RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse

Reverse Engineering of Genome-wide Gene Regulatory Networks from Gene Expression Data

(2015) Zhi-Ping Liu   CURRENT GENOMICS

Systematic identification of transcriptional and post-transcriptional regulations in human respiratory epithelial cells during influenza A virus infection

(2014) Zhi-Ping Liu et al.   BMC BIOINFORMATICS

Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks

(2013) Alex Greenfield et al.   BIOINFORMATICS

Gaussian graphical model for identifying significantly responsive regulatory networks from time course high-throughput data

(2013) Zhi-Ping Liu et al.   IET Systems Biology

Differential network biology

(2012) Trey Ideker et al.   Molecular Systems Biology

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2013 update

(2012) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

Boosting Signal-to-Noise in Complex Biology: Prior Knowledge Is Power

(2011) Trey Ideker et al.   CELL

Detecting and analyzing differentially activated pathways in brain regions of Alzheimer's disease patients

(2011) Zhi-Ping Liu et al.   Molecular BioSystems

GenBank

(2011) D. A. Benson et al.   NUCLEIC ACIDS RESEARCH

The IntAct molecular interaction database in 2012

(2011) S. Kerrien et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

The BioPAX community standard for pathway data sharing

(2010) Emek Demir et al.   NATURE BIOTECHNOLOGY

miRTarBase: a database curates experimentally validated microRNA–target interactions

(2010) Sheng-Da Hsu et al.   NUCLEIC ACIDS RESEARCH

Ongoing and future developments at the Universal Protein Resource

(2010)   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: update 2011

(2010) P. A. Fujita et al.   NUCLEIC ACIDS RESEARCH

Revealing strengths and weaknesses of methods for gene network inference

(2010) D. Marbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Literature-based priors for gene regulatory networks

(2009) E. Steele et al.   BIOINFORMATICS

MOODS: fast search for position weight matrix matches in DNA sequences

(2009) J. Korhonen et al.   BIOINFORMATICS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

TransmiR: a transcription factor–microRNA regulation database

(2009) Juan Wang et al.   NUCLEIC ACIDS RESEARCH

DIANA-microT web server: elucidating microRNA functions through target prediction

(2009) M. Maragkakis et al.   NUCLEIC ACIDS RESEARCH

Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells

(2008) Alexander Marson et al.   CELL

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

miRecords: an integrated resource for microRNA-target interactions

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