Cloud computing for genomic data analysis and collaboration

Don’t let useful data go to waste

(2017) Franziska Denk   NATURE

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Reproducible RNA-seq analysis using recount2

(2017) Leonardo Collado-Torres et al.   NATURE BIOTECHNOLOGY

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

Sharing Clinical and Genomic Data on Cancer — The Need for Global Solutions

(2017)   NEW ENGLAND JOURNAL OF MEDICINE

Should biomedical research be like Airbnb?

(2017) Vivien R. Bonazzi et al.   PLOS BIOLOGY

Singularity: Scientific containers for mobility of compute

(2017) Gregory M. Kurtzer et al.   PLoS One

Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce

(2016) Abhinav Nellore et al.   BIOINFORMATICS

Teaching Cloud Computing

(2016) Scott Campbell   COMPUTER

Million Veteran Program: A mega-biobank to study genetic influences on health and disease

(2016) John Michael Gaziano et al.   JOURNAL OF CLINICAL EPIDEMIOLOGY

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

Secure cloud computing for genomic data

(2016) Somalee Datta et al.   NATURE BIOTECHNOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

European Open Science Cloud

(2016)   NATURE GENETICS

Next-generation genotype imputation service and methods

(2016) Sayantan Das et al.   NATURE GENETICS

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

European Nucleotide Archive in 2016

(2016) Ana Luisa Toribio et al.   NUCLEIC ACIDS RESEARCH

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

A federated ecosystem for sharing genomic, clinical data

(2016)   SCIENCE

Tools and techniques for computational reproducibility

(2016) Stephen R. Piccolo et al.   GigaScience

A cloud-based workflow to quantify transcript-expression levels in public cancer compendia

(2016) PJ Tatlow et al.   Scientific Reports

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

(2015) Kathleen M. Fisch et al.   BIOINFORMATICS

Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results

(2015) Mumtahena Rahman et al.   BIOINFORMATICS

Perspective: Sustaining the big-data ecosystem

(2015) Philip E. Bourne et al.   NATURE

Data analysis: Create a cloud commons

(2015) Lincoln D. Stein et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

The European Genome-phenome Archive of human data consented for biomedical research

(2015) Ilkka Lappalainen et al.   NATURE GENETICS

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

A New Initiative on Precision Medicine

(2015) Francis S. Collins et al.   NEW ENGLAND JOURNAL OF MEDICINE

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

Dynamics of Wolbachia pipientis Gene Expression Across the Drosophila melanogaster Life Cycle

(2015) Florence Gutzwiller et al.   G3-Genes Genomes Genetics

Big Data: Astronomical or Genomical?

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

Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics

(2015) Benjamin J Kelly et al.   GENOME BIOLOGY

XSEDE: Accelerating Scientific Discovery

(2014) John Towns et al.   COMPUTING IN SCIENCE & ENGINEERING

Experiences building Globus Genomics: a next-generation sequencing analysis service using Galaxy, Globus, and Amazon Web Services

(2014) Ravi K. Madduri et al.   CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE

Globus platform-as-a-service for collaborative science applications

(2014) Rachana Ananthakrishnan et al.   CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE

Genomic cloud computing: legal and ethical points to consider

(2014) Edward S Dove et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses

(2014) Bo Liu et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Bionimbus: a cloud for managing, analyzing and sharing large genomics datasets

(2014) Allison P Heath et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Diversity and dynamics of the Drosophila transcriptome

(2014) James B. Brown et al.   NATURE

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

A simple and reproducible breast cancer prognostic test

(2013) Luigi Marchionni et al.   BMC GENOMICS

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Expression Atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

(2013) Robert Petryszak et al.   NUCLEIC ACIDS RESEARCH

NCBI’s Database of Genotypes and Phenotypes: dbGaP

(2013) Kimberly A. Tryka et al.   NUCLEIC ACIDS RESEARCH

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community

(2012) Konstantinos Krampis et al.   BMC BIOINFORMATICS

IaaS Cloud Architecture: From Virtualized Datacenters to Federated Cloud Infrastructures

(2012) Rafael Moreno-Vozmediano et al.   COMPUTER

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Next-generation sequencing data interpretation: enhancing reproducibility and accessibility

(2012) Anton Nekrutenko et al.   NATURE REVIEWS GENETICS

Galaxy CloudMan: delivering cloud compute clusters

(2011) Enis Afgan et al.   BMC BIOINFORMATICS

ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets

(2011) Alyssa C Frazee et al.   BMC BIOINFORMATICS

PeakRanger: A cloud-enabled peak caller for ChIP-seq data

(2011) Xin Feng et al.   BMC 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

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

The Proteome Folding Project: Proteome-scale prediction of structure and function

(2011) K. Drew et al.   GENOME RESEARCH

Globus Online: Accelerating and Democratizing Science through Cloud-Based Services

(2011) Ian Foster   IEEE INTERNET COMPUTING

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology

(2010) Keith A. Baggerly et al.   Annals of Applied Statistics

Frozen robust multiarray analysis (fRMA)

(2010) M. N. McCall et al.   BIOSTATISTICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

In silico research in the era of cloud computing

(2010) Joel T Dudley et al.   NATURE BIOTECHNOLOGY

Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci

(2010) Andre Franke et al.   NATURE GENETICS

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

The case for cloud computing in genome informatics

(2010) Lincoln D Stein   GENOME BIOLOGY

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton Graveley   GENOME BIOLOGY

Cloud-scale RNA-sequencing differential expression analysis with Myrna

(2010) Ben Langmead et al.   GENOME BIOLOGY

Unlocking the secrets of the genome

(2009) Susan E. Celniker et al.   NATURE

Repeatability of published microarray gene expression analyses

(2009) John P A Ioannidis et al.   NATURE GENETICS

Searching for SNPs with cloud computing

(2009) Ben Langmead et al.   GENOME BIOLOGY

MapReduce

(2008) Jeffrey Dean et al.   COMMUNICATIONS OF THE ACM

Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes

(2008) Eleftheria Zeggini et al.   NATURE GENETICS