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Jeffrey Grethe

Title(s)Associate Director, Neurosciences
SchoolHealth Sciences
Address9500 Gilman Drive #0608
La Jolla CA 92093
Phone858-822-0703
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    Emory UniversityPostdoctoralSchool of Medicine
    University of Southern CaliforniaPh.D.Biological Sciences / Neuroscience
    University of California, IrvineB.S.Applied Mathematics

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    Dr. Jeffrey Grethe has more than 2 decades of experience in providing collaborative data environments to biomedical researchers in order to advance scientific inquiry leading to new discoveries and treatments of human disorders. Within the Center for Research in Biological Systems (CRBS; http://crbs.ucsd.edu) at the University of California, San Diego he is the Principal Investigator for the NIDDK Information Network (dkNET; http://dknet.org), which serves the needs of basic and clinical investigators by providing seamless access to large pools of data, information, and resources relevant to the mission of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK). dkNET builds on an infrastructure foundation provided by the Neuroscience Information Framework (NIF; http://neuinfo.org), where Dr. Grethe, as Principal Invesitgator, led the development of the technical infrastructure. NIF, which provides the largest searchable collection of biomedical resources on the web, is an open source information framework enabling neuroscientists around the world to access a rich virtual environment identifying and providing access to neuroscience-relevant data and resources. Unlike more general search engines, NIF provides deeper access to a more focused set of resources that are relevant to neuroscience, provides search strategies tailored to neuroscience, and also provides access to content that is traditionally “hidden” from web search engines. The infrastructure underlying NIF and dkNET, SciCrunch (http://scicrunch.org), now supports a number of research communities. SciCrunch was designed to allow communities of researchers to create focused portals that provide access to resources, databases, information and tools of relevance to their research areas.

    Following a B.S. in Applied Mathematics from the University of California, Irvine, he received a doctorate in neurosciences with a focus on neuroinformatics and computational modeling from the University of Southern California. After a post-doc in non-invasive human imaging (PET, MRI, fMRI) at Emory University, Dr. Grethe joined the fMRI Data Center (fMRIDC) at Dartmouth College. At the fMRIDC (http://www.fmridc.org), he was one of the principal members responsible for bringing the Data Center online, the first publicly accessible repository of peer-reviewed fMRI studies. Throughout his career, he has been involved in enabling collaborative research, data sharing and discovery through the application of advanced informatics approaches. This started at USC with his involvement in the Human Brain Project and continues today with his work on NIF, dkNET, SciCrunch, and with standards bodies such as the International Neuroinformatics Coordinating Facility (where he is on the Oversight Committee for their Standards and Data Sharing Program). When he transitioned to the University of California, San Diego, he was the Executive Director of BIRN Coordinating Center. As part of the BIRN project he oversaw the deployment of an international collaborative network that supported hundreds of researchers and Terabytes of data spread across more than 30 institutions. Infrastructure from this work in BIRN has been applied to other projects such as the Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA) project, where he led the transition of the infrastructure to a workflow based analysis platform for metagenomic data. Most recently, he is the UCSD Principal Investigator for a newly funded NIH P41 Biomedical Technology Research Center – the Center for Reproducible Neuroimaging Computation (CRNC) – dedicated to establishing and promoting reproducible neuroimaging research.

    Collapse Research 
    Collapse Research Activities and Funding
    OPERATION, SUPPORT AND STRATEGIC ENHANCEMENT OF THE NEUROSCIENCE INFORMATION FRAMEWORK
    NIH/NIDA U24DA039832Apr 1, 2015 - Mar 31, 2017
    Role: Principal Investigator
    dkNET Coordinating Unit: An information network for FAIR resources and data
    NIH/NIDDK U24DK097771Dec 1, 2012 - Nov 30, 2017
    Role: Principal Investigator
    A Human Electrophysiology, Associated Anatomic Data and Integrated Tool Resource
    NIH/NIMH R01MH084819Apr 17, 2009 - Feb 28, 2013
    Role: Principal Investigator

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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Bio-AnswerFinder: a system to find answers to questions from biomedical texts. Database (Oxford). 2020 01 01; 2020. Ozyurt IB, Bandrowski A, Grethe JS. PMID: 31925435.
      View in: PubMed   Mentions:    Fields:    
    2. FAIR SCI Ahead: The Evolution of the Open Data Commons for Pre-Clinical Spinal Cord Injury Research. J Neurotrauma. 2020 Mar 15; 37(6):831-838. Fouad K, Bixby JL, Callahan A, Grethe JS, Jakeman LB, Lemmon VP, Magnuson DSK, Martone ME, Nielson JL, Schwab JM, Taylor-Burds C, Tetzlaff W, Torres-Espin A, Ferguson AR. PMID: 31608767.
      View in: PubMed   Mentions:    Fields:    
    3. A data citation roadmap for scholarly data repositories. Sci Data. 2019 04 10; 6(1):28. Fenner M, Crosas M, Grethe JS, Kennedy D, Hermjakob H, Rocca-Serra P, Durand G, Berjon R, Karcher S, Martone M, Clark T. PMID: 30971690.
      View in: PubMed   Mentions: 1     Fields:    
    4. Addendum: The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. 2019 03 19; 6(1):6. Wilkinson MD, Dumontier M, Jan Aalbersberg I, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJG, Groth P, Goble C, Grethe JS, Heringa J, Hoen PAC', Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone SA, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B. PMID: 30890711.
      View in: PubMed   Mentions: 3     Fields:    
    5. Everything Matters: The ReproNim Perspective on Reproducible Neuroimaging. Front Neuroinform. 2019; 13:1. Kennedy DN, Abraham SA, Bates JF, Crowley A, Ghosh S, Gillespie T, Goncalves M, Grethe JS, Halchenko YO, Hanke M, Haselgrove C, Hodge SM, Jarecka D, Kaczmarzyk J, Keator DB, Meyer K, Martone ME, Padhy S, Poline JB, Preuss N, Sincomb T, Travers M. PMID: 30792636.
      View in: PubMed   Mentions:
    6. Uniform resolution of compact identifiers for biomedical data. Sci Data. 2018 05 08; 5:180029. Wimalaratne SM, Juty N, Kunze J, Janée G, McMurry JA, Beard N, Jimenez R, Grethe JS, Hermjakob H, Martone ME, Clark T. PMID: 29737976.
      View in: PubMed   Mentions: 3     Fields:    
    7. DataMed - an open source discovery index for finding biomedical datasets. J Am Med Inform Assoc. 2018 Mar 01; 25(3):300-308. Chen X, Gururaj AE, Ozyurt B, Liu R, Soysal E, Cohen T, Tiryaki F, Li Y, Zong N, Jiang M, Rogith D, Salimi M, Kim HE, Rocca-Serra P, Gonzalez-Beltran A, Farcas C, Johnson T, Margolis R, Alter G, Sansone SA, Fore IM, Ohno-Machado L, Grethe JS, Xu H. PMID: 29346583.
      View in: PubMed   Mentions:    Fields:    
    8. Foundry: a message-oriented, horizontally scalable ETL system for scientific data integration and enhancement. Database (Oxford). 2018 01 01; 2018. Ozyurt IB, Grethe JS. PMID: 30576493.
      View in: PubMed   Mentions: 1     Fields:    
    9. Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLoS Biol. 2017 Jun; 15(6):e2001414. McMurry JA, Juty N, Blomberg N, Burdett T, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Grethe J, Hastings J, Hériché JK, Hermjakob H, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Rocca-Serra P, Sansone SA, Sariyar M, Snoep JL, Soiland-Reyes S, Stanford NJ, Swainston N, Washington N, Williams AR, Wimalaratne SM, Winfree LM, Wolstencroft K, Goble C, Mungall CJ, Haendel MA, Parkinson H. PMID: 28662064.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    10. DATS, the data tag suite to enable discoverability of datasets. Sci Data. 2017 06 06; 4:170059. Sansone SA, Gonzalez-Beltran A, Rocca-Serra P, Alter G, Grethe JS, Xu H, Fore IM, Lyle J, Gururaj AE, Chen X, Kim HE, Zong N, Li Y, Liu R, Ozyurt IB, Ohno-Machado L. PMID: 28585923.
      View in: PubMed   Mentions: 6     Fields:    
    11. Finding useful data across multiple biomedical data repositories using DataMed. Nat Genet. 2017 05 26; 49(6):816-819. Ohno-Machado L, Sansone SA, Alter G, Fore I, Grethe J, Xu H, Gonzalez-Beltran A, Rocca-Serra P, Gururaj AE, Bell E, Soysal E, Zong N, Kim HE. PMID: 28546571.
      View in: PubMed   Mentions: 14     Fields:    Translation:Humans
    12. The Resource Identification Initiative: A Cultural Shift in Publishing. Neuroinformatics. 2016 Apr; 14(2):169-82. Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan SS, Washington N, Zudilova-Seinstra E, Vasilevsky N. PMID: 26589523.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    13. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. 2016 Mar 15; 3:160018. Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJ, Groth P, Goble C, Grethe JS, Heringa J, 't Hoen PA, Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone SA, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Velterop J, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B. PMID: 26978244.
      View in: PubMed   Mentions: 324     Fields:    
    14. Resource Disambiguator for the Web: Extracting Biomedical Resources and Their Citations from the Scientific Literature. PLoS One. 2016; 11(1):e0146300. Ozyurt IB, Grethe JS, Martone ME, Bandrowski AE. PMID: 26730820.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    15. The Resource Identification Initiative: A Cultural Shift in Publishing. J Comp Neurol. 2016 Jan 01; 524(1):8-22. Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan SC, Washington N, Zudilova-Seinstra E, Vasilevsky N. PMID: 26599696.
      View in: PubMed   Mentions: 6     Fields:    Translation:Animals
    16. The Resource Identification Initiative: a cultural shift in publishing. Brain Behav. 2016 01; 6(1):e00417. Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan SC, Washington N, Zudilova-Seinstra E, Vasilevsky N. PMID: 27110440.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    17. The NIDDK Information Network: A Community Portal for Finding Data, Materials, and Tools for Researchers Studying Diabetes, Digestive, and Kidney Diseases. PLoS One. 2015; 10(9):e0136206. Whetzel PL, Grethe JS, Banks DE, Martone ME. PMID: 26393351.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    18. The Resource Identification Initiative: A cultural shift in publishing. F1000Res. 2015; 4:134. Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan S, Washington N, Zudilova-Seinstra E, Vasilevsky N. PMID: 26594330.
      View in: PubMed   Mentions:    Fields:    
    19. Extending the NIF DISCO framework to automate complex workflow: coordinating the harvest and integration of data from diverse neuroscience information resources. Front Neuroinform. 2014; 8:58. Marenco LN, Wang R, Bandrowski AE, Grethe JS, Shepherd GM, Miller PL. PMID: 25018728.
      View in: PubMed   Mentions:
    20. Development and use of Ontologies Inside the Neuroscience Information Framework: A Practical Approach. Front Genet. 2012; 3:111. Imam FT, Larson SD, Bandrowski A, Grethe JS, Gupta A, Martone ME. PMID: 22737162.
      View in: PubMed   Mentions:
    21. XCEDE: an extensible schema for biomedical data. Neuroinformatics. 2012 Jan; 10(1):19-32. Gadde S, Aucoin N, Grethe JS, Keator DB, Marcus DS, Pieper S. PMID: 21479735.
      View in: PubMed   Mentions: 22     Fields:    Translation:Humans
    22. A survey of the neuroscience resource landscape: perspectives from the neuroscience information framework. Int Rev Neurobiol. 2012; 103:39-68. Cachat J, Bandrowski A, Grethe JS, Gupta A, Astakhov V, Imam F, Larson SD, Martone ME. PMID: 23195120.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimals
    23. Data shopping in an open marketplace: Introducing the Ontogrator web application for marking up data using ontologies and browsing using facets. Stand Genomic Sci. 2011 Apr 29; 4(2):286-92. Morrison N, Hancock D, Hirschman L, Dawyndt P, Verslyppe B, Kyrpides N, Kottmann R, Yilmaz P, Glöckner FO, Grethe J, Booth T, Sterk P, Nenadic G, Field D. PMID: 21677865.
      View in: PubMed   Mentions:
    24. Federated web-accessible clinical data management within an extensible neuroimaging database. Neuroinformatics. 2010 Dec; 8(4):231-49. Ozyurt IB, Keator DB, Wei D, Fennema-Notestine C, Pease KR, Bockholt J, Grethe JS. PMID: 20567938.
      View in: PubMed   Mentions: 24     Fields:    Translation:Humans
    25. Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Res. 2011 Jan; 39(Database issue):D546-51. Sun S, Chen J, Li W, Altintas I, Lin A, Peltier S, Stocks K, Allen EE, Ellisman M, Grethe J, Wooley J. PMID: 21045053.
      View in: PubMed   Mentions: 133     Fields:    
    26. Derived Data Storage and Exchange Workflow for Large-Scale Neuroimaging Analyses on the BIRN Grid. Front Neuroinform. 2009; 3:30. Keator DB, Wei D, Gadde S, Bockholt J, Grethe JS, Marcus D, Aucoin N, Ozyurt IB. PMID: 19826494.
      View in: PubMed   Mentions:
    27. Mediator infrastructure for information integration and semantic data integration environment for biomedical research. Methods Mol Biol. 2009; 569:33-53. Grethe JS, Ross E, Little D, Sanders B, Gupta A, Astakhov V. PMID: 19623485.
      View in: PubMed   Mentions: 1     Fields:    
    28. Data federation in the Biomedical Informatics Research Network: tools for semantic annotation and query of distributed multiscale brain data. AMIA Annu Symp Proc. 2008 Nov 06; 1220. Bug W, Astahkov V, Boline J, Fennema-Notestine C, Grethe JS, Gupta A, Kennedy DN, Rubin DL, Sanders B, Turner JA, Martone ME. PMID: 18999211.
      View in: PubMed   Mentions: 7     Fields:    
    29. The Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC). AMIA Annu Symp Proc. 2008 Nov 06; 1000. Buccigrossi R, Ellisman M, Grethe J, Haselgrove C, Kennedy DN, Martone M, Preuss N, Reynolds K, Sullivan M, Turner J, Wagner K. PMID: 18999128.
      View in: PubMed   Mentions: 6     Fields:    
    30. The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience. Neuroinformatics. 2008 Sep; 6(3):175-94. Bug WJ, Ascoli GA, Grethe JS, Gupta A, Fennema-Notestine C, Laird AR, Larson SD, Rubin D, Shepherd GM, Turner JA, Martone ME. PMID: 18975148.
      View in: PubMed   Mentions: 75     Fields:    Translation:HumansAnimals
    31. Federated access to heterogeneous information resources in the Neuroscience Information Framework (NIF). Neuroinformatics. 2008 Sep; 6(3):205-17. Gupta A, Bug W, Marenco L, Qian X, Condit C, Rangarajan A, Müller HM, Miller PL, Sanders B, Grethe JS, Astakhov V, Shepherd G, Sternberg PW, Martone ME. PMID: 18958629.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansAnimals
    32. The neuroscience information framework: a data and knowledge environment for neuroscience. Neuroinformatics. 2008 Sep; 6(3):149-60. Gardner D, Akil H, Ascoli GA, Bowden DM, Bug W, Donohue DE, Goldberg DH, Grafstein B, Grethe JS, Gupta A, Halavi M, Kennedy DN, Marenco L, Martone ME, Miller PL, Müller HM, Robert A, Shepherd GM, Sternberg PW, Van Essen DC, Williams RW. PMID: 18946742.
      View in: PubMed   Mentions: 88     Fields:    Translation:HumansAnimals
    33. A general XML schema and SPM toolbox for storage of neuro-imaging results and anatomical labels. Neuroinformatics. 2006; 4(2):199-212. Keator DB, Gadde S, Grethe JS, Taylor DV, Potkin SG. PMID: 16845169.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansAnimals
    34. A web portal that enables collaborative use of advanced medical image processing and informatics tools through the Biomedical Informatics Research Network (BIRN). AMIA Annu Symp Proc. 2006; 579-83. Murphy SN, Mendis ME, Grethe JS, Gollub RL, Kennedy D, Rosen BR. PMID: 17238407.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    35. Biomedical informatics research network: building a national collaboratory to hasten the derivation of new understanding and treatment of disease. Stud Health Technol Inform. 2005; 112:100-9. Grethe JS, Baru C, Gupta A, James M, Ludaescher B, Martone ME, Papadopoulos PM, Peltier ST, Rajasekar A, Santini S, Zaslavsky IN, Ellisman MH. PMID: 15923720.
      View in: PubMed   Mentions: 24     Fields:    Translation:Humans
    36. Towards a formalization of disease-specific ontologies for neuroinformatics. Neural Netw. 2003 Nov; 16(9):1277-92. Gupta A, Ludäscher B, Grethe JS, Martone ME. PMID: 14622884.
      View in: PubMed   Mentions: 6     Fields:    
    37. Motor subcircuits mediating the control of movement extent and speed. J Neurophysiol. 2003 Dec; 90(6):3958-66. Turner RS, Desmurget M, Grethe J, Crutcher MD, Grafton ST. PMID: 12954606.
      View in: PubMed   Mentions: 42     Fields:    Translation:HumansCTClinical Trials
    38. The Functional Magnetic Resonance Imaging Data Center (fMRIDC): the challenges and rewards of large-scale databasing of neuroimaging studies. Philos Trans R Soc Lond B Biol Sci. 2001 Aug 29; 356(1412):1323-39. Van Horn JD, Grethe JS, Kostelec P, Woodward JB, Aslam JA, Rus D, Rockmore D, Gazzaniga MS. PMID: 11545705.
      View in: PubMed   Mentions: 40     Fields:    Translation:Humans
    39. Functional anatomy of nonvisual feedback loops during reaching: a positron emission tomography study. J Neurosci. 2001 Apr 15; 21(8):2919-28. Desmurget M, Gréa H, Grethe JS, Prablanc C, Alexander GE, Grafton ST. PMID: 11306644.
      View in: PubMed   Mentions: 41     Fields:    Translation:HumansCTClinical Trials
    40. Functional adaptation of reactive saccades in humans: a PET study. Exp Brain Res. 2000 May; 132(2):243-59. Desmurget M, Pélisson D, Grethe JS, Alexander GE, Urquizar C, Prablanc C, Grafton ST. PMID: 10853949.
      View in: PubMed   Mentions: 21     Fields:    Translation:Humans
    41. Essential neuronal pathways for reflex and conditioned response initiation in an intracerebellar stimulation paradigm and the impact of unconditioned stimulus preexposure on learning rate. Neurobiol Learn Mem. 1999 Mar; 71(2):167-93. Swain RA, Shinkman PG, Thompson JK, Grethe JS, Thompson RF. PMID: 10082638.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    42. Associative learning. Int Rev Neurobiol. 1997; 41:151-89. Thompson RF, Bao S, Chen L, Cipriano BD, Grethe JS, Kim JJ, Thompson JK, Tracy JA, Weninger MS, Krupa DJ. PMID: 9378587.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansAnimalsCells
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