GobyWeb: Simplified Management and Analysis of Gene Expression and DNA Methylation Sequencing Data

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Detection of Murine Leukemia Virus in the Epstein-Barr Virus-Positive Human B-Cell Line JY, Using a Computational RNA-Seq-Based Exogenous Agent Detection Pipeline, PARSES

(2012) Z. Lin et al.   JOURNAL OF VIROLOGY

Sequence Analysis of the Human Virome in Febrile and Afebrile Children

(2012) Kristine M. Wylie et al.   PLoS One

SIMPLEX: Cloud-Enabled Pipeline for the Comprehensive Analysis of Exome Sequencing Data

(2012) Maria Fischer et al.   PLoS One

Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing

(2012) Nathan L. Yozwiak et al.   PLoS Neglected Tropical Diseases

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Tabix: fast retrieval of sequence features from generic TAB-delimited files

(2011) H. Li   BIOINFORMATICS

CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing

(2011) Samuel V Angiuoli et al.   BMC BIOINFORMATICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Genes methylated by DNA methyltransferase 3b are similar in mouse intestine and human colon cancer

(2011) Eveline J. Steine et al.   JOURNAL OF CLINICAL INVESTIGATION

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Biases in Illumina transcriptome sequencing caused by random hexamer priming

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

Translational bioinformatics in the cloud: an affordable alternative

(2010) Joel T Dudley et al.   Genome Medicine

Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme

(2010) Kristian Ovaska et al.   Genome Medicine

Cloud-scale RNA-sequencing differential expression analysis with Myrna

(2010) Ben Langmead et al.   GENOME BIOLOGY

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

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Sensitive digital quantification of DNA methylation in clinical samples

(2009) Meng Li et al.   NATURE BIOTECHNOLOGY