Chromatin Landscape Dictates HSF Binding to Target DNA Elements

Nucleosome dynamics define transcriptional enhancers

(2010) Housheng Hansen He et al.   NATURE GENETICS

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

(2009) Chongzhi Zang et al.   BIOINFORMATICS

A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes

(2009) Stefan Kurtz et al.   BMC GENOMICS

ChIP-Seq of ERα and RNA polymerase II defines genes differentially responding to ligands

(2009) Willem-Jan Welboren et al.   EMBO JOURNAL

Spt6 enhances the elongation rate of RNA polymerase II in vivo

(2009) M Behfar Ardehali et al.   EMBO JOURNAL

Long-range spreading of dosage compensation in Drosophila captures transcribed autosomal genes inserted on X

(2009) A. A. Gorchakov et al.   GENES & DEVELOPMENT

Three subclasses of a Drosophila insulator show distinct and cell type-specific genomic distributions

(2009) A. M. Bushey et al.   GENES & DEVELOPMENT

Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation

(2009) T. E. Reddy et al.   GENOME RESEARCH

Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression

(2009) Y. Cheng et al.   GENOME RESEARCH

Hormonal Regulation of the E75 Gene in Drosophila: Identifying Functional Regulatory Elements through Computational and Biological Analysis

(2009) Travis J. Bernardo et al.   JOURNAL OF MOLECULAR BIOLOGY

Genome-Wide Mapping of Boundary Element-Associated Factor (BEAF) Binding Sites in Drosophila melanogaster Links BEAF to Transcription

(2009) N. Jiang et al.   MOLECULAR AND CELLULAR BIOLOGY

Insights into GATA-1-Mediated Gene Activation versus Repression via Genome-wide Chromatin Occupancy Analysis

(2009) Ming Yu et al.   MOLECULAR CELL

Unlocking the secrets of the genome

(2009) Susan E. Celniker et al.   NATURE

Defining mechanisms that regulate RNA polymerase II transcription in vivo

(2009) Nicholas J. Fuda et al.   NATURE

H3.3/H2A.Z double variant–containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions

(2009) Chunyuan Jin et al.   NATURE GENETICS

Tracking rates of transcription and splicing in vivo

(2009) M Behfar Ardehali et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mapping accessible chromatin regions using Sono-Seq

(2009) R. K. Auerbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery and Annotation of Functional Chromatin Signatures in the Human Genome

(2009) Gary Hon et al.   PLoS Computational Biology

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

(2009) Stewart MacArthur et al.   GENOME BIOLOGY

Rapid, Transcription-Independent Loss of Nucleosomes over a Large Chromatin Domain at Hsp70 Loci

(2008) Steven J. Petesch et al.   CELL

Caudal, a key developmental regulator, is a DPE-specific transcriptional factor

(2008) T. Juven-Gershon et al.   GENES & DEVELOPMENT

Proteotoxic stress and inducible chaperone networks in neurodegenerative disease and aging

(2008) R. I. Morimoto   GENES & DEVELOPMENT

Aberrant chromatin at genes encoding stem cell regulators in human mixed-lineage leukemia

(2008) M. G. Guenther et al.   GENES & DEVELOPMENT

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding

(2008) A. G. Robertson et al.   GENOME RESEARCH

Genome-wide profiling of salt fractions maps physical properties of chromatin

(2008) S. Henikoff et al.   GENOME RESEARCH

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

DOT1L/KMT4 Recruitment and H3K79 Methylation Are Ubiquitously Coupled with Gene Transcription in Mammalian Cells

(2008) D. J. Steger et al.   MOLECULAR AND CELLULAR BIOLOGY

NELF and GAGA Factor Are Linked to Promoter-Proximal Pausing at Many Genes in Drosophila

(2008) C. Lee et al.   MOLECULAR AND CELLULAR BIOLOGY

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

A large genome center's improvements to the Illumina sequencing system

(2008) Michael A Quail et al.   NATURE METHODS

Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments

(2008) X. Fan et al.   NUCLEIC ACIDS RESEARCH

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data

(2008) R. Jothi et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for high-throughput functional genomic data

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

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY