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

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A. D'Alessandro, Lorenza	Multilevel approach characterizing the progression of fatty liver disease Alterations in hepatocyte growth factor induced signal transduction in fatty liver disease foster cancer development
A. Knoblich, Jürgen	Understanding Stem Cell Growth Dynamics in Human Cerebral Organoids
A.Buchner, Bianca	Characterizing all feasible metabolic conversions of individual cells and microbial communities with elementary conversion modes.
Aaronson, Jeff	Precision machine-learning identifies a new paradigm for therapeutic discovery in Huntington’s disease: remodeling stress response to re-instate neuronal health and resilience.
Abdallah, Zahraa	Accelerating whole-cell modelling with surrogate machine learning models
Abdelilah-Seyfried, Salim	Development of a geometric blood vessel model to quantify morphological changes of endothelial cells in 3D during vascular remodeling
Abdullah, Yomn	Deciphering dysregulation in Erythroleukemia to design intervention strategies
Abizanda, Gloria	Characterization of cardiac fibroblast remodeling dynamics after myocardial infarction
Achar, Sooraj	Deep learning a model of cytotoxic T cell activation in the tumor microenvironment
Ackermann, Jörg	Agent-based modeling of spatiotemporal organization of bacteria in the human gut Modeling the adaptive immune response of a lymph node as Petri net Manatee invariants entailing signal transduction pathways in Petri nets of signaling networks A graph-based approach to analyze signal transduction involving cytokines and the JAK-STAT pathway in hepatocytes using Petri nets
Adams, Hollie	Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide images
Adler, Stephan O.	Control of COVID-19 Outbreaks under Stochastic Community Dynamics, Bimodality, or Limited Vaccination
Adlung, Lorenz	Cell-to-cell variability in JAK2/STAT5 pathway components and cytoplasmic volumes defines survival threshold in erythroid progenitor cells
Adriaens, Michiel	Analysis of multivariate longitudinal metabolomics data from meal challenges using RM-ASCA+
Afman, Lydia	The Mixed Meal Model; quantifying metabolic resilience in overweight and obesity
Agi, Egemen	A robust model of neural superposition sorting
Ainciburu, Marina	Characterization of cardiac fibroblast remodeling dynamics after myocardial infarction
Airoldi, Cristina	A low-granularity model integrating metabolism, growth and cell cycle: towards multi-level whole cell modeling of budding yeast
Akhshi, Amin	Deep learning a model of cytotoxic T cell activation in the tumor microenvironment
Alamoudi, Emad	FitMultiCell: Simulating and parameterizating computational models of multi-cellular processes
Alberghina, Lilia	A low-granularity model integrating metabolism, growth and cell cycle: towards multi-level whole cell modeling of budding yeast
Albers, Jonas	The potential of PBI for high resolution lung imaging in patients
Albrecht, Jan Phillipp	PolarityJaM: An image analysis toolbox for cell polarity, junction and morphology quantification
Alhussain, Mohamed	Investigating antagonistic chromatin remodeling by the Swi-Snf and Tup1-Cyc8 (Ssn6) complexes in yeast
Allister, Aldrige Bernardus	Exploring the “dark proteome” in hepatocellular carcinoma
Alonso-Pernas, Pol	An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness
Alonso-Roman, Raquel	Lactobacillus rhamnosus colonisation antagonizes Candida albicans by forcing metabolic adaptations that compromise pathogenicity
Aloy, Patrick	Microbial compound bioactivity descriptors enable large-scale prediction of small molecule impact on microbiota species and pathogens Formatting Biological Big Data to Enable Systems Pharmacology Improving drug-induced transcriptional descriptors and their biological connectivity
Alshoyokh, Mahdi	Inferring Gene Networks Rewiring of Naive and Primed Human Embryonic Stem Cells During Cellular Reprogramming Using Single-Cell RNA-seq Data
Altafini, Claudio	Proteomics profiling revealed a combination of protein biomarkers for predicting disease trajectory of multiple sclerosis
Altan-Bonnet, Grégoire	Deep learning a model of cytotoxic T cell activation in the tumor microenvironment
Altenburg, Tom	Explainable Machine Learning in Mass Spectrometry-based Proteomics
Altschmied, Lothar	Elucidating the role of TAS2R43 in HGT-1 cells – an integrated omics approach
Altschuler, Steven	Cancer cell fate decisions Avoiding errant activation of mitophagy: dual factor authentication of the Pink1/Parkin circuit
Alvarado, Alejandra	Mapping metabolic regulation in E. coli with a metabolism-wide CRISPRi library
Alves, Frauke	Quantification of imaging biomarkers in the extracellular matrix of left and right sided colon cancer tissues The potential of PBI for high resolution lung imaging in patients
Amiri, Behnam	On multistability and constitutive relations of cell motion on Fibronectin lanes
Anar, Sanchir	FISHing for Correlation
Angermair, Gerald	INSIDe: Integrative modeling of the spread of serious infectious diseases
Anglada-Girotto, Miquel	Harnessing cancer heterogeneity for the systematic discovery of treatable cancer-driver exons with spotter
Annerer-Walcher, Lukas	Patterns of differentially essential genetic interactions characterize functional modules across cancer types
Antczak, Philipp	Improving Our Understanding of ADPKD: Computational Analysis of Metabolome Data
Anton, Mihail	Metabolic Atlas - extending metabolic networks for model organisms with enzyme turnover predictions with GotEnzymes
Anttila, Ella	Tribus reveals the single-cell tumor architecture and effect of chemotherapy in ovarian cancer Single-cell spatial atlas of high-grade serous ovarian cancer
Arfelli, Fulvia	The potential of PBI for high resolution lung imaging in patients
Armstrong, Anthony	Targeted Proteomics-Driven Computational Modeling of the Mouse Macrophage Toll-like Receptor Signaling Pathway
Arora, Bharti	Quantification of imaging biomarkers in the extracellular matrix of left and right sided colon cancer tissues
Arslan, Janan	3D reconstruction and mathematical modelling of whole slide images to elucidate resistance to the targeted therapy in melanoma
Arts, Ilja	Analysis of multivariate longitudinal metabolomics data from meal challenges using RM-ASCA+ The Mixed Meal Model; quantifying metabolic resilience in overweight and obesity
Arutjunjan, Rafael	Exact Confidence Regions for Non-Linear Models Personalized Treatment of Anemia in Lung Carcinoma
Arutjunjan, Rafael	A powerful modelling approach tailored to cellular signalling
Astaburuaga-García, Rosario	Ionizing radiation triggers differential signaling dynamics of p-p53 and p-ERK1/2 in sensitive and resistant HNSCC cell clones
Aulehla, Alexander	A bottom-up investigation of emergence in a self-organizing model of embryonic pattern formation
Avar, Göksu	The pharmaco-epigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity
Ayar, Enes Sefa	Leveraging the Molecular Signatures of Cancer for Dynamic Network Modeling
Aydoğan, Hande Özge	Improving Our Understanding of ADPKD: Computational Analysis of Metabolome Data
Azevedo, Manuel	Multi-Omics Regulatory Network Inference in the Presence of Missing Data
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Backes, Thierry	Statistical estimation of enzyme kinetics and pathway cost predicts overflow metabolism
Badkas, Apurva	Model ensembling as a tool to form interpretable multi-omic predictors of cancer pharmacosensitivity Expanding the disease network of Glioblastoma Multiforme via topological analysis
Baebler, Špela	Stress Knowledge Map: A knowledge resource for modeling of plant stress responses
Baeumer, Lisa	Temporal Proteomics and Transcriptomics Unravels the Host-Pathogen Interaction Network of Macrophages and Corynebacterium diphtheriae.
Bahar, Yozlem	Logical modeling of signaling mechanisms in early development
Bakal, Chris	The Systems of Size and Shape Control
Bakuli, Abhishek	Seroepidemiology And Modeling Of SARS-CoV-2 In Ethiopia: Longitudinal Cohort Study Among Front-line Health-care Workers And Community
Balakrishnan, Sanjaay	FROG Analysis - a community standard to foster reproducibility and curation of constraint-based models
Balakrishnan, Shreedula	NETISCE: A dynamical systems and control theory approach to cell reprogramming
Balaur, Irina	FAIR assessment of biosimulation models - a cross-community project
Balderas, Robert	Technology advancements to enhance the future of Immune Health
Balsamy, Subash	Evaluation of methods to compute quasi-potential functions and their use as systems biology models Discovery of Hidden Control Variables and modeling Non-Linear Dynamical Biological Systems Towards a Computational Toolkit for Cell Fate Decision Detection
Balubaid, Ali	Evaluation of methods to compute quasi-potential functions and their use as systems biology models Discovery of Hidden Control Variables and modeling Non-Linear Dynamical Biological Systems On data-driven learning of an effective energy landscape from trajectories of nonlinear dynamical biological systems Towards a Computational Toolkit for Cell Fate Decision Detection Inferring Gene Networks Rewiring of Naive and Primed Human Embryonic Stem Cells During Cellular Reprogramming Using Single-Cell RNA-seq Data
Bamagoos, Atif	Investigating antagonistic chromatin remodeling by the Swi-Snf and Tup1-Cyc8 (Ssn6) complexes in yeast
Bang, Severin	More BANG for the buck: how to distribute measurements to optimize information gain for mathematical models Deciphering dysregulation in Erythroleukemia to design intervention strategies BlotIt - Optimal alignment of Western blot and qPCR experiments
Banga, Julio	Improving our Mechanistic Understanding of Cell Cycle Dynamics
Bankier, Sean	Identification of causal genes at GWAS loci with pleiotropic gene regulatory effects using instrumental variable sets
Bansal, Vikas	Transcription start site signal profiling improves transposable element RNA expression analysis at locus-level
Baratella, Ellisa	The potential of PBI for high resolution lung imaging in patients
Barbara, Majello	MultiOmics Network Embedding for SubType Analysis
Barber, Amelia	Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection
Barberis, Matteo	A Novel and Robust Molecular Switch Actuating the Quantitative Model of Eukaryotic Cell Cycle Control
Barlas, Afsar	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
Barry, Craig	Implementation of multiplexed single cell proteomics for the investigation of cellular heterogeneity in mammalian cell lines
Bartoszewicz, Jakub M.	Towards identification of new life cycle-associated regions in phage genomes using deep learning
Bastian, Peter	DUNE-COPASI: Multi-Compartment Diffusion-Reaction solver for Cell Biology
Batchelor, Eric	Coordination of p53 and MAPK dynamics controls heterogeneous responses to genotoxic agents in single cells
Bathe, Mark	Inference of a causal synaptic molecular network from multiplexed imaging and its perturbations in autism and schizophrenia
Bauer, Michael	An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness
Baum, Katharina	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
Baum, Katharina	Computational modeling of the Hes1 oscillator for the self-renewal of muscle stem cells
Baumbach, Jan	Inference of differential gene regulatory networks from gene expression data using boosted differential trees
Bayer, Florian	DecryptM: decrypting drug actions and protein modification by dose- and time-resolved proteomics
Bayer, Florian P	Decrypting drug actions and protein modifications by dose- and time-resolved proteomics
Beber, Moritz	FROG Analysis - a community standard to foster reproducibility and curation of constraint-based models
Beetz, Stephanie	Identification of a SARS-CoV-2 inhibitor by combining binary protein-protein interaction mapping, structure prediction and virtual screening
Behr, Juergen	Elucidating the role of TAS2R43 in HGT-1 cells – an integrated omics approach
Bej, Saptarshi	Elucidating the role of TAS2R43 in HGT-1 cells – an integrated omics approach
Bellec, Maelle	Mitotic Memory as Spontaneous Symmetry Breaking in the Cell
Benary, Uwe	Analysis of the impact of MYCN on the energy metabolism in neuroblastoma using metabolomics data and mathematical modeling
Benisty, Hannah	Tissue-specific codon usage: from systems to synthetic biology
Berdiel-Acer, Mireia	Disentangling Proliferation Signaling in Breast Cancer Subtypes based on an integrative modeling approach
Berg, Thomas	Multilevel approach characterizing the progression of fatty liver disease
Bergmann, Ariane	Dynamic metabolome profiling uncovers potential TOR signaling genes
Bergmann, Frank T.	FROG Analysis - a community standard to foster reproducibility and curation of constraint-based models
Berking, Carola	A disease network-based deep learning approach for characterizing melanoma
Bernal-Tamayo, Juan P.	Construction and Decomposition of Cellular Energy Landscapes using Hopfield Neural Networks Evaluation of methods to compute quasi-potential functions and their use as systems biology models Discovery of Hidden Control Variables and modeling Non-Linear Dynamical Biological Systems
Berner, Nicola	DecryptM: decrypting drug actions and protein modification by dose- and time-resolved proteomics
Bernhardt, Stephan	Disentangling Proliferation Signaling in Breast Cancer Subtypes based on an integrative modeling approach
Betts, Courtney	Quantitative Spatial Profiling Reveals Tumor Microenvironment Heterogeneity and Prognostic Biomarkers Associated with Immune Population Architectures
Beygi, Alireza	Universality of form: The case of retinal cone photoreceptor mosaics
Bhaskara, Ramachandra M.	Molecular principles governing substrate specificity of human SUMO E3 Ligases Analyzing human E3 ligome for efficient design of PROTACs
Bi, Shuangyu	Dynamic fluctuations in a bacterial metabolic network
Bias, Manish	Analysis of Heterogeneity in the Tumor Microenvironment in the 4NQO HNSCC Mouse Model
Bickenbach, Johannes	A training strategy for hybrid models to break the curse of dimensionality: An application in mortality estimation for cohorts of COVID-19 patients
Biederer, Jürgen	The potential of PBI for high resolution lung imaging in patients
Biermayer, Ina	Multilevel approach characterizing the progression of fatty liver disease Alterations in hepatocyte growth factor induced signal transduction in fatty liver disease foster cancer development
Bignell, Elaine	Latent variable models of fungal growth considering the data measurement process
Birchmeier, Carmen	Computational modeling of the Hes1 oscillator for the self-renewal of muscle stem cells
Biskupek, Iga	Studying conformational transitions of selected proteins using UNRES coarse-grained replica exchange molecular dynamics simulations with Lorentzian restraints.
Blank, Lars	A physiology-based model of bile acid metabolism in mice
Blavier, Jeremy	Identification of a SARS-CoV-2 inhibitor by combining binary protein-protein interaction mapping, structure prediction and virtual screening
Blee, Johanna	Defining Design Rules for Next-Generation Snakebite Antivenoms
Bleker, Carissa	Stress Knowledge Map: A knowledge resource for modeling of plant stress responses
Blinov, Michael	BioSimulations: integrated models, model languages, model repositories, simulation experiments, simulation tools and data visualization Virtual Cell Modeling and Simulation Software
Blumenthal, David B.	Inference of differential gene regulatory networks from gene expression data using boosted differential trees
Blüthgen, Nils	Ionizing radiation triggers differential signaling dynamics of p-p53 and p-ERK1/2 in sensitive and resistant HNSCC cell clones Modeling the tumor microenvironment in patient-derived organoid culture Modelling how mRNA flows through subcellular compartments
Bodeit, Oliver	Control of COVID-19 Outbreaks under Stochastic Community Dynamics, Bimodality, or Limited Vaccination
Boissel, Jean-Pierre	A multi-strain model of immunization against influenza A viruses after infection or vaccination Jinkō Knowledge: An integrated knowledge management tool prior to in silico multiscale model development
Bonn, Lasse	Control of COVID-19 Outbreaks under Stochastic Community Dynamics, Bimodality, or Limited Vaccination
Boone, Charles	Mapping Genetic and Chemical Genetic Interaction Networks in Yeast and Human Cells
Boor, Peter	Computational Pathology of Kidney Disease
Bork, Peer	Molecular eco-systems biology of microbiomes for human and planetary health
Borth, Nicole	Amino acid metabolism of Chinese Hamster Ovary cells: Comparison of growth and production phases in a fed-batch
Bosia, Carla	Frequency preference in miRNA-mRNA interaction models: competition and cooperativity effects
Bosshard, Lars	Cell type-specific gene co-expression modules define tumor heterogeneity in melanoma patients
Bourlier, Tanguy	Jinkō Knowledge: An integrated knowledge management tool prior to in silico multiscale model development
Bowler, Chris	Tara Oceans: Eco-Systems Biology at Planetary Scale
Branz, Pablo	Ionizing radiation triggers differential signaling dynamics of p-p53 and p-ERK1/2 in sensitive and resistant HNSCC cell clones
Braun, Felix	The abundance and cross-talk of EGFR and MET receptors in lung cancer cell lines is critical for the efficacy of tyrosine kinase inhibitors
Brice, Alexis	Exploring the missing heritability in SPG7 heterozygous carriers with Whole Genome Sequencing
Brickman, Joshua M.	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
Brombacher, Eva	Benchmarking of analysis strategies for data-independent acquisition proteomics data
Bruder, Johanna	Web-based analysis of indirect calorimetric data arising from metabolic phenotyping systems
Bruezière, Lara	A multi-strain model of immunization against influenza A viruses after infection or vaccination
Brun, Christine	What are the functions of the short open reading frame-encoded peptides in monocytes? An interactomic approach. Discovery of potential functional paths by integration of phospho-proteomics data in the PPI network using a RWR framework
Brunner, Patrick	Spatio-temporal modeling reveals a layer of tunable control circuits for the distribution of cytokines in tissues.
Brunnsåker, Daniel	Metabolic profile predictions using efficient and interpretable data descriptors generated with relational learning
Brunnsåker, Daniel	Automated improvement of genome-scale models using a first-order logical model of metabolism
Brusch, Lutz	Advanced Modelling of Multicellular Systems in Morpheus
Bryson, Bryan	Combinatorial effects of ligands are predicted by a genome-scale model of signaling based on artificial neural networks
Buecherl, Lukas	SynBioSuite: Web-based modeling and analysis of biological systems
Bujtár, Zsófia	Computational modeling of the Hes1 oscillator for the self-renewal of muscle stem cells
Burbano de Lara, Sebastian	Exploring the “dark proteome” in hepatocellular carcinoma Alterations in hepatocyte growth factor induced signal transduction in fatty liver disease foster cancer development
Burgos, Asdrubal	A modular concept for modeling of plant lipid metabolism
Burgstaller-Muehlbacher, Sebastian	Phylogeny and artificial neural networks
Burkovski, Andreas	Temporal Proteomics and Transcriptomics Unravels the Host-Pathogen Interaction Network of Macrophages and Corynebacterium diphtheriae.
Bursi, Roberta	Personalized medicine for Multiple Sclerosis treatment strategies at the individual and population level
Burt, Philipp	Data-driven modeling of cell-cell communication networks
Busti, Stefano	A low-granularity model integrating metabolism, growth and cell cycle: towards multi-level whole cell modeling of budding yeast
Byrne, Nicole	Investigating antagonistic chromatin remodeling by the Swi-Snf and Tup1-Cyc8 (Ssn6) complexes in yeast
Büttner, Maren	Integrational approaches for cross-species analysis of lung pathologies at single-cell resolution.
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C. Hernandez, Silvia	Characterization of cardiac fibroblast remodeling dynamics after myocardial infarction
Cai, James	A quantum circuit model for inferring gene regulatory networks with application to single-cell transcriptomic data
Calderwood, Michael A	Identification of a SARS-CoV-2 inhibitor by combining binary protein-protein interaction mapping, structure prediction and virtual screening
Califano, Andrea	Systematic elucidation and pharmacological targeting of non-oncogene dependencies at the single cell level.
Calzola, Jessica	Targeted Proteomics-Driven Computational Modeling of the Mouse Macrophage Toll-like Receptor Signaling Pathway
Campbell, Stuart	Predicting pathogenicity of TPM1 variants using multi-scale models
Carballo-Pacheco, Martin	Macroecological Laws Naturally Arise from Complex Chaotic Dynamics of Gut Microbiota
Carbonell-Caballero, José	Disentangling the internal composition of tumour activities through a hierarchical factorization model
Carillo, Daniel	Benchmarking Phage-Host Prediction Tools using Real Metagenomics Data
Carlhäll, Carl-Johan	Insights on hemodynamic changes in hypertension and T2D through non-invasive cardiovascular modeling
Carosati, Emanuele	Multi-Omics Visible Drug Activity prediction, interpreting the biological processes underlying drug sensitivity
Casado, Enrique	Personalized Treatment of Anemia in Lung Carcinoma
Casado, Julia	Tribus reveals the single-cell tumor architecture and effect of chemotherapy in ovarian cancer Single-cell spatial atlas of high-grade serous ovarian cancer
Cassonet, Patricia	Identification of a SARS-CoV-2 inhibitor by combining binary protein-protein interaction mapping, structure prediction and virtual screening
Castillo Alfonso, Freddy	From genome sequencing to the first draft of the genome scale metabolic model of the symbiont fungus Leucoagaricus gongylophorus LEU18496.
Castro, Anna	Stochasticity of Meiotic Entry in Xenopus Oocytes
Ceccarelli, Michele	Multi-Omics Visible Drug Activity prediction, interpreting the biological processes underlying drug sensitivity MultiOmics Network Embedding for SubType Analysis
Cedersund, Gunnar	Insights on hemodynamic changes in hypertension and T2D through non-invasive cardiovascular modeling Digital twins and hybrid modelling for simulation of physiological variables and stroke risk M4-health: digital twins that follow you throughout your health journey An interconnected multi-level mechanistic model of the human brain Mathematical modeling of cytokine interplay in human monocytes during LPS stimulation Connecting the Neurovascular coupling and Electrophysiological signaling – a modeling approach A comprehensive mechanistic model of adipocyte signaling with layers of confidence
Cevost, Jasmin	Precision machine-learning identifies a new paradigm for therapeutic discovery in Huntington’s disease: remodeling stress response to re-instate neuronal health and resilience.
Chadwick, Angus	Linking models of biochemical dynamics via mass-constrained neural ordinary differential equations
Chae, Junghun	Rhythmic protein degradation for cost-effective circadian oscillation
Chae, Seokjoo	Spatially-Coordinated Collective Protein Behaviors Enable Robust Circadian Timekeeping
Chairs, Session	Introduction Pitching for Classical modeling Pitching for AI / ML modeling Pitching for hybrid/data-driven modeling Panel Discussion Q&A Final remarks
Chalabi, Asma	Dynamic analysis framework to detect cell division and cell death in live-cell imaging, using signal processing and machine learning
Chaligne, Ronan	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
Chamakuri, Nagaiah	Multiscale Modeling of Dyadic Structure-Function Relation in Ventricular Cardiac Myocytes
Chan, Joseph	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
Chandra, Nagasuma	Identification of personalised driver gene panels in Melanoma
Chandrasegaran, Sharmilla	A Systems Biology Approach To Study The Spatiotemporal Dynamics Of Senescent Cells In Wound Healing And Tissue Repair
Chang, Jon	Neural Circuits Underlying Autism Spectrum Disorders
Chapman, Katy	Quantitative Impacts of Bumble Bee Ecology on Foraging Behaviour: An Economic Model
Chapuy, Björn	Patient- and cell line-specific modeling of diffuse large B-cell lymphoma
Charoentong, Pornpimol	Extracting knowledge from multi-omics and clinical datasets using graph machine learning
Chaudhary, Ojasvi	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
Chaves, Madalena	Analyzing single-cell trajectories with augmented machine learning methods predicts cancer drugs response in live-cell microscopy assays
Chaves, Sandra S.	A multi-strain model of immunization against influenza A viruses after infection or vaccination
Chen, Xiuqiang	Discovery of Robust and Highly Specific Microbiome Signatures for Non-Alcoholic Fatty Liver Disease
Chen, Yingdan	COVIDpro: Database for mining protein dysregulation in patients with COVID-19
Chen, Yu	Metabolic Atlas - extending metabolic networks for model organisms with enzyme turnover predictions with GotEnzymes
Chen, Yu	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
Chew, Yin Hoon	How can we unleash the potentials of whole-cell modelling?
Cho, Juyeon	Single cell pseudo-time inference based on copy number variants for identifying a tumor transition state Single cell analysis of a breast pre-cancerous state to explore critical tumor microenvironment interactions
Choi, Jungmin	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
Choi, Soon Gang	Identification of a SARS-CoV-2 inhibitor by combining binary protein-protein interaction mapping, structure prediction and virtual screening
Choo, Zi-Ning	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
Choteau, Sébastien A.	What are the functions of the short open reading frame-encoded peptides in monocytes? An interactomic approach.
Choufani, Charbel	Stochasticity of Meiotic Entry in Xenopus Oocytes
Christopoulos, Petros	Personalized Treatment of Anemia in Lung Carcinoma
Cinquemani, Eugenio	Quantification of bacterial resource allocation in changining environments on the single-cell level
Clas, Simone Menghai	Development of a mass-spectrometry based clinical proteomics pipeline allows absolute quantification of pathway components and provides insights in pathway activation The abundance and cross-talk of EGFR and MET receptors in lung cancer cell lines is critical for the efficacy of tyrosine kinase inhibitors
Clavel, Thomas	A physiology-based model of bile acid metabolism in mice
Clayton, Andrew	Periodic Forcing of the ERK pathway
Cloete, Ielyaas	Computational modeling of DLBCL predicts response to BH3-mimetics
Colin, Remy	Dynamic fluctuations in a bacterial metabolic network
Community Members,	FROG Analysis - a community standard to foster reproducibility and curation of constraint-based models
Conesa, David	Disentangling the internal composition of tumour activities through a hierarchical factorization model
Confalonieri, Marco	The potential of PBI for high resolution lung imaging in patients
Consortium, Hecatos	Multiple-omics based metabolic modelling reveals effects of drug-induced liver toxicity A systems pharmacology approach reveals robust drug metabolism and altered glucuronide disposition in a mouse model of liver cirrhosis A physiology-based model of bile acid metabolism in mice
Consortium, The Fitmulticell	FitMultiCell: Simulating and parameterizating computational models of multi-cellular processes
Contento, Lorenzo	Seroepidemiology And Modeling Of SARS-CoV-2 In Ethiopia: Longitudinal Cohort Study Among Front-line Health-care Workers And Community INSIDe: Integrative modeling of the spread of serious infectious diseases
Cook, Daniel	Are metastatic triple negative breast cancers closer to their parental tumors or primary tumors of their destination tissues?
Cooper, Sarah	Resolving Resolution Hindrances in Spatial Transcriptomics
Cordes, Henrik	Multiple-omics based metabolic modelling reveals effects of drug-induced liver toxicity
Cornet, Cas	Effect of dispersal by inundation on soil bacterial communities depends on soil developmental stage
Correa, Sandra	A modular concept for modeling of plant lipid metabolism
Cosi, Filippo G.	Multiscale Modeling of Dyadic Structure-Function Relation in Ventricular Cardiac Myocytes
Cottrell, Jeffrey	Inference of a causal synaptic molecular network from multiplexed imaging and its perturbations in autism and schizophrenia
Coudeville, Laurent	A multi-strain model of immunization against influenza A viruses after infection or vaccination
Courcelles, Eulalie	A multi-strain model of immunization against influenza A viruses after infection or vaccination
Coussens, Lisa	Quantitative Spatial Profiling Reveals Tumor Microenvironment Heterogeneity and Prognostic Biomarkers Associated with Immune Population Architectures
Coutelier, Marie	Exploring the missing heritability in SPG7 heterozygous carriers with Whole Genome Sequencing
Covert, Markus	A dynamic HIF1α-PPARγ circuit controls a paradoxical adipocyte regulatory landscape The E. coli Whole-Cell Modeling Project: Vision and Progress
Creixell, Pau	Mechanisms of Pro- and Anti-Oncogenic Signaling Downstream of Dual Tyrosine Protein Kinases
Cristiani, Alberto	Molecular principles governing substrate specificity of human SUMO E3 Ligases
Cristiani, Alberto	Analyzing human E3 ligome for efficient design of PROTACs
Crotty, Stephen M.	Phylogeny and artificial neural networks
Crowl, Sam	Inferring kinase activity of a tumor from phosphoproteomic data
Cvijovic, Marija	Scalable and flexible inference framework for stochastic dynamic single-cell models
Czaplewski, Cezary	Studying conformational transitions of selected proteins using UNRES coarse-grained replica exchange molecular dynamics simulations with Lorentzian restraints.
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Dalgic, Ertugrul	Mutually Antagonistic Protein Pairs of Cancer
Damiani, Chiara	Can we trust genome-wide metabolic models?
Dandou, Sarah	3D reconstruction and mathematical modelling of whole slide images to elucidate resistance to the targeted therapy in melanoma
Danielson, Eric	Inference of a causal synaptic molecular network from multiplexed imaging and its perturbations in autism and schizophrenia
Das, Sakshi	Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide images
Davoine, Claire-Sophie	Exploring the missing heritability in SPG7 heterozygous carriers with Whole Genome Sequencing
de Cesare, Irene	Model Predictive Control of Cancer Cellular Dynamics: A New Strategy For Therapy Design
De Decker, Yannick	Initial source of heterogeneity in a model for cell fate decision in the early mammalian embryo
de Jong, Hidde	Quantification of bacterial resource allocation in changining environments on the single-cell level
De Landtsheer, Sebastien	Model ensembling as a tool to form interpretable multi-omic predictors of cancer pharmacosensitivity
De Landtsheer, Sébastien	Expanding the disease network of Glioblastoma Multiforme via topological analysis Machine learning-based prediction of frailty in elderly people - Data from the Berlin Aging Study-II (BASE-II)
de Weerd, Hendrik	MODalyseR—a novel software for inference of disease module hub regulators identified a putative multiple sclerosis regulator supported by independent eQTL data
Debreuve, Eric	Dynamic analysis framework to detect cell division and cell death in live-cell imaging, using signal processing and machine learning
Demuth, Ilja	Machine learning-based prediction of frailty in elderly people - Data from the Berlin Aging Study-II (BASE-II)
Dervey, Roxane	When cells decide to give up on repairing DNA damage
Destaing, Olivier	Discovery of potential functional paths by integration of phospho-proteomics data in the PPI network using a RWR framework
Devenyi, Adrian	Mitotic Memory as Spontaneous Symmetry Breaking in the Cell
Deák, Flora	Non-linear mixed effects modeling of the T cell response in individuals infected with SARS-CoV-2
Di Pasquale, Pamela	The role of the kynurenine metabolism in chronic graft-versus-host-disease: Insights from computational modeling and patient data
Diaz, Juan M.	Evaluation of methods to compute quasi-potential functions and their use as systems biology models Discovery of Hidden Control Variables and modeling Non-Linear Dynamical Biological Systems
Didier, Jeff	Machine learning-based prediction of frailty in elderly people - Data from the Berlin Aging Study-II (BASE-II)
Diederen, Thomas	Simulation Based Metabolic Flux Inference
Diemer, Jorin	Non-monotonic Na+ dynamics in the malaria parasite Plasmodium falciparum
Dieter, Yannik	Development of a mass-spectrometry based clinical proteomics pipeline allows absolute quantification of pathway components and provides insights in pathway activation
Dimitriew, Wassili	Human host and pathogenic fungi: modeling and deciphering nested metabolic defense strategies
Dinh, Marc	Geometric programming to Solve Optimal Concentrations of Metabolites and Enzymes in Constraint-based modelling
Doerig, Christian	Structural proteomics evidence for a predicted glycolytic metabolon
Domenzain, Iván	Reconstruction of a catalogue of enzyme constrained models of metabolism using GECKO 2.0 and its applications to eukaryote metabolism
Domínguez-Hüttinger, Elisa	Mathematical modelling of the regulatory mechanisms of keratinocyte differentiation for epidermal homeostasis
Domínguez-Hüttinger, Elisa	Mathematical model of the immunopathological progression of tuberculosis
Dooley, Steven	Multilevel approach characterizing the progression of fatty liver disease
Dopazo, Joaquín	Disentangling the internal composition of tumour activities through a hierarchical factorization model
Doresic, Domagoj	Efficient parameter estimation for ODE models with semi-quantitative data using spline approximation
Doresic, Domagoj	Efficient brute-force model selection by iterative elimination of less useful model subspaces
Dorgham, Karim	Multi-dimensional immune correlates of early prediction of COVID-19 severe versus asymptomatic disease course
Douaihy, Maria	Mitotic Memory as Spontaneous Symmetry Breaking in the Cell
Doubleday, Peter F	Dynamic metabolome profiling uncovers potential TOR signaling genes
Dourado, Hugo	The limit on dry mass density is an organizing principle for cellular physiology The Economy and Control of Balanced Cellular Growth
Dreossi, Diego	The potential of PBI for high resolution lung imaging in patients
Drucks, Tamara	Phylogeny and artificial neural networks
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Durr, Alexandra	Exploring the missing heritability in SPG7 heterozygous carriers with Whole Genome Sequencing
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Dwivedi, Sanjiv	New data-driven gene representations using deep autoencoders at multiple omics to identify candidate disease genes and robust classifiers
Dyer, Martin J. S.	Computational modeling of DLBCL predicts response to BH3-mimetics
E
E. Samadi, Moein	A training strategy for hybrid models to break the curse of dimensionality: An application in mortality estimation for cohorts of COVID-19 patients
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Ejneby Silverå, Malin	An interconnected multi-level mechanistic model of the human brain
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El Hachem, Elie-Julien	Latent Dirichlet Allocation for Double Clustering (LDA-DC): Discovering patients phenotypes and cell populations within a single Bayesian framework
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Engqvist, Martin	Prediction of enzyme kinetic parameters and substrate scopes using artificial intelligence
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Ewald, Jan	Human host and pathogenic fungi: modeling and deciphering nested metabolic defense strategies
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Faber, Jennifer	Modeling disease progression in spinocerebellar ataxias
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Fendt, Rebekka	A systems pharmacology approach reveals robust drug metabolism and altered glucuronide disposition in a mouse model of liver cirrhosis
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Ferraro, Luigi	Multi-Omics Visible Drug Activity prediction, interpreting the biological processes underlying drug sensitivity MultiOmics Network Embedding for SubType Analysis
Ferro, Elsi	Frequency preference in miRNA-mRNA interaction models: competition and cooperativity effects
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Finke, Martin	Multilevel approach characterizing the progression of fatty liver disease
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Fischer-Holzhausen, Sophie	A mechanistic model for endocrine profiles of female puberty maturation
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Flinner, Nadine	Advantages of Ensemble CNN’s in Computational Pathology.
Flores-Garza, Eliezer	Mathematical model of the immunopathological progression of tuberculosis
Flors, Victor	Metabolome-wise analysis of plants exposed to abiotic stress conditions to identify potential metabolites inducers of cross-tolerance to biotic stressors
Fontanarrosa, Pedro	SynBioSuite: Web-based modeling and analysis of biological systems
Foresto, Giulio	A multi-strain model of immunization against influenza A viruses after infection or vaccination
Formichetti, Sara	The transcriptome dynamics of single cells during the cell cycle
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Fraser, Iain	Targeted Proteomics-Driven Computational Modeling of the Mouse Macrophage Toll-like Receptor Signaling Pathway
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Friedrich, Vincent D.	Integrational approaches for cross-species analysis of lung pathologies at single-cell resolution.
Frigessi, Arnoldo	Mechanistic modeling of patient-specific response to hormone therapy and CDK inhibitors in breast cancer
Frishberg, Amit	Reconstructing a quantitative measure of disease dynamics for discovery and clinical benefit
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Fromion, Vincent	Geometric programming to Solve Optimal Concentrations of Metabolites and Enzymes in Constraint-based modelling
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Fuchs, Alisa	Logical modeling of signaling mechanisms in early development
Färkkilä, Anniina	Tribus reveals the single-cell tumor architecture and effect of chemotherapy in ovarian cancer Single-cell spatial atlas of high-grade serous ovarian cancer
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Galindez, Gihanna	Inference of differential gene regulatory networks from gene expression data using boosted differential trees
Garcia Martinez, Guillermo	FISHing for Correlation
Garcia-Molina, Antoni	Metabolome-wise analysis of plants exposed to abiotic stress conditions to identify potential metabolites inducers of cross-tolerance to biotic stressors
Geiselmann, Hans	Quantification of bacterial resource allocation in changining environments on the single-cell level
Geldmacher, Christof	Non-linear mixed effects modeling of the T cell response in individuals infected with SARS-CoV-2
Georgii, Elisabeth	Modeling disease progression in spinocerebellar ataxias
Gerhardt, Holger	PolarityJaM: An image analysis toolbox for cell polarity, junction and morphology quantification
Geris, Liesbet	Hybrid cellular automaton representation of the influence of mechanical stimulation on the development of bone metastases
Germade, Tomas	Dynamic metabolome profiling uncovers potential TOR signaling genes
Germain, Ronald	Targeted Proteomics-Driven Computational Modeling of the Mouse Macrophage Toll-like Receptor Signaling Pathway
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Ghallab, Ahmed	A systems pharmacology approach reveals robust drug metabolism and altered glucuronide disposition in a mouse model of liver cirrhosis Alterations in hepatocyte growth factor induced signal transduction in fatty liver disease foster cancer development
Ghandian, Sina	Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide images
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Gherman, Ioana	Accelerating whole-cell modelling with surrogate machine learning models
Ghim, Cheol-Min	Rhythmic protein degradation for cost-effective circadian oscillation
Giese, Wolfgang	Multiscale Modeling of Dyadic Structure-Function Relation in Ventricular Cardiac Myocytes
Giese, Wolfgang	PolarityJaM: An image analysis toolbox for cell polarity, junction and morphology quantification
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Giovanni, Scala	Multi-Omics Visible Drug Activity prediction, interpreting the biological processes underlying drug sensitivity MultiOmics Network Embedding for SubType Analysis
Giri, Amitava	Unraveling the role of network motifs to decipher the origin of robust decision-making in biological systems
Giridhar, Maya	Elucidating the role of TAS2R43 in HGT-1 cells – an integrated omics approach
Gjertsen, BjØrn Tore	Deciphering dysregulation in Erythroleukemia to design intervention strategies
Glaab, Enrico	Machine learning based pathway deregulation analysis of metabolomics data for Parkinson's Disease
Glatter, Timo	Mapping metabolic regulation in E. coli with a metabolism-wide CRISPRi library
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Goekeri, Cengiz	Integrational approaches for cross-species analysis of lung pathologies at single-cell resolution.
Goldenbogen, Björn	Control of COVID-19 Outbreaks under Stochastic Community Dynamics, Bimodality, or Limited Vaccination
Golebiewski, Martin	The COmputational MOdeling in BIology NEtwork in 2022: Evolving needs in standardisation and model reuse
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Gollub, Mattia	Structural proteomics evidence for a predicted glycolytic metabolon
Golusik, Sabrina	Identification of a SARS-CoV-2 inhibitor by combining binary protein-protein interaction mapping, structure prediction and virtual screening
Gomez de Lope, Elisa	Machine learning based pathway deregulation analysis of metabolomics data for Parkinson's Disease
Gomez-Cabrero, David	Construction and Decomposition of Cellular Energy Landscapes using Hopfield Neural Networks Evaluation of methods to compute quasi-potential functions and their use as systems biology models Discovery of Hidden Control Variables and modeling Non-Linear Dynamical Biological Systems On data-driven learning of an effective energy landscape from trajectories of nonlinear dynamical biological systems Characterization of cardiac fibroblast remodeling dynamics after myocardial infarction Inferring Gene Networks Rewiring of Naive and Primed Human Embryonic Stem Cells During Cellular Reprogramming Using Single-Cell RNA-seq Data
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Gong, Bo	Directed cell migration by cortical actin and ER-PM contact site-mediated restriction of receptor signaling to the front
Gonze, Didier	Initial source of heterogeneity in a model for cell fate decision in the early mammalian embryo
Goodrich, David	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
Gopalan, Anuradha	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
Gorochov, Guy	Multi-dimensional immune correlates of early prediction of COVID-19 severe versus asymptomatic disease course
Gorochowski, Thomas E	The COmputational MOdeling in BIology NEtwork in 2022: Evolving needs in standardisation and model reuse Accelerating whole-cell modelling with surrogate machine learning models
Govindaraj, Vinodhini	Transcriptional fluctuations govern the serum dependent cell cycle duration heterogeneities in Mammalian cells
Gower, Alexander	Automated improvement of genome-scale models using a first-order logical model of metabolism
Gradl, Katrin	Elucidating the role of TAS2R43 in HGT-1 cells – an integrated omics approach
Graf, Dimitri	Model-based design of a synthetic oscillator based on an epigenetic memory system
Graff, John Paul	Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide images
Granada, Adrián E.	Dynamics of the circadian clock in models of cancer and its potential for treatment
Grdseloff, Nastasja	Development of a geometric blood vessel model to quantify morphological changes of endothelial cells in 3D during vascular remodeling
Greb, Thomas	Computational analysis of cambium activity during plant radial growth
Grein, Stephan	Efficient parameter estimation for ODE models with semi-quantitative data using spline approximation Web-based analysis of indirect calorimetric data arising from metabolic phenotyping systems
Grekova, Anastasiia	Multi-Omics Regulatory Network Inference in the Presence of Missing Data
Gresnigt, Mark S.	Lactobacillus rhamnosus colonisation antagonizes Candida albicans by forcing metabolic adaptations that compromise pathogenicity
Grierson, Claire	Accelerating whole-cell modelling with surrogate machine learning models
Gris, Barbara	Precision machine-learning identifies a new paradigm for therapeutic discovery in Huntington’s disease: remodeling stress response to re-instate neuronal health and resilience.
Groen, Bert	Combining machine learning and ODE’s to build multiscale models for estimation of metabolic trajectories
Grohe, Martin	Inference and dynamical simulation of the gene-regulatory network in single cells
Grozdani, Sonya	Benchmarking Phage-Host Prediction Tools using Real Metagenomics Data
Groß, Olaf	A powerful modelling approach tailored to cellular signalling
Großeholz, Ruth	Computational analysis of cambium activity during plant radial growth
Gruber, Andrea	Modelling of Pharmacokinetics and Pharmacodynamics for first-in-man dose selection of targeted alpha therapy
Gruden, Kristina	Stress Knowledge Map: A knowledge resource for modeling of plant stress responses
Grzegorzewski, Jan	Physiologically based pharmacokinetic (PBPK) models for metabolic phenotyping and evaluation of liver function
Gu, Wei	Composing and perturbing large-scale constraint-based metabolic models with COBREXA.jl
Guan, Yuanfang	Comparative analysis of molecular fingerprints in prediction of drug combination effects
Gudina, Esayas Kebede	Seroepidemiology And Modeling Of SARS-CoV-2 In Ethiopia: Longitudinal Cohort Study Among Front-line Health-care Workers And Community
Guillaud-Bataille, Marine	Exploring the missing heritability in SPG7 heterozygous carriers with Whole Genome Sequencing
Guillot-Noël, Léna	Exploring the missing heritability in SPG7 heterozygous carriers with Whole Genome Sequencing
Guo, Tiannan	COVIDpro: Database for mining protein dysregulation in patients with COVID-19
Gursanscky, Nial	Computational analysis of cambium activity during plant radial growth
Gusinow, Roy	Federated mathematical modelling and machine learning for a multi-national cohort of COVID-19 patients
Gustafsson, Mika	New data-driven gene representations using deep autoencoders at multiple omics to identify candidate disease genes and robust classifiers MODalyseR—a novel software for inference of disease module hub regulators identified a putative multiple sclerosis regulator supported by independent eQTL data
Gustafsson, Mika	Proteomics profiling revealed a combination of protein biomarkers for predicting disease trajectory of multiple sclerosis
Guzmán Maldonado, Jorge Alberto	Hybrid models for cellular signaling: meso-scale pathway identification
Gómez-Cabrero, David	Towards a Computational Toolkit for Cell Fate Decision Detection
Gödtel, Franziska	Development of a mass-spectrometry based clinical proteomics pipeline allows absolute quantification of pathway components and provides insights in pathway activation
Gökkaya, Mehmet	Multi-dimensional immune correlates of early prediction of COVID-19 severe versus asymptomatic disease course
Gütebier, Lea	A workflow for the creation of regulatory networks integrating miRNAs and lncRNAs associated with exposure to ionizing radiation using open source data and tools
H
H. de Groot, Daan	Characterizing all feasible metabolic conversions of individual cells and microbial communities with elementary conversion modes.
Haendeler, Simon	Understanding Stem Cell Growth Dynamics in Human Cerebral Organoids
Haffner, Johanna E.L.	Control of COVID-19 Outbreaks under Stochastic Community Dynamics, Bimodality, or Limited Vaccination
Haga, Masatoshi	Data-driven mathematical modeling of human skin aging and its application for natural compound screening
Hagel, Marc-Daniel	TREAT-SGS - a multi-omics approach to treat the rare neuro-developmental disorder Schinzel–Giedion syndrome
Haglund, Caj	Lipid metabolic reprogramming extends beyond histological tumor demarcations in human operable pancreatic cancer
Hagström, Jaana	Lipid metabolic reprogramming extends beyond histological tumor demarcations in human operable pancreatic cancer
Haj-Hassan, Maya	A deep learning-based approach for counting ovarian follicles
Hajizadeh, Siamak	Single-cell spatial atlas of high-grade serous ovarian cancer
Hall, Katie	Quantitative Impacts of Bumble Bee Ecology on Foraging Behaviour: An Economic Model
Hameed, Tara	Latent variable models of fungal growth considering the data measurement process
Hamilton, William	A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation
Hammad, Seddik	Multilevel approach characterizing the progression of fatty liver disease
Hamsafar, Yamah	Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide images
Hanke, Matthias	A multi-strain model of immunization against influenza A viruses after infection or vaccination
Hansmann, Marin-Leo	Modeling the adaptive immune response of a lymph node as Petri net
Hao, Tong	Identification of a SARS-CoV-2 inhibitor by combining binary protein-protein interaction mapping, structure prediction and virtual screening
Harrington, Kyle	PolarityJaM: An image analysis toolbox for cell polarity, junction and morphology quantification
Hartung, Niklas	A physiologically-structured population model for pharmacokinetics of orally inhaled drugs
Harvey, Danielle	Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide images
Hasenauer, Jan	Cell-to-cell variability in JAK2/STAT5 pathway components and cytoplasmic volumes defines survival threshold in erythroid progenitor cells Seroepidemiology And Modeling Of SARS-CoV-2 In Ethiopia: Longitudinal Cohort Study Among Front-line Health-care Workers And Community Federated mathematical modelling and machine learning for a multi-national cohort of COVID-19 patients INSIDe: Integrative modeling of the spread of serious infectious diseases Posterior marginalization accelerates Bayesian inference for dynamical systems Hybrid mechanistic and deep learning modeling in systems biology Efficient parameter estimation for ODE models with semi-quantitative data using spline approximation FitMultiCell: Simulating and parameterizating computational models of multi-cellular processes Moving Horizon Estimation for Patient-Specific Optimal Control of Blood Glucose in Intensive Care Units Web-based analysis of indirect calorimetric data arising from metabolic phenotyping systems Biological-informed multi-modality integration of unmatched single-cell-omics datasets to provide a multi-dimensional view Timelapse of Single Cell Lipidomics
Hasenauer, Jan	Efficient brute-force model selection by iterative elimination of less useful model subspaces
Hasenauer, Jan	Non-linear mixed effects modeling of the T cell response in individuals infected with SARS-CoV-2
Hasmann, Max	Disentangling Proliferation Signaling in Breast Cancer Subtypes based on an integrative modeling approach
Hass, Helge	The abundance and cross-talk of EGFR and MET receptors in lung cancer cell lines is critical for the efficacy of tyrosine kinase inhibitors
Hassan, Reham	A systems pharmacology approach reveals robust drug metabolism and altered glucuronide disposition in a mouse model of liver cirrhosis
Hauber, Adrian Lukas	Uncovering cell-type specific mechanisms across an arbitrary number of cell-types by adapting the clustered LASSO to differential equation models
Hauert, Sabine	Defining Design Rules for Next-Generation Snakebite Antivenoms
Hauptfield, Ernestina	Benchmarking Phage-Host Prediction Tools using Real Metagenomics Data
Hay Mele, Bruno	Computational analysis of cambium activity during plant radial growth
He, Mingjie	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
Head, Sarah A.	Harnessing cancer heterogeneity for the systematic discovery of treatable cancer-driver exons with spotter
Heckmann, David	Prediction of enzyme kinetic parameters and substrate scopes using artificial intelligence
Heiman, Myriam	Precision machine-learning identifies a new paradigm for therapeutic discovery in Huntington’s disease: remodeling stress response to re-instate neuronal health and resilience.
Heine, Markus	Web-based analysis of indirect calorimetric data arising from metabolic phenotyping systems
Heinen, Tobias	DeepCellRegMap: An interpretable deep learning framework for mapping genetic effects at cell subtype resolution using large-scale single-cell sequencing data
Heinonen, Markus	Continuous-time models under uncertainty
Heinz, Gitta A.	Integrational approaches for cross-species analysis of lung pathologies at single-cell resolution.
Heinzlmeir, Stephanie	DecryptM: decrypting drug actions and protein modification by dose- and time-resolved proteomics
Heirendt, Laurent	Composing and perturbing large-scale constraint-based metabolic models with COBREXA.jl
Held, Alexander	Multilevel approach characterizing the progression of fatty liver disease
Hellberg, Sandra	Proteomics profiling revealed a combination of protein biomarkers for predicting disease trajectory of multiple sclerosis
Helm, Barbara	Deciphering dysregulation in Erythroleukemia to design intervention strategies Multilevel approach characterizing the progression of fatty liver disease 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
Helm, Barbara	Development of a mass-spectrometry based clinical proteomics pipeline allows absolute quantification of pathway components and provides insights in pathway activation
Helm, Dominic	The abundance and cross-talk of EGFR and MET receptors in lung cancer cell lines is critical for the efficacy of tyrosine kinase inhibitors
Helm, Dominic	Alterations in hepatocyte growth factor induced signal transduction in fatty liver disease foster cancer development Development of a mass-spectrometry based clinical proteomics pipeline allows absolute quantification of pathway components and provides insights in pathway activation
Helming, Ticho	Cell Type view into tomato stem elongation in Shade avoidance response
Hemedan, Ahmed	Cohort-specific Boolean models highlight different regulatory modules during disease progression
Hempel de Ibarra, Natalie	Quantitative Impacts of Bumble Bee Ecology on Foraging Behaviour: An Economic Model
Henao, Juan	Multi-Omics Regulatory Network Inference in the Presence of Missing Data
Hengstler, Jan	Alterations in hepatocyte growth factor induced signal transduction in fatty liver disease foster cancer development
Hengstler, Jan	A systems pharmacology approach reveals robust drug metabolism and altered glucuronide disposition in a mouse model of liver cirrhosis
Henkel, Ron	MeDaX - our vision for bioMedical Data eXploration
Hennersdorf, Clara	FISHing for Correlation
Heppt, Markus	A disease network-based deep learning approach for characterizing melanoma
Hermes, Jacques	Non-parametric model-based estimation of the effective reproduction number for SARS-CoV-2
Hermjakob, Henning	FAIR sharing of reproducible COVID-19 models of epidemic and pandemic forecast FAIR assessment of biosimulation models - a cross-community project FROG Analysis - a community standard to foster reproducibility and curation of constraint-based models BioModels: an open repository of mathematical models of the biological and biomedical processes A Reproducibility Scorecard for Self-checking of Systems Biology Models
Hernandez-Alias, Xavier	Tissue-specific codon usage: from systems to synthetic biology
Hernández-Pando, Rogelio	Mathematical model of the immunopathological progression of tuberculosis
Herren, Jörg	Web-based analysis of indirect calorimetric data arising from metabolic phenotyping systems
Herrgårdh, Tilda	Digital twins and hybrid modelling for simulation of physiological variables and stroke risk
Herrmann, Carl	Integrative analysis on comorbid signatures in psychotic disorders using multi-rank non-negative matrix factorization based graph approach
Herten, Dirk Peter	The abundance and cross-talk of EGFR and MET receptors in lung cancer cell lines is critical for the efficacy of tyrosine kinase inhibitors
Heutink, Peter	Transcription start site signal profiling improves transposable element RNA expression analysis at locus-level
Heyn, Johannes C.J.	On multistability and constitutive relations of cell motion on Fibronectin lanes
Hidaka, Yoshimasa	Structural reduction of chemical reaction networks based on topology
Hiesinger, Peter Robin	A robust model of neural superposition sorting
Hill, David	Identification of a SARS-CoV-2 inhibitor by combining binary protein-protein interaction mapping, structure prediction and virtual screening
Himmelbach, Axel	Elucidating the role of TAS2R43 in HGT-1 cells – an integrated omics approach
Hindley, Hollie	A model of RNA repair to study antibiotic tolerance
Hippenstiel, Stefan	Integrational approaches for cross-species analysis of lung pathologies at single-cell resolution.
Hirono, Yuji	Structural reduction of chemical reaction networks based on topology
Hocke, Andreas C.	Integrational approaches for cross-species analysis of lung pathologies at single-cell resolution.
Hodgkinson, Arran	Mitotic Memory as Spontaneous Symmetry Breaking in the Cell 3D reconstruction and mathematical modelling of whole slide images to elucidate resistance to the targeted therapy in melanoma Quantitative Impacts of Bumble Bee Ecology on Foraging Behaviour: An Economic Model
Hoelscher, Michael	Non-linear mixed effects modeling of the T cell response in individuals infected with SARS-CoV-2
Hoelscher, Michael	Seroepidemiology And Modeling Of SARS-CoV-2 In Ethiopia: Longitudinal Cohort Study Among Front-line Health-care Workers And Community
Hoenzke, Katja	Integrational approaches for cross-species analysis of lung pathologies at single-cell resolution.
Hoffmann, Alexander	Multi-scale modeling of B-cell fate decisions required for antibody generation
Hofmann, Andreas	INSIDe: Integrative modeling of the spread of serious infectious diseases
Hofmann, Ute	A systems pharmacology approach reveals robust drug metabolism and altered glucuronide disposition in a mouse model of liver cirrhosis
Hojjati, Sara	Dimethyl fumarate shifts CSF protein profile in relapsing remitting MS: a proteomics approach for biomarker discovery
Hojjati, Sara	Proteomics profiling revealed a combination of protein biomarkers for predicting disease trajectory of multiple sclerosis
Holbrook-Smith, Duncan	Dynamic metabolome profiling uncovers potential TOR signaling genes
Holcik, Laurenz	GuaCAMOLE: fragment GC bias-aware abundance estimation from metagenomic data increases accuracy and comparability
Holdijk, Lars	Path Integral Stochastic Optimal Control for Sampling Transition Paths
Holetschek, Corinna	Multi-dimensional immune correlates of early prediction of COVID-19 severe versus asymptomatic disease course
Holstein, Tanja	A probabilistic graphical model for taxonomic profiling of viral and microbiome proteome samples
Homeyer, André	Multilevel approach characterizing the progression of fatty liver disease
Hong, Hyukpyo	Systematic inference identifies a major source of heterogeneity in non-Markovian cell signaling dynamics: the rate-limiting step number Universally valid reduction of multiscale stochastic biochemical systems with simple non-elementary propensities
Horlings, Hugo M.	Single-cell spatial atlas of high-grade serous ovarian cancer
Hornef, Mathias	A physiology-based model of bile acid metabolism in mice
Horvath, Peter	Lipid metabolic reprogramming extends beyond histological tumor demarcations in human operable pancreatic cancer
Hu, Xiao-Pan	An optimal RNA growth law and its relationship with genome organization in bacteria
Hu, Yan	Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide images
Hu, Zin	Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide images
Huang, Kexin	GEARS: Predicting transcriptional outcomes of novel multi-gene perturbations
Huang, Shan	Metabolic Atlas - extending metabolic networks for model organisms with enzyme turnover predictions with GotEnzymes
Hube, Bernhard	Lactobacillus rhamnosus colonisation antagonizes Candida albicans by forcing metabolic adaptations that compromise pathogenicity
Huber, Rudolf Maria	Personalized Treatment of Anemia in Lung Carcinoma
Huergo, Estefania	A robust clustering strategy for patient stratification in complex diseases
Huisinga, Wilhelm	Development of a geometric blood vessel model to quantify morphological changes of endothelial cells in 3D during vascular remodeling Towards rational design of antibiotic combination therapies
Huisinga, Wilhelm	From System Biology to Pharmacology: Identifying what is important
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Huo, Yu	Dynamics of growth and ribosome level in batch cultures of S. cerevisiae
Huth, Manuel	Federated mathematical modelling and machine learning for a multi-national cohort of COVID-19 patients
Hyltander, Ingrid	Metabolic Atlas - extending metabolic networks for model organisms with enzyme turnover predictions with GotEnzymes
Hänselmann, Siegfried	The abundance and cross-talk of EGFR and MET receptors in lung cancer cell lines is critical for the efficacy of tyrosine kinase inhibitors
Hölttä, Maarit	Lipid metabolic reprogramming extends beyond histological tumor demarcations in human operable pancreatic cancer
I
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Kronström, Filip	Metabolic profile predictions using efficient and interpretable data descriptors generated with relational learning
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Kuepfer, Lars	Multiple-omics based metabolic modelling reveals effects of drug-induced liver toxicity
Kukuruzinska, Maria	Analysis of Heterogeneity in the Tumor Microenvironment in the 4NQO HNSCC Mouse Model
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Kurzai, Oliver	Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection
Kurzawa, Nils	Microbial compound bioactivity descriptors enable large-scale prediction of small molecule impact on microbiota species and pathogens
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Kuster, Bernhard	DecryptM: decrypting drug actions and protein modification by dose- and time-resolved proteomics
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Labagnara, Marco	When cells decide to give up on repairing DNA damage
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Lagha, Mounia	Mitotic Memory as Spontaneous Symmetry Breaking in the Cell
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Lakrisenko, Polina	Data-driven modeling of mitochondrial metabolism
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Lang, Paul	Improving our Mechanistic Understanding of Cell Cycle Dynamics
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Larive, Romain	3D reconstruction and mathematical modelling of whole slide images to elucidate resistance to the targeted therapy in melanoma
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Lauber, Kirsten	Ionizing radiation triggers differential signaling dynamics of p-p53 and p-ERK1/2 in sensitive and resistant HNSCC cell clones
Lauber, Michael	Multi-Omics Regulatory Network Inference in the Presence of Missing Data
Lauffenburger, Douglas A.	Combinatorial effects of ligands are predicted by a genome-scale model of signaling based on artificial neural networks
Launonen, Inga-Maria	Tribus reveals the single-cell tumor architecture and effect of chemotherapy in ovarian cancer
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Lebovka, Ivan	Computational analysis of cambium activity during plant radial growth
LeCam, Laurent	3D reconstruction and mathematical modelling of whole slide images to elucidate resistance to the targeted therapy in melanoma
Lee, Cindy	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
Lee, Jonghyun	Single cell pseudo-time inference based on copy number variants for identifying a tumor transition 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
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Li, Huating	Resistant starch decreases intrahepatic triglycerides in NAFLD patients via the gut microbiome contribution to the branched-chain amino acids pool
Li, Jiahang	COVRECON: Combining Genome-scale Metabolic Network Reconstruction and Data-driven Inverse Modeling to Reveal Causal Biochemical Regulations
Li, Jun	Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection
Li, Linge	Cell Type view into tomato stem elongation in Shade avoidance response
Li, Qi	Resistant starch decreases intrahepatic triglycerides in NAFLD patients via the gut microbiome contribution to the branched-chain amino acids pool
Li, Xiaomeng	Deciphering dysregulation in Erythroleukemia to design intervention strategies
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Li, Zhi	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
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Lieb, Guilaume	Dynamic single cell analysis of a MAPK signaling cascade and its impact on transcriptional output
Liebermeister, Wolfram	The Economy and Control of Balanced Cellular Growth
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Lim, Najung	Single cell pseudo-time inference based on copy number variants for identifying a tumor transition state Single cell analysis of colorectal cancers with familial adenomatous polyposis for revealing differential pre-malignant programs
Lin, Jia-Ren	Tribus reveals the single-cell tumor architecture and effect of chemotherapy in ovarian cancer
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Link, Hannes	Dynamic fluctuations in a bacterial metabolic network
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Linkevicius, Domas	Linking models of biochemical dynamics via mass-constrained neural ordinary differential equations
Linkov, Irina	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
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List, Markus	Inference of differential gene regulatory networks from gene expression data using boosted differential trees Multi-Omics Regulatory Network Inference in the Presence of Missing Data
Liu, Xiaomin	Computational analysis of cambium activity during plant radial growth
Liu, Yan	Resistant starch decreases intrahepatic triglycerides in NAFLD patients via the gut microbiome contribution to the branched-chain amino acids pool
Liudahl, Shannon	Quantitative Spatial Profiling Reveals Tumor Microenvironment Heterogeneity and Prognostic Biomarkers Associated with Immune Population Architectures
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Loew, Leslie	Virtual Cell Modeling and Simulation Software
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Long, Xiaoxue	Resistant starch decreases intrahepatic triglycerides in NAFLD patients via the gut microbiome contribution to the branched-chain amino acids pool
Lopez, Carlos	Unified Tumor Growth Mechanisms from Multimodel Inference and Dataset Integration
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Love, Jillian	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
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Marfil Sánchez, Andrea	An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness
Marfil Sánchez, Andrea	Discovery of Robust and Highly Specific Microbiome Signatures for Non-Alcoholic Fatty Liver Disease
Marko-Varga, György	Lipid metabolic reprogramming extends beyond histological tumor demarcations in human operable pancreatic cancer
Markus, Andrea	Quantification of imaging biomarkers in the extracellular matrix of left and right sided colon cancer tissues
Martens, Lennart	A probabilistic graphical model for taxonomic profiling of viral and microbiome proteome samples
Martini, Alessandra C.	Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide images
Martis B, Shiny	Jinkō Knowledge: An integrated knowledge management tool prior to in silico multiscale model development
Martínez-Enguita, David	New data-driven gene representations using deep autoencoders at multiple omics to identify candidate disease genes and robust classifiers
Marucci, Lucia	Model Predictive Control of Cancer Cellular Dynamics: A New Strategy For Therapy Design Accelerating whole-cell modelling with surrogate machine learning models
Maruhashi, Koji	XAI × Fugaku uncovered EMT mechanisms via cancer characteristic specific gene network analysis
Marulli, Cathy	Structural proteomics evidence for a predicted glycolytic metabolon
Maseko, Sibusiso	Identification of a SARS-CoV-2 inhibitor by combining binary protein-protein interaction mapping, structure prediction and virtual screening
Mashreghi, Mir-Farzin	Integrational approaches for cross-species analysis of lung pathologies at single-cell resolution.
Masilionis, Ignas	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
Masison, Joseph	Quantify the role of DMT1 endocytosis, IRPs activity, and FT iron sequestration in duodenal enterocyte iron regulation
Matz, Timon W.	Topological properties accurately predict cell division events and organization of Arabidopsis thaliana’s shoot apical meristem
Matz-Soja, Madlen	Multilevel approach characterizing the progression of fatty liver disease
Mayali, Xavier	In silico analysis of metabolic capabilities in a synthetic community of phycosphere bacteria
Mazutis, Linas	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
McKnight, R Anthony	Cross-inhibitory feedbacks of nucleocytoplasmic transport give rise to divergent multicellular phenotype in ERBB2-activated breast epithelia
Megret, Lucile	Precision machine-learning identifies a new paradigm for therapeutic discovery in Huntington’s disease: remodeling stress response to re-instate neuronal health and resilience.
Meier-Schellersheim, Martin	Targeted Proteomics-Driven Computational Modeling of the Mouse Macrophage Toll-like Receptor Signaling Pathway
Meimetis, Nikolaos	Combinatorial effects of ligands are predicted by a genome-scale model of signaling based on artificial neural networks
Meister, Michael	The abundance and cross-talk of EGFR and MET receptors in lung cancer cell lines is critical for the efficacy of tyrosine kinase inhibitors
Mellergård, Johan	Dimethyl fumarate shifts CSF protein profile in relapsing remitting MS: a proteomics approach for biomarker discovery
Mellergård, Johan	Proteomics profiling revealed a combination of protein biomarkers for predicting disease trajectory of multiple sclerosis
Menden, Michael P.	The pharmaco-epigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity
Mendes, Pedro	Regulation of Mammalian Iron Physiology Across Scales Quantify the role of DMT1 endocytosis, IRPs activity, and FT iron sequestration in duodenal enterocyte iron regulation
Mercado, Maria	A new platform for deep multiplexed metabolomics with a DNA barcode readout
Merchant, Miller	In silico analysis of metabolic capabilities in a synthetic community of phycosphere bacteria
Merks, Roeland	Computational analysis of cambium activity during plant radial growth
Merkt, Simon	Seroepidemiology And Modeling Of SARS-CoV-2 In Ethiopia: Longitudinal Cohort Study Among Front-line Health-care Workers And Community
Merzbacher, Charlotte	Fast and scalable machine learning approach for dynamic metabolic engineering
Meyer, Joana	Inference and dynamical simulation of the gene-regulatory network in single cells
Meyer, Tobias	Directed cell migration by cortical actin and ER-PM contact site-mediated restriction of receptor signaling to the front
Mi, Haoyang	Quantitative Spatial Profiling Reveals Tumor Microenvironment Heterogeneity and Prognostic Biomarkers Associated with Immune Population Architectures
Michoel, Tom	Identification of causal genes at GWAS loci with pleiotropic gene regulatory effects using instrumental variable sets
Migh, Ede	Lipid metabolic reprogramming extends beyond histological tumor demarcations in human operable pancreatic cancer
Migueles Lozano, Oscar Arturo	Patient-specific modeling of the TP53 pathway in endometrial carcinoma patients
Milias-Argeitis, Andreas	Fast parameter estimation for ODE-based models of heterogeneous cell populations
Milman, Neta	Reconstructing a quantitative measure of disease dynamics for discovery and clinical benefit
Minaud, Lise	Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide images
Minaud, Lise	Rapid parallel model inference and on-the-fly tiling of digital pathology images
Miravet-Verde, Samuel	Harnessing cancer heterogeneity for the systematic discovery of treatable cancer-driver exons with spotter
Mirhakkak, Mohammad	An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness
Mirhakkak, Mohammad H.	Lactobacillus rhamnosus colonisation antagonizes Candida albicans by forcing metabolic adaptations that compromise pathogenicity
Mitchell, Simon	Computational modeling of DLBCL predicts response to BH3-mimetics Flow Cytometry Combined with Systems Biology Modelling Reveals Heterogeneous “NFkB Fingerprints” in DLBCL 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.
Miyano, Satoru	A novel drug response network analysis on supercomputers uncovered gastric cancer drug sensitivity mechanism XAI × Fugaku uncovered EMT mechanisms via cancer characteristic specific gene network analysis
Miyazaki, Hiroyasu	Structural reduction of chemical reaction networks based on topology
Moeller, Jens	Temporal Proteomics and Transcriptomics Unravels the Host-Pathogen Interaction Network of Macrophages and Corynebacterium diphtheriae.
Monteagudo, Edith	The role of the kynurenine metabolism in chronic graft-versus-host-disease: Insights from computational modeling and patient data
Monteiro, Claudio	Jinkō Knowledge: An integrated knowledge management tool prior to in silico multiscale model development
Monti, Stefano	Analysis of Heterogeneity in the Tumor Microenvironment in the 4NQO HNSCC Mouse Model
Monuki, Edwin S.	Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide images
Morales-Soto, Larisa	Evaluation of methods to compute quasi-potential functions and their use as systems biology models
Moran, Rafael	Amino Acid Impact on Protein Secretion in B. subtilis: an RBA Approach
Moraru, Ion	BioSimulations: integrated models, model languages, model repositories, simulation experiments, simulation tools and data visualization Virtual Cell Modeling and Simulation Software
Morkel, Markus	Modeling the tumor microenvironment in patient-derived organoid culture
Morris, Michael	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
Morris, Natalie	Defining Design Rules for Next-Generation Snakebite Antivenoms
Morán-Torres, Rafael	Control of COVID-19 Outbreaks under Stochastic Community Dynamics, Bimodality, or Limited Vaccination
Mostolizadeh, Reihaneh	New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells The metabolic community model of Staphylococcus aureus and four abundant human nasal microbes
Motsi, Natasha	Latent variable models of fungal growth considering the data measurement process
Motzfeldt, Inga Kirstine Flaaten	Deciphering dysregulation in Erythroleukemia to design intervention strategies
Mowry, Bryan	Investigating brain development using tissue and single-cell gene expression data
Mueller, Melinda	An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness
Muhlich, Jeremy	A Mechanistic model of EGFR and ERK signaling reveals how allostery and rewiring contribute to drug resistance
Muley, Thomas	The abundance and cross-talk of EGFR and MET receptors in lung cancer cell lines is critical for the efficacy of tyrosine kinase inhibitors
Muley, Thomas	Personalized Treatment of Anemia in Lung Carcinoma
Musella, Luca	Temporal Proteomics and Transcriptomics Unravels the Host-Pathogen Interaction Network of Macrophages and Corynebacterium diphtheriae.
Muth, Thilo	A probabilistic graphical model for taxonomic profiling of viral and microbiome proteome samples Explainable Machine Learning in Mass Spectrometry-based Proteomics
Muti, Hannah Sophie	Artificial Intelligence in Digital Pathology Research - Where do we come from and where do we go?
Mutlu, Samet	Ionizing radiation triggers differential signaling dynamics of p-p53 and p-ERK1/2 in sensitive and resistant HNSCC cell clones
Myers, Chris J	The COmputational MOdeling in BIology NEtwork in 2022: Evolving needs in standardisation and model reuse SynBioSuite: Web-based modeling and analysis of biological systems
Myllys, Maiju	A systems pharmacology approach reveals robust drug metabolism and altered glucuronide disposition in a mouse model of liver cirrhosis
Méreaux, Jean-Loup	Exploring the missing heritability in SPG7 heterozygous carriers with Whole Genome Sequencing
Mölders, Christina	Alterations in hepatocyte growth factor induced signal transduction in fatty liver disease foster cancer development
Mühl, Heiko	A graph-based approach to analyze signal transduction involving cytokines and the JAK-STAT pathway in hepatocytes using Petri nets
Müller, Julian	DecryptM: decrypting drug actions and protein modification by dose- and time-resolved proteomics
Müller, Roman-Ulrich	Improving Our Understanding of ADPKD: Computational Analysis of Metabolome Data
Müller, Stefan	Analyzing Optimal and Non-Optimal Resource Allocations in Whole-Cell Models
Müller, Wolfgang	Deep insight into SABIO-RK data via visualization
N
Naas, Julia	FLOVELO - Pushing Boundaries of Cell Dynamics Inference with Maximum Flow Networks
Naegle, Kristen	Inferring kinase activity of a tumor from phosphoproteomic data
Nair, Satish	Precision machine-learning identifies a new paradigm for therapeutic discovery in Huntington’s disease: remodeling stress response to re-instate neuronal health and resilience.
Nakonecnij, Vanessa	INSIDe: Integrative modeling of the spread of serious infectious diseases
Navid, Ali	In silico analysis of metabolic capabilities in a synthetic community of phycosphere bacteria
Neri, Christian	Precision machine-learning identifies a new paradigm for therapeutic discovery in Huntington’s disease: remodeling stress response to re-instate neuronal health and resilience.
Neubert, Wilhelm	Multiscale Modeling of Dyadic Structure-Function Relation in Ventricular Cardiac Myocytes
Neumann, Avidan	Multi-dimensional immune correlates of early prediction of COVID-19 severe versus asymptomatic disease course
Neuwirt, Emilia	A powerful modelling approach tailored to cellular signalling
Nguyen, My-Le	Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide images
Nguyen, Tung V. N.	FAIR sharing of reproducible COVID-19 models of epidemic and pandemic forecast BioModels: an open repository of mathematical models of the biological and biomedical processes A Reproducibility Scorecard for Self-checking of Systems Biology Models
Ni, Yueqiong	An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness
Ni, Yueqiong	Resistant starch decreases intrahepatic triglycerides in NAFLD patients via the gut microbiome contribution to the branched-chain amino acids pool
Ni, Yueqiong	Discovery of Robust and Highly Specific Microbiome Signatures for Non-Alcoholic Fatty Liver Disease
Nickerson, David	The COmputational MOdeling in BIology NEtwork in 2022: Evolving needs in standardisation and model reuse FAIR assessment of biosimulation models - a cross-community project
Nielsen, Alexander V.	A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation
Nielsen, Jens	Reconstruction of a catalogue of enzyme constrained models of metabolism using GECKO 2.0 and its applications to eukaryote metabolism Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction Are metastatic triple negative breast cancers closer to their parental tumors or primary tumors of their destination tissues? Metabolic Atlas - extending metabolic networks for model organisms with enzyme turnover predictions with GotEnzymes
Niggemann, Oliver	From Plants to Plants and Beyond: How Modeling Strategies from the Engineering Field Could Benefit Systems Biology
Nikaein, Niloofar	Mathematical modeling of cytokine interplay in human monocytes during LPS stimulation
Nikoloski, Zoran	A modular concept for modeling of plant lipid metabolism Topological properties accurately predict cell division events and organization of Arabidopsis thaliana’s shoot apical meristem
Nikoloski, Zoran	Predicting plasticity of rosette growth and metabolic fluxes in Arabidopsis thaliana
Nilsson, Avlant	Combinatorial effects of ligands are predicted by a genome-scale model of signaling based on artificial neural networks
Nishida, Kozo	Delivering Virtual Reality and Gaming Technologies to the Field of Systems Biology
Nita-Lazar, Aleksandra	Targeted Proteomics-Driven Computational Modeling of the Mouse Macrophage Toll-like Receptor Signaling Pathway
Norris, Richard	Modelling mutations in B-cell malignancies reveals how mutations synergise to contribute to aggressive disease.
Nouailles, Geraldine	Integrational approaches for cross-species analysis of lung pathologies at single-cell resolution.
Novak, Bela	Improving our Mechanistic Understanding of Cell Cycle Dynamics
Nowicka, Melania	Towards identification of new life cycle-associated regions in phage genomes using deep learning Learning synthetic cell classifier designs with genetic algorithms and logic programming
Nussinov, Ruth	Discovery of Latent Drivers from Double Mutations in Pan-Cancer Data
Nychas, Emmanouil	Resistant starch decreases intrahepatic triglycerides in NAFLD patients via the gut microbiome contribution to the branched-chain amino acids pool
Nychas, Emmanouil	Discovery of Robust and Highly Specific Microbiome Signatures for Non-Alcoholic Fatty Liver Disease
Nyman, Elin	Mathematical modeling of cytokine interplay in human monocytes during LPS stimulation A comprehensive mechanistic model of adipocyte signaling with layers of confidence
Nånberg, Eewa	Mathematical modeling of cytokine interplay in human monocytes during LPS stimulation
Nöh, Katharina	Integrating 13C labeling and thermodynamic data for thermodynamically consistent Bayesian Metabolic Flux Analysis (T13C-MFA)
O
O'Donovan, Shauna	Analysis of multivariate longitudinal metabolomics data from meal challenges using RM-ASCA+ The Mixed Meal Model; quantifying metabolic resilience in overweight and obesity
Obermayer, Benedikt	Integrational approaches for cross-species analysis of lung pathologies at single-cell resolution.
Ogris, Christoph	Multi-Omics Regulatory Network Inference in the Presence of Missing Data
Ohnmacht, Alexander J.	The pharmaco-epigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity
Okada, Mariko	Gene expression heterogeneity arises from signaling networks Data-driven mathematical modeling of human skin aging and its application for natural compound screening
Okada, Takashi	Structural reduction of chemical reaction networks based on topology
Olivares-Hernández, Roberto	From genome sequencing to the first draft of the genome scale metabolic model of the symbiont fungus Leucoagaricus gongylophorus LEU18496.
Oliver, Brett	FROG Analysis - a community standard to foster reproducibility and curation of constraint-based models
Olivet, Julien	Identification of a SARS-CoV-2 inhibitor by combining binary protein-protein interaction mapping, structure prediction and virtual screening
Olofsson, Charlotta S.	A comprehensive mechanistic model of adipocyte signaling with layers of confidence
Olsson, Tomas	Proteomics profiling revealed a combination of protein biomarkers for predicting disease trajectory of multiple sclerosis
On Behalf Of The X-Hide Consortium,	Mathematical modeling of cytokine interplay in human monocytes during LPS stimulation
Oppenheim, Olya	PolarityJaM: An image analysis toolbox for cell polarity, junction and morphology quantification
Orsatti, Laura	The role of the kynurenine metabolism in chronic graft-versus-host-disease: Insights from computational modeling and patient data
Ospina De Los Rios, Santiago	DUNE-COPASI: Multi-Compartment Diffusion-Reaction solver for Cell Biology
Ostaszewsk, Marek	Cohort-specific Boolean models highlight different regulatory modules during disease progression
Overmann, Jörg	Elucidating functions of microbial dark matter
Oyarzún, Diego	Fast and scalable machine learning approach for dynamic metabolic engineering Analyzing single-cell trajectories with augmented machine learning methods predicts cancer drugs response in live-cell microscopy assays
P
Pack, Arran	Computational Models of Heterogeneous Mutations in Diffuse Large B-cell Lymphoma.
Padmanabhan Nandan, Akhilesh	Dynamical basis of cellular sensing and responsiveness to spatial-temporal signals
Palanikumar, Indumathi	FROG Analysis - a community standard to foster reproducibility and curation of constraint-based models
Palazzin, Alberto	Personalized medicine for Multiple Sclerosis treatment strategies at the individual and population level
Palomino, Sara	A robust clustering strategy for patient stratification in complex diseases
Palumbo, Pasquale	A low-granularity model integrating metabolism, growth and cell cycle: towards multi-level whole cell modeling of budding yeast
Panagiotou, Gianni	Discovery of Robust and Highly Specific Microbiome Signatures for Non-Alcoholic Fatty Liver Disease
Panagiotou, Gianni	Lactobacillus rhamnosus colonisation antagonizes Candida albicans by forcing metabolic adaptations that compromise pathogenicity Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection
Panagiotou, Gianni	An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness
Panagiotou, Gianni	Candida expansion in the human gut is associated with an ecological signature that supports growth under dysbiotic conditions
Panagiotou, Gianni	Resistant starch decreases intrahepatic triglycerides in NAFLD patients via the gut microbiome contribution to the branched-chain amino acids pool
Pang, Tin Yau	Predicting metabolite accumulation in cancerous metabolic network
Pang, Wei	Accelerating whole-cell modelling with surrogate machine learning models
Pantazopoulou, Chrysoula K.	Cell Type view into tomato stem elongation in Shade avoidance response
Papa, Federico	A low-granularity model integrating metabolism, growth and cell cycle: towards multi-level whole cell modeling of budding yeast
Pappas, Nikolaos	Benchmarking Phage-Host Prediction Tools using Real Metagenomics Data
Pareja-Lorente, Elena	Improving drug-induced transcriptional descriptors and their biological connectivity
Parizot, Christoph	Multi-dimensional immune correlates of early prediction of COVID-19 severe versus asymptomatic disease course
Park, Heewon	A novel drug response network analysis on supercomputers uncovered gastric cancer drug sensitivity mechanism XAI × Fugaku uncovered EMT mechanisms via cancer characteristic specific gene network analysis
Park, JinSeok	Vasculogenic mimicry induced by multicellular interaction in a 3D glioblastoma model-on-a-chip
Parlitz, Ulrich	Multiscale Modeling of Dyadic Structure-Function Relation in Ventricular Cardiac Myocytes
Pascual Garcia, Elena	Towards rational design of antibiotic combination therapies
Pastor, Victoria	Metabolome-wise analysis of plants exposed to abiotic stress conditions to identify potential metabolites inducers of cross-tolerance to biotic stressors
Pathirana, Dilan	FAIR sharing of reproducible COVID-19 models of epidemic and pandemic forecast
Pathirana, Dilan	Efficient brute-force model selection by iterative elimination of less useful model subspaces Moving Horizon Estimation for Patient-Specific Optimal Control of Blood Glucose in Intensive Care Units
Patil, Ananya	NETISCE: A dynamical systems and control theory approach to cell reprogramming
Paudel, Bishal	Cross-inhibitory feedbacks of nucleocytoplasmic transport give rise to divergent multicellular phenotype in ERBB2-activated breast epithelia
Pauling, Josch K	Lipid network and moiety analysis for revealing enzymatic dysregulation and mechanistic alterations from lipidomics data
Pauling, Josch Konstantin	LipiDetective: a Deep Learning Model for the Detection of Lipid Species in Mass Spectra
Pavlou, Antrea	Quantification of bacterial resource allocation in changining environments on the single-cell level
Pe'Er, Dana	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
Peidli, Stefan	Modeling the tumor microenvironment in patient-derived organoid culture
Peiter, Clemens	Non-linear mixed effects modeling of the T cell response in individuals infected with SARS-CoV-2
Peleke, Fritz Forbang	Deep convolutional neural networks capture the relationship between genetic variation and gene expression in plants
Pelkmans, Lucas	Multimodal perception links cellular state to decision making in single cells
Penas, David	Improving our Mechanistic Understanding of Cell Cycle Dynamics
Pennitz, Peter	Integrational approaches for cross-species analysis of lung pathologies at single-cell resolution.
Pentimalli, Tancredi	Dissecting the Developing Mouse Brain at Spatial Single-Cell Resolution Using PASTA-seq
Pepper, Andrea	Flow Cytometry Combined with Systems Biology Modelling Reveals Heterogeneous “NFkB Fingerprints” in DLBCL
Pepper, Andrea	Computational modeling of DLBCL predicts response to BH3-mimetics
Pepper, Chris	Computational modeling of DLBCL predicts response to BH3-mimetics Flow Cytometry Combined with Systems Biology Modelling Reveals Heterogeneous “NFkB Fingerprints” in DLBCL
Peres, Sabine	Geometric programming to Solve Optimal Concentrations of Metabolites and Enzymes in Constraint-based modelling
Perez de Arce, Karen	Inference of a causal synaptic molecular network from multiplexed imaging and its perturbations in autism and schizophrenia
Perez-Rosendahl, Mari	Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide images
Perez-Villatoro, Fernando	Single-cell spatial atlas of high-grade serous ovarian cancer
Periyasamy, Sathish	Investigating brain development using tissue and single-cell gene expression data
Perrin, Jérémie	Discovery of potential functional paths by integration of phospho-proteomics data in the PPI network using a RWR framework
Persad, Sitara	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
Persson, Alexander	Mathematical modeling of cytokine interplay in human monocytes during LPS stimulation
Persson, Katarina	Building the knowledge base to understand cellular signal transduction in different inflammatory phenotypes
Persson, Sebastian	Scalable and flexible inference framework for stochastic dynamic single-cell models
Peränen, Johan	Lipid metabolic reprogramming extends beyond histological tumor demarcations in human operable pancreatic cancer
Peters, Joshua M.	Combinatorial effects of ligands are predicted by a genome-scale model of signaling based on artificial neural networks
Petrova, Veronika	Using multi-omics data and machine learning to unravel alternative splicing regulation
Peyronnet, Emmanuel	A multi-strain model of immunization against influenza A viruses after infection or vaccination
Pflug, Florian	GuaCAMOLE: fragment GC bias-aware abundance estimation from metagenomic data increases accuracy and comparability
Pflug, Florian	Understanding Stem Cell Growth Dynamics in Human Cerebral Organoids
Philipps, Maren	Hybrid mechanistic and deep learning modeling in systems biology
Picchini, Umberto	Scalable and flexible inference framework for stochastic dynamic single-cell models
Picotti, Paola	Proteomes in 3D: Structural proteome snapshots as a new functional ‘omics readout
Picotti, Paola	Structural proteomics evidence for a predicted glycolytic metabolon
Piehl, Fredrik	Proteomics profiling revealed a combination of protein biomarkers for predicting disease trajectory of multiple sclerosis
Pierik, Ronald	Cell Type view into tomato stem elongation in Shade avoidance response
Pierre, Philippe	What are the functions of the short open reading frame-encoded peptides in monocytes? An interactomic approach.
Pignodel, Christine	3D reconstruction and mathematical modelling of whole slide images to elucidate resistance to the targeted therapy in melanoma
Piraud, Marie	Modeling disease progression in spinocerebellar ataxias
Pires Pacheco, Maria	Machine learning-based prediction of frailty in elderly people - Data from the Berlin Aging Study-II (BASE-II)
Pirhonen, Juho	Lipid metabolic reprogramming extends beyond histological tumor demarcations in human operable pancreatic cancer
Pitkänen, Esa	Comparative analysis of molecular fingerprints in prediction of drug combination effects
Planell, Nuria	Characterization of cardiac fibroblast remodeling dynamics after myocardial infarction A robust clustering strategy for patient stratification in complex diseases
Plata, German	Optimization of functional efficiency in key tissues constrains protein rate of evolution in multicellular species
Podell, Brendan	Resolving Resolution Hindrances in Spatial Transcriptomics
Podpecan, Vid	Stress Knowledge Map: A knowledge resource for modeling of plant stress responses
Podéus, Henrik	M4-health: digital twins that follow you throughout your health journey An interconnected multi-level mechanistic model of the human brain Connecting the Neurovascular coupling and Electrophysiological signaling – a modeling approach
Polenkowski, Mareike	Exploring the “dark proteome” in hepatocellular carcinoma
Polychronidou, Maria	From bench to scientific publishing
Ponchon, Jean	Jinkō Knowledge: An integrated knowledge management tool prior to in silico multiscale model development
Popel, Aleksander	Quantitative Spatial Profiling Reveals Tumor Microenvironment Heterogeneity and Prognostic Biomarkers Associated with Immune Population Architectures
Popp, Ferdinand	Extracting knowledge from multi-omics and clinical datasets using graph machine learning
Porubsky, Veronica	Using graph theory and recurrent neural network models to investigate the anxiety circuit
Posas, Francesc	Dissecting the principles underlying transcriptional heterogeneity
Poulton, Jenny	Optimal prediction of a noisy signal
Prawitz, Hannah	Control of COVID-19 Outbreaks under Stochastic Community Dynamics, Bimodality, or Limited Vaccination
Preusser, Tobias	Multilevel approach characterizing the progression of fatty liver disease
Prista von Bonhorst, Francisco	Initial source of heterogeneity in a model for cell fate decision in the early mammalian embryo Impact of Amyloid-Beta Induced Disruption on Ca2+ Homeostasis in a Simple model of Neuronal Activity
Pritzel, Alex	The workings and impact of AlphaFold
Proks, Martin	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
Prummer, Michael	Cell type-specific gene co-expression modules define tumor heterogeneity in melanoma patients
Prósper, Felipe	Characterization of cardiac fibroblast remodeling dynamics after myocardial infarction
Psaroudakis, Dennis	GO Term-based Comparative Functional Genomics in Plants
Puolakkainen, Pauli	Lipid metabolic reprogramming extends beyond histological tumor demarcations in human operable pancreatic cancer
Purwar, Rahul	Transcriptional fluctuations govern the serum dependent cell cycle duration heterogeneities in Mammalian cells
Puzović, Nataša	Being noisy in a crowd: differential selective pressure on gene expression noise in model gene regulatory networks
Péré, Marielle	Analyzing single-cell trajectories with augmented machine learning methods predicts cancer drugs response in live-cell microscopy assays
Q
Qian, Lingling	Resistant starch decreases intrahepatic triglycerides in NAFLD patients via the gut microbiome contribution to the branched-chain amino acids pool
Qiang, Yu	The abundance and cross-talk of EGFR and MET receptors in lung cancer cell lines is critical for the efficacy of tyrosine kinase inhibitors
R
Raajaraam, Lavanya	FROG Analysis - a community standard to foster reproducibility and curation of constraint-based models
Racoceanu, Daniel	3D reconstruction and mathematical modelling of whole slide images to elucidate resistance to the targeted therapy in melanoma
Radde, Nicole	Quasi-Entropy Closure: A Fast and Reliable Approach to Close the Moment Equations of the Chemical Master Equation Model-based design of a synthetic oscillator based on an epigenetic memory system
Radulescu, Ovidiu	Mitotic Memory as Spontaneous Symmetry Breaking in the Cell Stochasticity of Meiotic Entry in Xenopus Oocytes 3D reconstruction and mathematical modelling of whole slide images to elucidate resistance to the targeted therapy in melanoma
Raffetseder, Johanna	Dimethyl fumarate shifts CSF protein profile in relapsing remitting MS: a proteomics approach for biomarker discovery
Raffetseder, Johanna	Proteomics profiling revealed a combination of protein biomarkers for predicting disease trajectory of multiple sclerosis
Raghu, Aswathy	FROG Analysis - a community standard to foster reproducibility and curation of constraint-based models
Rahi, Sahand Jamal	When cells decide to give up on repairing DNA damage
Raimúndez, Elba	FAIR sharing of reproducible COVID-19 models of epidemic and pandemic forecast Posterior marginalization accelerates Bayesian inference for dynamical systems
Rajamani, Anantha Ramanan	The pharmaco-epigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity
Rajewsky, Nikolaus	Dissecting the Developing Mouse Brain at Spatial Single-Cell Resolution Using PASTA-seq The transcriptome dynamics of single cells during the cell cycle
Ralser, Markus	The metabolic and proteomic landscape of genome-scale genetic perturbation
Ramachandran, Kausthubh	FAIR sharing of reproducible COVID-19 models of epidemic and pandemic forecast
Raman, Karthik	FROG Analysis - a community standard to foster reproducibility and curation of constraint-based models
Ramirez de Molina, Ana	Personalized Treatment of Anemia in Lung Carcinoma
Ramos, Fernanda	Quantification of imaging biomarkers in the extracellular matrix of left and right sided colon cancer tissues
Ramsak, Ziva	Stress Knowledge Map: A knowledge resource for modeling of plant stress responses
Rands, Sean	Quantitative Impacts of Bumble Bee Ecology on Foraging Behaviour: An Economic Model
Rasko, John E.J.	Using multi-omics data and machine learning to unravel alternative splicing regulation
Ratto, Nicolas	A multi-strain model of immunization against influenza A viruses after infection or vaccination
Raue, Andreas	The abundance and cross-talk of EGFR and MET receptors in lung cancer cell lines is critical for the efficacy of tyrosine kinase inhibitors
Raue, Andreas	Personalized Treatment of Anemia in Lung Carcinoma
Rautou, Pierre-Emmanuel	A robust clustering strategy for patient stratification in complex diseases
Razzaq, Misbah	A deep learning-based approach for counting ovarian follicles
Reichel, Andreas	Modelling of Pharmacokinetics and Pharmacodynamics for first-in-man dose selection of targeted alpha therapy
Reichling, Stella	Dynamic metabolome profiling uncovers potential TOR signaling genes
Reifenstein, Eric	A robust model of neural superposition sorting
Reinz, Eileen	Disentangling Proliferation Signaling in Breast Cancer Subtypes based on an integrative modeling approach
Reiser, Johanna	The potential of PBI for high resolution lung imaging in patients
Reiter, Eric	A deep learning-based approach for counting ovarian follicles
Renard, Bernhard Y.	Towards identification of new life cycle-associated regions in phage genomes using deep learning Explainable Machine Learning in Mass Spectrometry-based Proteomics
Renson, Ludovic	Model Predictive Control of Cancer Cellular Dynamics: A New Strategy For Therapy Design
Renz, Alina	New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
Repsilber, Dirk	Mathematical modeling of cytokine interplay in human monocytes during LPS stimulation
Rey, Maja	Deep insight into SABIO-RK data via visualization
Rezeli, Melinda	Lipid metabolic reprogramming extends beyond histological tumor demarcations in human operable pancreatic cancer
Richtmann, Sarah	Development of a mass-spectrometry based clinical proteomics pipeline allows absolute quantification of pathway components and provides insights in pathway activation
Ripalda-Cemboráin, Purificación	Characterization of cardiac fibroblast remodeling dynamics after myocardial infarction
Rizzo, Paride	Elucidating the role of TAS2R43 in HGT-1 cells – an integrated omics approach
Robert, Corentin	Initial source of heterogeneity in a model for cell fate decision in the early mammalian embryo
Robinson, Jonathan L.	Are metastatic triple negative breast cancers closer to their parental tumors or primary tumors of their destination tissues?
Rocha, Camilo	Hierarchical gene function prediction using a novel topology-based threshold and comparing 6 correlation metrics. Study case: Rice
Rodriguez Gonzalez, Agustin	Personalized Treatment of Anemia in Lung Carcinoma
Roeblitz, Susanna	A mechanistic model for endocrine profiles of female puberty maturation
Rohr, Karl	The abundance and cross-talk of EGFR and MET receptors in lung cancer cell lines is critical for the efficacy of tyrosine kinase inhibitors
Rolfsson, Óttar	Molecular regulators of catecholamine response in human pulmonary microvascular endothelial cells
Rolle-Kampczyk, Ulrike	A physiology-based model of bile acid metabolism in mice
Roman Garcia, Susana	Bias and reproducibility in a Computational Neurobiology PhD’s journey
Roman-Vicharra, Cristhian	A quantum circuit model for inferring gene regulatory networks with application to single-cell transcriptomic data
Romano, Nicola	Bias and reproducibility in a Computational Neurobiology PhD’s journey
Rombouts, Jan	A bottom-up investigation of emergence in a self-organizing model of embryonic pattern formation
Romero, Jose A.H.	Deciphering transcriptional drivers of stem cell differentiation using causal inference
Romero, Miguel	Hierarchical gene function prediction using a novel topology-based threshold and comparing 6 correlation metrics. Study case: Rice
Roohani, Yusuf	GEARS: Predicting transcriptional outcomes of novel multi-gene perturbations
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Vicent, Cristian	Metabolome-wise analysis of plants exposed to abiotic stress conditions to identify potential metabolites inducers of cross-tolerance to biotic stressors
Vidal, Marc	Identification of a SARS-CoV-2 inhibitor by combining binary protein-protein interaction mapping, structure prediction and virtual screening
Viehof, Alina	A physiology-based model of bile acid metabolism in mice
Vigueras-Ramírez, Gabriel	From genome sequencing to the first draft of the genome scale metabolic model of the symbiont fungus Leucoagaricus gongylophorus LEU18496.
Vilas Zornoza, Amaia	Characterization of cardiac fibroblast remodeling dynamics after myocardial infarction
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Villette, Claire	Hybrid cellular automaton representation of the influence of mechanical stimulation on the development of bone metastases
Vinters, Harry V.	Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide images
Viola, Federica	Insights on hemodynamic changes in hypertension and T2D through non-invasive cardiovascular modeling
Viswanathan, Ganesh	Boolean dynamic modeling of TNFR1 signaling predicts a nested feedback loop regulating the apoptotic response at single-cell level (EXCEPTION - ZOOM)
Vitkup, Dennis	Optimization of functional efficiency in key tissues constrains protein rate of evolution in multicellular species Macroecological Laws Naturally Arise from Complex Chaotic Dynamics of Gut Microbiota Neural Circuits Underlying Autism Spectrum Disorders
Vitkup, Dennis	Cancer cells depend on environmental lipids for proliferation when electron acceptors are limited
Vlasov, Artyom	Alterations in hepatocyte growth factor induced signal transduction in fatty liver disease foster cancer development
Vogel, Arndt	Exploring the “dark proteome” in hepatocellular carcinoma
Vogler, Meike	Computational modeling of DLBCL predicts response to BH3-mimetics
Vogt, Tom	Precision machine-learning identifies a new paradigm for therapeutic discovery in Huntington’s disease: remodeling stress response to re-instate neuronal health and resilience.
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Vrethem, Magnus	Dimethyl fumarate shifts CSF protein profile in relapsing remitting MS: a proteomics approach for biomarker discovery
Vural, Merve	Mutually Antagonistic Protein Pairs of Cancer
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Wagner, Willi	The potential of PBI for high resolution lung imaging in patients
Wahlsten, Madison	Deep learning a model of cytotoxic T cell activation in the tumor microenvironment
Waldherr, Steffen	COVRECON: Combining Genome-scale Metabolic Network Reconstruction and Data-driven Inverse Modeling to Reveal Causal Biochemical Regulations
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Wamhoff, Eike	Inference of a causal synaptic molecular network from multiplexed imaging and its perturbations in autism and schizophrenia
Wang, Jiayao	Neural Circuits Underlying Autism Spectrum Disorders
Wang, Junyu	Numerical approaches for the rapid analysis of prophylactic efficacy against HIV
Wang, Lixin	Cross-inhibitory feedbacks of nucleocytoplasmic transport give rise to divergent multicellular phenotype in ERBB2-activated breast epithelia
Wang, Shangqian	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
Wang, Wenyu	Gene-essentiality based drug signature helps repurposing non-cancer drugs
Wang, Xiao	Dynamics of growth and ribosome level in batch cultures of S. cerevisiae
Wang, Xiao	Genome-wide analysis of genetic variants affecting metabolomic abundance in pigs divergent for feed efficiency
Wang, Xiaolin	Resistant starch decreases intrahepatic triglycerides in NAFLD patients via the gut microbiome contribution to the branched-chain amino acids pool
Wang, Yang	Topological properties accurately predict cell division events and organization of Arabidopsis thaliana’s shoot apical meristem
Wang, Yang	Identification of a SARS-CoV-2 inhibitor by combining binary protein-protein interaction mapping, structure prediction and virtual screening
Wang, Yu	Inferring individual interactions in gene regulatory networks with delays from time-series experiments
Wang, Ziyan	Comparative analysis of molecular fingerprints in prediction of drug combination effects
Wanker, Erich	The genotype-phenotype nexus: uncovering causal mechanisms in neurodegenerative disease with experimental and theoretical approaches
Wanker, Erich E	Identification of a SARS-CoV-2 inhibitor by combining binary protein-protein interaction mapping, structure prediction and virtual screening
Warth, Arne	The abundance and cross-talk of EGFR and MET receptors in lung cancer cell lines is critical for the efficacy of tyrosine kinase inhibitors
Waters, Chris	Avoiding errant activation of mitophagy: dual factor authentication of the Pink1/Parkin circuit
Weckwerth, Wolfram	COVRECON: Combining Genome-scale Metabolic Network Reconstruction and Data-driven Inverse Modeling to Reveal Causal Biochemical Regulations
Wegner, Andre	Data-driven modeling of mitochondrial metabolism
Weidemann, Andreas	Deep insight into SABIO-RK data via visualization
Weindl, Daniel	Data-driven modeling of mitochondrial metabolism Improving our Mechanistic Understanding of Cell Cycle Dynamics
Weiner, January	The insidious trappings of gene set enrichments
Weirich, Sara	Model-based design of a synthetic oscillator based on an epigenetic memory system
Weiße, Andrea	Towards rational design of antibiotic combination therapies
Weiße, Andrea	A model of RNA repair to study antibiotic tolerance
Welsch, Christoph	A graph-based approach to analyze signal transduction involving cytokines and the JAK-STAT pathway in hepatocytes using Petri nets
Welter, Danielle	FAIR assessment of biosimulation models - a cross-community project
Wertz, Mary	Precision machine-learning identifies a new paradigm for therapeutic discovery in Huntington’s disease: remodeling stress response to re-instate neuronal health and resilience.
Wessely, Anja	A disease network-based deep learning approach for characterizing melanoma
Westerhuis, Johan	Analysis of multivariate longitudinal metabolomics data from meal challenges using RM-ASCA+
Wiechmann, Svenja	Decrypting drug actions and protein modifications by dose- and time-resolved proteomics
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Wiemann, Stefan	Disentangling Proliferation Signaling in Breast Cancer Subtypes based on an integrative modeling approach
Wieser, Andreas	Non-linear mixed effects modeling of the T cell response in individuals infected with SARS-CoV-2
Wieser, Andreas	INSIDe: Integrative modeling of the spread of serious infectious diseases
Wieser, Andreas	Seroepidemiology And Modeling Of SARS-CoV-2 In Ethiopia: Longitudinal Cohort Study Among Front-line Health-care Workers And Community
Wilhelm, Mathias	DecryptM: decrypting drug actions and protein modification by dose- and time-resolved proteomics
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Wilkinson, Hillary	Precision machine-learning identifies a new paradigm for therapeutic discovery in Huntington’s disease: remodeling stress response to re-instate neuronal health and resilience.
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Williams, Christopher	Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide images
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Witting, Michael	LipiDetective: a Deep Learning Model for the Detection of Lipid Species in Mass Spectra
Witzenrath, Martin	Integrational approaches for cross-species analysis of lung pathologies at single-cell resolution.
Wodke, Judith	MeDaX - our vision for bioMedical Data eXploration
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Wolkenhauer, Olaf	A workflow for the creation of regulatory networks integrating miRNAs and lncRNAs associated with exposure to ionizing radiation using open source data and tools Become an ICSB - an Interdisciplinary Champion of Systems & Biology
Wong, Daniel R.	Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide images
Wong, Justin J.-L.	Using multi-omics data and machine learning to unravel alternative splicing regulation
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Wortel, Meike	A low-granularity model integrating metabolism, growth and cell cycle: towards multi-level whole cell modeling of budding yeast
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Wäsch, Marvin	Multilevel approach characterizing the progression of fatty liver disease
Wöhrle, Svenja	A powerful modelling approach tailored to cellular signalling
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Xia, Yufan	Manually curated genome-scale metabolic reconstructions of the multi-drug resistant Gram-negative pathogens A. baumannii and K. pneumoniae
Xie, Ren	Analysis of multivariate longitudinal metabolomics data from meal challenges using RM-ASCA+
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Xu, Guowang	Resistant starch decreases intrahepatic triglycerides in NAFLD patients via the gut microbiome contribution to the branched-chain amino acids pool
Xu, Tianhao	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
Y
Yadav, Manish	Theory of biochemical information processing with transients
Yaffe, Michael	Systems Approaches to Deciphering Kinase Signaling and the Phosphoproteome: A Focus on Cancer, Inflammation, and DNA Damage
Yamaguchi, Tomoyuki	Reinforcement learning and Monte-Carlo tree search in gene expression enable the entire gene regulation in a cell
Yang, Qiong	Building a synthetic cell: search for the minimal requirements for robust, sustainable, and tunable cell cycles
Yavuz, Bengi Ruken	Discovery of Latent Drivers from Double Mutations in Pan-Cancer Data
Young, Jamey	Amino acid metabolism of Chinese Hamster Ovary cells: Comparison of growth and production phases in a fed-batch
Youssef, Pierre	Investigating brain development using tissue and single-cell gene expression data
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Z
Zadora, Piotr	Development of a mass-spectrometry based clinical proteomics pipeline allows absolute quantification of pathway components and provides insights in pathway activation
Zagidullin, Bulat	Comparative analysis of molecular fingerprints in prediction of drug combination effects
Zagorščak, Maja	Stress Knowledge Map: A knowledge resource for modeling of plant stress responses
Zaidi, Samir	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
Zakieva, Alexandra	Computational analysis of cambium activity during plant radial growth
Zamboni, Nicola	Simulation Based Metabolic Flux Inference
Zampieri, Mattia	CRISPRi meets metabolomics: a platform for rapid functional annotation of compound libraries
Zanghellini, Jürgen	Analyzing Optimal and Non-Optimal Resource Allocations in Whole-Cell Models Amino acid metabolism of Chinese Hamster Ovary cells: Comparison of growth and production phases in a fed-batch Characterizing all feasible metabolic conversions of individual cells and microbial communities with elementary conversion modes.
Zanzoni, Andreas	What are the functions of the short open reading frame-encoded peptides in monocytes? An interactomic approach.
Zecchin, Marina	FISHing for Correlation
Zecha, Jana	Decrypting drug actions and protein modifications by dose- and time-resolved proteomics
Zecha, Jana	DecryptM: decrypting drug actions and protein modification by dose- and time-resolved proteomics
Zenkner, Martina	Identification of a SARS-CoV-2 inhibitor by combining binary protein-protein interaction mapping, structure prediction and virtual screening
Zetter, Mario	Mathematical model of the immunopathological progression of tuberculosis
Zhang, Fangfei	COVIDpro: Database for mining protein dysregulation in patients with COVID-19
Zhang, Lanxin	Numerical approaches for the rapid analysis of prophylactic efficacy against HIV
Zhang, Le	A disease network-based deep learning approach for characterizing melanoma
Zhang, Lu	An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness
Zhang, Yao	Computational modeling of the Hes1 oscillator for the self-renewal of muscle stem cells
Zhang, Youcheng	Integrative analysis on comorbid signatures in psychotic disorders using multi-rank non-negative matrix factorization based graph approach
Zhao, Jimmy	Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling
Zhao, Michael	A dynamic HIF1α-PPARγ circuit controls a paradoxical adipocyte regulatory landscape A bottom-up investigation of emergence in a self-organizing model of embryonic pattern formation
Zhou, Jinfei	A disease network-based deep learning approach for characterizing melanoma
Zhou, Lina	Resistant starch decreases intrahepatic triglycerides in NAFLD patients via the gut microbiome contribution to the branched-chain amino acids pool
Zhu, Feng	A modular concept for modeling of plant lipid metabolism
Zia, Asima	Inferring Gene Networks Rewiring of Naive and Primed Human Embryonic Stem Cells During Cellular Reprogramming Using Single-Cell RNA-seq Data
Zinzen, Robert Patrick	Logical modeling of signaling mechanisms in early development
Zörnig, Inka	Extracting knowledge from multi-omics and clinical datasets using graph machine learning
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Åkesson, Julia	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
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Štor, Jerneja	Amino acid metabolism of Chinese Hamster Ovary cells: Comparison of growth and production phases in a fed-batch