping, structure prediction and virtual screening
protein-protein interactions (PPIs)	What are the functions of the short open reading frame-encoded peptides in monocytes? An interactomic approach.
proteome	Decrypting drug actions and protein modifications by dose- and time-resolved proteomics Co-expression analysis of transcriptome and proteome identifies LRR-VIII-1 kinase and MAPK-kinase (MEK1) regulatory modules associated with P-deficiency adaptation and P use efficiency in maize
Proteomes in 3D	Proteomes in 3D: Structural proteome snapshots as a new functional ‘omics readout
proteomics	Multiple-omics based metabolic modelling reveals effects of drug-induced liver toxicity Multilevel approach characterizing the progression of fatty liver disease The abundance and cross-talk of EGFR and MET receptors in lung cancer cell lines is critical for the efficacy of tyrosine kinase inhibitors A probabilistic graphical model for taxonomic profiling of viral and microbiome proteome samples Decrypting drug actions and protein modifications by dose- and time-resolved proteomics Benchmarking of analysis strategies for data-independent acquisition proteomics data Mapping metabolic regulation in E. coli with a metabolism-wide CRISPRi library Mutually Antagonistic Protein Pairs of Cancer Temporal Proteomics and Transcriptomics Unravels the Host-Pathogen Interaction Network of Macrophages and Corynebacterium diphtheriae. Predicting metabolite accumulation in cancerous metabolic network Targeted Proteomics-Driven Computational Modeling of the Mouse Macrophage Toll-like Receptor Signaling Pathway The metabolic and proteomic landscape of genome-scale genetic perturbation DecryptM: decrypting drug actions and protein modification by dose- and time-resolved proteomics COVIDpro: Database for mining protein dysregulation in patients with COVID-19 Proteomes in 3D: Structural proteome snapshots as a new functional ‘omics readout Dimethyl fumarate shifts CSF protein profile in relapsing remitting MS: a proteomics approach for biomarker discovery
Proteomics profiling	Proteomics profiling revealed a combination of protein biomarkers for predicting disease trajectory of multiple sclerosis
pseudo-time	Single cell pseudo-time inference based on copy number variants for identifying a tumor transition state
psychotic disorders	Integrative analysis on comorbid signatures in psychotic disorders using multi-rank non-negative matrix factorization based graph approach
PTA-toolbox	Integrating 13C labeling and thermodynamic data for thermodynamically consistent Bayesian Metabolic Flux Analysis (T13C-MFA)
PTMs	Explainable Machine Learning in Mass Spectrometry-based Proteomics Decrypting drug actions and protein modifications by dose- and time-resolved proteomics
publishing	From bench to scientific publishing
PUE	Co-expression analysis of transcriptome and proteome identifies LRR-VIII-1 kinase and MAPK-kinase (MEK1) regulatory modules associated with P-deficiency adaptation and P use efficiency in maize
Pyruvate	Dynamic fluctuations in a bacterial metabolic network
Python	New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
pytorch lightning	Rapid parallel model inference and on-the-fly tiling of digital pathology images
Q
q/a	Q&A Q&A and Open Discussion
Quality control and quality assurance	Computationally Modeling the Human Microbiome of the Respiratory Tract
quantitative biology	The E. coli Whole-Cell Modeling Project: Vision and Progress When cells decide to give up on repairing DNA damage
Quantum computing	A quantum circuit model for inferring gene regulatory networks with application to single-cell transcriptomic data
quasi-potential	Evaluation of methods to compute quasi-potential functions and their use as systems biology models
Queueing theory	Systematic inference identifies a major source of heterogeneity in non-Markovian cell signaling dynamics: the rate-limiting step number
R
R package	BlotIt - Optimal alignment of Western blot and qPCR experiments
Radiation resistance	Ionizing radiation triggers differential signaling dynamics of p-p53 and p-ERK1/2 in sensitive and resistant HNSCC cell clones
Random sampling	Can we trust genome-wide metabolic models?
random walk with restart	Discovery of potential functional paths by integration of phospho-proteomics data in the PPI network using a RWR framework
rare biosphere	Effect of dispersal by inundation on soil bacterial communities depends on soil developmental stage
rare disease	TREAT-SGS - a multi-omics approach to treat the rare neuro-developmental disorder Schinzel–Giedion syndrome
Rare diseases	Modeling disease progression in spinocerebellar ataxias
rates	Modelling how mRNA flows through subcellular compartments
reaction kinetics	Deep insight into SABIO-RK data via visualization DUNE-COPASI: Multi-Compartment Diffusion-Reaction solver for Cell Biology
reaction knockout	New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
Real-time dynamic information processing	Theory of biochemical information processing with transients
Real-time Engine	Delivering Virtual Reality and Gaming Technologies to the Field of Systems Biology
real-time navigation	Dynamical basis of cellular sensing and responsiveness to spatial-temporal signals
Receptor activation signaling	Cross-inhibitory feedbacks of nucleocytoplasmic transport give rise to divergent multicellular phenotype in ERBB2-activated breast epithelia
Receptor Networks	Cells use molecular working memory to navigate in changing chemoattractant fields
receptor signaling	Directed cell migration by cortical actin and ER-PM contact site-mediated restriction of receptor signaling to the front
Receptor tyrosine kinases	Cells use molecular working memory to navigate in changing chemoattractant fields
recurrent neural networks	Using graph theory and recurrent neural network models to investigate the anxiety circuit
regulatory genomics	DeepCellRegMap: An interpretable deep learning framework for mapping genetic effects at cell subtype resolution using large-scale single-cell sequencing data
regulatory network	A workflow for the creation of regulatory networks integrating miRNAs and lncRNAs associated with exposure to ionizing radiation using open source data and tools
Regulatory network model	Mathematical modelling of the regulatory mechanisms of keratinocyte differentiation for epidermal homeostasis
Reinforcement learning	Reinforcement learning and Monte-Carlo tree search in gene expression enable the entire gene regulation in a cell
Relapsing Remitting Multiple Sclerosis	Personalized medicine for Multiple Sclerosis treatment strategies at the individual and population level
Relational Learning	Metabolic profile predictions using efficient and interpretable data descriptors generated with relational learning
Relative measurements	BlotIt - Optimal alignment of Western blot and qPCR experiments
remarks	Final remarks
REMD	Studying conformational transitions of selected proteins using UNRES coarse-grained replica exchange molecular dynamics simulations with Lorentzian restraints.
