ASEQ: fast allele-specific studies from next-generation sequencing data

Tumor clone dynamics in lethal prostate cancer

(2014) S. Carreira et al.   Science Translational Medicine

Punctuated Evolution of Prostate Cancer Genomes

(2013) Sylvan C. Baca et al.   CELL

Variants at IRX4 as prostate cancer expression quantitative trait loci

(2013) Xing Xu et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Allelic imbalance metre (Allim), a new tool for measuring allele-specific gene expression with RNA-seq data

(2013) Ram Vinay Pandey et al.   Molecular Ecology Resources

Germline Allele-Specific Expression of DAPK1 in Chronic Lymphocytic Leukemia

(2013) Quan-Xiang Wei et al.   PLoS One

A novel hierarchical clustering algorithm for gene sequences

(2012) Dan Wei et al.   BMC BIOINFORMATICS

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer

(2012) Christopher E Barbieri et al.   NATURE GENETICS

Monoallelic Expression Determines Oncogenic Progression and Outcome in Benign and Malignant Brain Tumors

(2011) E. J. Walker et al.   CANCER RESEARCH

A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data

(2011) D. A. Skelly et al.   GENOME RESEARCH

The genomic complexity of primary human prostate cancer

(2011) Michael F. Berger et al.   NATURE

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries

(2010) Lukas Habegger et al.   BIOINFORMATICS

RNA sequencing reveals the role of splicing polymorphisms in regulating human gene expression

(2010) E. Lalonde et al.   GENOME RESEARCH

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

(2010) A. McKenna et al.   GENOME RESEARCH

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

(2009) Jacob F. Degner et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Allele-Specific Up-Regulation of FGFR2 Increases Susceptibility to Breast Cancer

(2008) Kerstin B Meyer et al.   PLOS BIOLOGY