Jeffrey Sean Grethe, Ph.D. - Publications

Affiliations: 
Center for Research in Biological Systems University of California, San Diego, La Jolla, CA 
Area:
neuroinformatics

57 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 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, ... ... Grethe JS, et al. Addendum: The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data. 6: 6. PMID 30890711 DOI: 10.1038/s41597-019-0009-6  1
2019 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, et al. Everything Matters: The ReproNim Perspective on Reproducible Neuroimaging. Frontiers in Neuroinformatics. 13: 1. PMID 30792636 DOI: 10.3389/fninf.2019.00001  1
2018 Ozyurt IB, Grethe JS. Foundry: a message-oriented, horizontally scalable ETL system for scientific data integration and enhancement. Database : the Journal of Biological Databases and Curation. 2018. PMID 30576493 DOI: 10.1093/database/bay130  1
2018 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. Scientific Data. 5: 180029. PMID 29737976 DOI: 10.1038/sdata.2018.29  1
2018 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, ... ... Grethe JS, et al. DataMed - an open source discovery index for finding biomedical datasets. Journal of the American Medical Informatics Association : Jamia. PMID 29346583 DOI: 10.1093/jamia/ocx121  1
2017 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, et al. DATS, the data tag suite to enable discoverability of datasets. Scientific Data. 4: 170059. PMID 28585923 DOI: 10.1038/sdata.2017.59  1
2016 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 and Behavior. 6: e00417. PMID 27110440 DOI: 10.1002/brb3.417  1
2016 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, ... ... Grethe JS, et al. The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data. 3: 160018. PMID 26978244 DOI: 10.1038/sdata.2016.18  1
2016 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. 11: e0146300. PMID 26730820 DOI: 10.1371/journal.pone.0146300  1
2016 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. The Journal of Comparative Neurology. 524: 8-22. PMID 26599696 DOI: 10.1002/cne.23913  1
2016 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 and Behavior. 6: 1-14. DOI: 10.1002/brb3.417  1
2015 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. F1000research. 4: 134. PMID 26594330 DOI: 10.12688/f1000research.6555.1  1
2015 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. PMID 26589523 DOI: 10.1007/s12021-015-9284-3  1
2015 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. 10: e0136206. PMID 26393351 DOI: 10.1371/journal.pone.0136206  1
2014 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. Frontiers in Neuroinformatics. 8: 58. PMID 25018728 DOI: 10.3389/fninf.2014.00058  1
2014 Whetzel PL, Grethe JS, Bandrowski A, Banks D, