Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems

The Simmune Modeler visual interface for creating signaling networks based on bi-molecular interactions

(2013) Fengkai Zhang et al.   BIOINFORMATICS

Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits

(2013) Mario Marchisio et al.   BMC Systems Biology

Encoding and Decoding Cellular Information through Signaling Dynamics

(2013) Jeremy E. Purvis et al.   CELL

Conformational Coupling across the Plasma Membrane in Activation of the EGF Receptor

(2013) Nicholas F. Endres et al.   CELL

Dynamics and adaptive benefits of modular protein evolution

(2013) Erich Bornberg-Bauer et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Perspective: Stochastic algorithms for chemical kinetics

(2013) Daniel T. Gillespie et al.   JOURNAL OF CHEMICAL PHYSICS

Constraining rule-based dynamics with types

(2013) VINCENT DANOS et al.   MATHEMATICAL STRUCTURES IN COMPUTER SCIENCE

Equilibrium and termination II: the case of Petri nets

(2013) VINCENT DANOS et al.   MATHEMATICAL STRUCTURES IN COMPUTER SCIENCE

Phosphotyrosine Signaling Proteins that Drive Oncogenesis Tend to be Highly Interconnected

(2013) Grigoriy Koytiger et al.   MOLECULAR & CELLULAR PROTEOMICS

Exploring higher-order EGFR oligomerisation and phosphorylation—a combined experimental and theoretical approach

(2013) Noga Kozer et al.   Molecular BioSystems

Programming biological models in Python using PySB

(2013) C. F. Lopez et al.   Molecular Systems Biology

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

Time-ordered product expansions for computational stochastic system biology

(2013) Eric Mjolsness   PHYSICAL BIOLOGY

Markovian dynamics on complex reaction networks

(2013) J. Goutsias et al.   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

Single-Cell Measurements of IgE-Mediated FcεRI Signaling Using an Integrated Microfluidic Platform

(2013) Yanli Liu et al.   PLoS One

The evolutionary origins of modularity

(2013) J. Clune et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Rule-based modeling and simulations of the inner kinetochore structure

(2013) Sergej Tschernyschkow et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Decoding the Language of Phosphorylation Site Dynamics

(2013) L. A. Chylek   Science Signaling

Monovalent and Multivalent Ligation of the B Cell Receptor Exhibit Differential Dependence upon Syk and Src Family Kinases

(2013) S. Mukherjee et al.   Science Signaling

Reliable Prediction of Complex Phenotypes from a Modular Design in Free Energy Space: An Extensive Exploration of the lac Operon

(2013) Jose M. G. Vilar et al.   ACS Synthetic Biology

Computational Analysis of Rho GTPase Cycling

(2013) Cibele Vieira Falkenberg et al.   PLoS Computational Biology

Systems Model of T Cell Receptor Proximal Signaling Reveals Emergent Ultrasensitivity

(2013) Himadri Mukhopadhyay et al.   PLoS Computational Biology

Interface-Resolved Network of Protein-Protein Interactions

(2013) Margaret E. Johnson et al.   PLoS Computational Biology

Engineering Biomass Conversion Processes: A Systems Perspective

(2012) Prodromos Daoutidis et al.   AICHE JOURNAL

Multivalent Binding and Facilitated Diffusion Account for the Formation of the Grb2–Sos1 Signaling Complex in a Cooperative Manner

(2012) Caleb B. McDonald et al.   BIOCHEMISTRY

Measurement and Modeling of Signaling at the Single-Cell Level

(2012) Sarah E. Kolitz et al.   BIOCHEMISTRY

Crosstalk and Competition in Signaling Networks

(2012) Michael A. Rowland et al.   BIOPHYSICAL JOURNAL

A coarse-grained model for synergistic action of multiple enzymes on cellulose

(2012) Andrea Asztalos et al.   Biotechnology for Biofuels

Accelerated maximum likelihood parameter estimation for stochastic biochemical systems

(2012) Bernie J Daigle et al.   BMC BIOINFORMATICS

RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry

(2012) Adam M Smith et al.   BMC BIOINFORMATICS

Exact model reduction of combinatorial reaction networks

(2012) Holger Conzelmann et al.   BMC Systems Biology

Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks

(2012) Daniel C Kirouac et al.   BMC Systems Biology

Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling

(2012) Matthew S Creamer et al.   BMC Systems Biology

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

MYC on the Path to Cancer

(2012) Chi V. Dang   CELL

Constructing structural networks of signaling pathways on the proteome scale

(2012) Guray Kuzu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Coarse-graining of multiprotein assemblies

(2012) Marissa G Saunders et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Logic-based models in systems biology: a predictive and parameter-free network analysis method

(2012) Michelle L. Wynn et al.   Integrative Biology

Specification, construction, and exact reduction of state transition system models of biochemical processes

(2012) Scott M. Bugenhagen et al.   JOURNAL OF CHEMICAL PHYSICS

A Computational Model for Early Events in B Cell Antigen Receptor Signaling: Analysis of the Roles of Lyn and Fyn

(2012) D. Barua et al.   JOURNAL OF IMMUNOLOGY

A predictive mathematical model of the DNA damage G2 checkpoint

(2012) Kevin J. Kesseler et al.   JOURNAL OF THEORETICAL BIOLOGY

A framework for mapping, visualisation and automatic model creation of signal-transduction networks

(2012) Carl-Fredrik Tiger et al.   Molecular Systems Biology

Multilevel Monte Carlo for Continuous Time Markov Chains, with Applications in Biochemical Kinetics

(2012) David F. Anderson et al.   MULTISCALE MODELING & SIMULATION

The spatial architecture of protein function and adaptation

(2012) Richard N. McLaughlin Jr et al.   NATURE

Unresponsiveness of colon cancer to BRAF(V600E) inhibition through feedback activation of EGFR

(2012) Anirudh Prahallad et al.   NATURE

Structure-based prediction of protein–protein interactions on a genome-wide scale

(2012) Qiangfeng Cliff Zhang et al.   NATURE

Computational modeling of cellular signaling processes embedded into dynamic spatial contexts

(2012) Bastian R Angermann et al.   NATURE METHODS

PrePPI: a structure-informed database of protein–protein interactions

(2012) Qiangfeng Cliff Zhang et al.   NUCLEIC ACIDS RESEARCH

Modular evolution of phosphorylation-based signalling systems

(2012) J. Jin et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

CaMKII activation and dynamics are independent of the holoenzyme structure: an infinite subunit holoenzyme approximation

(2012) P J Michalski et al.   PHYSICAL BIOLOGY

Combinatorial Complexity and Compositional Drift in Protein Interaction Networks

(2012) Eric J. Deeds et al.   PLoS One

Modeling and Simulation of Aggregation of Membrane Protein LAT with Molecular Variability in the Number of Binding Sites for Cytosolic Grb2-SOS1-Grb2

(2012) Ambarish Nag et al.   PLoS One

Comprehensive Binary Interaction Mapping of SH2 Domains via Fluorescence Polarization Reveals Novel Functional Diversification of ErbB Receptors

(2012) Ronald J. Hause et al.   PLoS One

A Mechanistic Model of Early FcεRI Signaling: Lipid Rafts and the Question of Protection from Dephosphorylation

(2012) Dipak Barua et al.   PLoS One

The Response of Cancers to BRAF Inhibition Underscores the Importance of Cancer Systems Biology

(2012) E. C. Stites   Science Signaling

Computational Approaches for Analyzing Information Flow in Biological Networks

(2012) B. Kholodenko et al.   Science Signaling

Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology

(2011) Jürgen Cox et al.   Annual Review of Biochemistry

RuleBender: a visual interface for rule-based modeling

(2011) Wen Xu et al.   BIOINFORMATICS

Ultrasensitivity in Multisite Phosphorylation of Membrane-Anchored Proteins

(2011) Omer Dushek et al.   BIOPHYSICAL JOURNAL

Timescale analysis of rule-based biochemical reaction networks

(2011) David J. Klinke et al.   BIOTECHNOLOGY PROGRESS

Hierarchical graphs for rule-based modeling of biochemical systems

(2011) Nathan W Lemons et al.   BMC BIOINFORMATICS

Toward a comprehensive language for biological systems

(2011) James R Faeder   BMC BIOLOGY

Measuring and Modeling Apoptosis in Single Cells

(2011) Sabrina L. Spencer et al.   CELL

Regulation of the catalytic activity of the EGF receptor

(2011) Nicholas F Endres et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The interplay of double phosphorylation and scaffolding in MAPK pathways

(2011) PaweŁ Kocieniewski et al.   JOURNAL OF THEORETICAL BIOLOGY

Guidelines for visualizing and annotating rule-based models

(2011) Lily A. Chylek et al.   Molecular BioSystems

Rapid Phospho-Turnover by Receptor Tyrosine Kinases Impacts Downstream Signaling and Drug Binding

(2011) Laura B. Kleiman et al.   MOLECULAR CELL

ErbB1 dimerization is promoted by domain co-confinement and stabilized by ligand binding

(2011) Shalini T Low-Nam et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A Computational Analysis of the Dynamic Roles of Talin, Dok1, and PIPKI for Integrin Activation

(2011) Florian Geier et al.   PLoS One

Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range

(2011) T. M. Thomson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transient protein-protein interactions

(2011) S. E. Acuner Ozbabacan et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Information Transduction Capacity of Noisy Biochemical Signaling Networks

(2011) R. Cheong et al.   SCIENCE

Quantifying Intramolecular Binding in Multivalent Interactions: A Structure-Based Synergistic Study on Grb2-Sos1 Complex

(2011) Anurag Sethi et al.   PLoS Computational Biology

Functional Motifs in Biochemical Reaction Networks

(2010) John J. Tyson et al.   Annual Review of Physical Chemistry

Modeling Multivalent Ligand-Receptor Interactions with Steric Constraints on Configurations of Cell-Surface Receptor Aggregates

(2010) Michael I. Monine et al.   BIOPHYSICAL JOURNAL

RuleMonkey: software for stochastic simulation of rule-based models

(2010) Joshua Colvin et al.   BMC BIOINFORMATICS

Analysis and verification of the HMGB1 signaling pathway

(2010) Haijun Gong et al.   BMC BIOINFORMATICS

Rule-based spatial modeling with diffusing, geometrically constrained molecules

(2010) Gerd Gruenert et al.   BMC BIOINFORMATICS

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

(2010) Chen Li et al.   BMC Systems Biology

Ligand-Specific c-Fos Expression Emerges from the Spatiotemporal Control of ErbB Network Dynamics

(2010) Takashi Nakakuki et al.   CELL

Phosphotyrosine Signaling: Evolving a New Cellular Communication System

(2010) Wendell A. Lim et al.   CELL

Cell Signaling by Receptor Tyrosine Kinases

(2010) Mark A. Lemmon et al.   CELL

Intrinsic information carriers in combinatorial dynamical systems

(2010) Russ Harmer et al.   CHAOS

Rule-based modelling and simulation of biochemical systems with molecular finite automata

(2010) J. Yang et al.   IET Systems Biology

Shaping the response: the role of FcεRI and Syk expression levels in mast cell signalling

(2010) A. Nag et al.   IET Systems Biology

A Detailed Mathematical Model Predicts That Serial Engagement of IgE-Fc RI Complexes Can Enhance Syk Activation in Mast Cells

