Navigating the Multilayered Organization of Eukaryotic Signaling: A New Trend in Data Integration

A self-updating road map of The Cancer Genome Atlas

(2013) D. E. Robbins et al.   BIOINFORMATICS

SignaLink 2 – a signaling pathway resource with multi-layered regulatory networks

(2013) Dávid Fazekas et al.   BMC Systems Biology

Molecular genetic testing and the future of clinical genomics

(2013) Sara Huston Katsanis et al.   NATURE REVIEWS GENETICS

NRF2-ome: An Integrated Web Resource to Discover Protein Interaction and Regulatory Networks of NRF2

(2013) Dénes Türei et al.   Oxidative Medicine and Cellular Longevity

TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks

(2012) Cyrille Lepoivre et al.   BMC BIOINFORMATICS

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

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

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms

(2012) Camille Terfve et al.   BMC Systems Biology

Semantic Web meets Integrative Biology: a survey

(2012) H. Chen et al.   BRIEFINGS IN BIOINFORMATICS

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

The Therapeutic Target Database: an Internet resource for the primary targets of approved, clinical trial and experimental drugs

(2011) Xin Liu et al.   EXPERT OPINION ON THERAPEUTIC TARGETS

Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery

(2011) F. Zhu et al.   NUCLEIC ACIDS RESEARCH

The IntAct molecular interaction database in 2012

(2011) S. Kerrien 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

Cytoscape Web: an interactive web-based network browser

(2010) Christian T. Lopes et al.   BIOINFORMATICS

PuTmiR: A database for extracting neighboring transcription factors of human microRNAs

(2010) Sanghamitra Bandyopadhyay et al.   BMC BIOINFORMATICS

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

(2010) Takashi Nakakuki et al.   CELL

The BioPAX community standard for pathway data sharing

(2010) Emek Demir et al.   NATURE BIOTECHNOLOGY

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

(2010) Michael W Sneddon et al.   NATURE METHODS

Signalling ballet in space and time

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

SPIKE: a database of highly curated human signaling pathways

(2010) Arnon Paz et al.   NUCLEIC ACIDS RESEARCH

Phospho.ELM: a database of phosphorylation sites--update 2011

(2010) H. Dinkel et al.   NUCLEIC ACIDS RESEARCH

PHOSIDA 2011: the posttranslational modification database

(2010) F. Gnad et al.   NUCLEIC ACIDS RESEARCH

REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila

(2010) S. M. Gallo et al.   NUCLEIC ACIDS RESEARCH

YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface

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

The BioGRID Interaction Database: 2011 update

(2010) C. Stark et al.   NUCLEIC ACIDS RESEARCH

ConsensusPathDB: toward a more complete picture of cell biology

(2010) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs

(2010) C. Knox et al.   NUCLEIC ACIDS RESEARCH

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

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

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

(2010) S. A. Forbes et al.   NUCLEIC ACIDS RESEARCH

The Mammalian MAPK/ERK Pathway Exhibits Properties of a Negative Feedback Amplifier

(2010) O. E. Sturm et al.   Science Signaling

HER2 Phosphorylation Is Maintained by a PKB Negative Feedback Loop in Response to Anti-HER2 Herceptin in Breast Cancer

(2010) Merel Gijsen et al.   PLOS BIOLOGY

Logical modelling of regulatory networks with GINsim 2.3

(2009) A. Naldi et al.   BIOSYSTEMS

Proteome-wide Prediction of Signal Flow Direction in Protein Interaction Networks Based on Interacting Domains

(2009) Wei Liu et al.   MOLECULAR & CELLULAR PROTEOMICS

Update of TTD: Therapeutic Target Database

(2009) Feng Zhu et al.   NUCLEIC ACIDS RESEARCH

TransmiR: a transcription factor–microRNA regulation database

(2009) Juan Wang et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites

(2008) Neil FW Saunders et al.   BMC BIOINFORMATICS

DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions

(2008) Jingkai Yu et al.   BMC GENOMICS

Domain-oriented reduction of rule-based network models

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

PRINCESS, a Protein Interaction Confidence Evaluation System with Multiple Data Sources

(2008) Dong Li et al.   MOLECULAR & CELLULAR PROTEOMICS

Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network

(2008) Nicolas Simonis et al.   NATURE METHODS

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

miRecords: an integrated resource for microRNA-target interactions

(2008) F. Xiao et al.   NUCLEIC ACIDS RESEARCH

TranscriptomeBrowser: A Powerful and Flexible Toolbox to Explore Productively the Transcriptional Landscape of the Gene Expression Omnibus Database

(2008) Fabrice Lopez et al.   PLoS One