ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets

(2011) Chao Cheng et al.   GENOME BIOLOGY

Frozen robust multiarray analysis (fRMA)

(2010) M. N. McCall et al.   BIOSTATISTICS

Diverse Targets of the Transcription Factor STAT3 Contribute to T Cell Pathogenicity and Homeostasis

(2010) Lydia Durant et al.   IMMUNITY

A global map of human gene expression

(2010) Margus Lukk et al.   NATURE BIOTECHNOLOGY

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

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

The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes

(2010) Matthew N. McCall et al.   NUCLEIC ACIDS RESEARCH

Evaluation of Algorithm Performance in ChIP-Seq Peak Detection

(2010) Elizabeth G. Wilbanks et al.   PLoS One

Bayesian approach to transforming public gene expression repositories into disease diagnosis databases

(2010) H. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inactive yet indispensable: the tale of Jarid2

(2010) David Landeira et al.   TRENDS IN CELL BIOLOGY

A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments

(2009) Teemu D Laajala et al.   BMC GENOMICS

Positive Cross-Talk between Estrogen Receptor and NF- B in Breast Cancer

(2009) J. Frasor et al.   CANCER RESEARCH

Analysis of Interleukin-21-Induced Prdm1 Gene Regulation Reveals Functional Cooperation of STAT3 and IRF4 Transcription Factors

(2009) Hyokjoon Kwon et al.   IMMUNITY

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

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

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

(2008) Xi Chen et al.   CELL

Experimental Malaria Infection Triggers Early Expansion of Natural Killer Cells

(2008) C. C. Kim et al.   INFECTION AND IMMUNITY

Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

(2008) Jun Zhu et al.   NATURE GENETICS

NCBI GEO: archive for high-throughput functional genomic data

(2008) T. Barrett et al.   NUCLEIC ACIDS RESEARCH