Jeffrey Grethe

TitleAssociate Director
InstitutionUniversity of California San Diego
DepartmentCenter for Research in Biological Systems
Address9500 Gilman Drive #0608
La Jolla CA 92093
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    Collapse Biography 
    Collapse Education and Training
    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
    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 - Jun 30, 2023
    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.
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    1. Wimalaratne SM, Juty N, Kunze J, Janée G, McMurry JA, Beard N, Jimenez R, Grethe JS, Hermjakob H, Martone ME, Clark T. Uniform resolution of compact identifiers for biomedical data. Sci Data. 2018 May 08; 5:180029. PMID: 29737976.
      View in: PubMed
    2. 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. DataMed - an open source discovery index for finding biomedical datasets. J Am Med Inform Assoc. 2018 Jan 13. PMID: 29346583.
      View in: PubMed
    3. 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. 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. PMID: 28662064.
      View in: PubMed
    4. 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. DATS, the data tag suite to enable discoverability of datasets. Sci Data. 2017 06 06; 4:170059. PMID: 28585923.
      View in: PubMed
    5. 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. Finding useful data across multiple biomedical data repositories using DataMed. Nat Genet. 2017 May 26; 49(6):816-819. PMID: 28546571.
      View in: PubMed
    6. 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. The Resource Identification Initiative: A Cultural Shift in Publishing. Neuroinformatics. 2016 Apr; 14(2):169-82. PMID: 26589523.
      View in: PubMed
    7. 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. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. 2016 Mar 15; 3:160018. PMID: 26978244; PMCID: PMC4792175.
    8. Ozyurt IB, Grethe JS, Martone ME, Bandrowski AE. Resource Disambiguator for the Web: Extracting Biomedical Resources and Their Citations from the Scientific Literature. PLoS One. 2016; 11(1):e0146300. PMID: 26730820.
      View in: PubMed
    9. 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. The Resource Identification Initiative: A Cultural Shift in Publishing. J Comp Neurol. 2016 Jan 01; 524(1):8-22. PMID: 26599696; PMCID: PMC4684178.
    10. 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. The Resource Identification Initiative: a cultural shift in publishing. Brain Behav. 2016 Jan; 6(1):e00417. PMID: 27110440.
      View in: PubMed
    11. Whetzel PL, Grethe JS, Banks DE, Martone ME. 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. PMID: 26393351; PMCID: PMC4578941.
    12. 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. The Resource Identification Initiative: A cultural shift in publishing. F1000Res. 2015; 4:134. PMID: 26594330.
      View in: PubMed
    13. Marenco LN, Wang R, Bandrowski AE, Grethe JS, Shepherd GM, Miller PL. 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. PMID: 25018728; PMCID: PMC4071641.
    14. Imam FT, Larson SD, Bandrowski A, Grethe JS, Gupta A, Martone ME. Development and use of Ontologies Inside the Neuroscience Information Framework: A Practical Approach. Front Genet. 2012; 3:111. PMID: 22737162; PMCID: PMC3381282.
    15. Gadde S, Aucoin N, Grethe JS, Keator DB, Marcus DS, Pieper S. XCEDE: an extensible schema for biomedical data. Neuroinformatics. 2012 Jan; 10(1):19-32. PMID: 21479735; PMCID: PMC3836560.
    16. Cachat J, Bandrowski A, Grethe JS, Gupta A, Astakhov V, Imam F, Larson SD, Martone ME. A survey of the neuroscience resource landscape: perspectives from the neuroscience information framework. Int Rev Neurobiol. 2012; 103:39-68. PMID: 23195120.
      View in: PubMed
    17. 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. 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. PMID: 21677865; PMCID: PMC3111990.
    18. Ozyurt IB, Keator DB, Wei D, Fennema-Notestine C, Pease KR, Bockholt J, Grethe JS. Federated web-accessible clinical data management within an extensible neuroimaging database. Neuroinformatics. 2010 Dec; 8(4):231-49. PMID: 20567938; PMCID: PMC2974931.
    19. Sun S, Chen J, Li W, Altintas I, Lin A, Peltier S, Stocks K, Allen EE, Ellisman M, Grethe J, Wooley J. Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Res. 2011 Jan; 39(Database issue):D546-51. PMID: 21045053; PMCID: PMC3013694.
    20. Keator DB, Wei D, Gadde S, Bockholt J, Grethe JS, Marcus D, Aucoin N, Ozyurt IB. Derived Data Storage and Exchange Workflow for Large-Scale Neuroimaging Analyses on the BIRN Grid. Front Neuroinform. 2009; 3:30. PMID: 19826494; PMCID: PMC2759340.
    21. Grethe JS, Ross E, Little D, Sanders B, Gupta A, Astakhov V. Mediator infrastructure for information integration and semantic data integration environment for biomedical research. Methods Mol Biol. 2009; 569:33-53. PMID: 19623485.
      View in: PubMed
    22. Bug W, Astahkov V, Boline J, Fennema-Notestine C, Grethe JS, Gupta A, Kennedy DN, Rubin DL, Sanders B, Turner JA, Martone ME. 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. PMID: 18999211.
      View in: PubMed
    23. Buccigrossi R, Ellisman M, Grethe J, Haselgrove C, Kennedy DN, Martone M, Preuss N, Reynolds K, Sullivan M, Turner J, Wagner K. The Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC). AMIA Annu Symp Proc. 2008 Nov 06; 1000. PMID: 18999128.
      View in: PubMed
    24. Bug WJ, Ascoli GA, Grethe JS, Gupta A, Fennema-Notestine C, Laird AR, Larson SD, Rubin D, Shepherd GM, Turner JA, Martone ME. The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience. Neuroinformatics. 2008 Sep; 6(3):175-94. PMID: 18975148; PMCID: PMC2743139.
    25. 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. Federated access to heterogeneous information resources in the Neuroscience Information Framework (NIF). Neuroinformatics. 2008 Sep; 6(3):205-17. PMID: 18958629; PMCID: PMC2689790.
    26. 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. The neuroscience information framework: a data and knowledge environment for neuroscience. Neuroinformatics. 2008 Sep; 6(3):149-60. PMID: 18946742; PMCID: PMC2661130.
    27. Keator DB, Gadde S, Grethe JS, Taylor DV, Potkin SG. A general XML schema and SPM toolbox for storage of neuro-imaging results and anatomical labels. Neuroinformatics. 2006; 4(2):199-212. PMID: 16845169.
      View in: PubMed
    28. Murphy SN, Mendis ME, Grethe JS, Gollub RL, Kennedy D, Rosen BR. 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. PMID: 17238407; PMCID: PMC1839506.
    29. Grethe JS, Baru C, Gupta A, James M, Ludaescher B, Martone ME, Papadopoulos PM, Peltier ST, Rajasekar A, Santini S, Zaslavsky IN, Ellisman MH. 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. PMID: 15923720.
      View in: PubMed
    30. Gupta A, Ludäscher B, Grethe JS, Martone ME. Towards a formalization of disease-specific ontologies for neuroinformatics. Neural Netw. 2003 Nov; 16(9):1277-92. PMID: 14622884.
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    31. Turner RS, Desmurget M, Grethe J, Crutcher MD, Grafton ST. Motor subcircuits mediating the control of movement extent and speed. J Neurophysiol. 2003 Dec; 90(6):3958-66. PMID: 12954606.
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    32. Van Horn JD, Grethe JS, Kostelec P, Woodward JB, Aslam JA, Rus D, Rockmore D, Gazzaniga MS. 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. PMID: 11545705; PMCID: PMC1088517.
    33. Desmurget M, Gréa H, Grethe JS, Prablanc C, Alexander GE, Grafton ST. Functional anatomy of nonvisual feedback loops during reaching: a positron emission tomography study. J Neurosci. 2001 Apr 15; 21(8):2919-28. PMID: 11306644.
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    34. Desmurget M, Pélisson D, Grethe JS, Alexander GE, Urquizar C, Prablanc C, Grafton ST. Functional adaptation of reactive saccades in humans: a PET study. Exp Brain Res. 2000 May; 132(2):243-59. PMID: 10853949.
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    35. Swain RA, Shinkman PG, Thompson JK, Grethe JS, Thompson RF. 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. PMID: 10082638.
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    36. Thompson RF, Bao S, Chen L, Cipriano BD, Grethe JS, Kim JJ, Thompson JK, Tracy JA, Weninger MS, Krupa DJ. Associative learning. Int Rev Neurobiol. 1997; 41:151-89. PMID: 9378587.
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