replica exchange	Studying conformational transitions of selected proteins using UNRES coarse-grained replica exchange molecular dynamics simulations with Lorentzian restraints.
reproducibility	BioSimulations: integrated models, model languages, model repositories, simulation experiments, simulation tools and data visualization FROG Analysis - a community standard to foster reproducibility and curation of constraint-based models The COmputational MOdeling in BIology NEtwork in 2022: Evolving needs in standardisation and model reuse A Reproducibility Scorecard for Self-checking of Systems Biology Models
Reproducibility in Science	Bias and reproducibility in a Computational Neurobiology PhD’s journey
reproducible modelling	BioModels: an open repository of mathematical models of the biological and biomedical processes
reproduction	A deep learning-based approach for counting ovarian follicles
residual feed intake	Genome-wide analysis of genetic variants affecting metabolomic abundance in pigs divergent for feed efficiency
Resolution	Resolving Resolution Hindrances in Spatial Transcriptomics
resource allocation	Amino Acid Impact on Protein Secretion in B. subtilis: an RBA Approach Analyzing Optimal and Non-Optimal Resource Allocations in Whole-Cell Models Quantification of bacterial resource allocation in changining environments on the single-cell level Geometric programming to Solve Optimal Concentrations of Metabolites and Enzymes in Constraint-based modelling
Reusable modelling	Improving our Mechanistic Understanding of Cell Cycle Dynamics
reversible binding	Universally valid reduction of multiscale stochastic biochemical systems with simple non-elementary propensities
RhoGTPase	Decoding cellular deformation from pseudo-simultaneously observed RhoGTPase activities
Ribosome	An optimal RNA growth law and its relationship with genome organization in bacteria
ribosome composition	Analyzing Optimal and Non-Optimal Resource Allocations in Whole-Cell Models
ribosome level	Dynamics of growth and ribosome level in batch cultures of S. cerevisiae
ribosomes	Quantification of bacterial resource allocation in changining environments on the single-cell level
Rice	Hierarchical gene function prediction using a novel topology-based threshold and comparing 6 correlation metrics. Study case: Rice
risk	When cells decide to give up on repairing DNA damage
risk factors	Machine learning-based prediction of frailty in elderly people - Data from the Berlin Aging Study-II (BASE-II)
RMR	Web-based analysis of indirect calorimetric data arising from metabolic phenotyping systems
RNA composition	An optimal RNA growth law and its relationship with genome organization in bacteria
RNA repair	A model of RNA repair to study antibiotic tolerance
RNA velocity	Inference and dynamical simulation of the gene-regulatory network in single cells FLOVELO - Pushing Boundaries of Cell Dynamics Inference with Maximum Flow Networks
RNA-seq	Transcription start site signal profiling improves transposable element RNA expression analysis at locus-level
robotics	Deep learning a model of cytotoxic T cell activation in the tumor microenvironment
Robustness	A robust model of neural superposition sorting Robust oscillations against spatial-temporal noise in intra-inter cellular kinetics
root	Co-expression analysis of transcriptome and proteome identifies LRR-VIII-1 kinase and MAPK-kinase (MEK1) regulatory modules associated with P-deficiency adaptation and P use efficiency in maize
Rtc system	A model of RNA repair to study antibiotic tolerance
RTS	PlantEd - a serious game about plant growth that aims to support metabolic modeling with citizen science
rule-based	Virtual Cell Modeling and Simulation Software
Rule-based modelling	Improving our Mechanistic Understanding of Cell Cycle Dynamics Data-driven modeling of mitochondrial metabolism
rxncon	Building the knowledge base to understand cellular signal transduction in different inflammatory phenotypes
S
SABIO-RK	Deep insight into SABIO-RK data via visualization
Saccharomyces cerevisiae	Metabolic profile predictions using efficient and interpretable data descriptors generated with relational learning
salt marsh	Effect of dispersal by inundation on soil bacterial communities depends on soil developmental stage
Sampling	Integrating 13C labeling and thermodynamic data for thermodynamically consistent Bayesian Metabolic Flux Analysis (T13C-MFA)
Sampling noise	Accounting for low transcript sampling rates in scRNA-seq using the Good-Turing estimator
Sampling Transition Paths	Path Integral Stochastic Optimal Control for Sampling Transition Paths
SARS-CoV-2	Non-linear mixed effects modeling of the T cell response in individuals infected with SARS-CoV-2 Non-parametric model-based estimation of the effective reproduction number for SARS-CoV-2 Multi-dimensional immune correlates of early prediction of COVID-19 severe versus asymptomatic disease course Computationally Modeling the Human Microbiome of the Respiratory Tract New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells Identification of a SARS-CoV-2 inhibitor by combining binary protein-protein interaction mapping, structure prediction and virtual screening
SBGN	The COmputational MOdeling in BIology NEtwork in 2022: Evolving needs in standardisation and model reuse
SBML	Virtual Cell Modeling and Simulation Software Advanced Modelling of Multicellular Systems in Morpheus The COmputational MOdeling in BIology NEtwork in 2022: Evolving needs in standardisation and model reuse Physiologically based pharmacokinetic (PBPK) models for metabolic phenotyping and evaluation of liver function
SBOL	The COmputational MOdeling in BIology NEtwork in 2022: Evolving needs in standardisation and model reuse
Scatter search	Improving our Mechanistic Understanding of Cell Cycle Dynamics
scBLender	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
schizophrenia	Integrative analysis on comorbid signatures in psychotic disorders using multi-rank non-negative matrix factorization based graph approach Inference of a causal synaptic molecular network from multiplexed imaging and its perturbations in autism and schizophrenia
scientific machine learning	Hybrid mechanistic and deep learning modeling in systems biology
scientist	Introduction
scMS	Implementation of multiplexed single cell proteomics for the investigation of cellular heterogeneity in mammalian cell lines
SCOPE2-MS	Implementation of multiplexed single cell proteomics for the investigation of cellular heterogeneity in mammalian cell lines
scRNA-seq	On the relation between input and output distributions of scRNA-seq experiments The transcriptome dynamics of single cells during the cell cycle Accounting for low transcript sampling rates in scRNA-seq using the Good-Turing estimator
scRNA-seq analysis	FLOVELO - Pushing Boundaries of Cell Dynamics Inference with Maximum Flow Networks
scRNAseq	Inference and dynamical simulation of the gene-regulatory network in single cells
Second harmonic generation	Quantification of imaging biomarkers in the extracellular matrix of left and right sided colon cancer tissues
SED-ML	Virtual Cell Modeling and Simulation Software The COmputational MOdeling in BIology NEtwork in 2022: Evolving needs in standardisation and model reuse
SEIR Models	Seroepidemiology And Modeling Of SARS-CoV-2 In Ethiopia: Longitudinal Cohort Study Among Front-line Health-care Workers And Community
self-replicator model	Dynamics of growth and ribosome level in batch cultures of S. cerevisiae
semi-automatic FAIR evaluation tool	FAIR assessment of biosimulation models - a cross-community project
semi-mechanistic modeling	Hybrid mechanistic and deep learning modeling in systems biology
Senescence	Cancer cell fate decisions Systems Approaches to Deciphering Kinase Signaling and the Phosphoproteome: A Focus on Cancer, Inflammation, and DNA Damage
senior editor	From bench to scientific publishing
Sensitivity analysis	Defining Design Rules for Next-Generation Snakebite Antivenoms
sepsis	Machine learning-based sepsis risk prediction modeling using electronic health records of cancer patients
session	Introduction Q&A
session chairs	Final remarks
Shade avoidance response	Cell Type view into tomato stem elongation in Shade avoidance response
Shape analysis	Precision machine-learning identifies a new paradigm for therapeutic discovery in Huntington’s disease: remodeling stress response to re-instate neuronal health and resilience.
shape control	The Systems of Size and Shape Control
Shiny	Web-based analysis of indirect calorimetric data arising from metabolic phenotyping systems
shoot apical meristem	Topological properties accurately predict cell division events and organization of Arabidopsis thaliana’s shoot apical meristem
short linear motifs	Proteome-scale mapping of binding sites in the intrinsically disordered regions of human and viral proteomes
short linear motifs (SLiMs)	What are the functions of the short open reading frame-encoded peptides in monocytes? An interactomic approach.
short open reading frames (sORFs)	What are the functions of the short open reading frame-encoded peptides in monocytes? An interactomic approach.
Signal flow	Combinatorial effects of ligands are predicted by a genome-scale model of signaling based on artificial neural networks
Signal flow path variability	Boolean dynamic modeling of TNFR1 signaling predicts a nested feedback loop regulating the apoptotic response at single-cell level (EXCEPTION - ZOOM)
Signal Flow Propagation	NETISCE: A dynamical systems and control theory approach to cell reprogramming
signal transduction	Multimodal perception links cellular state to decision making in single cells Manatee invariants entailing signal transduction pathways in Petri nets of signaling networks Alterations in hepatocyte growth factor induced signal transduction in fatty liver disease foster cancer development The abundance and cross-talk of EGFR and MET receptors in lung cancer cell lines is critical for the efficacy of tyrosine kinase inhibitors Deciphering dysregulation in Erythroleukemia to design intervention strategies Computational modeling for the elucidation of cell fate decisions in early development Cell-to-cell variability in JAK2/STAT5 pathway components and cytoplasmic volumes defines survival threshold in erythroid progenitor cells Building the knowledge base to understand cellular signal transduction in different inflammatory phenotypes A powerful modelling approach tailored to cellular signalling More BANG for the buck: how to distribute measurements to optimize information gain for mathematical models A Mechanistic model of EGFR and ERK signaling reveals how allostery and rewiring contribute to drug resistance Disentangling Proliferation Signaling in Breast Cancer Subtypes based on an integrative modeling approach
signaling	Discovery of potential functional paths by integration of phospho-proteomics data in the PPI network using a RWR framework A bottom-up investigation of emergence in a self-organizing model of embryonic pattern formation Combining multi-omics and biological knowledge to understand signaling deregulation in disease Gene expression heterogeneity arises from signaling networks A comprehensive mechanistic model of adipocyte signaling with layers of confidence A graph-based approach to analyze signal transduction involving cytokines and the JAK-STAT pathway in hepatocytes using Petri nets
signaling dynamics	Multi-scale modeling of B-cell fate decisions required for antibody generation
Signaling pathway	Mechanistic modeling of patient-specific response to hormone therapy and CDK inhibitors in breast cancer
Signaling pathways	Manatee invariants entailing signal transduction pathways in Petri nets of signaling networks
signalling	Digital Twin models for the precision diagnosis and therapy of cancer Computational modeling of DLBCL predicts response to BH3-mimetics
Signalling Networks	Cells use molecular working memory to navigate in changing chemoattractant fields
Signalling pathways	Hybrid models for cellular signaling: meso-scale pathway identification Ionizing radiation triggers differential signaling dynamics of p-p53 and p-ERK1/2 in sensitive and resistant HNSCC cell clones
Simmune	Targeted Proteomics-Driven Computational Modeling of the Mouse Macrophage Toll-like Receptor Signaling Pathway
Simulation	PlantEd - a serious game about plant growth that aims to support metabolic modeling with citizen science Virtual Cell Modeling and Simulation Software Delivering Virtual Reality and Gaming Technologies to the Field of Systems Biology Stochastic Model of Intra-Tumor Heterogeneity (SMITH) Modeling the adaptive immune response of a lymph node as Petri net Agent-based modeling of spatiotemporal organization of bacteria in the human gut Transcription start site signal profiling improves transposable element RNA expression analysis at locus-level DUNE-COPASI: Multi-Compartment Diffusion-Reaction solver for Cell Biology
simulation algorithms	BioSimulations: integrated models, model languages, model repositories, simulation experiments, simulation tools and data visualization
Simulation Based Inference	Simulation Based Metabolic Flux Inference
Simulations	Dynamic fluctuations in a bacterial metabolic network
single cell	Coordination of p53 and MAPK dynamics controls heterogeneous responses to genotoxic agents in single cells Quantification of bacterial resource allocation in changining environments on the single-cell level Characterization of cardiac fibroblast remodeling dynamics after myocardial infarction
single cell analysis	TREAT-SGS - a multi-omics approach to treat the rare neuro-developmental disorder Schinzel–Giedion syndrome Combining single-cell imaging techniques to probe surface-adhesion-dependent morphological features of disease state Cell type-specific gene co-expression modules define tumor heterogeneity in melanoma patients
single cell behavior and cell variability	Foundations for a theory of IP3 induced Ca2+ signalling - re-inventing a classic.
Single Cell Imaging	Robust oscillations against spatial-temporal noise in intra-inter cellular kinetics
Single cell metabolomics	A new platform for deep multiplexed metabolomics with a DNA barcode readout
single cell methods	Modeling the tumor microenvironment in patient-derived organoid culture
single cell modeling	Mitotic Memory as Spontaneous Symmetry Breaking in the Cell
Single cell modelling	Timelapse of Single Cell Lipidomics
single cell polarization	Dynamical basis of cellular sensing and responsiveness to spatial-temporal signals
single cell proteomics	Implementation of multiplexed single cell proteomics for the investigation of cellular heterogeneity in mammalian cell lines
single cell RNA-seq	Analysis of Heterogeneity in the Tumor Microenvironment in the 4NQO HNSCC Mouse Model
Single-cell	Logical modeling of signaling mechanisms in early development Dynamic analysis framework to detect cell division and cell death in live-cell imaging, using signal processing and machine learning Biological-informed multi-modality integration of unmatched single-cell-omics datasets to provide a multi-dimensional view Multi-dimensional immune correlates of early prediction of COVID-19 severe versus asymptomatic disease course Analyzing single-cell trajectories with augmented machine learning methods predicts cancer drugs response in live-cell microscopy assays Scalable and flexible inference framework for stochastic dynamic single-cell models The transcriptome dynamics of single cells during the cell cycle Predicting developmental states in zebrafish using transfer learning How do single bacterial cells make decisions?
single-cell analysis	Single cell analysis of a breast pre-cancerous state to explore critical tumor microenvironment interactions Single cell analysis of colorectal cancers with familial adenomatous polyposis for revealing differential pre-malignant programs Single cell pseudo-time inference based on copy number variants for identifying a tumor transition state When cells decide to give up on repairing DNA damage
single-cell data	Fast parameter estimation for ODE-based models of heterogeneous cell populations
Single-cell Genomics	GEARS: Predicting transcriptional outcomes of novel multi-gene perturbations
single-cell modeling	Cell-to-cell variability in JAK2/STAT5 pathway components and cytoplasmic volumes defines survival threshold in erythroid progenitor cells
single-cell multi-omics	DeepCellRegMap: An interpretable deep learning framework for mapping genetic effects at cell subtype resolution using large-scale single-cell sequencing data
single-cell RNA sequencing	A quantum circuit model for inferring gene regulatory networks with application to single-cell transcriptomic data Integrational approaches for cross-species analysis of lung pathologies at single-cell resolution.
single-cell RNA-seq	Deciphering transcriptional drivers of stem cell differentiation using causal inference
Single-cell sequencing	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
single-cell transcriptomics	Investigating brain development using tissue and single-cell gene expression data Towards a Computational Toolkit for Cell Fate Decision Detection
SIR modelling	FAIR sharing of reproducible COVID-19 models of epidemic and pandemic forecast
SIRD compartmental model	Non-parametric model-based estimation of the effective reproduction number for SARS-CoV-2
size control	The Systems of Size and Shape Control
skin aging	Data-driven mathematical modeling of human skin aging and its application for natural compound screening
SLiMs	Proteome-scale mapping of binding sites in the intrinsically disordered regions of human and viral proteomes
Snakebite	Defining Design Rules for Next-Generation Snakebite Antivenoms
SNP-heritability	Genome-wide analysis of genetic variants affecting metabolomic abundance in pigs divergent for feed efficiency
sodium dynamics	Non-monotonic Na+ dynamics in the malaria parasite Plasmodium falciparum
Software	MODalyseR—a novel software for inference of disease module hub regulators identified a putative multiple sclerosis regulator supported by independent eQTL data
software development	PolarityJaM: An image analysis toolbox for cell polarity, junction and morphology quantification
software engineering	New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
sORF-encoded peptides (sPEPs)	What are the functions of the short open reading frame-encoded peptides in monocytes? An interactomic approach.
Spatial architecture	Quantitative Spatial Profiling Reveals Tumor Microenvironment Heterogeneity and Prognostic Biomarkers Associated with Immune Population Architectures
spatial modeling	Virtual Cell Modeling and Simulation Software Stochasticity of Meiotic Entry in Xenopus Oocytes Spatio-temporal modeling reveals a layer of tunable control circuits for the distribution of cytokines in tissues.
Spatial Patterning	Dissecting the Developing Mouse Brain at Spatial Single-Cell Resolution Using PASTA-seq
spatial reconstruction	Reconstruction of regulatory networks driving patterned expression in the Drosophila embryo based on spatially resolved single-cell sequencing data​
Spatial Transcriptomics	Resolving Resolution Hindrances in Spatial Transcriptomics Characterization of cardiac fibroblast remodeling dynamics after myocardial infarction Dissecting the Developing Mouse Brain at Spatial Single-Cell Resolution Using PASTA-seq
Spatio-Temporal Models	Investigating brain development using tissue and single-cell gene expression data
Spatio-temporal noise	Robust oscillations against spatial-temporal noise in intra-inter cellular kinetics
spatiotemporal heterogeneity	Spatially-Coordinated Collective Protein Behaviors Enable Robust Circadian Timekeeping
Species Networks	Discovery of Robust and Highly Specific Microbiome Signatures for Non-Alcoholic Fatty Liver Disease
spectral flow cytometry	Deep learning a model of cytotoxic T cell activation in the tumor microenvironment
SPG7	Exploring the missing heritability in SPG7 heterozygous carriers with Whole Genome Sequencing
Spiking neural network model	Connecting the Neurovascular coupling and Electrophysiological signaling – a modeling approach
splicing code	Using multi-omics data and machine learning to unravel alternative splicing regulation
Spread of COVID-19	Seroepidemiology And Modeling Of SARS-CoV-2 In Ethiopia: Longitudinal Cohort Study Among Front-line Health-care Workers And Community
standardisation	The COmputational MOdeling in BIology NEtwork in 2022: Evolving needs in standardisation and model reuse
Standardization	Computationally Modeling the Human Microbiome of the Respiratory Tract
standards	FROG Analysis - a community standard to foster reproducibility and curation of constraint-based models
Staphylococcus aureus	The metabolic community model of Staphylococcus aureus and four abundant human nasal microbes
State transition graph	Boolean dynamic modeling of TNFR1 signaling predicts a nested feedback loop regulating the apoptotic response at single-cell level (EXCEPTION - ZOOM)
statistical inference	Efficient brute-force model selection by iterative elimination of less useful model subspaces
Statistical modeling	Multimodal perception links cellular state to decision making in single cells
statistical physics	Stochasticity of Meiotic Entry in Xenopus Oocytes Mitotic Memory as Spontaneous Symmetry Breaking in the Cell
statistical scaling laws	Macroecological Laws Naturally Arise from Complex Chaotic Dynamics of Gut Microbiota
statistics	The insidious trappings of gene set enrichments
stem cell differentiation	Inference and dynamical simulation of the gene-regulatory network in single cells
Stem Cell Growth Dynamics	Understanding Stem Cell Growth Dynamics in Human Cerebral Organoids
stem cell transplantation	The role of the kynurenine metabolism in chronic graft-versus-host-disease: Insights from computational modeling and patient data
Stem cells	Inferring Gene Networks Rewiring of Naive and Primed Human Embryonic Stem Cells During Cellular Reprogramming Using Single-Cell RNA-seq Data
stem elongation	Cell Type view into tomato stem elongation in Shade avoidance response
stepwise regression	Efficient brute-force model selection by iterative elimination of less useful model subspaces
stochastic	FitMultiCell: Simulating and parameterizating computational models of multi-cellular processes
stochastic adaptation	How do single bacterial cells make decisions?
Stochastic model	A robust model of neural superposition sorting Stochasticity of Meiotic Entry in Xenopus Oocytes
Stochastic Modelling	Understanding Stem Cell Growth Dynamics in Human Cerebral Organoids
Stochastic reaction networks	A generic framework to coarse-grain stochastic reaction networks by Abstract Interpretation
stochastic simulation	COVRECON: Combining Genome-scale Metabolic Network Reconstruction and Data-driven Inverse Modeling to Reveal Causal Biochemical Regulations Universally valid reduction of multiscale stochastic biochemical systems with simple non-elementary propensities
Strain-specific model reconstruction	Computationally Modeling the Human Microbiome of the Respiratory Tract
stress responses	Dissecting the principles underlying transcriptional heterogeneity
stress signaling network	Stress Knowledge Map: A knowledge resource for modeling of plant stress responses
stroke	Digital twins and hybrid modelling for simulation of physiological variables and stroke risk
Structural proteomics	Structural proteomics evidence for a predicted glycolytic metabolon
structural reduction	Structural reduction of chemical reaction networks based on topology
structure	The workings and impact of AlphaFold
Structured population equations	A physiologically-structured population model for pharmacokinetics of orally inhaled drugs
subcellular compartments	Modelling how mRNA flows through subcellular compartments
subcritical pitchfork bifurcation	Dynamical basis of cellular sensing and responsiveness to spatial-temporal signals
Substrate scope	Prediction of enzyme kinetic parameters and substrate scopes using artificial intelligence
Subtype Analysis	MultiOmics Network Embedding for SubType Analysis
succession	Effect of dispersal by inundation on soil bacterial communities depends on soil developmental stage
Sucrose synthase 1	Co-expression analysis of transcriptome and proteome identifies LRR-VIII-1 kinase and MAPK-kinase (MEK1) regulatory modules associated with P-deficiency adaptation and P use efficiency in maize
SUMO E3 ligases	Molecular principles governing substrate specificity of human SUMO E3 Ligases
Supercomputer Fugaku	XAI × Fugaku uncovered EMT mechanisms via cancer characteristic specific gene network analysis
support vector machine	Using multi-omics data and machine learning to unravel alternative splicing regulation
surrogate models	Accelerating whole-cell modelling with surrogate machine learning models
Survival models	Modeling disease progression in spinocerebellar ataxias
Swi-Snf	Investigating antagonistic chromatin remodeling by the Swi-Snf and Tup1-Cyc8 (Ssn6) complexes in yeast
Switch-like responses	Mathematical modelling of the regulatory mechanisms of keratinocyte differentiation for epidermal homeostasis
Synapse	Inference of a causal synaptic molecular network from multiplexed imaging and its perturbations in autism and schizophrenia
Syntheic Biology	Robust oscillations against spatial-temporal noise in intra-inter cellular kinetics
synthetic biology	Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction Learning synthetic cell classifier designs with genetic algorithms and logic programming Towards identification of new life cycle-associated regions in phage genomes using deep learning Fast and scalable machine learning approach for dynamic metabolic engineering
synthetic oscillator	Model-based design of a synthetic oscillator based on an epigenetic memory system
Synthetic oscillators	Robust oscillations against spatial-temporal noise in intra-inter cellular kinetics
System	System Pathology of Cancer
System biology	Reconstructing a quantitative measure of disease dynamics for discovery and clinical benefit
System identification	Decoding cellular deformation from pseudo-simultaneously observed RhoGTPase activities Discovery of Hidden Control Variables and modeling Non-Linear Dynamical Biological Systems
System pharmacology	From System Biology to Pharmacology: Identifying what is important Numerical approaches for the rapid analysis of prophylactic efficacy against HIV
system scale omics	The metabolic and proteomic landscape of genome-scale genetic perturbation
system-level modeling	In silico analysis of metabolic capabilities in a synthetic community of phycosphere bacteria
systems biology	Disentangling the internal composition of tumour activities through a hierarchical factorization model Virtual Cell Modeling and Simulation Software Mathematical modeling of cytokine interplay in human monocytes during LPS stimulation Amino Acid Impact on Protein Secretion in B. subtilis: an RBA Approach Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction Modelling mutations in B-cell malignancies reveals how mutations synergise to contribute to aggressive disease. Deep insight into SABIO-RK data via visualization A mechanistic model for endocrine profiles of female puberty maturation On the relation between input and output distributions of scRNA-seq experiments Temporal Proteomics and Transcriptomics Unravels the Host-Pathogen Interaction Network of Macrophages and Corynebacterium diphtheriae. A dynamic HIF1α-PPARγ circuit controls a paradoxical adipocyte regulatory landscape Manually curated genome-scale metabolic reconstructions of the multi-drug resistant Gram-negative pathogens A. baumannii and K. pneumoniae Expanding the disease network of Glioblastoma Multiforme via topological analysis BioCypher: an ontology-driven framework for flexible harmonisation of large-scale biomedical knowledge graphs Cancer cell fate decisions CRISPRi meets metabolomics: a platform for rapid functional annotation of compound libraries Disentangling Proliferation Signaling in Breast Cancer Subtypes based on an integrative modeling approach Harnessing cancer heterogeneity for the systematic discovery of treatable cancer-driver exons with spotter Efficient brute-force model selection by iterative elimination of less useful model subspaces The transcriptome dynamics of single cells during the cell cycle Metabolome-wise analysis of plants exposed to abiotic stress conditions to identify potential metabolites inducers of cross-tolerance to biotic stressors Systems Approaches to Deciphering Kinase Signaling and the Phosphoproteome: A Focus on Cancer, Inflammation, and DNA Damage GEARS: Predicting transcriptional outcomes of novel multi-gene perturbations On data-driven learning of an effective energy landscape from trajectories of nonlinear dynamical biological systems Quantitative Spatial Profiling Reveals Tumor Microenvironment Heterogeneity and Prognostic Biomarkers Associated with Immune Population Architectures Patterns of differentially essential genetic interactions characterize functional modules across cancer types Metabolic Atlas - extending metabolic networks for model organisms with enzyme turnover predictions with GotEnzymes A comprehensive mechanistic model of adipocyte signaling with layers of confidence Composing and perturbing large-scale constraint-based metabolic models with COBREXA.jl
Systems Biology Markup Language (SBML)	SynBioSuite: Web-based modeling and analysis of biological systems
Systems biology modelling	A Reproducibility Scorecard for Self-checking of Systems Biology Models
Systems Control	NETISCE: A dynamical systems and control theory approach to cell reprogramming
systems development	Metabolic Atlas - extending metabolic networks for model organisms with enzyme turnover predictions with GotEnzymes
systems medicine	Deciphering dysregulation in Erythroleukemia to design intervention strategies Mathematical model of the immunopathological progression of tuberculosis A systems pharmacology approach reveals robust drug metabolism and altered glucuronide disposition in a mouse model of liver cirrhosis Information Processing by Homo-Oligomeric Proteins: From First Principles to Cardiac Disease The COmputational MOdeling in BIology NEtwork in 2022: Evolving needs in standardisation and model reuse A disease network-based deep learning approach for characterizing melanoma Computational modeling of DLBCL predicts response to BH3-mimetics Cohort-specific Boolean models highlight different regulatory modules during disease progression
Systems pharmacokinetics	Defining Design Rules for Next-Generation Snakebite Antivenoms
Systems pharmacology	A framework for predicting the effect of multiple factors on HIV protection from heterosexual transmission through truvada-based pre-exposure prophylaxis (PrEP) in women A systems pharmacology approach reveals robust drug metabolism and altered glucuronide disposition in a mouse model of liver cirrhosis CRISPRi meets metabolomics: a platform for rapid functional annotation of compound libraries Formatting Biological Big Data to Enable Systems Pharmacology
T
T cell clustering	Spatio-temporal modeling reveals a layer of tunable control circuits for the distribution of cytokines in tissues.
T cells	Deep learning a model of cytotoxic T cell activation in the tumor microenvironment
Tandem Mass Spectrometry	LipiDetective: a Deep Learning Model for the Detection of Lipid Species in Mass Spectra
target engagement	Decrypting drug actions and protein modifications by dose- and time-resolved proteomics
target selection	Harnessing cancer heterogeneity for the systematic discovery of treatable cancer-driver exons with spotter
Targeted therapies	Patient-specific modeling of the TP53 pathway in endometrial carcinoma patients
targeted therapy	3D reconstruction and mathematical modelling of whole slide images to elucidate resistance to the targeted therapy in melanoma Disentangling Proliferation Signaling in Breast Cancer Subtypes based on an integrative modeling approach
task-specific synthetic sample generation	Elucidating the role of TAS2R43 in HGT-1 cells – an integrated omics approach
taxonomic inference	A probabilistic graphical model for taxonomic profiling of viral and microbiome proteome samples
TBS1	Technology advancements to enhance the future of Immune Health The Transforming Growth Factor beta Riddle – From the Cellular to the Patient Scale Elucidating functions of microbial dark matter The genotype-phenotype nexus: uncovering causal mechanisms in neurodegenerative disease with experimental and theoretical approaches Therapy-related senescence signatures in lymphoma Systematic elucidation and pharmacological targeting of non-oncogene dependencies at the single cell level.
TBS2	Technology advancements to enhance the future of Immune Health The Transforming Growth Factor beta Riddle – From the Cellular to the Patient Scale Elucidating functions of microbial dark matter The genotype-phenotype nexus: uncovering causal mechanisms in neurodegenerative disease with experimental and theoretical approaches Therapy-related senescence signatures in lymphoma Systematic elucidation and pharmacological targeting of non-oncogene dependencies at the single cell level.
TBS3	Technology advancements to enhance the future of Immune Health The Transforming Growth Factor beta Riddle – From the Cellular to the Patient Scale Elucidating functions of microbial dark matter The genotype-phenotype nexus: uncovering causal mechanisms in neurodegenerative disease with experimental and theoretical approaches Therapy-related senescence signatures in lymphoma Systematic elucidation and pharmacological targeting of non-oncogene dependencies at the single cell level.
TCGA	Patient-specific modeling of the TP53 pathway in endometrial carcinoma patients
TEE	Web-based analysis of indirect calorimetric data arising from metabolic phenotyping systems
temporal turnover	Effect of dispersal by inundation on soil bacterial communities depends on soil developmental stage
The principle of maximum entropy	Universality of form: The case of retinal cone photoreceptor mosaics
Therapeutic target	Cohort-specific Boolean models highlight different regulatory modules during disease progression
therapy resistance	A Mechanistic model of EGFR and ERK signaling reveals how allostery and rewiring contribute to drug resistance
Thermodynamic models	Structural proteomics evidence for a predicted glycolytic metabolon
Thermodynamics-based Flux Analysis	Integrating 13C labeling and thermodynamic data for thermodynamically consistent Bayesian Metabolic Flux Analysis (T13C-MFA)
thermodynamics-based parameterization	Data-driven modeling of mitochondrial metabolism
thread-safe	Rapid parallel model inference and on-the-fly tiling of digital pathology images
tidal regime	Effect of dispersal by inundation on soil bacterial communities depends on soil developmental stage
time-course transcriptomics	Data-driven modeling of cell-cell communication networks
Time-series analysis	Dynamics of the circadian clock in models of cancer and its potential for treatment
Time-series Classification	Analyzing single-cell trajectories with augmented machine learning methods predicts cancer drugs response in live-cell microscopy assays
time-series data	Nonstationary Biomedical Signal Feature Extraction
time-series experiments	Inferring individual interactions in gene regulatory networks with delays from time-series experiments
Time-varying extracellular signals	Theory of biochemical information processing with transients
tissue architecture	Spatio-temporal modeling reveals a layer of tunable control circuits for the distribution of cytokines in tissues.
tissue-specific model	New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
tissue-specificity	Tissue-specific codon usage: from systems to synthetic biology
TNFα	Boolean dynamic modeling of TNFR1 signaling predicts a nested feedback loop regulating the apoptotic response at single-cell level (EXCEPTION - ZOOM)
Toll-like receptor	Targeted Proteomics-Driven Computational Modeling of the Mouse Macrophage Toll-like Receptor Signaling Pathway
tomatoes	Cell Type view into tomato stem elongation in Shade avoidance response
tool	Stress Knowledge Map: A knowledge resource for modeling of plant stress responses
topology	Topological properties accurately predict cell division events and organization of Arabidopsis thaliana’s shoot apical meristem
Topology-based Enrichment	Temporal Proteomics and Transcriptomics Unravels the Host-Pathogen Interaction Network of Macrophages and Corynebacterium diphtheriae.
TOR signaling	Dynamic metabolome profiling uncovers potential TOR signaling genes
TP53	Patient-specific modeling of the TP53 pathway in endometrial carcinoma patients
trajectory inference	FLOVELO - Pushing Boundaries of Cell Dynamics Inference with Maximum Flow Networks
Trajectory reconstruction	Improving our Mechanistic Understanding of Cell Cycle Dynamics
Trans-omic network	Transomic network analysis of glucose metabolism and its dysfunction associated with obesity
transciptional heterogeneity	Dissecting the principles underlying transcriptional heterogeneity
Transcription	Dynamic single cell analysis of a MAPK signaling cascade and its impact on transcriptional output A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation
transcription factor	Cell-to-cell variability in JAK2/STAT5 pathway components and cytoplasmic volumes defines survival threshold in erythroid progenitor cells
transcription factors	Being noisy in a crowd: differential selective pressure on gene expression noise in model gene regulatory networks
transcriptional fluctuations	Transcriptional fluctuations govern the serum dependent cell cycle duration heterogeneities in Mammalian cells
transcriptional regulation	A Novel and Robust Molecular Switch Actuating the Quantitative Model of Eukaryotic Cell Cycle Control
transcriptional repression	Combined multiple transcriptional repression mechanisms generate ultrasensitivity and oscillations
transcriptome	Neural Circuits Underlying Autism Spectrum Disorders The transcriptome dynamics of single cells during the cell cycle Co-expression analysis of transcriptome and proteome identifies LRR-VIII-1 kinase and MAPK-kinase (MEK1) regulatory modules associated with P-deficiency adaptation and P use efficiency in maize
Transcriptomics	Multiple-omics based metabolic modelling reveals effects of drug-induced liver toxicity Temporal Proteomics and Transcriptomics Unravels the Host-Pathogen Interaction Network of Macrophages and Corynebacterium diphtheriae. Accounting for low transcript sampling rates in scRNA-seq using the Good-Turing estimator A workflow for the creation of regulatory networks integrating miRNAs and lncRNAs associated with exposure to ionizing radiation using open source data and tools GEARS: Predicting transcriptional outcomes of novel multi-gene perturbations Molecular regulators of catecholamine response in human pulmonary microvascular endothelial cells
transfer function	Periodic Forcing of the ERK pathway
Transfer learning	Explainable Machine Learning in Mass Spectrometry-based Proteomics Predicting developmental states in zebrafish using transfer learning New data-driven gene representations using deep autoencoders at multiple omics to identify candidate disease genes and robust classifiers
transferability	Advantages of Ensemble CNN’s in Computational Pathology.
transition state	Single cell pseudo-time inference based on copy number variants for identifying a tumor transition state
translation	Tissue-specific codon usage: from systems to synthetic biology
Translation of knowledge	From System Biology to Pharmacology: Identifying what is important
translation rate	Dynamics of growth and ribosome level in batch cultures of S. cerevisiae
Translational Modeling	Multi-platform model training reduces bias in translational drug sensitivity models for cancer patients
transposable elements	Transcription start site signal profiling improves transposable element RNA expression analysis at locus-level
transposons	Transcription start site signal profiling improves transposable element RNA expression analysis at locus-level
Tri-stability	Unraveling the role of network motifs to decipher the origin of robust decision-making in biological systems
Trigger waves	Stochasticity of Meiotic Entry in Xenopus Oocytes
Triple-negative breast cancer	Are metastatic triple negative breast cancers closer to their parental tumors or primary tumors of their destination tissues?
