Xenome--a tool for classifying reads from xenograft samples

Comparative studies of de novo assembly tools for next-generation sequencing technologies

(2011) Yong Lin et al.   BIOINFORMATICS

Succinct data structures for assembling large genomes

(2011) Thomas C. Conway et al.   BIOINFORMATICS

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

AREM: Aligning Short Reads from ChIP-Sequencing by Expectation Maximization

(2011) Daniel Newkirk et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data

(2011) Dongjun Chung et al.   PLoS Computational Biology

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery

(2010) Fereydoun Hormozdiari et al.   BIOINFORMATICS

Validation of a mouse xenograft model system for gene expression analysis of human acute lymphoblastic leukaemia

(2010) Amy L Samuels et al.   BMC GENOMICS

Genome remodelling in a basal-like breast cancer metastasis and xenograft

(2010) Li Ding et al.   NATURE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH