State–time spectrum of signal transduction logic models

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

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

Querying quantitative logic models (Q2LM) to study intracellular signaling networks and cell-cytokine interactions

(2011) Melody K. Morris et al.   Biotechnology Journal

Comparing Signaling Networks between Normal and Transformed Hepatocytes Using Discrete Logical Models

(2011) J. Saez-Rodriguez et al.   CANCER RESEARCH

Setting the Standards for Signal Transduction Research

(2011) J. Saez-Rodriguez et al.   Science Signaling

A Directed Protein Interaction Network for Investigating Intracellular Signal Transduction

(2011) A. Vinayagam et al.   Science Signaling

Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database

(2011) George A. Khoury et al.   Scientific Reports

Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli

(2011) Melody K. Morris et al.   PLoS Computational Biology

Logic-Based Models for the Analysis of Cell Signaling Networks

(2010) Melody K. Morris et al.   BIOCHEMISTRY

Odefy -- From discrete to continuous models

(2010) Jan Krumsiek et al.   BMC BIOINFORMATICS

Simplistic pathways or complex networks?

(2010) Claus Jørgensen et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Boolean models of within-host immune interactions

(2010) Juilee Thakar et al.   CURRENT OPINION IN MICROBIOLOGY

Classic and contemporary approaches to modeling biochemical reactions

(2010) W. W. Chen et al.   GENES & DEVELOPMENT

Competitors Try Collaboration To Speed Drug Development

(2010) Margie Patlak   JNCI-Journal of the National Cancer Institute

A Boolean Approach to Linear Prediction for Signaling Network Modeling

(2010) Federica Eduati et al.   PLoS One

Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement

(2010) Laurence Calzone et al.   PLoS Computational Biology

Know your limits: Assumptions, constraints and interpretation in systems biology

(2009) Garth R. Ilsley et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling

(2009) Dominik M Wittmann et al.   BMC Systems Biology

Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance

(2009) Özgür Sahin et al.   BMC Systems Biology

Cancer systems biology: a network modeling perspective

(2009) P. K. Kreeger et al.   CARCINOGENESIS

An evolutionary method for complex-process optimization

(2009) Jose A. Egea et al.   COMPUTERS & OPERATIONS RESEARCH

Tissue specificity and the human protein interaction network

(2009) Alice Bossi et al.   Molecular Systems Biology

Pathway databases and tools for their exploitation: benefits, current limitations and challenges

(2009) Anna Bauer-Mehren et al.   Molecular Systems Biology

Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction

(2009) Julio Saez-Rodriguez et al.   Molecular Systems Biology

The Systems Biology Graphical Notation

(2009) Nicolas Le Novère et al.   NATURE BIOTECHNOLOGY

Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data

(2009) Alexander Mitsos et al.   PLoS Computational Biology

ON/OFF and Beyond - A Boolean Model of Apoptosis

(2009) Rebekka Schlatter et al.   PLoS Computational Biology

Protein Kinases: Starting a Molecular Systems View of Endocytosis

(2008) Prisca Liberali et al.   Annual Review of Cell and Developmental Biology

Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc

(2008) A. Gonzalez et al.   BIOINFORMATICS

Synchronous versus asynchronous modeling of gene regulatory networks

(2008) A. Garg et al.   BIOINFORMATICS

Optimization in computational systems biology

(2008) Julio R Banga   BMC Systems Biology

Logic models of pathway biology

(2008) Steven Watterson et al.   DRUG DISCOVERY TODAY

Modelling cellular signalling systems

(2008) Padmini Rangamani et al.   Essays in Biochemistry

A comprehensive modular map of molecular interactions in RB/E2F pathway

(2008) Laurence Calzone et al.   Molecular Systems Biology

Emergent decision-making in biological signal transduction networks

(2008) T. Helikar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein networking: insights into global functional organization of proteomes

(2008) Enrico Pieroni et al.   PROTEOMICS