SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines

Tracking the NGS revolution: managing life science research on shared high-performance computing clusters

(2018) Martin Dahlö et al.   GigaScience

Container-based bioinformatics with Pachyderm

(2018) Jon Ander Novella et al.   BIOINFORMATICS

Predicting Off-Target Binding Profiles With Confidence Using Conformal Prediction

(2018) Samuel Lampa et al.   Frontiers in Pharmacology

Computation semantics of the functional scientific workflow language Cuneiform

(2017) JÖRGEN BRANDT et al.   JOURNAL OF FUNCTIONAL PROGRAMMING

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

Toil enables reproducible, open source, big biomedical data analyses

(2017) John Vivian et al.   NATURE BIOTECHNOLOGY

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Apache Spark

(2016) Matei Zaharia et al.   COMMUNICATIONS OF THE ACM

Large-scale ligand-based predictive modelling using support vector machines

(2016) Jonathan Alvarsson et al.   Journal of Cheminformatics

Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles

(2016) Samuel Lampa et al.   Journal of Cheminformatics

Experiences with workflows for automating data-intensive bioinformatics

(2015) Ola Spjuth et al.   Biology Direct

Methods of integrating data to uncover genotype–phenotype interactions

(2015) Marylyn D. Ritchie et al.   NATURE REVIEWS GENETICS

Big Data: Astronomical or Genomical?

(2015) Zachary D. Stephens et al.   PLOS BIOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

The big challenges of big data

(2013) Vivien Marx   NATURE

Bpipe: a tool for running and managing bioinformatics pipelines

(2012) Simon P. Sadedin et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Nipype: A Flexible, Lightweight and Extensible Neuroimaging Data Processing Framework in Python

(2011) Krzysztof Gorgolewski et al.   Frontiers in Neuroinformatics

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

(2010) A. McKenna et al.   GENOME RESEARCH

Visualization of omics data for systems biology

(2010) Nils Gehlenborg et al.   NATURE METHODS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS