Genome-wide study of correlations between genomic features and their relationship with the regulation of gene expression

The ENCODE Project and Perspectives on Pathways

(2014) Vinicius Tragante et al.   GENETIC EPIDEMIOLOGY

A promoter-level mammalian expression atlas

(2014)   NATURE

CpG domains downstream of TSSs promote high levels of gene expression

(2014) Simone Krinner et al.   NUCLEIC ACIDS RESEARCH

Cooperativity, Specificity, and Evolutionary Stability of Polycomb Targeting in Drosophila

(2014) Bernd Schuettengruber et al.   Cell Reports

H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation

(2013) Shannon M. Lauberth et al.   CELL

Architectural and Functional Diversity of Polycomb Group Response Elements in Drosophila

(2013) J. L. Brown et al.   GENETICS

Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing

(2013) Nicola Crosetto et al.   NATURE METHODS

How bidirectional becomes unidirectional

(2013) Patricia Richard et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Genomic HyperBrowser: an analysis web server for genome-scale data

(2013) Geir K. Sandve et al.   NUCLEIC ACIDS RESEARCH

Statistics of genome architecture

(2013) V.R. Chechetkin   PHYSICS LETTERS A

DNA Double-Strand Breaks Coupled with PARP1 and HNRNPA2B1 Binding Sites Flank Coordinately Expressed Domains in Human Chromosomes

(2013) Nickolai A. Tchurikov et al.   PLoS Genetics

Human-specific CpG “beacons” identify loci associated with human-specific traits and disease

(2012) Christopher G. Bell et al.   Epigenetics

EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era

(2012) René Dreos et al.   NUCLEIC ACIDS RESEARCH

ArrayExpress update—trends in database growth and links to data analysis tools

(2012) Gabriella Rustici et al.   NUCLEIC ACIDS RESEARCH

Exploring Massive, Genome Scale Datasets with the GenometriCorr Package

(2012) Alexander Favorov et al.   PLoS Computational Biology

Chapter 11: Genome-Wide Association Studies

(2012) William S. Bush et al.   PLoS Computational Biology

Shape-based peak identification for ChIP-Seq

(2011) Valerie Hower et al.   BMC BIOINFORMATICS

Genome-wide profiling of forum domains in Drosophila melanogaster

(2011) Nickolai A. Tchurikov et al.   NUCLEIC ACIDS RESEARCH

DBTSS: DataBase of Transcriptional Start Sites progress report in 2012

(2011) R. Yamashita et al.   NUCLEIC ACIDS RESEARCH

Spectral sum rules and search for periodicities in DNA sequences

(2011) V.R. Chechetkin   PHYSICS LETTERS A

The Genomic HyperBrowser: inferential genomics at the sequence level

(2011) Geir K Sandve et al.   GENOME BIOLOGY

Redefining CpG islands using hidden Markov models

(2010) H. Wu et al.   BIOSTATISTICS

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Evaluation of Algorithm Performance in ChIP-Seq Peak Detection

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

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets

(2009) J. W. Nicol et al.   BIOINFORMATICS

CpG islands - ‘A rough guide’

(2009) Robert S. Illingworth et al.   FEBS LETTERS

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

An overview of recent developments in genomics and associated statistical methods

(2009) P. J. Bickel et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Evidence for RNA synthesis in the intergenic region between enhancer and promoter and its inhibition by insulators in Drosophila melanogaster

(2008) Nickolai A. Tchurikov et al.   NUCLEIC ACIDS RESEARCH

Stability and Dynamics of Polycomb Target Sites in Drosophila Development

(2008) Camilla Kwong et al.   PLoS Genetics

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY