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

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

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

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

Crosstalk between transcription factors and microRNAs in human protein interaction network

(2012) Chen-Ching Lin 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

The NRF2-related interactome and regulome contain multifunctional proteins and fine-tuned autoregulatory loops

(2012) Diána Papp et al.   FEBS LETTERS

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

DIANA miRPath v.2.0: investigating the combinatorial effect of microRNAs in pathways

(2012) Ioannis S. Vlachos et al.   NUCLEIC ACIDS RESEARCH

Integrating Phosphorylation Network with Transcriptional Network Reveals Novel Functional Relationships

(2012) Lin Wang et al.   PLoS One

Context-dependent transcriptional regulations between signal transduction pathways

(2011) Sohyun Hwang et al.   BMC BIOINFORMATICS

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support

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

ELM--the database of eukaryotic linear motifs

(2011) H. Dinkel et al.   NUCLEIC ACIDS RESEARCH

NAViGaTing the Micronome – Using Multiple MicroRNA Prediction Databases to Identify Signalling Pathway-Associated MicroRNAs

(2011) Elize A. Shirdel et al.   PLoS One

Signalogs: Orthology-Based Identification of Novel Signaling Pathway Components in Three Metazoans

(2011) Tamás Korcsmáros et al.   PLoS One

Network-Based Tools for the Identification of Novel Drug Targets

(2011) I. J. Farkas et al.   Science Signaling

Allo-network drugs: harnessing allostery in cellular networks

(2011) Ruth Nussinov et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Uniformly curated signaling pathways reveal tissue-specific cross-talks and support drug target discovery

(2010) Tamás Korcsmáros et al.   BIOINFORMATICS

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

An improved method for scoring protein-protein interactions using semantic similarity within the Gene Ontology

(2010) Shobhit Jain et al.   BMC BIOINFORMATICS

Ultrasensitive Responses and Specificity in Cell Signaling

(2010) Seth Haney et al.   BMC Systems Biology

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

SPIKE: a database of highly curated human signaling pathways

(2010) Arnon Paz 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

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

miRBase: integrating microRNA annotation and deep-sequencing data

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

Network analyses in systems pharmacology

(2009) S. I. Berger et al.   BIOINFORMATICS

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

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

Navigating the network: signaling cross-talk in hematopoietic cells

(2009) Iain D C Fraser et al.   NATURE IMMUNOLOGY

Mechanisms of drug combinations: interaction and network perspectives

(2009) Jia Jia et al.   NATURE REVIEWS DRUG DISCOVERY

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

Integrating Proteomic, Transcriptional, and Interactome Data Reveals Hidden Components of Signaling and Regulatory Networks

(2009) S.-s. C. Huang et al.   Science Signaling

Finding scaffold proteins in interactomes

(2009) Fidel Ramírez et al.   TRENDS IN CELL BIOLOGY

Network modeling of signal transduction: establishing the global view

(2008) Hans A. Kestler et al.   BIOESSAYS

Signaling cross-talk between TGF-β/BMP and other pathways

(2008) Xing Guo et al.   CELL RESEARCH

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

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

De novo DNA synthesis using single molecule PCR

(2008) Tuval Ben Yehezkel et al.   NUCLEIC ACIDS RESEARCH

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

DrugBank and its relevance to pharmacogenomics

(2008) David S Wishart   PHARMACOGENOMICS

The quest for orthologs: finding the corresponding gene across genomes

(2008) Arnold Kuzniar et al.   TRENDS IN GENETICS