Using Biological Pathway Data with Paxtools

Software support for SBGN maps: SBGN-ML and LibSBGN

(2012) M. P. van Iersel et al.   BIOINFORMATICS

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

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

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

BioPAX support in CellDesigner

(2011) Huaiyu Mi et al.   BIOINFORMATICS

Mutual exclusivity analysis identifies oncogenic network modules

(2011) G. Ciriello et al.   GENOME RESEARCH

IPAVS: Integrated Pathway Resources, Analysis and Visualization System

(2011) Pradeep Kumar Sreenivasaiah et al.   NUCLEIC ACIDS RESEARCH

hiPathDB: a human-integrated pathway database with facile visualization

(2011) N. Yu et al.   NUCLEIC ACIDS RESEARCH

PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

(2011) P. V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

Editing, validating and translating of SBGN maps

(2010) T. Czauderna et al.   BIOINFORMATICS

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM

(2010) Charles J. Vaske et al.   BIOINFORMATICS

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

(2010) Chen Li et al.   BMC Systems Biology

The BioPAX community standard for pathway data sharing

(2010) Emek Demir et al.   NATURE BIOTECHNOLOGY

Discovering modulators of gene expression

(2010) Özgün Babur et al.   NUCLEIC ACIDS RESEARCH

Pathway Commons, a web resource for biological pathway data

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

Reactome: a database of reactions, pathways and biological processes

(2010) D. Croft et al.   NUCLEIC ACIDS RESEARCH

Finding the Right Questions: Exploratory Pathway Analysis to Enhance Biological Discovery in Large Datasets

(2010) Thomas Kelder et al.   PLOS BIOLOGY

ChiBE: interactive visualization and manipulation of BioPAX pathway models

(2009) Ozgun Babur et al.   BIOINFORMATICS

Algorithms for effective querying of compound graph-based pathway databases

(2009) Ugur Dogrusoz et al.   BMC BIOINFORMATICS

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium

(2009) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2009) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

(2009) J. Chen et al.   NUCLEIC ACIDS RESEARCH

Insights into the Organization of Biochemical Regulatory Networks Using Graph Theory Analyses

(2008) Avi Ma'ayan   JOURNAL OF BIOLOGICAL CHEMISTRY

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH

Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses

(2008) S. Jones et al.   SCIENCE