Modelling the Structure and Dynamics of Biological Pathways

MONALISA for stochastic simulations of Petri net models of biochemical systems

(2015) Pavel Balazki et al.   BMC BIOINFORMATICS

WikiPathways: capturing the full diversity of pathway knowledge

(2015) Martina Kutmon et al.   NUCLEIC ACIDS RESEARCH

Yeast pheromone pathway modeling using Petri nets

(2014) Abhishek Majumdar et al.   BMC BIOINFORMATICS

Stochasticity of metabolism and growth at the single-cell level

(2014) Daniel J. Kiviet et al.   NATURE

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps

(2013) Inna Kuperstein et al.   BMC Systems Biology

Programming biological models in Python using PySB

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

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway knowledgebase

(2013) David Croft et al.   NUCLEIC ACIDS RESEARCH

VANTED v2: a framework for systems biology applications

(2012) Hendrik Rohn et al.   BMC Systems Biology

Creating interactive, web-based and data-enriched maps with the Systems Biology Graphical Notation

(2012) Astrid Junker et al.   Nature Protocols

The ConsensusPathDB interaction database: 2013 update

(2012) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways

(2011) Luca Beltrame et al.   BIOINFORMATICS

iPath2.0: interactive pathway explorer

(2011) Takuji Yamada et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Construction of a large scale integrated map of macrophage pathogen recognition and effector systems

(2010) Sobia Raza et al.   BMC Systems Biology

The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways

(2010) Tom C Freeman et al.   BMC Systems Biology

Signaling network of dendritic cells in response to pathogens: a community-input supported knowledgebase

(2010) Sonali Patil et al.   BMC Systems Biology

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

(2010) Chen Li et al.   BMC Systems Biology

SnapShot: Network Motifs

(2010) Oren Shoval et al.   CELL

The BioPAX community standard for pathway data sharing

(2010) Emek Demir et al.   NATURE BIOTECHNOLOGY

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

(2010) David Warde-Farley et al.   NUCLEIC ACIDS RESEARCH

Dynamical approaches to modeling developmental gene regulatory networks

(2009) Nicholas Geard et al.   BIRTH DEFECTS RESEARCH PART C-EMBRYO TODAY-REVIEWS

The Systems Biology Graphical Notation

(2009) Nicolas Le Novère et al.   NATURE BIOTECHNOLOGY

A logic-based diagram of signalling pathways central to macrophage activation

(2008) Sobia Raza et al.   BMC Systems Biology

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

(2008) Laurence Calzone et al.   Molecular Systems Biology

The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks

(2008) Derek Ruths et al.   PLoS Computational Biology