System for Quality-Assured Data Analysis: Flexible, reproducible scientific workflows

Strategies for identification of somatic variants using the Ion Torrent deep targeted sequencing platform

(2018) Aditya Deshpande et al.   BMC BIOINFORMATICS

Oral microbiota reveals signs of acculturation in Mexican American women

(2018) Kristi L. Hoffman et al.   PLoS One

Rapid and powerful detection of subtle allelic imbalance from exome sequencing data withhapLOHseq

(2016) F. Anthony San Lucas et al.   BIOINFORMATICS

NEAT: a framework for building fully automated NGS pipelines and analyses

(2016) Patrick Schorderet   BMC BIOINFORMATICS

Genomic Landscape of Colorectal Mucosa and Adenomas

(2016) E. Borras et al.   Cancer Prevention Research

Genomic Landscape Established by Allelic Imbalance in the Cancerization Field of a Normal Appearing Airway

(2016) Yasminka Jakubek et al.   CANCER RESEARCH

Omics Pipe: a community-based framework for reproducible multi-omics data analysis

(2015) Kathleen M. Fisch et al.   BIOINFORMATICS

NGSANE: a lightweight production informatics framework for high-throughput data analysis

(2014) Fabian A. Buske et al.   BIOINFORMATICS

Preliminary whole-exome sequencing reveals mutations that imply common tumorigenicity pathways in multiple endocrine neoplasia type 1 patients

(2014) Minerva Angélica Romero Arenas et al.   SURGERY

Identification of Allelic Imbalance with a Statistical Model for Subtle Genomic Mosaicism

(2014) Rui Xia et al.   PLoS Computational Biology

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Ten Simple Rules for Reproducible Computational Research

(2013) Geir Kjetil Sandve et al.   PLoS Computational Biology

Bpipe: a tool for running and managing bioinformatics pipelines

(2012) Simon P. Sadedin et al.   BIOINFORMATICS

Haplotype-based profiling of subtle allelic imbalance with SNP arrays

(2012) S. Vattathil et al.   GENOME RESEARCH

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Next-generation sequencing data interpretation: enhancing reproducibility and accessibility

(2012) Anton Nekrutenko et al.   NATURE REVIEWS GENETICS

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools

(2011) F. A. San Lucas et al.   BIOINFORMATICS

ContEst: estimating cross-contamination of human samples in next-generation sequencing data

(2011) Kristian Cibulskis et al.   BIOINFORMATICS

Chipster: user-friendly analysis software for microarray and other high-throughput data

(2011) M Aleksi Kallio et al.   BMC GENOMICS

Ruffus: a lightweight Python library for computational pipelines

(2010) Leo Goodstadt   BIOINFORMATICS

MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes

(2010) Yun Li et al.   GENETIC EPIDEMIOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

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

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs

(2008) Joshua M Korn et al.   NATURE GENETICS