Literature DB >> 26198305

Big biomedical data as the key resource for discovery science.

Arthur W Toga1, Ian Foster2, Carl Kesselman3, Ravi Madduri2, Kyle Chard2, Eric W Deutsch4, Nathan D Price4, Gustavo Glusman4, Benjamin D Heavner4, Ivo D Dinov5, Joseph Ames6, John Van Horn6, Roger Kramer4, Leroy Hood4.   

Abstract

Modern biomedical data collection is generating exponentially more data in a multitude of formats. This flood of complex data poses significant opportunities to discover and understand the critical interplay among such diverse domains as genomics, proteomics, metabolomics, and phenomics, including imaging, biometrics, and clinical data. The Big Data for Discovery Science Center is taking an "-ome to home" approach to discover linkages between these disparate data sources by mining existing databases of proteomic and genomic data, brain images, and clinical assessments. In support of this work, the authors developed new technological capabilities that make it easy for researchers to manage, aggregate, manipulate, integrate, and model large amounts of distributed data. Guided by biological domain expertise, the Center's computational resources and software will reveal relationships and patterns, aiding researchers in identifying biomarkers for the most confounding conditions and diseases, such as Parkinson's and Alzheimer's.
© 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.

Entities:  

Keywords:  Alzheimer's disease (ID); BD2K; Parkinson's disease; analytics; big; big data; biomedical; data; discovery; discovery science; resource; science, neuroscience (ja)

Mesh:

Year:  2015        PMID: 26198305      PMCID: PMC5009918          DOI: 10.1093/jamia/ocv077

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


  18 in total

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Authors:  G Glusman; D Lancet
Journal:  Bioinformatics       Date:  2000-05       Impact factor: 6.937

2.  Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.

Authors:  Andrew Keller; Alexey I Nesvizhskii; Eugene Kolker; Ruedi Aebersold
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3.  Science brick by brick.

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4.  Accelerating medical research using the swift workflow system.

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Journal:  Stud Health Technol Inform       Date:  2007

5.  Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline.

Authors:  Joseph Slagel; Luis Mendoza; David Shteynberg; Eric W Deutsch; Robert L Moritz
Journal:  Mol Cell Proteomics       Date:  2014-11-23       Impact factor: 5.911

6.  Analysis of genetic inheritance in a family quartet by whole-genome sequencing.

Authors:  Jared C Roach; Gustavo Glusman; Arian F A Smit; Chad D Huff; Robert Hubley; Paul T Shannon; Lee Rowen; Krishna P Pant; Nathan Goodman; Michael Bamshad; Jay Shendure; Radoje Drmanac; Lynn B Jorde; Leroy Hood; David J Galas
Journal:  Science       Date:  2010-03-10       Impact factor: 47.728

Review 7.  The Alzheimer's Disease Neuroimaging Initiative informatics core: A decade in review.

Authors:  Arthur W Toga; Karen L Crawford
Journal:  Alzheimers Dement       Date:  2015-07       Impact factor: 21.566

8.  Global Data Sharing in Alzheimer Disease Research.

Authors:  Naveen Ashish; Priya Bhatt; Arthur W Toga
Journal:  Alzheimer Dis Assoc Disord       Date:  2016 Apr-Jun       Impact factor: 2.703

9.  Neuroimaging study designs, computational analyses and data provenance using the LONI pipeline.

Authors:  Ivo Dinov; Kamen Lozev; Petros Petrosyan; Zhizhong Liu; Paul Eggert; Jonathan Pierce; Alen Zamanyan; Shruthi Chakrapani; John Van Horn; D Stott Parker; Rico Magsipoc; Kelvin Leung; Boris Gutman; Roger Woods; Arthur Toga
Journal:  PLoS One       Date:  2010-09-28       Impact factor: 3.240

10.  Identification of copy number variants in whole-genome data using Reference Coverage Profiles.

Authors:  Gustavo Glusman; Alissa Severson; Varsha Dhankani; Max Robinson; Terry Farrah; Denise E Mauldin; Anna B Stittrich; Seth A Ament; Jared C Roach; Mary E Brunkow; Dale L Bodian; Joseph G Vockley; Ilya Shmulevich; John E Niederhuber; Leroy Hood
Journal:  Front Genet       Date:  2015-02-17       Impact factor: 4.599

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  29 in total

1.  Highly Reproducible Automated Proteomics Sample Preparation Workflow for Quantitative Mass Spectrometry.

Authors:  Qin Fu; Michael P Kowalski; Mitra Mastali; Sarah J Parker; Kimia Sobhani; Irene van den Broek; Christie L Hunter; Jennifer E Van Eyk
Journal:  J Proteome Res       Date:  2017-11-10       Impact factor: 4.466

2.  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

Review 3.  Crowdsourcing biomedical research: leveraging communities as innovation engines.

Authors:  Julio Saez-Rodriguez; James C Costello; Stephen H Friend; Michael R Kellen; Lara Mangravite; Pablo Meyer; Thea Norman; Gustavo Stolovitzky
Journal:  Nat Rev Genet       Date:  2016-07-15       Impact factor: 53.242

4.  Big Data Science Training Program at a Minority Serving Institution: Processes and Initial Outcomes.

Authors:  Archana Jaiswal McEligot; Math P Cuajungco; Sam Behseta; Laura Chandler; Harmanpreet Chauhan; Sinjini Mitra; Pimbucha Rusmevichientong; Shana Charles
Journal:  Calif J Health Promot       Date:  2018

5.  Envisioning the future of 'big data' biomedicine.

Authors:  Alex A T Bui; John Darrell Van Horn
Journal:  J Biomed Inform       Date:  2017-03-30       Impact factor: 6.317

Review 6.  Using Administrative Data to Examine Health Disparities and Outcomes in Neurological Diseases of the Elderly.

Authors:  Allison W Willis
Journal:  Curr Neurol Neurosci Rep       Date:  2015-11       Impact factor: 5.081

7.  Imputation Strategy for Reliable Regional MRI Morphological Measurements.

Authors:  Shaina Sta Cruz; Ivo D Dinov; Megan M Herting; Clio González-Zacarías; Hosung Kim; Arthur W Toga; Farshid Sepehrband
Journal:  Neuroinformatics       Date:  2020-01

8.  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

9.  How Will Big Data Improve Clinical and Basic Research in Radiation Therapy?

Authors:  Barry S Rosenstein; Jacek Capala; Jason A Efstathiou; Jeff Hammerbacher; Sarah L Kerns; Feng-Ming Spring Kong; Harry Ostrer; Fred W Prior; Bhadrasain Vikram; John Wong; Ying Xiao
Journal:  Int J Radiat Oncol Biol Phys       Date:  2015-11-11       Impact factor: 7.038

10.  A generic method for improving the spatial interoperability of medical and ecological databases.

Authors:  A Ghenassia; J B Beuscart; G Ficheur; F Occelli; E Babykina; E Chazard; M Genin
Journal:  Int J Health Geogr       Date:  2017-10-03       Impact factor: 3.918

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