Literature DB >> 28366789

Envisioning the future of 'big data' biomedicine.

Alex A T Bui1, John Darrell Van Horn2.   

Abstract

Through the increasing availability of more efficient data collection procedures, biomedical scientists are now confronting ever larger sets of data, often finding themselves struggling to process and interpret what they have gathered. This, while still more data continues to accumulate. This torrent of biomedical information necessitates creative thinking about how the data are being generated, how they might be best managed, analyzed, and eventually how they can be transformed into further scientific understanding for improving patient care. Recognizing this as a major challenge, the National Institutes of Health (NIH) has spearheaded the "Big Data to Knowledge" (BD2K) program - the agency's most ambitious biomedical informatics effort ever undertaken to date. In this commentary, we describe how the NIH has taken on "big data" science head-on, how a consortium of leading research centers are developing the means for handling large-scale data, and how such activities are being marshalled for the training of a new generation of biomedical data scientists. All in all, the NIH BD2K program seeks to position data science at the heart of 21st Century biomedical research.
Copyright © 2017 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Biomedicine; Computing; Data science; Software; Training

Mesh:

Year:  2017        PMID: 28366789      PMCID: PMC5613673          DOI: 10.1016/j.jbi.2017.03.017

Source DB:  PubMed          Journal:  J Biomed Inform        ISSN: 1532-0464            Impact factor:   6.317


  20 in total

1.  Center of excellence for mobile sensor data-to-knowledge (MD2K).

Authors:  Santosh Kumar; Gregory D Abowd; William T Abraham; Mustafa al'Absi; J Gayle Beck; Duen Horng Chau; Tyson Condie; David E Conroy; Emre Ertin; Deborah Estrin; Deepak Ganesan; Cho Lam; Benjamin Marlin; Clay B Marsh; Susan A Murphy; Inbal Nahum-Shani; Kevin Patrick; James M Rehg; Moushumi Sharmin; Vivek Shetty; Ida Sim; Bonnie Spring; Mani Srivastava; David W Wetter
Journal:  J Am Med Inform Assoc       Date:  2015-07-03       Impact factor: 4.497

Review 2.  Administrative Databases in Orthopaedic Research: Pearls and Pitfalls of Big Data.

Authors:  Alpesh A Patel; Kern Singh; Ryan M Nunley; Shobhit V Minhas
Journal:  J Am Acad Orthop Surg       Date:  2016-03       Impact factor: 3.020

3.  Is it time to re-prioritize neuroimaging databases and digital repositories?

Authors:  John Darrell Van Horn; Arthur W Toga
Journal:  Neuroimage       Date:  2009-04-14       Impact factor: 6.556

4.  The big medical data miss: challenges in establishing an open medical resource.

Authors:  Eric J Topol
Journal:  Nat Rev Genet       Date:  2015-05       Impact factor: 53.242

5.  KnowEnG: a knowledge engine for genomics.

Authors:  Saurabh Sinha; Jun Song; Richard Weinshilboum; Victor Jongeneel; Jiawei Han
Journal:  J Am Med Inform Assoc       Date:  2015-07-23       Impact factor: 4.497

Review 6.  Scaling Up Scientific Discovery in Sleep Medicine: The National Sleep Research Resource.

Authors:  Dennis A Dean; Ary L Goldberger; Remo Mueller; Matthew Kim; Michael Rueschman; Daniel Mobley; Satya S Sahoo; Catherine P Jayapandian; Licong Cui; Michael G Morrical; Susan Surovec; Guo-Qiang Zhang; Susan Redline
Journal:  Sleep       Date:  2016-05-01       Impact factor: 5.849

7.  Opinion: Big data biomedicine offers big higher education opportunities.

Authors:  John Darrell Van Horn
Journal:  Proc Natl Acad Sci U S A       Date:  2016-06-07       Impact factor: 11.205

8.  The center for expanded data annotation and retrieval.

Authors:  Mark A Musen; Carol A Bean; Kei-Hoi Cheung; Michel Dumontier; Kim A Durante; Olivier Gevaert; Alejandra Gonzalez-Beltran; Purvesh Khatri; Steven H Kleinstein; Martin J O'Connor; Yannick Pouliot; Philippe Rocca-Serra; Susanna-Assunta Sansone; Jeffrey A Wiser
Journal:  J Am Med Inform Assoc       Date:  2015-06-25       Impact factor: 4.497

9.  Common genetic variants influence human subcortical brain structures.

Authors:  Derrek P Hibar; Jason L Stein; Miguel E Renteria; Alejandro Arias-Vasquez; Sylvane Desrivières; Neda Jahanshad; Roberto Toro; Katharina Wittfeld; Lucija Abramovic; Micael Andersson; Benjamin S Aribisala; Nicola J Armstrong; Manon Bernard; Marc M Bohlken; Marco P Boks; Janita Bralten; Andrew A Brown; M Mallar Chakravarty; Qiang Chen; Christopher R K Ching; Gabriel Cuellar-Partida; Anouk den Braber; Sudheer Giddaluru; Aaron L Goldman; Oliver Grimm; Tulio Guadalupe; Johanna Hass; Girma Woldehawariat; Avram J Holmes; Martine Hoogman; Deborah Janowitz; Tianye Jia; Sungeun Kim; Marieke Klein; Bernd Kraemer; Phil H Lee; Loes M Olde Loohuis; Michelle Luciano; Christine Macare; Karen A Mather; Manuel Mattheisen; Yuri Milaneschi; Kwangsik Nho; Martina Papmeyer; Adaikalavan Ramasamy; Shannon L Risacher; Roberto Roiz-Santiañez; Emma J Rose; Alireza Salami; Philipp G Sämann; Lianne Schmaal; Andrew J Schork; Jean Shin; Lachlan T Strike; Alexander Teumer; Marjolein M J van Donkelaar; Kristel R van Eijk; Raymond K Walters; Lars T Westlye; Christopher D Whelan; Anderson M Winkler; Marcel P Zwiers; Saud Alhusaini; Lavinia Athanasiu; Stefan Ehrlich; Marina M H Hakobjan; Cecilie B Hartberg; Unn K Haukvik; Angelien J G A M Heister; David Hoehn; Dalia Kasperaviciute; David C M Liewald; Lorna M Lopez; Remco R R Makkinje; Mar Matarin; Marlies A M Naber; D Reese McKay; Margaret Needham; Allison C Nugent; Benno Pütz; Natalie A Royle; Li Shen; Emma Sprooten; Daniah Trabzuni; Saskia S L van der Marel; Kimm J E van Hulzen; Esther Walton; Christiane Wolf; Laura Almasy; David Ames; Sampath Arepalli; Amelia A Assareh; Mark E Bastin; Henry Brodaty; Kazima B Bulayeva; Melanie A Carless; Sven Cichon; Aiden Corvin; Joanne E Curran; Michael Czisch; Greig I de Zubicaray; Allissa Dillman; Ravi Duggirala; Thomas D Dyer; Susanne Erk; Iryna O Fedko; Luigi Ferrucci; Tatiana M Foroud; Peter T Fox; Masaki Fukunaga; J Raphael Gibbs; Harald H H Göring; Robert C Green; Sebastian Guelfi; Narelle K Hansell; Catharina A Hartman; Katrin Hegenscheid; Andreas Heinz; Dena G Hernandez; Dirk J Heslenfeld; Pieter J Hoekstra; Florian Holsboer; Georg Homuth; Jouke-Jan Hottenga; Masashi Ikeda; Clifford R Jack; Mark Jenkinson; Robert Johnson; Ryota Kanai; Maria Keil; Jack W Kent; Peter Kochunov; John B Kwok; Stephen M Lawrie; Xinmin Liu; Dan L Longo; Katie L McMahon; Eva Meisenzahl; Ingrid Melle; Sebastian Mohnke; Grant W Montgomery; Jeanette C Mostert; Thomas W Mühleisen; Michael A Nalls; Thomas E Nichols; Lars G Nilsson; Markus M Nöthen; Kazutaka Ohi; Rene L Olvera; Rocio Perez-Iglesias; G Bruce Pike; Steven G Potkin; Ivar Reinvang; Simone Reppermund; Marcella Rietschel; Nina Romanczuk-Seiferth; Glenn D Rosen; Dan Rujescu; Knut Schnell; Peter R Schofield; Colin Smith; Vidar M Steen; Jessika E Sussmann; Anbupalam Thalamuthu; Arthur W Toga; Bryan J Traynor; Juan Troncoso; Jessica A Turner; Maria C Valdés Hernández; Dennis van 't Ent; Marcel van der Brug; Nic J A van der Wee; Marie-Jose van Tol; Dick J Veltman; Thomas H Wassink; Eric Westman; Ronald H Zielke; Alan B Zonderman; David G Ashbrook; Reinmar Hager; Lu Lu; Francis J McMahon; Derek W Morris; Robert W Williams; Han G Brunner; Randy L Buckner; Jan K Buitelaar; Wiepke Cahn; Vince D Calhoun; Gianpiero L Cavalleri; Benedicto Crespo-Facorro; Anders M Dale; Gareth E Davies; Norman Delanty; Chantal Depondt; Srdjan Djurovic; Wayne C Drevets; Thomas Espeseth; Randy L Gollub; Beng-Choon Ho; Wolfgang Hoffmann; Norbert Hosten; René S Kahn; Stephanie Le Hellard; Andreas Meyer-Lindenberg; Bertram Müller-Myhsok; Matthias Nauck; Lars Nyberg; Massimo Pandolfo; Brenda W J H Penninx; Joshua L Roffman; Sanjay M Sisodiya; Jordan W Smoller; Hans van Bokhoven; Neeltje E M van Haren; Henry Völzke; Henrik Walter; Michael W Weiner; Wei Wen; Tonya White; Ingrid Agartz; Ole A Andreassen; John Blangero; Dorret I Boomsma; Rachel M Brouwer; Dara M Cannon; Mark R Cookson; Eco J C de Geus; Ian J Deary; Gary Donohoe; Guillén Fernández; Simon E Fisher; Clyde Francks; David C Glahn; Hans J Grabe; Oliver Gruber; John Hardy; Ryota Hashimoto; Hilleke E Hulshoff Pol; Erik G Jönsson; Iwona Kloszewska; Simon Lovestone; Venkata S Mattay; Patrizia Mecocci; Colm McDonald; Andrew M McIntosh; Roel A Ophoff; Tomas Paus; Zdenka Pausova; Mina Ryten; Perminder S Sachdev; Andrew J Saykin; Andy Simmons; Andrew Singleton; Hilkka Soininen; Joanna M Wardlaw; Michael E Weale; Daniel R Weinberger; Hieab H H Adams; Lenore J Launer; Stephan Seiler; Reinhold Schmidt; Ganesh Chauhan; Claudia L Satizabal; James T Becker; Lisa Yanek; Sven J van der Lee; Maritza Ebling; Bruce Fischl; W T Longstreth; Douglas Greve; Helena Schmidt; Paul Nyquist; Louis N Vinke; Cornelia M van Duijn; Luting Xue; Bernard Mazoyer; Joshua C Bis; Vilmundur Gudnason; Sudha Seshadri; M Arfan Ikram; Nicholas G Martin; Margaret J Wright; Gunter Schumann; Barbara Franke; Paul M Thompson; Sarah E Medland
Journal:  Nature       Date:  2015-01-21       Impact factor: 49.962

10.  The FAIR Guiding Principles for scientific data management and stewardship.

Authors:  Mark D Wilkinson; Michel Dumontier; I Jsbrand Jan Aalbersberg; Gabrielle Appleton; Myles Axton; Arie Baak; Niklas Blomberg; Jan-Willem Boiten; Luiz Bonino da Silva Santos; Philip E Bourne; Jildau Bouwman; Anthony J Brookes; Tim Clark; Mercè Crosas; Ingrid Dillo; Olivier Dumon; Scott Edmunds; Chris T Evelo; Richard Finkers; Alejandra Gonzalez-Beltran; Alasdair J G Gray; Paul Groth; Carole Goble; Jeffrey S Grethe; Jaap Heringa; Peter A C 't Hoen; Rob Hooft; Tobias Kuhn; Ruben Kok; Joost Kok; Scott J Lusher; Maryann E Martone; Albert Mons; Abel L Packer; Bengt Persson; Philippe Rocca-Serra; Marco Roos; Rene van Schaik; Susanna-Assunta Sansone; Erik Schultes; Thierry Sengstag; Ted Slater; George Strawn; Morris A Swertz; Mark Thompson; Johan van der Lei; Erik van Mulligen; Jan Velterop; Andra Waagmeester; Peter Wittenburg; Katherine Wolstencroft; Jun Zhao; Barend Mons
Journal:  Sci Data       Date:  2016-03-15       Impact factor: 6.444

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  13 in total

Review 1.  Progress in data interoperability to support computational toxicology and chemical safety evaluation.

Authors:  Sean Watford; Stephen Edwards; Michelle Angrish; Richard S Judson; Katie Paul Friedman
Journal:  Toxicol Appl Pharmacol       Date:  2019-08-09       Impact factor: 4.219

2.  Platform for Automated Real-Time High Performance Analytics on Medical Image Data.

Authors:  William J Allen; Refaat E Gabr; Getaneh B Tefera; Amol S Pednekar; Matthew W Vaughn; Ponnada A Narayana
Journal:  IEEE J Biomed Health Inform       Date:  2018-03       Impact factor: 5.772

Review 3.  Assessing health risks from multiple environmental stressors: Moving from G×E to I×E.

Authors:  Cliona M McHale; Gwendolyn Osborne; Rachel Morello-Frosch; Andrew G Salmon; Martha S Sandy; Gina Solomon; Luoping Zhang; Martyn T Smith; Lauren Zeise
Journal:  Mutat Res Rev Mutat Res       Date:  2017-11-24       Impact factor: 5.657

4.  Exploring completeness in clinical data research networks with DQe-c.

Authors:  Hossein Estiri; Kari A Stephens; Jeffrey G Klann; Shawn N Murphy
Journal:  J Am Med Inform Assoc       Date:  2018-01-01       Impact factor: 4.497

Review 5.  Neurotrauma as a big-data problem.

Authors:  J Russell Huie; Carlos A Almeida; Adam R Ferguson
Journal:  Curr Opin Neurol       Date:  2018-12       Impact factor: 5.710

6.  Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls.

Authors:  Alexandra R Buckley; Kristopher A Standish; Kunal Bhutani; Trey Ideker; Roger S Lasken; Hannah Carter; Olivier Harismendy; Nicholas J Schork
Journal:  BMC Genomics       Date:  2017-06-12       Impact factor: 3.969

7.  The National Institutes of Health funding for clinical research applying machine learning techniques in 2017.

Authors:  Amarnath R Annapureddy; Suveen Angraal; Cesar Caraballo; Alyssa Grimshaw; Chenxi Huang; Bobak J Mortazavi; Harlan M Krumholz
Journal:  NPJ Digit Med       Date:  2020-01-31

8.  mHealth for the Detection and Intervention in Adolescent and Young Adult Substance Use Disorder.

Authors:  Stephanie Carreiro; Peter R Chai; Jennifer Carey; Jeffrey Lai; David Smelson; Edward W Boyer
Journal:  Curr Addict Rep       Date:  2018-02-15

9.  Recon3D enables a three-dimensional view of gene variation in human metabolism.

Authors:  Elizabeth Brunk; Swagatika Sahoo; Daniel C Zielinski; Ali Altunkaya; Andreas Dräger; Nathan Mih; Francesco Gatto; Avlant Nilsson; German Andres Preciat Gonzalez; Maike Kathrin Aurich; Andreas Prlić; Anand Sastry; Anna D Danielsdottir; Almut Heinken; Alberto Noronha; Peter W Rose; Stephen K Burley; Ronan M T Fleming; Jens Nielsen; Ines Thiele; Bernhard O Palsson
Journal:  Nat Biotechnol       Date:  2018-02-19       Impact factor: 54.908

10.  Knowledge-guided analysis of "omics" data using the KnowEnG cloud platform.

Authors:  Charles Blatti; Amin Emad; Matthew J Berry; Lisa Gatzke; Milt Epstein; Daniel Lanier; Pramod Rizal; Jing Ge; Xiaoxia Liao; Omar Sobh; Mike Lambert; Corey S Post; Jinfeng Xiao; Peter Groves; Aidan T Epstein; Xi Chen; Subhashini Srinivasan; Erik Lehnert; Krishna R Kalari; Liewei Wang; Richard M Weinshilboum; Jun S Song; C Victor Jongeneel; Jiawei Han; Umberto Ravaioli; Nahil Sobh; Colleen B Bushell; Saurabh Sinha
Journal:  PLoS Biol       Date:  2020-01-23       Impact factor: 8.029

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