Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses

The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud

(2013) Katherine Wolstencroft et al.   NUCLEIC ACIDS RESEARCH

Unipro UGENE: a unified bioinformatics toolkit

(2012) Konstantin Okonechnikov et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Cole Trapnell et al.   Nature Protocols

Cistrome: an integrative platform for transcriptional regulation studies

(2011) Tao Liu et al.   GENOME BIOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

myExperiment: a repository and social network for the sharing of bioinformatics workflows

(2010) Carole A. Goble et al.   NUCLEIC ACIDS RESEARCH

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

hPDI: a database of experimental human protein-DNA interactions

(2009) Z. Xie et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

High-resolution DNA-binding specificity analysis of yeast transcription factors

(2009) C. Zhu et al.   GENOME RESEARCH

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY