MolBioLib: a C++11 framework for rapid development and deployment of bioinformatics tasks

Next-Generation Sequencing Strategies Enable Routine Detection of Balanced Chromosome Rearrangements for Clinical Diagnostics and Genetic Research

(2011) Michael E. Talkowski et al.   AMERICAN JOURNAL OF HUMAN GENETICS

GenomicTools: a computational platform for developing high-throughput analytics in genomics

(2011) Aristotelis Tsirigos et al.   BIOINFORMATICS

BamTools: a C++ API and toolkit for analyzing and managing BAM files

(2011) D. W. Barnett et al.   BIOINFORMATICS

Functional analysis of the microtubule-interacting transcriptome

(2011) Judith A. Sharp et al.   MOLECULAR BIOLOGY OF THE CELL

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

(2011)   PLOS BIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Genome-wide Identification of Polycomb-Associated RNAs by RIP-seq

(2010) Jing Zhao et al.   MOLECULAR CELL

Ensembl 2011

(2010) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: update 2011

(2010) P. A. Fujita et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BioMart – biological queries made easy

(2009) Damian Smedley et al.   BMC GENOMICS

Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi

(2009) Nelson C Lau et al.   EMBO JOURNAL

Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs

(2008) Julien Dutheil et al.   BMC EVOLUTIONARY BIOLOGY

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

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY