PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

Software support for SBGN maps: SBGN-ML and LibSBGN

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

Gene expression profiling and pathway analysis identify the integrin signaling pathway to be altered by IL-1β in human pancreatic cancer cells: Role of JNK

(2012) Gaurav Verma et al.   CANCER LETTERS

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium

(2011) P. Gaudet et al.   BRIEFINGS IN BIOINFORMATICS

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

WikiPathways: building research communities on biological pathways

(2011) T. Kelder et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology: enhancements for 2011

(2011)   NUCLEIC ACIDS RESEARCH

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

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

Correction: HPRT Deficiency Coordinately Dysregulates Canonical Wnt and Presenilin-1 Signaling: A Neuro-Developmental Regulatory Role for a Housekeeping Gene?

(2011) Tae Hyuk Kang et al.   PLoS One

GIGA: a simple, efficient algorithm for gene tree inference in the genomic age

(2010) Paul D Thomas   BMC BIOINFORMATICS

A Global In Vivo Drosophila RNAi Screen Identifies NOT3 as a Conserved Regulator of Heart Function

(2010) G. Gregory Neely et al.   CELL

Research Resource: Gonadotropin-Releasing Hormone Receptor-Mediated Signaling Network in LβT2 Cells: A Pathway-Based Web-Accessible Knowledgebase

(2010) Marc Y. Fink et al.   MOLECULAR ENDOCRINOLOGY

The BioPAX community standard for pathway data sharing

(2010) Emek Demir et al.   NATURE BIOTECHNOLOGY

Ensembl 2011

(2010) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Entrez Gene: gene-centered information at NCBI

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

Reactome: a database of reactions, pathways and biological processes

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

The Systems Biology Graphical Notation

(2009) Nicolas Le Novère et al.   NATURE BIOTECHNOLOGY

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

(2009) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species

(2009)   PLoS Computational Biology

PID: the Pathway Interaction Database

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

CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks

(2008) A. Funahashi et al.   PROCEEDINGS OF THE IEEE