diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

DIME: R-package for identifying differential ChIP-seq based on an ensemble of mixture models

(2011) C. Taslim et al.   BIOINFORMATICS

Detecting differential binding of transcription factors with ChIP-seq

(2011) Kun Liang et al.   BIOINFORMATICS

An Epigenetic Signature for Monoallelic Olfactory Receptor Expression

(2011) Angeliki Magklara et al.   CELL

Epigenetics in Alternative Pre-mRNA Splicing

(2011) Reini F. Luco et al.   CELL

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

ChIP-Seq: technical considerations for obtaining high-quality data

(2011) Benjamin L Kidder et al.   NATURE IMMUNOLOGY

Cocaine dynamically regulates heterochromatin and repetitive element unsilencing in nucleus accumbens

(2011) I. Maze et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

A signal–noise model for significance analysis of ChIP-seq with negative control

(2010) Han Xu et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Ras-Guanine Nucleotide-Releasing Factor 1 (Ras-GRF1) Controls Activation of Extracellular Signal-Regulated Kinase (ERK) Signaling in the Striatum and Long-Term Behavioral Responses to Cocaine

(2009) Stefania Fasano et al.   BIOLOGICAL PSYCHIATRY

Determination of enriched histone modifications in non-genic portions of the human genome

(2009) Jeffrey A Rosenfeld et al.   BMC GENOMICS

Cocaine self-administration alters the expression of chromatin-remodelling proteins; modulation by histone deacetylase inhibition

(2009) Lionel Host et al.   JOURNAL OF PSYCHOPHARMACOLOGY

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

HDAC2: a critical factor in health and disease

(2009) Oliver H. Krämer   TRENDS IN PHARMACOLOGICAL SCIENCES

An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data

(2008) Han Xu et al.   BIOINFORMATICS

Hypoinsulinemia Alleviates the Grf1/Ras/Akt Anti-Apoptotic Pathway and Induces Alterations of Mitochondrial Ras Trafficking in Neuronal Cells

(2008) E. Zhuravliova et al.   NEUROCHEMICAL RESEARCH