Literature DB >> 29379135

Cloud computing for genomic data analysis and collaboration.

Ben Langmead1, Abhinav Nellore2.   

Abstract

Next-generation sequencing has made major strides in the past decade. Studies based on large sequencing data sets are growing in number, and public archives for raw sequencing data have been doubling in size every 18 months. Leveraging these data requires researchers to use large-scale computational resources. Cloud computing, a model whereby users rent computers and storage from large data centres, is a solution that is gaining traction in genomics research. Here, we describe how cloud computing is used in genomics for research and large-scale collaborations, and argue that its elasticity, reproducibility and privacy features make it ideally suited for the large-scale reanalysis of publicly available archived data, including privacy-protected data.

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Year:  2018        PMID: 29379135      PMCID: PMC6452449          DOI: 10.1038/nrg.2017.113

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  59 in total

1.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

Authors:  Aaron McKenna; Matthew Hanna; Eric Banks; Andrey Sivachenko; Kristian Cibulskis; Andrew Kernytsky; Kiran Garimella; David Altshuler; Stacey Gabriel; Mark Daly; Mark A DePristo
Journal:  Genome Res       Date:  2010-07-19       Impact factor: 9.043

2.  Data analysis: Create a cloud commons.

Authors:  Lincoln D Stein; Bartha M Knoppers; Peter Campbell; Gad Getz; Jan O Korbel
Journal:  Nature       Date:  2015-07-09       Impact factor: 49.962

3.  Cloud computing.

Authors:  Alex Bateman; Matt Wood
Journal:  Bioinformatics       Date:  2009-05-12       Impact factor: 6.937

4.  Reproducibility of computational workflows is automated using continuous analysis.

Authors:  Brett K Beaulieu-Jones; Casey S Greene
Journal:  Nat Biotechnol       Date:  2017-03-13       Impact factor: 54.908

5.  Human genomics. The human transcriptome across tissues and individuals.

Authors:  Marta Melé; Pedro G Ferreira; Ferran Reverter; David S DeLuca; Jean Monlong; Michael Sammeth; Taylor R Young; Jakob M Goldmann; Dmitri D Pervouchine; Timothy J Sullivan; Rory Johnson; Ayellet V Segrè; Sarah Djebali; Anastasia Niarchou; Fred A Wright; Tuuli Lappalainen; Miquel Calvo; Gad Getz; Emmanouil T Dermitzakis; Kristin G Ardlie; Roderic Guigó
Journal:  Science       Date:  2015-05-08       Impact factor: 47.728

6.  ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets.

Authors:  Alyssa C Frazee; Ben Langmead; Jeffrey T Leek
Journal:  BMC Bioinformatics       Date:  2011-11-16       Impact factor: 3.169

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

Authors:  Jordi Barretina; Giordano Caponigro; Nicolas Stransky; Kavitha Venkatesan; Adam A Margolin; Sungjoon Kim; Christopher J Wilson; Joseph Lehár; Gregory V Kryukov; Dmitriy Sonkin; Anupama Reddy; Manway Liu; Lauren Murray; Michael F Berger; John E Monahan; Paula Morais; Jodi Meltzer; Adam Korejwa; Judit Jané-Valbuena; Felipa A Mapa; Joseph Thibault; Eva Bric-Furlong; Pichai Raman; Aaron Shipway; Ingo H Engels; Jill Cheng; Guoying K Yu; Jianjun Yu; Peter Aspesi; Melanie de Silva; Kalpana Jagtap; Michael D Jones; Li Wang; Charles Hatton; Emanuele Palescandolo; Supriya Gupta; Scott Mahan; Carrie Sougnez; Robert C Onofrio; Ted Liefeld; Laura MacConaill; Wendy Winckler; Michael Reich; Nanxin Li; Jill P Mesirov; Stacey B Gabriel; Gad Getz; Kristin Ardlie; Vivien Chan; Vic E Myer; Barbara L Weber; Jeff Porter; Markus Warmuth; Peter Finan; Jennifer L Harris; Matthew Meyerson; Todd R Golub; Michael P Morrissey; William R Sellers; Robert Schlegel; Levi A Garraway
Journal:  Nature       Date:  2012-03-28       Impact factor: 49.962

8.  A global reference for human genetic variation.

Authors:  Adam Auton; Lisa D Brooks; Richard M Durbin; Erik P Garrison; Hyun Min Kang; Jan O Korbel; Jonathan L Marchini; Shane McCarthy; Gil A McVean; Gonçalo R Abecasis
Journal:  Nature       Date:  2015-10-01       Impact factor: 49.962

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

Authors:  Eleftheria Zeggini; Laura J Scott; Richa Saxena; Benjamin F Voight; Jonathan L Marchini; Tianle Hu; Paul I W de Bakker; Gonçalo R Abecasis; Peter Almgren; Gitte Andersen; Kristin Ardlie; Kristina Bengtsson Boström; Richard N Bergman; Lori L Bonnycastle; Knut Borch-Johnsen; Noël P Burtt; Hong Chen; Peter S Chines; Mark J Daly; Parimal Deodhar; Chia-Jen Ding; Alex S F Doney; William L Duren; Katherine S Elliott; Michael R Erdos; Timothy M Frayling; Rachel M Freathy; Lauren Gianniny; Harald Grallert; Niels Grarup; Christopher J Groves; Candace Guiducci; Torben Hansen; Christian Herder; Graham A Hitman; Thomas E Hughes; Bo Isomaa; Anne U Jackson; Torben Jørgensen; Augustine Kong; Kari Kubalanza; Finny G Kuruvilla; Johanna Kuusisto; Claudia Langenberg; Hana Lango; Torsten Lauritzen; Yun Li; Cecilia M Lindgren; Valeriya Lyssenko; Amanda F Marvelle; Christa Meisinger; Kristian Midthjell; Karen L Mohlke; Mario A Morken; Andrew D Morris; Narisu Narisu; Peter Nilsson; Katharine R Owen; Colin N A Palmer; Felicity Payne; John R B Perry; Elin Pettersen; Carl Platou; Inga Prokopenko; Lu Qi; Li Qin; Nigel W Rayner; Matthew Rees; Jeffrey J Roix; Anelli Sandbaek; Beverley Shields; Marketa Sjögren; Valgerdur Steinthorsdottir; Heather M Stringham; Amy J Swift; Gudmar Thorleifsson; Unnur Thorsteinsdottir; Nicholas J Timpson; Tiinamaija Tuomi; Jaakko Tuomilehto; Mark Walker; Richard M Watanabe; Michael N Weedon; Cristen J Willer; Thomas Illig; Kristian Hveem; Frank B Hu; Markku Laakso; Kari Stefansson; Oluf Pedersen; Nicholas J Wareham; Inês Barroso; Andrew T Hattersley; Francis S Collins; Leif Groop; Mark I McCarthy; Michael Boehnke; David Altshuler
Journal:  Nat Genet       Date:  2008-03-30       Impact factor: 38.330

10.  CloudBurst: highly sensitive read mapping with MapReduce.

Authors:  Michael C Schatz
Journal:  Bioinformatics       Date:  2009-04-08       Impact factor: 6.937

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  49 in total

1.  Swarm: A federated cloud framework for large-scale variant analysis.

Authors:  Amir Bahmani; Kyle Ferriter; Vandhana Krishnan; Arash Alavi; Amir Alavi; Philip S Tsao; Michael P Snyder; Cuiping Pan
Journal:  PLoS Comput Biol       Date:  2021-05-12       Impact factor: 4.475

2.  Remote e-Work and Distance Learning for Academic Medicine: Best Practices and Opportunities for the Future.

Authors:  Shuhan He; Debbie Lai; Sarah Mott; Andrew Little; Andrew Grock; Mary R C Haas; Teresa M Chan
Journal:  J Grad Med Educ       Date:  2020-06

3.  Meeting the challenge: Health information technology's essential role in achieving precision medicine.

Authors:  Teresa Zayas-Cabán; Kevin J Chaney; Courtney C Rogers; Joshua C Denny; P Jon White
Journal:  J Am Med Inform Assoc       Date:  2021-06-12       Impact factor: 4.497

Review 4.  Data integration strategies for predictive analytics in precision medicine.

Authors:  Lewis J Frey
Journal:  Per Med       Date:  2018-11-02       Impact factor: 2.512

5.  GalaxyCloudRunner: enhancing scalable computing for Galaxy.

Authors:  Nuwan Goonasekera; Alexandru Mahmoud; John Chilton; Enis Afgan
Journal:  Bioinformatics       Date:  2021-07-19       Impact factor: 6.937

6.  ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses.

Authors:  Natasha Pavlovikj; Joao Carlos Gomes-Neto; Jitender S Deogun; Andrew K Benson
Journal:  PeerJ       Date:  2021-05-21       Impact factor: 2.984

7.  Cardioinformatics: the nexus of bioinformatics and precision cardiology.

Authors:  Bohdan B Khomtchouk; Diem-Trang Tran; Kasra A Vand; Matthew Might; Or Gozani; Themistocles L Assimes
Journal:  Brief Bioinform       Date:  2020-12-01       Impact factor: 11.622

8.  An imputed whole-genome sequence-based GWAS approach pinpoints causal mutations for complex traits in a specific swine population.

Authors:  Guorong Yan; Xianxian Liu; Shijun Xiao; Wenshui Xin; Wenwu Xu; Yiping Li; Tao Huang; Jiangtao Qin; Lei Xie; Junwu Ma; Zhiyan Zhang; Lusheng Huang
Journal:  Sci China Life Sci       Date:  2021-08-11       Impact factor: 6.038

Review 9.  Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance.

Authors:  Aquillah M Kanzi; James Emmanuel San; Benjamin Chimukangara; Eduan Wilkinson; Maryam Fish; Veron Ramsuran; Tulio de Oliveira
Journal:  Front Genet       Date:  2020-10-23       Impact factor: 4.599

Review 10.  Banking with precision: transfusion medicine as a potential universal application in clinical genomics.

Authors:  Celina Montemayor; Patricia A R Brunker; Margaret A Keller
Journal:  Curr Opin Hematol       Date:  2019-11       Impact factor: 3.284

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