LLM3D: a log-linear modeling-based method to predict functional gene regulatory interactions from genome-wide expression data

Learning transcriptional networks from the integration of ChIP–chip and expression data in a non-parametric model

(2010) Ahrim Youn et al.   BIOINFORMATICS

TF-finder: A software package for identifying transcription factors involved in biological processes using microarray data and existing knowledge base

(2010) Xiaoqi Cui et al.   BMC BIOINFORMATICS

Integrating multiple evidence sources to predict transcription factor binding in the human genome

(2010) J. Ernst et al.   GENOME RESEARCH

A Molecular Mechanism for Ibuprofen-Mediated RhoA Inhibition in Neurons

(2010) J. Dill et al.   JOURNAL OF NEUROSCIENCE

NFIL3 and cAMP Response Element-Binding Protein Form a Transcriptional Feedforward Loop that Controls Neuronal Regeneration-Associated Gene Expression

(2009) H. D. MacGillavry et al.   JOURNAL OF NEUROSCIENCE

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

PPARγ stimulation promotes neurite outgrowth in SH-SY5Y human neuroblastoma cells

(2009) Gianluca Miglio et al.   NEUROSCIENCE LETTERS

GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information

(2009) R. Nogales-Cadenas et al.   NUCLEIC ACIDS RESEARCH

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

An Integrated Approach to Identifying Cis-Regulatory Modules in the Human Genome

(2009) Kyoung-Jae Won et al.   PLoS One

ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells

(2009) Z. Ouyang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Eukaryotic transcription factor binding sites--modeling and integrative search methods

(2008) S. Hannenhalli   BIOINFORMATICS

Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences

(2008) Lucas D. Ward et al.   BIOINFORMATICS

Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: A three factor design

(2008) Alessandro Fazio et al.   BMC GENOMICS

Gene-set approach for expression pattern analysis

(2008) D. Nam et al.   BRIEFINGS IN BIOINFORMATICS

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

Omega-3 polyunsaturated fatty acids increase the neurite outgrowth of rat sensory neurones throughout development and in aged animals

(2008) Lesley G. Robson et al.   NEUROBIOLOGY OF AGING

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Potential Therapeutic Targets for PPAR after Spinal Cord Injury

(2008) Dana M. McTigue   PPAR Research