Streaming fragment assignment for real-time analysis of sequencing experiments

Mixture models for analysis of the taxonomic composition of metagenomes

(2011) Peter Meinicke et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Hobbes: optimized gram-based methods for efficient read alignment

(2011) Athena Ahmadi et al.   NUCLEIC ACIDS RESEARCH

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

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts 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

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

Accurate quantification of transcriptome from RNA-Seq data by effective length normalization

(2010) Soohyun Lee et al.   NUCLEIC ACIDS RESEARCH

The case for cloud computing in genome informatics

(2010) Lincoln D Stein   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite

(2009) T. Hashimoto et al.   BIOINFORMATICS

On-line expectation-maximization algorithm for latent data models

(2009) Olivier Cappé et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

The potential and challenges of nanopore sequencing

(2008) Daniel Branton et al.   NATURE BIOTECHNOLOGY