Literature DB >> 26174866

The NIH BD2K center for big data in translational genomics.

Benedict Paten1, Mark Diekhans2, Brian J Druker3, Stephen Friend4, Justin Guinney4, Nadine Gassner2, Mitchell Guttman5, W James Kent2, Patrick Mantey6, Adam A Margolin7, Matt Massie8, Adam M Novak2, Frank Nothaft8, Lior Pachter9, David Patterson8, Maciej Smuga-Otto2, Joshua M Stuart2, Laura Van't Veer10, Barbara Wold11, David Haussler12.   

Abstract

The world's genomics data will never be stored in a single repository - rather, it will be distributed among many sites in many countries. No one site will have enough data to explain genotype to phenotype relationships in rare diseases; therefore, sites must share data. To accomplish this, the genetics community must forge common standards and protocols to make sharing and computing data among many sites a seamless activity. Through the Global Alliance for Genomics and Health, we are pioneering the development of shared application programming interfaces (APIs) to connect the world's genome repositories. In parallel, we are developing an open source software stack (ADAM) that uses these APIs. This combination will create a cohesive genome informatics ecosystem. Using containers, we are facilitating the deployment of this software in a diverse array of environments. Through benchmarking efforts and big data driver projects, we are ensuring ADAM's performance and utility.
© The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Keywords:  APIs; big data; computational genomics; genome informatics; genomics

Mesh:

Year:  2015        PMID: 26174866      PMCID: PMC5009913          DOI: 10.1093/jamia/ocv047

Source DB:  PubMed          Journal:  J Am Med Inform Assoc        ISSN: 1067-5027            Impact factor:   4.497


  5 in total

1.  Initial sequencing and analysis of the human genome.

Authors:  E S Lander; L M Linton; B Birren; C Nusbaum; M C Zody; J Baldwin; K Devon; K Dewar; M Doyle; W FitzHugh; R Funke; D Gage; K Harris; A Heaford; J Howland; L Kann; J Lehoczky; R LeVine; P McEwan; K McKernan; J Meldrim; J P Mesirov; C Miranda; W Morris; J Naylor; C Raymond; M Rosetti; R Santos; A Sheridan; C Sougnez; Y Stange-Thomann; N Stojanovic; A Subramanian; D Wyman; J Rogers; J Sulston; R Ainscough; S Beck; D Bentley; J Burton; C Clee; N Carter; A Coulson; R Deadman; P Deloukas; A Dunham; I Dunham; R Durbin; L French; D Grafham; S Gregory; T Hubbard; S Humphray; A Hunt; M Jones; C Lloyd; A McMurray; L Matthews; S Mercer; S Milne; J C Mullikin; A Mungall; R Plumb; M Ross; R Shownkeen; S Sims; R H Waterston; R K Wilson; L W Hillier; J D McPherson; M A Marra; E R Mardis; L A Fulton; A T Chinwalla; K H Pepin; W R Gish; S L Chissoe; M C Wendl; K D Delehaunty; T L Miner; A Delehaunty; J B Kramer; L L Cook; R S Fulton; D L Johnson; P J Minx; S W Clifton; T Hawkins; E Branscomb; P Predki; P Richardson; S Wenning; T Slezak; N Doggett; J F Cheng; A Olsen; S Lucas; C Elkin; E Uberbacher; M Frazier; R A Gibbs; D M Muzny; S E Scherer; J B Bouck; E J Sodergren; K C Worley; C M Rives; J H Gorrell; M L Metzker; S L Naylor; R S Kucherlapati; D L Nelson; G M Weinstock; Y Sakaki; A Fujiyama; M Hattori; T Yada; A Toyoda; T Itoh; C Kawagoe; H Watanabe; Y Totoki; T Taylor; J Weissenbach; R Heilig; W Saurin; F Artiguenave; P Brottier; T Bruls; E Pelletier; C Robert; P Wincker; D R Smith; L Doucette-Stamm; M Rubenfield; K Weinstock; H M Lee; J Dubois; A Rosenthal; M Platzer; G Nyakatura; S Taudien; A Rump; H Yang; J Yu; J Wang; G Huang; J Gu; L Hood; L Rowen; A Madan; S Qin; R W Davis; N A Federspiel; A P Abola; M J Proctor; R M Myers; J Schmutz; M Dickson; J Grimwood; D R Cox; M V Olson; R Kaul; C Raymond; N Shimizu; K Kawasaki; S Minoshima; G A Evans; M Athanasiou; R Schultz; B A Roe; F Chen; H Pan; J Ramser; H Lehrach; R Reinhardt; W R McCombie; M de la Bastide; N Dedhia; H Blöcker; K Hornischer; G Nordsiek; R Agarwala; L Aravind; J A Bailey; A Bateman; S Batzoglou; E Birney; P Bork; D G Brown; C B Burge; L Cerutti; H C Chen; D Church; M Clamp; R R Copley; T Doerks; S R Eddy; E E Eichler; T S Furey; J Galagan; J G Gilbert; C Harmon; Y Hayashizaki; D Haussler; H Hermjakob; K Hokamp; W Jang; L S Johnson; T A Jones; S Kasif; A Kaspryzk; S Kennedy; W J Kent; P Kitts; E V Koonin; I Korf; D Kulp; D Lancet; T M Lowe; A McLysaght; T Mikkelsen; J V Moran; N Mulder; V J Pollara; C P Ponting; G Schuler; J Schultz; G Slater; A F Smit; E Stupka; J Szustakowki; D Thierry-Mieg; J Thierry-Mieg; L Wagner; J Wallis; R Wheeler; A Williams; Y I Wolf; K H Wolfe; S P Yang; R F Yeh; F Collins; M S Guyer; J Peterson; A Felsenfeld; K A Wetterstrand; A Patrinos; M J Morgan; P de Jong; J J Catanese; K Osoegawa; H Shizuya; S Choi; Y J Chen; J Szustakowki
Journal:  Nature       Date:  2001-02-15       Impact factor: 49.962

2.  The Cancer Genome Atlas Pan-Cancer analysis project.

Authors:  John N Weinstein; Eric A Collisson; Gordon B Mills; Kenna R Mills Shaw; Brad A Ozenberger; Kyle Ellrott; Ilya Shmulevich; Chris Sander; Joshua M Stuart
Journal:  Nat Genet       Date:  2013-10       Impact factor: 38.330

3.  The UCSC Genome Browser database: 2015 update.

Authors:  Kate R Rosenbloom; Joel Armstrong; Galt P Barber; Jonathan Casper; Hiram Clawson; Mark Diekhans; Timothy R Dreszer; Pauline A Fujita; Luvina Guruvadoo; Maximilian Haeussler; Rachel A Harte; Steve Heitner; Glenn Hickey; Angie S Hinrichs; Robert Hubley; Donna Karolchik; Katrina Learned; Brian T Lee; Chin H Li; Karen H Miga; Ngan Nguyen; Benedict Paten; Brian J Raney; Arian F A Smit; Matthew L Speir; Ann S Zweig; David Haussler; Robert M Kuhn; W James Kent
Journal:  Nucleic Acids Res       Date:  2014-11-26       Impact factor: 19.160

4.  Best practices for scientific computing.

Authors:  Greg Wilson; D A Aruliah; C Titus Brown; Neil P Chue Hong; Matt Davis; Richard T Guy; Steven H D Haddock; Kathryn D Huff; Ian M Mitchell; Mark D Plumbley; Ben Waugh; Ethan P White; Paul Wilson
Journal:  PLoS Biol       Date:  2014-01-07       Impact factor: 8.029

5.  The UCSC Cancer Genomics Browser: update 2015.

Authors:  Mary Goldman; Brian Craft; Teresa Swatloski; Melissa Cline; Olena Morozova; Mark Diekhans; David Haussler; Jingchun Zhu
Journal:  Nucleic Acids Res       Date:  2014-11-11       Impact factor: 19.160

  5 in total
  13 in total

1.  Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop.

Authors:  Kathleen M Jagodnik; Simon Koplev; Sherry L Jenkins; Lucila Ohno-Machado; Benedict Paten; Stephan C Schurer; Michel Dumontier; Ruben Verborgh; Alex Bui; Peipei Ping; Neil J McKenna; Ravi Madduri; Ajay Pillai; Avi Ma'ayan
Journal:  J Biomed Inform       Date:  2017-05-10       Impact factor: 6.317

2.  Visual Omics Explorer (VOE): a cross-platform portal for interactive data visualization.

Authors:  Baekdoo Kim; Thahmina Ali; Samuel Hosmer; Konstantinos Krampis
Journal:  Bioinformatics       Date:  2016-03-07       Impact factor: 6.937

Review 3.  Leveraging European infrastructures to access 1 million human genomes by 2022.

Authors:  Gary Saunders; Michael Baudis; Regina Becker; Sergi Beltran; Christophe Béroud; Ewan Birney; Cath Brooksbank; Søren Brunak; Marc Van den Bulcke; Rachel Drysdale; Salvador Capella-Gutierrez; Paul Flicek; Francesco Florindi; Peter Goodhand; Ivo Gut; Jaap Heringa; Petr Holub; Jef Hooyberghs; Nick Juty; Thomas M Keane; Jan O Korbel; Ilkka Lappalainen; Brane Leskosek; Gert Matthijs; Michaela Th Mayrhofer; Andres Metspalu; Arcadi Navarro; Steven Newhouse; Tommi Nyrönen; Angela Page; Bengt Persson; Aarno Palotie; Helen Parkinson; Jordi Rambla; David Salgado; Erik Steinfelder; Morris A Swertz; Alfonso Valencia; Susheel Varma; Niklas Blomberg; Serena Scollen
Journal:  Nat Rev Genet       Date:  2019-08-27       Impact factor: 53.242

4.  VariantSpark: population scale clustering of genotype information.

Authors:  Aidan R O'Brien; Neil F W Saunders; Yi Guo; Fabian A Buske; Rodney J Scott; Denis C Bauer
Journal:  BMC Genomics       Date:  2015-12-10       Impact factor: 3.969

5.  Fused Regression for Multi-source Gene Regulatory Network Inference.

Authors:  Kari Y Lam; Zachary M Westrick; Christian L Müller; Lionel Christiaen; Richard Bonneau
Journal:  PLoS Comput Biol       Date:  2016-12-06       Impact factor: 4.475

6.  Facilitating a culture of responsible and effective sharing of cancer genome data.

Authors:  Lillian L Siu; Mark Lawler; David Haussler; Bartha Maria Knoppers; Jeremy Lewin; Daniel J Vis; Rachel G Liao; Fabrice Andre; Ian Banks; J Carl Barrett; Carlos Caldas; Anamaria Aranha Camargo; Rebecca C Fitzgerald; Mao Mao; John E Mattison; William Pao; William R Sellers; Patrick Sullivan; Bin Tean Teh; Robyn L Ward; Jean Claude ZenKlusen; Charles L Sawyers; Emile E Voest
Journal:  Nat Med       Date:  2016-05-05       Impact factor: 53.440

Review 7.  Challenges of Identifying Clinically Actionable Genetic Variants for Precision Medicine.

Authors:  Tonia C Carter; Max M He
Journal:  J Healthc Eng       Date:  2016       Impact factor: 2.682

8.  GenAp: a distributed SQL interface for genomic data.

Authors:  Christos Kozanitis; David A Patterson
Journal:  BMC Bioinformatics       Date:  2016-02-04       Impact factor: 3.169

9.  MMTF-An efficient file format for the transmission, visualization, and analysis of macromolecular structures.

Authors:  Anthony R Bradley; Alexander S Rose; Antonín Pavelka; Yana Valasatava; Jose M Duarte; Andreas Prlić; Peter W Rose
Journal:  PLoS Comput Biol       Date:  2017-06-02       Impact factor: 4.475

10.  Identification of Liver Cancer Stem Cell Stemness Markers Using a Comparative Analysis of Public Data Sets.

Authors:  Kirill Borziak; Joseph Finkelstein
Journal:  Stem Cells Cloning       Date:  2021-06-16
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.