Tristability	Initial source of heterogeneity in a model for cell fate decision in the early mammalian embryo
tRNA	An optimal RNA growth law and its relationship with genome organization in bacteria Tissue-specific codon usage: from systems to synthetic biology
tropomyosin	Predicting pathogenicity of TPM1 variants using multi-scale models
tryptophan	The role of the kynurenine metabolism in chronic graft-versus-host-disease: Insights from computational modeling and patient data
TSE	Web-based analysis of indirect calorimetric data arising from metabolic phenotyping systems
TSS	Transcription start site signal profiling improves transposable element RNA expression analysis at locus-level
Tuberculosis	Mathematical model of the immunopathological progression of tuberculosis
Tumor architecture	Tribus reveals the single-cell tumor architecture and effect of chemotherapy in ovarian cancer
Tumor environment	Vasculogenic mimicry induced by multicellular interaction in a 3D glioblastoma model-on-a-chip
tumor heterogeneity	Cell type-specific gene co-expression modules define tumor heterogeneity in melanoma patients
Tumor microenvironment	Modeling the tumor microenvironment in patient-derived organoid culture Tribus reveals the single-cell tumor architecture and effect of chemotherapy in ovarian cancer
Tumor-immune microenvironment	Quantitative Spatial Profiling Reveals Tumor Microenvironment Heterogeneity and Prognostic Biomarkers Associated with Immune Population Architectures
Tumor-microenvironment	Single-cell spatial atlas of high-grade serous ovarian cancer
Tup1-Cyc8	Investigating antagonistic chromatin remodeling by the Swi-Snf and Tup1-Cyc8 (Ssn6) complexes in yeast
Turnover number	Prediction of enzyme kinetic parameters and substrate scopes using artificial intelligence
Type-1 Interferon	Multi-dimensional immune correlates of early prediction of COVID-19 severe versus asymptomatic disease course
U
ubiquitin	Decrypting drug actions and protein modifications by dose- and time-resolved proteomics
ubiquitination	Rhythmic protein degradation for cost-effective circadian oscillation
ultrasensitivity	Combined multiple transcriptional repression mechanisms generate ultrasensitivity and oscillations
uncertainty	Posterior marginalization accelerates Bayesian inference for dynamical systems
Uncertainty Quantification	Exact Confidence Regions for Non-Linear Models
unmeasured components	Inferring individual interactions in gene regulatory networks with delays from time-series experiments
UNRES force field	Studying conformational transitions of selected proteins using UNRES coarse-grained replica exchange molecular dynamics simulations with Lorentzian restraints.
Unsupervised clustering	Analyzing human E3 ligome for efficient design of PROTACs
unsupervised learning	Predicting developmental states in zebrafish using transfer learning
V
vaccines	A multi-strain model of immunization against influenza A viruses after infection or vaccination Machine learning for hard biological problems Preventing & limiting pandemics through vaccination: what have we learned from COVID-19 and MPX?
vascular remodeling	Development of a geometric blood vessel model to quantify morphological changes of endothelial cells in 3D during vascular remodeling
Vasculogenic mimicry	Vasculogenic mimicry induced by multicellular interaction in a 3D glioblastoma model-on-a-chip
venn diagrams	The insidious trappings of gene set enrichments
vesicle fusion dynamics	Variance of filtered signals: characterization for linear reaction networks and application to neurotransmission dynamics
vessel geometry	Development of a geometric blood vessel model to quantify morphological changes of endothelial cells in 3D during vascular remodeling
Virtual Patients	Personalized medicine for Multiple Sclerosis treatment strategies at the individual and population level
Virtual Reality	Delivering Virtual Reality and Gaming Technologies to the Field of Systems Biology
Virtual Screening / Docking	Identification of a SARS-CoV-2 inhibitor by combining binary protein-protein interaction mapping, structure prediction and virtual screening
VirtualLeaf	Computational analysis of cambium activity during plant radial growth
virus mutations	New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
virus proteomics	A probabilistic graphical model for taxonomic profiling of viral and microbiome proteome samples
virus-host interactions	Proteome-scale mapping of binding sites in the intrinsically disordered regions of human and viral proteomes
visualization	Delivering Virtual Reality and Gaming Technologies to the Field of Systems Biology Deep insight into SABIO-RK data via visualization
vitamin B6	The role of the kynurenine metabolism in chronic graft-versus-host-disease: Insights from computational modeling and patient data
W
Waddington's Landscape	Construction and Decomposition of Cellular Energy Landscapes using Hopfield Neural Networks
Wastewater Monitoring	INSIDe: Integrative modeling of the spread of serious infectious diseases
web application	Web-based analysis of indirect calorimetric data arising from metabolic phenotyping systems BioSimulations: integrated models, model languages, model repositories, simulation experiments, simulation tools and data visualization COVIDpro: Database for mining protein dysregulation in patients with COVID-19
Weiner Filtering	Optimal prediction of a noisy signal
Western blot	BlotIt - Optimal alignment of Western blot and qPCR experiments
Whole gene expression	Reinforcement learning and Monte-Carlo tree search in gene expression enable the entire gene regulation in a cell
whole genome sequencing	Exploring the missing heritability in SPG7 heterozygous carriers with Whole Genome Sequencing
whole-cell model	A low-granularity model integrating metabolism, growth and cell cycle: towards multi-level whole cell modeling of budding yeast
whole-cell modeling	The E. coli Whole-Cell Modeling Project: Vision and Progress
whole-cell modelling	Accelerating whole-cell modelling with surrogate machine learning models How can we unleash the potentials of whole-cell modelling?
Working Memory	Cells use molecular working memory to navigate in changing chemoattractant fields
Wound healing	A Systems Biology Approach To Study The Spatiotemporal Dynamics Of Senescent Cells In Wound Healing And Tissue Repair Morphometric analysis of macrophage populations in response to animal-derived extracellular matrices
Y
Yeast	Mapping Genetic and Chemical Genetic Interaction Networks in Yeast and Human Cells
young	Introduction
Z
zarr	Rapid parallel model inference and on-the-fly tiling of digital pathology images
zebrafish development	Predicting developmental states in zebrafish using transfer learning
Zm00001d038522	Co-expression analysis of transcriptome and proteome identifies LRR-VIII-1 kinase and MAPK-kinase (MEK1) regulatory modules associated with P-deficiency adaptation and P use efficiency in maize
Zm00001d043609	Co-expression analysis of transcriptome and proteome identifies LRR-VIII-1 kinase and MAPK-kinase (MEK1) regulatory modules associated with P-deficiency adaptation and P use efficiency in maize
Zm00001d045042	Co-expression analysis of transcriptome and proteome identifies LRR-VIII-1 kinase and MAPK-kinase (MEK1) regulatory modules associated with P-deficiency adaptation and P use efficiency in maize