HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis

A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs

(2013) G. Andrey et al.   SCIENCE

The UCSC genome browser and associated tools

(2012) R. M. Kuhn et al.   BRIEFINGS IN BIOINFORMATICS

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles

(2012) Gwendal Le Martelot et al.   PLOS BIOLOGY

Chipster: user-friendly analysis software for microarray and other high-throughput data

(2011) M Aleksi Kallio et al.   BMC GENOMICS

Processing and analyzing ChIP-seq data: from short reads to regulatory interactions

(2011) M. Leleu et al.   Briefings in Functional Genomics

Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L

(2011) Alexandre Huber et al.   EMBO JOURNAL

The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA

(2011) E. Splinter et al.   GENES & DEVELOPMENT

Analysis of HIV-1 Expression Level and Sense of Transcription by High-Throughput Sequencing of the Infected Cell

(2011) G. Lefebvre et al.   JOURNAL OF VIROLOGY

GeneProf: analysis of high-throughput sequencing experiments

(2011) Florian Halbritter et al.   NATURE METHODS

Probable Zoonotic Leprosy in the Southern United States

(2011) Richard W. Truman et al.   NEW ENGLAND JOURNAL OF MEDICINE

The Dynamic Architecture of Hox Gene Clusters

(2011) D. Noordermeer et al.   SCIENCE

Genome-Wide and Phase-Specific DNA-Binding Rhythms of BMAL1 Control Circadian Output Functions in Mouse Liver

(2011) Guillaume Rey et al.   PLOS BIOLOGY

SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data

(2011) Songbo Huang et al.   Frontiers in Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Telomere-Binding Protein Tbf1 Demarcates snoRNA Gene Promoters in Saccharomyces cerevisiae

(2010) Milena Preti et al.   MOLECULAR CELL

KAP1 controls endogenous retroviruses in embryonic stem cells

(2010) Helen M. Rowe et al.   NATURE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Comparative genomic and phylogeographic analysis of Mycobacterium leprae

(2009) Marc Monot et al.   NATURE GENETICS

MEME SUITE: tools for motif discovery and searching

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

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

A universal classification of eukaryotic transposable elements implemented in Repbase

(2008) Vladimir V. Kapitonov et al.   NATURE REVIEWS GENETICS

Global Chromatin Domain Organization of the Drosophila Genome

(2008) Elzo de Wit et al.   PLoS Genetics

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY