ICSB 2017: INTERNATIONAL CONFERENCE ON SYSTEMS BIOLOGY 2017

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

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13C metabolic flux analysis	Investigate metabolic reprogramming of Saccharomyces cerevisiae for xylose-based fatty alcohol production via 13C metabolic flux Analysis
13C MFA	Investigate metabolic reprogramming of Saccharomyces cerevisiae for xylose-based fatty alcohol production via 13C metabolic flux Analysis
A
ABC	Global regulation of transcription by cell size
actin	Multiphysics models of actin regulation
actinobacteria	Extended GEM of Streptomyces Coelicolor for production of secondary metabolites
activation threshold	Circadian clock protein Cry regulates cellular quiescence depth
Adaptation	Stress-adaptive decision-making and dispersal behaviors in nematodes involve coordinated neuropeptide signaling
Adult stem cell	Intercellular Coupling of the Cell Cycle and Circadian Clock in Adult Stem Cell Culture
ageing	Towards a Computational Model of the Dermal Extracellular Matrix in Ageing
Ageing strategy	Large scale simulations of a damage accumulation model in Saccharomyces cerevisiae reveal the benefit of dynamic damage retention in unicellular ageing
algorithms	Reconstructing dynamic processes from high dimensional snap-shot data
Amyloid	Nano-scale imaging and systems modelling of amyloid protein self-assembly
analog computing	Using action potential simulations to explore the possible cause-effect relationships between gain and loss of cardiac ion channel function and generation of proarrhythmic early afterdepolarizations
Analysis	COPASI Tutorial
Anaphase regulatory proteins	Evaluating the Robustness of the Temporal Order of Anaphase Events using an Ensemble of Single Cell Models
Anti-cancer drug	Predicting anticancer drug responses using deep learning based on cancer cell line gene expression profiles and drug molecular fingerprints
antibiotic resistance	Modeling the Metabolic Response to Antibiotic Stress in Bacterial Pathogens
antibiotics	Extended GEM of Streptomyces Coelicolor for production of secondary metabolites Modeling the Metabolic Response to Antibiotic Stress in Bacterial Pathogens
Antimicrobials	Genome mining of Bacillus licheniformis strains from the Red Sea with focus on the biosynthesis of antimicrobial products
apoptosis	Fundamental Trade-offs between Information Flow in Single Cells and Cell Populations Identifying non-genetic origins of cell-to-cell variability in B-lymphocyte proliferation through systems biology
Arabidopsis	CoReg: Identification of co-regulators in genome scale transcription regulatory
Arabidopsis thaliana	Genome scale metabolic model of Arabidopsis thalina for isoprenoid production
arrhythmia	Using action potential simulations to explore the possible cause-effect relationships between gain and loss of cardiac ion channel function and generation of proarrhythmic early afterdepolarizations
artificial neural network	Emulating mechanism-based models with artificial neural networks for applications in synthetic biology and systems biology
ATAC-seq	Transcriptional regulatory network inference from gene expression and chromatin accessibility measurements
Atomic force microscopy	Nano-scale imaging and systems modelling of amyloid protein self-assembly
Attractor landscape	Cell-type specific optimized therapy for colorectal cancer based on dynamical analysis of variant network models
Attractors	Analysis of a dynamic model of guard cell signaling reveals the stability of signal propagation
automated experimental planning	Using high-throughput genetics to test mathematical models of the yeast cell cycle
Autonomous Oscillations	UNCOVERING A NETWORK MOTIF UNDERLYING A MINIMAL AUTONOMOUS OSCILLATOR OF THE BUDDING YEAST CELL CYCLE
auxotrophy predictions	Automated pathway curation and improving metabolic model reconstruction based on phylogenetic analysis of pathway conservation
B
B. licheniformis	Genome mining of Bacillus licheniformis strains from the Red Sea with focus on the biosynthesis of antimicrobial products
bacteria	The PATRIC bioinformatics resource center for omic data analysis
Bacterial conjugation	Predictive modelling of a batch filter mating process
bacterial pathogens	Modeling the Metabolic Response to Antibiotic Stress in Bacterial Pathogens
bar-code deletion library	Global Outlook on Survival of Escherichia coli Mutants during Long-Term Stationary Phase
Barcode	Computational framework for endogenous barcoding of hematopoietic stem cells in vivo
bifurcation	Cells read TGF-beta temporal information through a nested relay mechanism Multi-Objective Optimization in Biology and Biomedicine
bifurcation analysis	Deciphering the dynamical origin of mixed population during neural stem cell development Modeling the Interactions of Sense and Antisense Transcripts in the Mammalian Circadian Clock Network
bifurcation theory	Network Dynamics and Cell Physiology
Biochemical Modeling	Tutorial on StochSS: An Integrated Development Environment for Simulation and Analysis of Discrete Stochastic Biochemical Models
Biochemical networks	Model reduction under parameter uncertainty
bioinformatics	The PATRIC bioinformatics resource center for omic data analysis The Undergraduate Degree in Systems Biology at Virginia Tech
Biological networks	SigNetSim : A web platform for building and analyzing mathematical models of molecular signaling networks
biological noise	The dual role of microRNA in boundary formation of the spinal cord
Biological oscillators	Incoherent inputs enhance robustness of biological oscillators
biomarker identification	Identification of potential tissue-specific cancer biomarkers and development of cancer versus normal genomic classifiers
bioproduction	E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria
Biosensor	A Synthetic Biosensor to Determine Peroxisomal Acetyl-CoA Concentration for Compartmentalized Metabolic Engineering.
Bistability	Two interlinked bistable mechanisms generate a robust M phase
bistable switch	Keynote Talk: Cell cycle regulation by systems-level feedback controls
bistable switches	A common role for stoichiometric inhibitors in cell cycle transitions
black box model	A Black Box Model of Patient Response to Hemodialysis
blood pressure regulation	A Black Box Model of Patient Response to Hemodialysis
BMP signaling	Mapping BMP pairwise interactions describes how cells compute responses to BMP mixtures
BOLD response	Multi-level modelling for a new physiologically based interpretation of fMRI data
boolean model	A comprehensive dynamical network model of the human immune system
Boolean Modeling	DECIPHERING CELL CYCLE ROBUSTNESS BY A MULTI-SCALE FRAMEWORK INTEGRATING CELL CYCLE AND METABOLISM IN BUDDING YEAST
Boolean modeling and simulation	Systems modeling of interplay among extracellular cytokines regulating phenotypic plasticity of CD4+ T-cell differentiation
Boolean network	Compensatory interactions to stabilize multiple steady states or mitigate the effects of multiple deregulations in biological networks Identifying synergistic control targets of a biological network based on a merged state transition map
bottleneck	Crosstalk between diverse synthetic protein degradation tags in Escherichia coli
Bottom Up	Towards a Computational Model of the Dermal Extracellular Matrix in Ageing
BPA	miRNA expression shifts as an initiator event in carcinogenesis induced by Bisphenol A in human prostate cells
Breast cancer	Insulin receptor substrate (IRS) dictates differential responses to insulin and insulin-like growth factor I (IGF1) stimulation
Budding Yeast	THE MULTIPLEX PHASE INTERLOCKER – A NOVEL AND ROBUST MOLECULAR DESIGN SYNCHRONIZING TRANSCRIPTIONAL CELL CYCLE DYNAMICS DECIPHERING CELL CYCLE ROBUSTNESS BY A MULTI-SCALE FRAMEWORK INTEGRATING CELL CYCLE AND METABOLISM IN BUDDING YEAST Cell Cycle Control in Budding Yeast: Robustness of Model Predictions Dilution of the cell cycle inhibitor Whi5 alone cannot account for size control in budding yeast Enhancing the Visualization of Budding Yeast Cell Cycles UNCOVERING A NETWORK MOTIF UNDERLYING A MINIMAL AUTONOMOUS OSCILLATOR OF THE BUDDING YEAST CELL CYCLE
budding yeast cell cycle model	Hybrid ODE/SSA Model of the Budding Yeast Cell Cycle Control Mechanism with Mutant Case Study
Bullous Pemphigoid	A distinct cutaneous microbiota profile in autoimmune bullous disease patients
bursts	Stochastic model of HPV early promoter predicts bursts like pattern of gene expression
C
c-MYC	Circadian clock protein Cry regulates cellular quiescence depth
C. elegans	High-throughput platforms for deep phenotyping
CAD	Data-Driven Design of Cell Factories and Communities
Caenorhabditis elegans	Stress-adaptive decision-making and dispersal behaviors in nematodes involve coordinated neuropeptide signaling
cameo	Tutorial: Metabolic flux modeling and computer aided strain design with cobrapy, cameo and DD-DeCaF
cancer	Computational Model of Melanoma Cancer Reconstructing dynamic processes from high dimensional snap-shot data
cancer biomarker	Identification of potential tissue-specific cancer biomarkers and development of cancer versus normal genomic classifiers
Cancer biomarkers	Cell Cycle Model System for the Identification of Molecular Markers of Cancer
Cancer cell line	Predicting anticancer drug responses using deep learning based on cancer cell line gene expression profiles and drug molecular fingerprints
Cancer cell lines	Dynamic network entropy as predictor of drug response in cancer cells.
cancer classification	Identification of potential tissue-specific cancer biomarkers and development of cancer versus normal genomic classifiers
Cancer development	Analysis of phenotypic network changes along with the sequential occurrence of driver mutations during colorectal tumorigenesis
Cancer drugs	Dynamic network entropy as predictor of drug response in cancer cells.
Cancer evolution	Clonal evolution in glioblastoma
cancer initiation	Clonal evolution in glioblastoma
Cancer Phenotype	Heparin-based hydrogel as a biomimetic 3D matrix for solid-phase growth factor presentation and cultivation of breast cancer cells
Cancer signalling	Patient-specific modelling and cell-to-cell variability of the JNK-p53 activation dynamics in primary and relapsed tumours.
cancer systems biology	Workshop: Developing Tutorials For Research Tools And Methods Defining subtype taxonomies and functional architectures of the breast cancer kinome Quantifying epithelial-mesenchymal plasticity in cancer and its association with patient survival
cancer treatment	Understanding the self-renewal, differentiation and death of intestinal cells
Carcinogenesis	miRNA expression shifts as an initiator event in carcinogenesis induced by Bisphenol A in human prostate cells
Caulobacter Cell Cycle	A Model of the Control Mechanism for the Genetic Circuit in Caulobacter Cell Cycle
CD4+ T-cell differentiation	Systems modeling of interplay among extracellular cytokines regulating phenotypic plasticity of CD4+ T-cell differentiation
CDK inhibitors	Circadian clock protein Cry regulates cellular quiescence depth
cell cycle	THE MULTIPLEX PHASE INTERLOCKER – A NOVEL AND ROBUST MOLECULAR DESIGN SYNCHRONIZING TRANSCRIPTIONAL CELL CYCLE DYNAMICS Cell Cycle Model System for the Identification of Molecular Markers of Cancer DECIPHERING CELL CYCLE ROBUSTNESS BY A MULTI-SCALE FRAMEWORK INTEGRATING CELL CYCLE AND METABOLISM IN BUDDING YEAST Keynote Talk: Cell cycle regulation by systems-level feedback controls Evaluating the Robustness of the Temporal Order of Anaphase Events using an Ensemble of Single Cell Models Mathematical modeling of an “ectopic” spindle assembly checkpoint Enhancing the Visualization of Budding Yeast Cell Cycles Exploring the dynamic regulation underlying synchronous chromosome splitting in anaphase Reconstructing dynamic processes from high dimensional snap-shot data Two interlinked bistable mechanisms generate a robust M phase UNCOVERING A NETWORK MOTIF UNDERLYING A MINIMAL AUTONOMOUS OSCILLATOR OF THE BUDDING YEAST CELL CYCLE Cell size homeostasis is critical for maintaining a permissive DNA:Cytoplasm ratio Intercellular Coupling of the Cell Cycle and Circadian Clock in Adult Stem Cell Culture
cell cycle checkpoints	A common role for stoichiometric inhibitors in cell cycle transitions
Cell Cycle Control	Cell Cycle Control in Budding Yeast: Robustness of Model Predictions
cell cycle regulation	Network Dynamics and Cell Physiology Using high-throughput genetics to test mathematical models of the yeast cell cycle
cell cycles	Incoherent inputs enhance robustness of biological oscillators
cell division	Exploring the dynamic regulation underlying synchronous chromosome splitting in anaphase
Cell factories	Data-Driven Design of Cell Factories and Communities
Cell fate decision	The link between dynamic modes of p53 and cell-fate decision in the DNA damage response Coupled feed-forward and feedback of ATM/p53/Mdm2/Wip1 control cell type-dependent bimodal p53 dynamics and cell fate response
cell growth	Modeling the nutrient signaling network in Saccharomyces cerevisiae
cell mass quantification	Proliferating mammalian cells modulate growth rate to reduce size variability
cell polarity	Exploring the inhibitory effect of membrane tension on cell polarization
cell signaling	Defining subtype taxonomies and functional architectures of the breast cancer kinome Oscillatory stimuli differentiate adapting circuit topologies
Cell size	Global regulation of transcription by cell size Cell size homeostasis is critical for maintaining a permissive DNA:Cytoplasm ratio
cell size control	Dilution of the cell cycle inhibitor Whi5 alone cannot account for size control in budding yeast Proliferating mammalian cells modulate growth rate to reduce size variability
Cell-cell adhesion	Automatic Inference of Dynamic Regulatory Networks Controlling Shape And Form
CellDesigner	COMBINE Tutorial - Modelling and Simulation Tools in Systems Biology
cellular death	Building a Mechanistic Understanding of Cell Death or Survival Decisions in L929 Cells
cellular heterogeneities	Evaluating the Robustness of the Temporal Order of Anaphase Events using an Ensemble of Single Cell Models
Cellular Signaling	Computational Construction of Toxicant Signaling Networks
Cellular signalling networks	A strategy for modelling and visualising phosphoproteomic datasets Mechanistic interplay between ceramide and insulin resistance
Cellular Signalling Pathway	Integration of a cellular signalling model with a whole-body pharmacokinetic model: Estimating cellular responses to administered interferon alpha doses in humans.
cellular survival	Building a Mechanistic Understanding of Cell Death or Survival Decisions in L929 Cells
cellular variability	Fundamental Trade-offs between Information Flow in Single Cells and Cell Populations
chemotaxis	Chemotropism in yeast
chemotropsim	Chemotropism in yeast
Circadian clock	A Dynamic KaiA-KaiC Interaction Maintains the Oscillation of the KaiABC Circadian Clock Intercellular Coupling of the Cell Cycle and Circadian Clock in Adult Stem Cell Culture Circadian clock protein Cry regulates cellular quiescence depth
circadian rhythm	Modeling the Interactions of Sense and Antisense Transcripts in the Mammalian Circadian Clock Network
cloud computing	Tutorial on StochSS: An Integrated Development Environment for Simulation and Analysis of Discrete Stochastic Biochemical Models Tutorial: GraphSpace: Interdisciplinary Collaborations in Network Biology
Clustering	Model reduction under parameter uncertainty
Clustering Biological Systems	Clustering Biological Systems Using Correlation Matrices
co-expression quasicliques	Finding coordinated expression motifs in RNA-seq data
co-infection	A comprehensive dynamical network model of the human immune system
Co-receptor CD8	Specificity and sensitivity of antigen sensing by the T cell receptor is enhanced by the co-receptor CD8
Co-regulation	CoReg: Identification of co-regulators in genome scale transcription regulatory
Co-target identification	Co-target identification from context specific kinetic models of folate metabolism in methotrexate resistant cancers
cobra	Tutorial: Metabolic flux modeling and computer aided strain design with cobrapy, cameo and DD-DeCaF Memote - A testing suite for constraint-based metabolic models Fast, easy, interoperable and reusable – the cobrapy infrastructure for constraints-based analysis of metabolic flux
cobrapy	Tutorial: Metabolic flux modeling and computer aided strain design with cobrapy, cameo and DD-DeCaF Fast, easy, interoperable and reusable – the cobrapy infrastructure for constraints-based analysis of metabolic flux
collaborations	Tutorial: GraphSpace: Interdisciplinary Collaborations in Network Biology
Combination Therapy	A Simple Formula for Fractional Killing
combinatorial perturbations	CrossPlan: Systematic Planning of Genetic Crosses to Validate Mathematical Models
Combinatorial signal processing	Mapping BMP pairwise interactions describes how cells compute responses to BMP mixtures
Combine	COMBINE Tutorial - Modelling and Simulation Tools in Systems Biology SigNetSim : A web platform for building and analyzing mathematical models of molecular signaling networks
comet tails	Multiphysics models of actin regulation
comparative omic analysis	The PATRIC bioinformatics resource center for omic data analysis
Comparing correlation matrices	Clustering Biological Systems Using Correlation Matrices
Compartmentalized Metabolic Engineering	A Synthetic Biosensor to Determine Peroxisomal Acetyl-CoA Concentration for Compartmentalized Metabolic Engineering.
Compartmentalized signaling	Functional diversification of signaling by GPCR localization
Complex systems	Ecological Dynamics of Gut Microbiota
Computational	Identifying non-genetic origins of cell-to-cell variability in B-lymphocyte proliferation through systems biology
computational biology	Workshop: 4th International Hands-on Tutorial on Logical Modeling​​​​​​​
Computational cancer biology
Computational Model	A comprehensive dynamical network model of the human immune system Towards a Computational Model of the Dermal Extracellular Matrix in Ageing
computational modeling	E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria Compartmentalization of lignin biosynthesis using either phenylalanine or tyrosine in Brachypodium distachyon Computational Model of Melanoma Cancer Coupled feed-forward and feedback of ATM/p53/Mdm2/Wip1 control cell type-dependent bimodal p53 dynamics and cell fate response
Computational models	Mechanistic interplay between ceramide and insulin resistance
computational simulation	Overrepresentation of feed forward loops can be driven by simple signal recognition, without the need for noise filtering
computer simulation	Network Dynamics and Cell Physiology
connections between courses
constraint based modeling	Genome scale metabolic model of Arabidopsis thalina for isoprenoid production
constraint-based modeling	DECIPHERING CELL CYCLE ROBUSTNESS BY A MULTI-SCALE FRAMEWORK INTEGRATING CELL CYCLE AND METABOLISM IN BUDDING YEAST Modeling the Metabolic Response to Antibiotic Stress in Bacterial Pathogens
constraints	Total enzyme activity constraint and homeostatic constraint impact on the best adjustable parameter sets of a kinetic model
constraints-based models	Tutorial: Metabolic flux modeling and computer aided strain design with cobrapy, cameo and DD-DeCaF
Control theory	Mathematical modeling of regulatory interactions in the fatty acid synthesis pathway
COPASI	COMBINE Tutorial - Modelling and Simulation Tools in Systems Biology
Coupled oscillator	Intercellular Coupling of the Cell Cycle and Circadian Clock in Adult Stem Cell Culture
CRISPR	An efficient procedure to generate plasmid for endogenous CRISPR-based knockin Systematic Optimization of Protein Secretory Pathways in Saccharomyces cerevisiae to Increase Expression of Hepatitis B Small Antigen
crosstalk	Building a Mechanistic Understanding of Cell Death or Survival Decisions in L929 Cells Crosstalk between diverse synthetic protein degradation tags in Escherichia coli
Curriculum	Systems biology education – When to start?
Cytokines	A Dynamic Model of Granulocyte-Monocyte Progenitor Differentiation
cytoskeleton	Multiphysics models of actin regulation
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Damage accumulation theory	Large scale simulations of a damage accumulation model in Saccharomyces cerevisiae reveal the benefit of dynamic damage retention in unicellular ageing
Damage retention	Large scale simulations of a damage accumulation model in Saccharomyces cerevisiae reveal the benefit of dynamic damage retention in unicellular ageing
Data aggregation	KineticDatanator: Tools for Aggregating Data for Biochemical Modeling
Data integration	Data Needs Structure: Data and Model Management for Distributed Systems Biology Projects
Data management	Data Needs Structure: Data and Model Management for Distributed Systems Biology Projects
database	Kinetics data information retrieval from the literature as public service
Databases	Data Needs Structure: Data and Model Management for Distributed Systems Biology Projects
Dauer	Stress-adaptive decision-making and dispersal behaviors in nematodes involve coordinated neuropeptide signaling
Decay rates	Integrated regulation of mRNA synthesis and decay decodes TNF signaling during inflammatory muscle-atrophy.
decision-support
deep learning	Segmenting four-dimensional fluorescence microscopic image using Convolutional Neural Network Automating cell segmentation and tracking with deep learning algorithms Predicting anticancer drug responses using deep learning based on cancer cell line gene expression profiles and drug molecular fingerprints
Deterministic	COPASI Tutorial
developing tutorials	Workshop: Developing Tutorials For Research Tools And Methods
Development	Stress-adaptive decision-making and dispersal behaviors in nematodes involve coordinated neuropeptide signaling
Differentiation	A Dynamic Model of Granulocyte-Monocyte Progenitor Differentiation
diffusion	Chemotropism in yeast
Discrete dynamic model	Analysis of a dynamic model of guard cell signaling reveals the stability of signal propagation
Disease	A distinct cutaneous microbiota profile in autoimmune bullous disease patients
Division	Identifying non-genetic origins of cell-to-cell variability in B-lymphocyte proliferation through systems biology
DNA construct	An efficient procedure to generate plasmid for endogenous CRISPR-based knockin
DNA damage response	The link between dynamic modes of p53 and cell-fate decision in the DNA damage response
DNA Replication	A Model of the Control Mechanism for the Genetic Circuit in Caulobacter Cell Cycle
Drug combination	Workshop on Drug Response Measurement and Analysis
Drug response	Workshop on Drug Response Measurement and Analysis Dynamic network entropy as predictor of drug response in cancer cells.
Drug response prediction	Predicting anticancer drug responses using deep learning based on cancer cell line gene expression profiles and drug molecular fingerprints
Drug sensitivity	Workshop on Drug Response Measurement and Analysis
drug simulations
Drug transport	In-silico prioritization of transporter-drug relationships from drug sensitivity screens
dwSSA	dwSSA++: efficient rare event probability estimation algorithm with leaping
Dynamic modelling	Patient-specific modelling and cell-to-cell variability of the JNK-p53 activation dynamics in primary and relapsed tumours.
Dynamic stability	Dynamic network entropy as predictor of drug response in cancer cells.
Dynamical analysis	SigNetSim : A web platform for building and analyzing mathematical models of molecular signaling networks
dynamical modeling	Workshop: 4th International Hands-on Tutorial on Logical Modeling​​​​​​​ KineticDatanator: Tools for Aggregating Data for Biochemical Modeling Toward A Whole-Cell Model of H1 Human Embryonic Stem Cells (hESCs): A Genome-Scale Metabolic Model
dynamical models	Stochastic model of HPV early promoter predicts bursts like pattern of gene expression
Dynamical systems	Mechanistic interplay between ceramide and insulin resistance Oscillatory stimuli differentiate adapting circuit topologies Two interlinked bistable mechanisms generate a robust M phase
dynamical systems theory	Network Dynamics and Cell Physiology
Dynamics	Identifying non-genetic origins of cell-to-cell variability in B-lymphocyte proliferation through systems biology
dynamics treatment design	The Transition from Acute Kidney Injury to Chronic Kidney Diseases Comes from Evolutionary Compromise
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E. coli	Global Outlook on Survival of Escherichia coli Mutants during Long-Term Stationary Phase
early developmental embryos	Segmenting four-dimensional fluorescence microscopic image using Convolutional Neural Network
Ecological dynamics	Ecological Dynamics of Gut Microbiota
education	Educational experiences in systems and synthetic biology: a mathematician’s perspective
Efficient chemotactic performance	Optimal methylation noise for best chemotactic performance of E. coli
Elastic Net	In-silico prioritization of transporter-drug relationships from drug sensitivity screens
Elementary modes	Detection of all possible signaling pathways in complex networks at steady state using Manatee invariants
Emulating mechanism-based models	Emulating mechanism-based models with artificial neural networks for applications in synthetic biology and systems biology
Endocrine therapies resistance	Mathematical modeling of the unfolded protein response in different breast cancer cell lines
Energy landscape analysis	A study on frequency-dependent state transition patterns in brain networks using energy landscape analysis
enhancer	Multi-Objective Optimization in Biology and Biomedicine
Enhancer landscape	A data-driven correlation measure model for epigenetic network inference in T cells
ensemble of single cell models	Evaluating the Robustness of the Temporal Order of Anaphase Events using an Ensemble of Single Cell Models
enzyme	Kinetics data information retrieval from the literature as public service
Enzyme promiscuity	Nontargeted in vitro metabolomics identifies wide-spread enyzme promiscuity in Escherichia coli
Epigenetic regulatory network	A data-driven correlation measure model for epigenetic network inference in T cells
Epigenetics	Multi-Objective Optimization in Biology and Biomedicine
Epithelial-mesenchymal plasticity	Quantifying epithelial-mesenchymal plasticity in cancer and its association with patient survival
ER+ breast cancer	Mathematical modeling of the unfolded protein response in different breast cancer cell lines
Error models	Evaluating the effects of measurement noise on the inference of biological regulatory networks using Modular Response Analysis
escher	Tutorial: Metabolic flux modeling and computer aided strain design with cobrapy, cameo and DD-DeCaF
Eukaryotes	Modeling the spatio-temporal replication program
evolution	Simulating the Evolutionary Dynamics of Single-stranded RNA Virus Populations The spatiotemporal network dynamics of acquired resistance in an engineered microecology Overrepresentation of feed forward loops can be driven by simple signal recognition, without the need for noise filtering
experiment planning	CrossPlan: Systematic Planning of Genetic Crosses to Validate Mathematical Models
Experimental design	Structural identifiability of kinetic parameters
experimental validation	CrossPlan: Systematic Planning of Genetic Crosses to Validate Mathematical Models Using high-throughput genetics to test mathematical models of the yeast cell cycle
Extracellular Matrix	Heparin-based hydrogel as a biomimetic 3D matrix for solid-phase growth factor presentation and cultivation of breast cancer cells
Extreme pathways	Structural identifiability of kinetic parameters
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FAIRDOM	Data Needs Structure: Data and Model Management for Distributed Systems Biology Projects COMBINE Tutorial - Modelling and Simulation Tools in Systems Biology
Fatty acid synthesis	Mathematical modeling of regulatory interactions in the fatty acid synthesis pathway
fatty alcohols	Investigate metabolic reprogramming of Saccharomyces cerevisiae for xylose-based fatty alcohol production via 13C metabolic flux Analysis
feed-forward loops	Overrepresentation of feed forward loops can be driven by simple signal recognition, without the need for noise filtering
feedback	Cells read TGF-beta temporal information through a nested relay mechanism
feedback regulation	Exploring the dynamic regulation underlying synchronous chromosome splitting in anaphase
fibrosis	Multi-Objective Optimization in Biology and Biomedicine
filopodia	Multiphysics models of actin regulation
Fisher information	Structural identifiability of kinetic parameters
fission yeast	Global regulation of transcription by cell size
flipped classroom
flow cytometry	Reconstructing dynamic processes from high dimensional snap-shot data
Fluctuation in signalling pathway	Optimal methylation noise for best chemotactic performance of E. coli
fluorescence protein tagging	An efficient procedure to generate plasmid for endogenous CRISPR-based knockin
Flux Balance Analysis	Nontargeted in vitro metabolomics identifies wide-spread enyzme promiscuity in Escherichia coli
Flux-balance analysis	The metabolic reconstruction of a minimal cell
Fluxomics	Data-Driven Design of Cell Factories and Communities
Folate pathway	Co-target identification from context specific kinetic models of folate metabolism in methotrexate resistant cancers
four-dimensional microscopic image	Segmenting four-dimensional fluorescence microscopic image using Convolutional Neural Network
Fractional Killing	A Simple Formula for Fractional Killing
FRET biosensor	GEF-H1 regulation by microtubule dynamics unveiled by fluctuation analysis of biosensor images
Functional genomics	Extracting dysregulated subnetworks in the non-small cell lung carcinoma tumor microenvironment
G
G protein-coupled receptor	Functional diversification of signaling by GPCR localization
G2 checkpoint	Understanding the effect of radiation on the cell cycle through mathematical modelling
gapfilling algorithms based on phylogeny	Automated pathway curation and improving metabolic model reconstruction based on phylogenetic analysis of pathway conservation
GEF-H1	GEF-H1 regulation by microtubule dynamics unveiled by fluctuation analysis of biosensor images
gene expression	Stochastic model of HPV early promoter predicts bursts like pattern of gene expression
Gene expression prediction	Transcriptional regulatory network inference from gene expression and chromatin accessibility measurements
Gene networks	High-throughput platforms for deep phenotyping
gene regulation	Modeling the Interactions of Sense and Antisense Transcripts in the Mammalian Circadian Clock Network
gene regulatory networks	The dual role of microRNA in boundary formation of the spinal cord Stochastic model of HPV early promoter predicts bursts like pattern of gene expression Reverse-Engineering Gene regulatory Networks as Threshold Boolean Networks
Genetic Circuit	A Model of the Control Mechanism for the Genetic Circuit in Caulobacter Cell Cycle
genetic crosses	CrossPlan: Systematic Planning of Genetic Crosses to Validate Mathematical Models
Genetic regulation	Automatic Inference of Dynamic Regulatory Networks Controlling Shape And Form
Genome mining	Genome mining of Bacillus licheniformis strains from the Red Sea with focus on the biosynthesis of antimicrobial products
Genome scale metabolic modeling
Genome scale model	Genome scale metabolic model of Arabidopsis thalina for isoprenoid production
Genome-scale metabolic models	Automated pathway curation and improving metabolic model reconstruction based on phylogenetic analysis of pathway conservation
Genome-scale model	Extended GEM of Streptomyces Coelicolor for production of secondary metabolites
genome-scale modeling	Modeling the Metabolic Response to Antibiotic Stress in Bacterial Pathogens
genomic instability	Evaluating the Robustness of the Temporal Order of Anaphase Events using an Ensemble of Single Cell Models
Genotype-phenotype	High-throughput platforms for deep phenotyping
Gillespie's stochastic simulation algorithm	Network Dynamics and Cell Physiology
glioblastoma	Clonal evolution in glioblastoma
GO semantic similarity	Finding coordinated expression motifs in RNA-seq data
GPU	Sequential Monte Carlo learning of Bayesian gene regulatory network models from RNA-seq data
gradients	Chemotropism in yeast
graphs	Tutorial: GraphSpace: Interdisciplinary Collaborations in Network Biology
growth rate modulation	Proliferating mammalian cells modulate growth rate to reduce size variability
Gut microbiome	Ecological Dynamics of Gut Microbiota
Gut microbiota
H
H2O2	Systematic Approach to Understanding Selective Cancer Susceptibility to Pharmacological Ascorbate Therapy
half lifes	Integrated regulation of mRNA synthesis and decay decodes TNF signaling during inflammatory muscle-atrophy.
HBsAg	Systematic Optimization of Protein Secretory Pathways in Saccharomyces cerevisiae to Increase Expression of Hepatitis B Small Antigen
Hematopoiesis	Computational framework for endogenous barcoding of hematopoietic stem cells in vivo
Heparin Hydrogel	Heparin-based hydrogel as a biomimetic 3D matrix for solid-phase growth factor presentation and cultivation of breast cancer cells
Hepcidin	A mathematical model of iron dynamics in a mouse
Heterogeneity	Characterizing Phenotypic Heterogeneity in Small Cell Lung Cancer Controlling Quiescence Heterogeneity by an Rb-E2F Network Switch
high performance computing	Simulating the Evolutionary Dynamics of Single-stranded RNA Virus Populations
high-throughput experiments	Quantitative methods for detecting origins of interferons signalling sensitivity
Hilbert-Huang transform	An Adaptive Spatiotemporal Spectrum Decomposition Approach for Cellular Morphodynamic Profiling
host-pathogen	A comprehensive dynamical network model of the human immune system
Host-pathogen dynamics	Spatiotemporal model for pattern formation in phage-bacteria system
HPV	Stochastic model of HPV early promoter predicts bursts like pattern of gene expression
HRS/IRR	Understanding the effect of radiation on the cell cycle through mathematical modelling
hume genome	An efficient procedure to generate plasmid for endogenous CRISPR-based knockin
Hybrid epithelial/mesenchymal	Quantifying epithelial-mesenchymal plasticity in cancer and its association with patient survival
hybrid modelling
hybrid ODE/SSA method	Hybrid ODE/SSA Model of the Budding Yeast Cell Cycle Control Mechanism with Mutant Case Study
Hypergraph
Hyperpath
hysteresis	Keynote Talk: Cell cycle regulation by systems-level feedback controls
I
iBioSim	COMBINE Tutorial - Modelling and Simulation Tools in Systems Biology
IGF1	Insulin receptor substrate (IRS) dictates differential responses to insulin and insulin-like growth factor I (IGF1) stimulation
image analysis	GEF-H1 regulation by microtubule dynamics unveiled by fluctuation analysis of biosensor images
image processing	Segmenting four-dimensional fluorescence microscopic image using Convolutional Neural Network
immune response	A comprehensive dynamical network model of the human immune system
immune system	A comprehensive dynamical network model of the human immune system
Immunology	A Dynamic Model of Granulocyte-Monocyte Progenitor Differentiation
in vivo	Computational framework for endogenous barcoding of hematopoietic stem cells in vivo
Infectious Diseases	Mathematical and computational foundations of infectious disease epidemiology
information	Cells read TGF-beta temporal information through a nested relay mechanism
information theory	Fundamental Trade-offs between Information Flow in Single Cells and Cell Populations
Innate Immunology	Measuring neutrophil migration patterns using microfluidic devices and ODE modeling of the mechanistic molecular pathways
Insulin	Insulin receptor substrate (IRS) dictates differential responses to insulin and insulin-like growth factor I (IGF1) stimulation
Interactome
Interdependency	Clustering Biological Systems Using Correlation Matrices
Interdisciplinary education	Systems biology education – When to start?
interferons	Quantitative methods for detecting origins of interferons signalling sensitivity
Intestinal stem cells	Understanding the self-renewal, differentiation and death of intestinal cells
intrinsic stochasticity	Stochastic model of HPV early promoter predicts bursts like pattern of gene expression
Iron metabolism	A mathematical model of iron dynamics in a mouse
Isoform	Comprehensive Proteogenomic Characterization of Human Prostate Cancer Cells Reveals Many Missing Proteins and Novel Protein Variants
isoprenoids	Genome scale metabolic model of Arabidopsis thalina for isoprenoid production
J
JWS Online	COMBINE Tutorial - Modelling and Simulation Tools in Systems Biology
K
KaiABC	A Dynamic KaiA-KaiC Interaction Maintains the Oscillation of the KaiABC Circadian Clock
kcat
KEGG	Extended GEM of Streptomyces Coelicolor for production of secondary metabolites
Key words	Simulation of a Petri net Based Model of the Menthol Biosynthesis
Killer	The spatiotemporal network dynamics of acquired resistance in an engineered microecology
kinetic constants
Kinetic data	COMBINE Tutorial - Modelling and Simulation Tools in Systems Biology KineticDatanator: Tools for Aggregating Data for Biochemical Modeling
kinetic model	Co-target identification from context specific kinetic models of folate metabolism in methotrexate resistant cancers Total enzyme activity constraint and homeostatic constraint impact on the best adjustable parameter sets of a kinetic model
kinetics	Kinetics data information retrieval from the literature as public service
kockin	An efficient procedure to generate plasmid for endogenous CRISPR-based knockin
L
Large scale dynamical modelling	Large scale simulations of a damage accumulation model in Saccharomyces cerevisiae reveal the benefit of dynamic damage retention in unicellular ageing
large-scale analysis using KBase	Automated pathway curation and improving metabolic model reconstruction based on phylogenetic analysis of pathway conservation
LCC1	Mathematical modeling of the unfolded protein response in different breast cancer cell lines
LCC9	Mathematical modeling of the unfolded protein response in different breast cancer cell lines
Lesion-like brain disorder	Increasing the network communicability of a damaged brain network for rehabilitation
Ligand discrimination	Specificity and sensitivity of antigen sensing by the T cell receptor is enhanced by the co-receptor CD8
lignin biosynthetic pathway	Compartmentalization of lignin biosynthesis using either phenylalanine or tyrosine in Brachypodium distachyon
linear system approximation modeling	Predicting the perturbation effects in biological networks based on linear system approximation modeling
Lipopeptides	Genome mining of Bacillus licheniformis strains from the Red Sea with focus on the biosynthesis of antimicrobial products
local communication	The minimum dominating sets in a brain network critically determine the efficiency of local communication of the network
logical modeling	Workshop: 4th International Hands-on Tutorial on Logical Modeling​​​​​​​
low-dose radiation	Understanding the effect of radiation on the cell cycle through mathematical modelling
M
machine learning	Segmenting four-dimensional fluorescence microscopic image using Convolutional Neural Network Identification of potential tissue-specific cancer biomarkers and development of cancer versus normal genomic classifiers Finding coordinated expression motifs in RNA-seq data A data-driven correlation measure model for epigenetic network inference in T cells
Malnutrition
Manatee invariants	Detection of all possible signaling pathways in complex networks at steady state using Manatee invariants
Markov Chain Monte Carlo	Sequential Monte Carlo learning of Bayesian gene regulatory network models from RNA-seq data
Master Regulators	A Model of the Control Mechanism for the Genetic Circuit in Caulobacter Cell Cycle
Master's and bachelor degrees	Systems biology education – When to start?
Mathematical Epidemiology	Mathematical and computational foundations of infectious disease epidemiology
Mathematical Mdodeling	Quantitative Systems Pharmacology
Mathematical Model	A Model of the Control Mechanism for the Genetic Circuit in Caulobacter Cell Cycle
mathematical modeling	Measuring neutrophil migration patterns using microfluidic devices and ODE modeling of the mechanistic molecular pathways Spatiotemporal model for pattern formation in phage-bacteria system Specificity and sensitivity of antigen sensing by the T cell receptor is enhanced by the co-receptor CD8 Tutorial: Metabolic flux modeling and computer aided strain design with cobrapy, cameo and DD-DeCaF Network Dynamics and Cell Physiology Dilution of the cell cycle inhibitor Whi5 alone cannot account for size control in budding yeast A Simple Formula for Fractional Killing Dynamics of T cell memory generation inferred from single cell fate mapping in vivo Mathematical modeling of regulatory interactions in the fatty acid synthesis pathway SigNetSim : A web platform for building and analyzing mathematical models of molecular signaling networks Quantifying epithelial-mesenchymal plasticity in cancer and its association with patient survival The Undergraduate Degree in Systems Biology at Virginia Tech Using high-throughput genetics to test mathematical models of the yeast cell cycle
Mathematical modelling	Predictive modelling of a batch filter mating process Educational experiences in systems and synthetic biology: a mathematician’s perspective Computational framework for endogenous barcoding of hematopoietic stem cells in vivo
Maximum entropy model	A study on frequency-dependent state transition patterns in brain networks using energy landscape analysis
MCF7	Mathematical modeling of the unfolded protein response in different breast cancer cell lines
Mechanistic modeling	Insulin receptor substrate (IRS) dictates differential responses to insulin and insulin-like growth factor I (IGF1) stimulation
MEG	A study on frequency-dependent state transition patterns in brain networks using energy landscape analysis
melanoma	Computational Model of Melanoma Cancer
membrane tension	Exploring the inhibitory effect of membrane tension on cell polarization
Menthol biosynthesis	Simulation of a Petri net Based Model of the Menthol Biosynthesis
Merged state transition map	Identifying synergistic control targets of a biological network based on a merged state transition map
Meta-genomics	Data-Driven Design of Cell Factories and Communities
metabolic	Memote - A testing suite for constraint-based metabolic models
metabolic adaptation	Modeling the Metabolic Response to Antibiotic Stress in Bacterial Pathogens
Metabolic control analysis	Co-target identification from context specific kinetic models of folate metabolism in methotrexate resistant cancers
metabolic engineering	Total enzyme activity constraint and homeostatic constraint impact on the best adjustable parameter sets of a kinetic model Workshop: Multi-scale metabolic modeling and engineering
Metabolic model	Modeling Methanotrophy: A genome-scale metabolic model of Methylococcus capsulatus
Metabolic modeling	Data-Driven Design of Cell Factories and Communities Modeling the Metabolic Response to Antibiotic Stress in Bacterial Pathogens
metabolic modelling	COMBINE Tutorial - Modelling and Simulation Tools in Systems Biology
Metabolic network	Extended GEM of Streptomyces Coelicolor for production of secondary metabolites
Metabolic networks	Nontargeted in vitro metabolomics identifies wide-spread enyzme promiscuity in Escherichia coli
Metabolic reconstruction	The metabolic reconstruction of a minimal cell
Metabolism	DECIPHERING CELL CYCLE ROBUSTNESS BY A MULTI-SCALE FRAMEWORK INTEGRATING CELL CYCLE AND METABOLISM IN BUDDING YEAST Aggregating RNA-Seq reads from multiple genes in KEGG metabolic pathways improves interpretability in gene expression pathway analysis
Metabolomics	Data-Driven Design of Cell Factories and Communities Nontargeted in vitro metabolomics identifies wide-spread enyzme promiscuity in Escherichia coli Systems Biology of Herbal Medicine: Pharmacological property of complex herbal formulation
Methanotrophy	Modeling Methanotrophy: A genome-scale metabolic model of Methylococcus capsulatus
Methotrexate resistance	Co-target identification from context specific kinetic models of folate metabolism in methotrexate resistant cancers
microalgae	E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria
Microarray	Towards a Computational Model of the Dermal Extracellular Matrix in Ageing
microarray gene expression	Identification of potential tissue-specific cancer biomarkers and development of cancer versus normal genomic classifiers
Microbial ecology	The spatiotemporal network dynamics of acquired resistance in an engineered microecology Predictive modelling of a batch filter mating process
microbial phenotypes	Automated pathway curation and improving metabolic model reconstruction based on phylogenetic analysis of pathway conservation
Microbiome	Data-Driven Design of Cell Factories and Communities A distinct cutaneous microbiota profile in autoimmune bullous disease patients
Microfluidic Device	Measuring neutrophil migration patterns using microfluidic devices and ODE modeling of the mechanistic molecular pathways
Microfluidics	High-throughput platforms for deep phenotyping
Microscopy	Identifying non-genetic origins of cell-to-cell variability in B-lymphocyte proliferation through systems biology Multiphysics models of actin regulation
microtubule disassembly	GEF-H1 regulation by microtubule dynamics unveiled by fluctuation analysis of biosensor images
Minardo web tool	A strategy for modelling and visualising phosphoproteomic datasets
minimal Cdk network	Understanding the effect of radiation on the cell cycle through mathematical modelling
Minimal cell	The metabolic reconstruction of a minimal cell
minimize computational cost	Emulating mechanism-based models with artificial neural networks for applications in synthetic biology and systems biology
minimum dominating set	The minimum dominating sets in a brain network critically determine the efficiency of local communication of the network
MIRIAM	SigNetSim : A web platform for building and analyzing mathematical models of molecular signaling networks
miRNA	miRNA expression shifts as an initiator event in carcinogenesis induced by Bisphenol A in human prostate cells
Missing Protein	Comprehensive Proteogenomic Characterization of Human Prostate Cancer Cells Reveals Many Missing Proteins and Novel Protein Variants
Mitophagy in human	Detection of all possible signaling pathways in complex networks at steady state using Manatee invariants
mitosis	The biochemical design of the mitotic checkpoint Keynote Talk: Cell cycle regulation by systems-level feedback controls Two interlinked bistable mechanisms generate a robust M phase
mitotic checkpoint	The biochemical design of the mitotic checkpoint
model discrimination	Oscillatory stimuli differentiate adapting circuit topologies
Model fitting	SigNetSim : A web platform for building and analyzing mathematical models of molecular signaling networks
model integration	Toward A Whole-Cell Model of H1 Human Embryonic Stem Cells (hESCs): A Genome-Scale Metabolic Model
Model reduction	Model reduction under parameter uncertainty
Model selection	Model reduction under parameter uncertainty
Model simulation	SigNetSim : A web platform for building and analyzing mathematical models of molecular signaling networks
modeling	Tutorial: Metabolic flux modeling and computer aided strain design with cobrapy, cameo and DD-DeCaF Modeling the spatio-temporal replication program Identifying non-genetic origins of cell-to-cell variability in B-lymphocyte proliferation through systems biology Workshop: Multi-scale metabolic modeling and engineering Multiphysics models of actin regulation
Modelling	Kinetics data information retrieval from the literature as public service COPASI Tutorial COMBINE Tutorial - Modelling and Simulation Tools in Systems Biology Fast, easy, interoperable and reusable – the cobrapy infrastructure for constraints-based analysis of metabolic flux
Modelling standards	COMBINE Tutorial - Modelling and Simulation Tools in Systems Biology
Modelling tools	COMBINE Tutorial - Modelling and Simulation Tools in Systems Biology
models	Memote - A testing suite for constraint-based metabolic models
Modular Response Analysis	Evaluating the effects of measurement noise on the inference of biological regulatory networks using Modular Response Analysis
Molecular networks	Defining subtype taxonomies and functional architectures of the breast cancer kinome
Monte Carlo Simulation	Optimal methylation noise for best chemotactic performance of E. coli
Morphodynamic profiling	An Adaptive Spatiotemporal Spectrum Decomposition Approach for Cellular Morphodynamic Profiling
morphology	Automating cell segmentation and tracking with deep learning algorithms
mRNA dynamics	Integrated regulation of mRNA synthesis and decay decodes TNF signaling during inflammatory muscle-atrophy.
multi-algorithm	Toward A Whole-Cell Model of H1 Human Embryonic Stem Cells (hESCs): A Genome-Scale Metabolic Model
multi-cellular model	A comprehensive dynamical network model of the human immune system
multi-omics integration	Multi-omics analysis of T helper 22 cells
multi-scale	Toward A Whole-Cell Model of H1 Human Embryonic Stem Cells (hESCs): A Genome-Scale Metabolic Model
Multicellular Systems Biology	DECIPHERING CELL CYCLE ROBUSTNESS BY A MULTI-SCALE FRAMEWORK INTEGRATING CELL CYCLE AND METABOLISM IN BUDDING YEAST Integration of a cellular signalling model with a whole-body pharmacokinetic model: Estimating cellular responses to administered interferon alpha doses in humans.
Multiple Phase Interlocker	THE MULTIPLEX PHASE INTERLOCKER – A NOVEL AND ROBUST MOLECULAR DESIGN SYNCHRONIZING TRANSCRIPTIONAL CELL CYCLE DYNAMICS
multiple-objective optimization	The Transition from Acute Kidney Injury to Chronic Kidney Diseases Comes from Evolutionary Compromise
Multistable Dynamics	A data-driven correlation measure model for epigenetic network inference in T cells
multivalency	Multiphysics models of actin regulation
muscle atrophy	Integrated regulation of mRNA synthesis and decay decodes TNF signaling during inflammatory muscle-atrophy.
Mycoplasma mycoides	The metabolic reconstruction of a minimal cell
Myeloid-Derived Suppressor Cells	A Dynamic Model of Granulocyte-Monocyte Progenitor Differentiation
N
network attack simulation	The minimum dominating sets in a brain network critically determine the efficiency of local communication of the network Increasing the network communicability of a damaged brain network for rehabilitation
Network communicability	Increasing the network communicability of a damaged brain network for rehabilitation
Network control	Compensatory interactions to stabilize multiple steady states or mitigate the effects of multiple deregulations in biological networks Identifying synergistic control targets of a biological network based on a merged state transition map Cell-type specific optimized therapy for colorectal cancer based on dynamical analysis of variant network models
Network Dynamics	THE MULTIPLEX PHASE INTERLOCKER – A NOVEL AND ROBUST MOLECULAR DESIGN SYNCHRONIZING TRANSCRIPTIONAL CELL CYCLE DYNAMICS
Network entropy	Dynamic network entropy as predictor of drug response in cancer cells.
Network inference	Towards a Computational Model of the Dermal Extracellular Matrix in Ageing Sequential Monte Carlo learning of Bayesian gene regulatory network models from RNA-seq data Evaluating the effects of measurement noise on the inference of biological regulatory networks using Modular Response Analysis
network model	A comprehensive dynamical network model of the human immune system
network motifs	A common role for stoichiometric inhibitors in cell cycle transitions
Network reduction	Analysis of a dynamic model of guard cell signaling reveals the stability of signal propagation
network structures and motifs	Incoherent inputs enhance robustness of biological oscillators
Network switch	Controlling Quiescence Heterogeneity by an Rb-E2F Network Switch
Network topology	Predicting the perturbation effects in biological networks based on linear system approximation modeling A data-driven correlation measure model for epigenetic network inference in T cells
networks	Tutorial: GraphSpace: Interdisciplinary Collaborations in Network Biology
Neural development	Deciphering the dynamical origin of mixed population during neural stem cell development
Neural Networks	Reverse-Engineering Gene regulatory Networks as Threshold Boolean Networks
Neuropeptide	Stress-adaptive decision-making and dispersal behaviors in nematodes involve coordinated neuropeptide signaling
Neutrophil	Measuring neutrophil migration patterns using microfluidic devices and ODE modeling of the mechanistic molecular pathways
Noise	mRNA Production Noise in Eukaryotic Cells Identifying non-genetic origins of cell-to-cell variability in B-lymphocyte proliferation through systems biology
noise in gene expression	Overrepresentation of feed forward loops can be driven by simple signal recognition, without the need for noise filtering
Non-linear Dynamics	A Simple Formula for Fractional Killing
Non-targeted metabolomics	Systems biology of multi-herbal formulations: Addressing condition-dependent prescription selection by comparing pharmacological and compound traits of related formulations
NRPs	Genome mining of Bacillus licheniformis strains from the Red Sea with focus on the biosynthesis of antimicrobial products
NTBI	A mathematical model of iron dynamics in a mouse
nutrient signaling	Modeling the nutrient signaling network in Saccharomyces cerevisiae
O
ODE modelling	Towards a Computational Model of the Dermal Extracellular Matrix in Ageing
olfaction	Multi-Objective Optimization in Biology and Biomedicine
Oncogenic Signaling Pathway	Phosphoproteomics-Guided Discovery of Effective Combination Therapies in Cancer
optimistic	Simulating the Evolutionary Dynamics of Single-stranded RNA Virus Populations
optimization	E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria Total enzyme activity constraint and homeostatic constraint impact on the best adjustable parameter sets of a kinetic model
Optogenetic perturbation	An Adaptive Spatiotemporal Spectrum Decomposition Approach for Cellular Morphodynamic Profiling
Optogenetics	Functional diversification of signaling by GPCR localization
Organoid	Intercellular Coupling of the Cell Cycle and Circadian Clock in Adult Stem Cell Culture
P
P-invariant	Simulation of a Petri net Based Model of the Menthol Biosynthesis
p53 regulation	Coupled feed-forward and feedback of ATM/p53/Mdm2/Wip1 control cell type-dependent bimodal p53 dynamics and cell fate response
pairwise interactions
parallel discrete event simulation	Simulating the Evolutionary Dynamics of Single-stranded RNA Virus Populations
Parameter Estimation	COPASI Tutorial Tutorial on StochSS: An Integrated Development Environment for Simulation and Analysis of Discrete Stochastic Biochemical Models
Parameter Sensitivity	Tutorial on StochSS: An Integrated Development Environment for Simulation and Analysis of Discrete Stochastic Biochemical Models
Parameter uncertainty	Model reduction under parameter uncertainty
parametric space exploration	Emulating mechanism-based models with artificial neural networks for applications in synthetic biology and systems biology
Parasitic Nematodes	Stress-adaptive decision-making and dispersal behaviors in nematodes involve coordinated neuropeptide signaling
Pathway analysis	Aggregating RNA-Seq reads from multiple genes in KEGG metabolic pathways improves interpretability in gene expression pathway analysis
pattern detection	Identifying frequent patterns in biochemical reaction networks using graph-mining
Pattern formation	Spatiotemporal model for pattern formation in phage-bacteria system
Peroxiporins	Systematic Approach to Understanding Selective Cancer Susceptibility to Pharmacological Ascorbate Therapy
Peroxisome	A Synthetic Biosensor to Determine Peroxisomal Acetyl-CoA Concentration for Compartmentalized Metabolic Engineering. Investigate metabolic reprogramming of Saccharomyces cerevisiae for xylose-based fatty alcohol production via 13C metabolic flux Analysis
persister	Analysis and classification of differential production within toxin-antitoxin systems using large datasets
Petri net	Simulation of a Petri net Based Model of the Menthol Biosynthesis
Pharmacological Ascorbate	Systematic Approach to Understanding Selective Cancer Susceptibility to Pharmacological Ascorbate Therapy
Pharmacology	Systems biology of multi-herbal formulations: Addressing condition-dependent prescription selection by comparing pharmacological and compound traits of related formulations Workshop on Drug Response Measurement and Analysis
phase field model	Exploring the inhibitory effect of membrane tension on cell polarization
phase plane analysis	Network Dynamics and Cell Physiology
Phenotype transition	Nonequilibrium stochastic dynamics at single cell level
Phenotypic attractors	Identifying synergistic control targets of a biological network based on a merged state transition map
Phenotypic network	Analysis of phenotypic network changes along with the sequential occurrence of driver mutations during colorectal tumorigenesis
Phenotyping	High-throughput platforms for deep phenotyping
Phosphoproteomic time series datasets	A strategy for modelling and visualising phosphoproteomic datasets
Phosphoproteomics	Phosphoproteomics-Guided Discovery of Effective Combination Therapies in Cancer
photosynthesis	E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria
Physiology	Quantitative Systems Pharmacology
plasmid	An efficient procedure to generate plasmid for endogenous CRISPR-based knockin
Poisson Point Process	GEF-H1 regulation by microtubule dynamics unveiled by fluctuation analysis of biosensor images
Polarity establishment	Principles that govern competition or co-existence in Rho-GTPase driven polarization
population dynamics	Simulating the Evolutionary Dynamics of Single-stranded RNA Virus Populations Global Outlook on Survival of Escherichia coli Mutants during Long-Term Stationary Phase
positive feedback loops	A common role for stoichiometric inhibitors in cell cycle transitions
post-transcription	Stochastic model of HPV early promoter predicts bursts like pattern of gene expression
Precision medicine	Patient-specific modelling and cell-to-cell variability of the JNK-p53 activation dynamics in primary and relapsed tumours. Cell-type specific optimized therapy for colorectal cancer based on dynamical analysis of variant network models Predicting anticancer drug responses using deep learning based on cancer cell line gene expression profiles and drug molecular fingerprints
predicting the perturbation effects	Predicting the perturbation effects in biological networks based on linear system approximation modeling
Prey	The spatiotemporal network dynamics of acquired resistance in an engineered microecology
professional development	The Undergraduate Degree in Systems Biology at Virginia Tech
programming	Fast, easy, interoperable and reusable – the cobrapy infrastructure for constraints-based analysis of metabolic flux
proliferating mammalian cell	Proliferating mammalian cells modulate growth rate to reduce size variability
proliferation	Controlling Quiescence Heterogeneity by an Rb-E2F Network Switch Circadian clock protein Cry regulates cellular quiescence depth
Prostate Cancer	Comprehensive Proteogenomic Characterization of Human Prostate Cancer Cells Reveals Many Missing Proteins and Novel Protein Variants Aggregating RNA-Seq reads from multiple genes in KEGG metabolic pathways improves interpretability in gene expression pathway analysis
protease	Crosstalk between diverse synthetic protein degradation tags in Escherichia coli
Protein aggregation	Nano-scale imaging and systems modelling of amyloid protein self-assembly
Protein assembly	Nano-scale imaging and systems modelling of amyloid protein self-assembly
Protein design	A Dynamic KaiA-KaiC Interaction Maintains the Oscillation of the KaiABC Circadian Clock
protein express pathway	Systematic Optimization of Protein Secretory Pathways in Saccharomyces cerevisiae to Increase Expression of Hepatitis B Small Antigen
Protein interaction network	Dynamic network entropy as predictor of drug response in cancer cells.
Protein Interaction Networks	Computational Construction of Toxicant Signaling Networks
Protein-protein interaction	A Dynamic KaiA-KaiC Interaction Maintains the Oscillation of the KaiABC Circadian Clock
Proteogenomics	Comprehensive Proteogenomic Characterization of Human Prostate Cancer Cells Reveals Many Missing Proteins and Novel Protein Variants
Proteomics	Cell Cycle Model System for the Identification of Molecular Markers of Cancer Data-Driven Design of Cell Factories and Communities Comprehensive Proteogenomic Characterization of Human Prostate Cancer Cells Reveals Many Missing Proteins and Novel Protein Variants
python	Tutorial: Metabolic flux modeling and computer aided strain design with cobrapy, cameo and DD-DeCaF Fast, easy, interoperable and reusable – the cobrapy infrastructure for constraints-based analysis of metabolic flux
Q
Quantitative biology	Mapping BMP pairwise interactions describes how cells compute responses to BMP mixtures
quantitative phase microscopy	Proliferating mammalian cells modulate growth rate to reduce size variability
Quantitative Systems Pharmacology	Quantitative Systems Pharmacology
queueing theory	Crosstalk between diverse synthetic protein degradation tags in Escherichia coli
quiescence	Controlling Quiescence Heterogeneity by an Rb-E2F Network Switch Reconstructing dynamic processes from high dimensional snap-shot data Circadian clock protein Cry regulates cellular quiescence depth
R
radiogenomics
rare event	dwSSA++: efficient rare event probability estimation algorithm with leaping
Rb-E2F bistable switch network	Circadian clock protein Cry regulates cellular quiescence depth
Rb-E2F pathway	Controlling Quiescence Heterogeneity by an Rb-E2F Network Switch
reaction	Kinetics data information retrieval from the literature as public service Chemotropism in yeast
reaction diffusion	Exploring the inhibitory effect of membrane tension on cell polarization
reaction networks	Identifying frequent patterns in biochemical reaction networks using graph-mining
real scientific B.Sc. projects
Regularized linear regression	In-silico prioritization of transporter-drug relationships from drug sensitivity screens
regularized regression models	Multi-omics analysis of T helper 22 cells
Regulatory Network	THE MULTIPLEX PHASE INTERLOCKER – A NOVEL AND ROBUST MOLECULAR DESIGN SYNCHRONIZING TRANSCRIPTIONAL CELL CYCLE DYNAMICS CoReg: Identification of co-regulators in genome scale transcription regulatory
Regulatory network topology	Evaluating the effects of measurement noise on the inference of biological regulatory networks using Modular Response Analysis
Replication	Modeling the spatio-temporal replication program
Replicative life span	Large scale simulations of a damage accumulation model in Saccharomyces cerevisiae reveal the benefit of dynamic damage retention in unicellular ageing
Resting-state network	A study on frequency-dependent state transition patterns in brain networks using energy landscape analysis
restriction enzyme	An efficient procedure to generate plasmid for endogenous CRISPR-based knockin
Reverse-engineering	Reverse-Engineering Gene regulatory Networks as Threshold Boolean Networks Automatic Inference of Dynamic Regulatory Networks Controlling Shape And Form
Rho-GTPase	Principles that govern competition or co-existence in Rho-GTPase driven polarization
RhoA GTPase	GEF-H1 regulation by microtubule dynamics unveiled by fluctuation analysis of biosensor images
Ribo-Seq	Analysis and classification of differential production within toxin-antitoxin systems using large datasets
ribosome profiling	Analysis and classification of differential production within toxin-antitoxin systems using large datasets
RNA Regulatory strategies	Integrated regulation of mRNA synthesis and decay decodes TNF signaling during inflammatory muscle-atrophy.
RNA splicing	mRNA Production Noise in Eukaryotic Cells
RNA virus	Simulating the Evolutionary Dynamics of Single-stranded RNA Virus Populations
RNA-seq	Analysis and classification of differential production within toxin-antitoxin systems using large datasets Stress-adaptive decision-making and dispersal behaviors in nematodes involve coordinated neuropeptide signaling Transcriptional regulatory network inference from gene expression and chromatin accessibility measurements Finding coordinated expression motifs in RNA-seq data Sequential Monte Carlo learning of Bayesian gene regulatory network models from RNA-seq data
RNA-sequencing	Aggregating RNA-Seq reads from multiple genes in KEGG metabolic pathways improves interpretability in gene expression pathway analysis
robustness	Incoherent inputs enhance robustness of biological oscillators miRNA expression shifts as an initiator event in carcinogenesis induced by Bisphenol A in human prostate cells
robustness of temporal order	Evaluating the Robustness of the Temporal Order of Anaphase Events using an Ensemble of Single Cell Models
S
S. cerevisiae	Investigate metabolic reprogramming of Saccharomyces cerevisiae for xylose-based fatty alcohol production via 13C metabolic flux Analysis
SABIO-RK	COMBINE Tutorial - Modelling and Simulation Tools in Systems Biology
Saccharomyces cerevisiae	Investigate metabolic reprogramming of Saccharomyces cerevisiae for xylose-based fatty alcohol production via 13C metabolic flux Analysis
SBGN	COMBINE Tutorial - Modelling and Simulation Tools in Systems Biology
SBML	COMBINE Tutorial - Modelling and Simulation Tools in Systems Biology SigNetSim : A web platform for building and analyzing mathematical models of molecular signaling networks Identifying frequent patterns in biochemical reaction networks using graph-mining
Scaling	Cell size homeostasis is critical for maintaining a permissive DNA:Cytoplasm ratio
SED-ML	SigNetSim : A web platform for building and analyzing mathematical models of molecular signaling networks
self-renewal	Understanding the self-renewal, differentiation and death of intestinal cells
sense-antisense transcripts interactions	Modeling the Interactions of Sense and Antisense Transcripts in the Mammalian Circadian Clock Network
Sensitivity Analysis	Cell Cycle Control in Budding Yeast: Robustness of Model Predictions
Sepsis	Measuring neutrophil migration patterns using microfluidic devices and ODE modeling of the mechanistic molecular pathways
service	Kinetics data information retrieval from the literature as public service
Shape formation	Automatic Inference of Dynamic Regulatory Networks Controlling Shape And Form
signal transduction	Fundamental Trade-offs between Information Flow in Single Cells and Cell Populations
Signal transduction pathways	Detection of all possible signaling pathways in complex networks at steady state using Manatee invariants
Signaling	The biochemical design of the mitotic checkpoint Identifying non-genetic origins of cell-to-cell variability in B-lymphocyte proliferation through systems biology
Signaling Network	A Dynamic Model of Granulocyte-Monocyte Progenitor Differentiation Understanding the effect of radiation on the cell cycle through mathematical modelling UNCOVERING A NETWORK MOTIF UNDERLYING A MINIMAL AUTONOMOUS OSCILLATOR OF THE BUDDING YEAST CELL CYCLE
Signalling pathway	Optimal methylation noise for best chemotactic performance of E. coli
signalling pathways	Quantitative methods for detecting origins of interferons signalling sensitivity
simulation	Simulating the Evolutionary Dynamics of Single-stranded RNA Virus Populations Kinetics data information retrieval from the literature as public service COPASI Tutorial Multiphysics models of actin regulation Simulation of a Petri net Based Model of the Menthol Biosynthesis
Simulation tools	COMBINE Tutorial - Modelling and Simulation Tools in Systems Biology
single cell	Exploring the dynamic regulation underlying synchronous chromosome splitting in anaphase
Single cell chemotaxis	Optimal methylation noise for best chemotactic performance of E. coli
Single cell dynamics	Automating cell segmentation and tracking with deep learning algorithms Coupled feed-forward and feedback of ATM/p53/Mdm2/Wip1 control cell type-dependent bimodal p53 dynamics and cell fate response
Single cell protein	Modeling Methanotrophy: A genome-scale metabolic model of Methylococcus capsulatus
single-cell biology	Reconstructing dynamic processes from high dimensional snap-shot data
Single-cell dynamics	Nonequilibrium stochastic dynamics at single cell level
Single-Cell Fate Mapping	Dynamics of T cell memory generation inferred from single cell fate mapping in vivo
SIR models	Mathematical and computational foundations of infectious disease epidemiology
Skin	A distinct cutaneous microbiota profile in autoimmune bullous disease patients
SLCs	In-silico prioritization of transporter-drug relationships from drug sensitivity screens
small cell lunger cancer	Characterizing Phenotypic Heterogeneity in Small Cell Lung Cancer
smFISH	Global regulation of transcription by cell size
snap-shot data	Reconstructing dynamic processes from high dimensional snap-shot data
Software	Data-Driven Design of Cell Factories and Communities
Software Tool	COPASI Tutorial
SParSE++	dwSSA++: efficient rare event probability estimation algorithm with leaping
Spatial mathematical modeling	Automatic Inference of Dynamic Regulatory Networks Controlling Shape And Form
Spatial Stochastic Simulation	Tutorial on StochSS: An Integrated Development Environment for Simulation and Analysis of Discrete Stochastic Biochemical Models
spatially-resolved eukaryotic cell models	mRNA Production Noise in Eukaryotic Cells
Spatio-temporal	Modeling the spatio-temporal replication program
spatiotemporal model	The dual role of microRNA in boundary formation of the spinal cord
Spectral decomposition	An Adaptive Spatiotemporal Spectrum Decomposition Approach for Cellular Morphodynamic Profiling
Spindle assembly checkpoint	Mathematical modeling of an “ectopic” spindle assembly checkpoint
SSA	dwSSA++: efficient rare event probability estimation algorithm with leaping
Stable Motif	Analysis of a dynamic model of guard cell signaling reveals the stability of signal propagation
Standards	COPASI Tutorial Memote - A testing suite for constraint-based metabolic models
Start transition	Dilution of the cell cycle inhibitor Whi5 alone cannot account for size control in budding yeast
stationary phase	Global Outlook on Survival of Escherichia coli Mutants during Long-Term Stationary Phase
Statistical region merging	An Adaptive Spatiotemporal Spectrum Decomposition Approach for Cellular Morphodynamic Profiling
Steady state analysis	Mathematical modeling of regulatory interactions in the fatty acid synthesis pathway
Stem Cell	Computational framework for endogenous barcoding of hematopoietic stem cells in vivo
Stochastic	COPASI Tutorial
stochastic modeling	Network Dynamics and Cell Physiology Mathematical modeling of an “ectopic” spindle assembly checkpoint Stochastic model of HPV early promoter predicts bursts like pattern of gene expression Deciphering the dynamical origin of mixed population during neural stem cell development
stochastic modelling	Quantitative methods for detecting origins of interferons signalling sensitivity
Stochastic Simulation	Tutorial on StochSS: An Integrated Development Environment for Simulation and Analysis of Discrete Stochastic Biochemical Models dwSSA++: efficient rare event probability estimation algorithm with leaping
stochastic simulation algorithm (SSA)	Hybrid ODE/SSA Model of the Budding Yeast Cell Cycle Control Mechanism with Mutant Case Study
Streptomyces	Extended GEM of Streptomyces Coelicolor for production of secondary metabolites
Stress	Stress-adaptive decision-making and dispersal behaviors in nematodes involve coordinated neuropeptide signaling
Structural identifiability	Structural identifiability of kinetic parameters
Synergistic control targets	Identifying synergistic control targets of a biological network based on a merged state transition map
Synergy	Systematic Optimization of Protein Secretory Pathways in Saccharomyces cerevisiae to Increase Expression of Hepatitis B Small Antigen Workshop on Drug Response Measurement and Analysis
synthetic biology	The spatiotemporal network dynamics of acquired resistance in an engineered microecology Data-Driven Design of Cell Factories and Communities Emulating mechanism-based models with artificial neural networks for applications in synthetic biology and systems biology Crosstalk between diverse synthetic protein degradation tags in Escherichia coli Educational experiences in systems and synthetic biology: a mathematician’s perspective Workshop: Multi-scale metabolic modeling and engineering
System Biology	Compensatory interactions to stabilize multiple steady states or mitigate the effects of multiple deregulations in biological networks
system dynamics	Using action potential simulations to explore the possible cause-effect relationships between gain and loss of cardiac ion channel function and generation of proarrhythmic early afterdepolarizations
system identification	A Black Box Model of Patient Response to Hemodialysis
systems biology	Tutorial: Metabolic flux modeling and computer aided strain design with cobrapy, cameo and DD-DeCaF Integration of a cellular signalling model with a whole-body pharmacokinetic model: Estimating cellular responses to administered interferon alpha doses in humans. Compartmentalization of lignin biosynthesis using either phenylalanine or tyrosine in Brachypodium distachyon A Dynamic Model of Granulocyte-Monocyte Progenitor Differentiation Analysis of phenotypic network changes along with the sequential occurrence of driver mutations during colorectal tumorigenesis Educational experiences in systems and synthetic biology: a mathematician’s perspective Fast, easy, interoperable and reusable – the cobrapy infrastructure for constraints-based analysis of metabolic flux Quantitative Systems Pharmacology Quantitative methods for detecting origins of interferons signalling sensitivity Functional diversification of signaling by GPCR localization
systems biology education	Workshop: Developing Tutorials For Research Tools And Methods
Systems Biology of Herbal Medicine	Systems Biology of Herbal Medicine: Pharmacological property of complex herbal formulation
Systems immunology	Multi-omics analysis of T helper 22 cells
systems medicine	Multi-level modelling for a new physiologically based interpretation of fMRI data
Systems neuroscience	A study on frequency-dependent state transition patterns in brain networks using energy landscape analysis
systems pharmacology	Integration of a cellular signalling model with a whole-body pharmacokinetic model: Estimating cellular responses to administered interferon alpha doses in humans. Multi-level modelling for a new physiologically based interpretation of fMRI data
Systems’ structures and functions	Clustering Biological Systems Using Correlation Matrices
T
T cell activation	Specificity and sensitivity of antigen sensing by the T cell receptor is enhanced by the co-receptor CD8
T Cell Differentiation	Dynamics of T cell memory generation inferred from single cell fate mapping in vivo
T helper 22 cell	Multi-omics analysis of T helper 22 cells
T-cell differentiation plasticity	Systems modeling of interplay among extracellular cytokines regulating phenotypic plasticity of CD4+ T-cell differentiation
T-helper cells	A data-driven correlation measure model for epigenetic network inference in T cells
T-invariant	Simulation of a Petri net Based Model of the Menthol Biosynthesis
Targeted metabolomics	Systems biology of multi-herbal formulations: Addressing condition-dependent prescription selection by comparing pharmacological and compound traits of related formulations
Temporally ordered progression	Evaluating the Robustness of the Temporal Order of Anaphase Events using an Ensemble of Single Cell Models
testing	Memote - A testing suite for constraint-based metabolic models
Threshold Boolean Networks	Reverse-Engineering Gene regulatory Networks as Threshold Boolean Networks
Time Course Clustering	Towards a Computational Model of the Dermal Extracellular Matrix in Ageing
Timing	THE MULTIPLEX PHASE INTERLOCKER – A NOVEL AND ROBUST MOLECULAR DESIGN SYNCHRONIZING TRANSCRIPTIONAL CELL CYCLE DYNAMICS
tissue patterning	The dual role of microRNA in boundary formation of the spinal cord
TNF signaling	Integrated regulation of mRNA synthesis and decay decodes TNF signaling during inflammatory muscle-atrophy.
Top Down	Towards a Computational Model of the Dermal Extracellular Matrix in Ageing
Toxicology	Computational Construction of Toxicant Signaling Networks
toxin-antitoxin systems	Analysis and classification of differential production within toxin-antitoxin systems using large datasets
tradeoff	The Transition from Acute Kidney Injury to Chronic Kidney Diseases Comes from Evolutionary Compromise
Traditional Japanese medicine (Kampo)	Systems biology of multi-herbal formulations: Addressing condition-dependent prescription selection by comparing pharmacological and compound traits of related formulations
Traditional Japanese medicine(Kampo)	Systems Biology of Herbal Medicine: Pharmacological property of complex herbal formulation
transcription	Global regulation of transcription by cell size Stochastic model of HPV early promoter predicts bursts like pattern of gene expression
Transcriptional burst	Nonequilibrium stochastic dynamics at single cell level
transcriptional regulatory network	Overrepresentation of feed forward loops can be driven by simple signal recognition, without the need for noise filtering
Transcriptional regulatory network inference	Transcriptional regulatory network inference from gene expression and chromatin accessibility measurements
Transcriptomics	Data-Driven Design of Cell Factories and Communities Systems Biology of Herbal Medicine: Pharmacological property of complex herbal formulation miRNA expression shifts as an initiator event in carcinogenesis induced by Bisphenol A in human prostate cells
Transient Oscillations	UNCOVERING A NETWORK MOTIF UNDERLYING A MINIMAL AUTONOMOUS OSCILLATOR OF THE BUDDING YEAST CELL CYCLE
Transition invariants	Detection of all possible signaling pathways in complex networks at steady state using Manatee invariants
Trasncription rates	Integrated regulation of mRNA synthesis and decay decodes TNF signaling during inflammatory muscle-atrophy.
Tumor dynamics	Heparin-based hydrogel as a biomimetic 3D matrix for solid-phase growth factor presentation and cultivation of breast cancer cells
Tumor microenvironment	Heparin-based hydrogel as a biomimetic 3D matrix for solid-phase growth factor presentation and cultivation of breast cancer cells Extracting dysregulated subnetworks in the non-small cell lung carcinoma tumor microenvironment
Tumor suppressor p53	The link between dynamic modes of p53 and cell-fate decision in the DNA damage response
Tumor-Specific Combination Therapy	Phosphoproteomics-Guided Discovery of Effective Combination Therapies in Cancer
Tumor-stromal interactions	Extracting dysregulated subnetworks in the non-small cell lung carcinoma tumor microenvironment
turing	Chemotropism in yeast
Turing pattern formation	Principles that govern competition or co-existence in Rho-GTPase driven polarization
turnover number
Two-phase dynamics	The link between dynamic modes of p53 and cell-fate decision in the DNA damage response
U
undergraduate degree	The Undergraduate Degree in Systems Biology at Virginia Tech
undergraduate research	The Undergraduate Degree in Systems Biology at Virginia Tech
unfair competition	A common role for stoichiometric inhibitors in cell cycle transitions
Unfolded protein response	Mathematical modeling of the unfolded protein response in different breast cancer cell lines
Unicellular ageing	Large scale simulations of a damage accumulation model in Saccharomyces cerevisiae reveal the benefit of dynamic damage retention in unicellular ageing
V
Variant	Comprehensive Proteogenomic Characterization of Human Prostate Cancer Cells Reveals Many Missing Proteins and Novel Protein Variants
Virtual Cell	COMBINE Tutorial - Modelling and Simulation Tools in Systems Biology Multiphysics models of actin regulation
viruses	Stochastic model of HPV early promoter predicts bursts like pattern of gene expression
Visualization	Data-Driven Design of Cell Factories and Communities Enhancing the Visualization of Budding Yeast Cell Cycles
W
wave pinning model	Exploring the inhibitory effect of membrane tension on cell polarization
Waves of Cyclins	THE MULTIPLEX PHASE INTERLOCKER – A NOVEL AND ROBUST MOLECULAR DESIGN SYNCHRONIZING TRANSCRIPTIONAL CELL CYCLE DYNAMICS UNCOVERING A NETWORK MOTIF UNDERLYING A MINIMAL AUTONOMOUS OSCILLATOR OF THE BUDDING YEAST CELL CYCLE
web-based	Tutorial: GraphSpace: Interdisciplinary Collaborations in Network Biology
WGCNA	Characterizing Phenotypic Heterogeneity in Small Cell Lung Cancer
whole-brain structural network	The minimum dominating sets in a brain network critically determine the efficiency of local communication of the network Increasing the network communicability of a damaged brain network for rehabilitation
Whole-cell simulations	mRNA Production Noise in Eukaryotic Cells
Wnt
workflow	Identifying frequent patterns in biochemical reaction networks using graph-mining
wSSA	dwSSA++: efficient rare event probability estimation algorithm with leaping
X
xylose	Investigate metabolic reprogramming of Saccharomyces cerevisiae for xylose-based fatty alcohol production via 13C metabolic flux Analysis
Y
yeast	Chemotropism in yeast Modeling the nutrient signaling network in Saccharomyces cerevisiae
yeast genetics	CrossPlan: Systematic Planning of Genetic Crosses to Validate Mathematical Models
Yeast knockout	Systematic Optimization of Protein Secretory Pathways in Saccharomyces cerevisiae to Increase Expression of Hepatitis B Small Antigen
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“Snake vectors”	Clustering Biological Systems Using Correlation Matrices

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