(2010) A. Nag et al.   JOURNAL OF IMMUNOLOGY

Structural Evidence for Loose Linkage between Ligand Binding and Kinase Activation in the Epidermal Growth Factor Receptor

(2010) C. Lu et al.   MOLECULAR AND CELLULAR BIOLOGY

Efficient modeling, simulation and coarse-graining of biological complexity with NFsim

(2010) Michael W Sneddon et al.   NATURE METHODS

Systems analysis of EGF receptor signaling dynamics with microwestern arrays

(2010) Mark F Ciaccio et al.   NATURE METHODS

Signalling ballet in space and time

(2010) Boris N. Kholodenko et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

CD4 and CD8 binding to MHC molecules primarily acts to enhance Lck delivery

(2010) M. N. Artyomov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid Diversification of Cell Signaling Phenotypes by Modular Domain Recombination

(2010) S. G. Peisajovich et al.   SCIENCE

Transient Protein-Protein Interactions: Structural, Functional, and Network Properties

(2010) James R. Perkins et al.   STRUCTURE

Detailed Simulations of Cell Biology with Smoldyn 2.1

(2010) Steven S. Andrews et al.   PLoS Computational Biology

Adaptable Functionality of Transcriptional Feedback in Bacterial Two-Component Systems

(2010) J. Christian J. Ray et al.   PLoS Computational Biology

NetPath: a public resource of curated signal transduction pathways

(2010) Kumaran Kandasamy et al.   GENOME BIOLOGY

Assembly of the Sos1–Grb2–Gab1 ternary signaling complex is under allosteric control

(2009) Caleb B. McDonald et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Simulation of large-scale rule-based models

(2009) Joshua Colvin et al.   BIOINFORMATICS

Efficient stochastic simulation of reaction–diffusion processes via direct compilation

(2009) Mieszko Lis et al.   BIOINFORMATICS

Digital Signaling and Hysteresis Characterize Ras Activation in Lymphoid Cells

(2009) Jayajit Das et al.   CELL

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

How to deal with large models?

(2009) William S Hlavacek   Molecular Systems Biology

Harmonic oscillator model of the insulin and IGF1 receptors’ allosteric binding and activation

(2009) Vladislav V Kiselyov et al.   Molecular Systems Biology

Input–output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data

(2009) William W Chen et al.   Molecular Systems Biology

Protein promiscuity and its implications for biotechnology

(2009) Irene Nobeli et al.   NATURE BIOTECHNOLOGY

The Systems Biology Graphical Notation

(2009) Nicolas Le Novère et al.   NATURE BIOTECHNOLOGY

Internal coarse-graining of molecular systems

(2009) J. Feret et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cell Signaling in Space and Time: Where Proteins Come Together and When They're Apart

(2009) J. D. Scott et al.   SCIENCE

P120-Ras GTPase activating protein (RasGAP): A multi-interacting protein in downstream signaling

(2008) Perayot Pamonsinlapatham et al.   BIOCHIMIE

LibSBML: an API Library for SBML

(2008) B. J. Bornstein et al.   BIOINFORMATICS

Virtual Cell modelling and simulation software environment

(2008) I.I. Moraru et al.   IET Systems Biology

Domain-oriented reduction of rule-based network models

(2008) N.M. Borisov et al.   IET Systems Biology

Laser Capture Microdissection and Protein Microarray Analysis of Human Non-small Cell Lung Cancer

(2008) Amy J. VanMeter et al.   MOLECULAR & CELLULAR PROTEOMICS

Kinase-Selective Enrichment Enables Quantitative Phosphoproteomics of the Kinome across the Cell Cycle

(2008) Henrik Daub et al.   MOLECULAR CELL

Life, logic and information

(2008) Paul Nurse   NATURE

Kinetic Monte Carlo method for rule-based modeling of biochemical networks

(2008) Jin Yang et al.   PHYSICAL REVIEW E

The T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATP

(2008) C.-H. Yun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces

(2008) Rex A. Kerr et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING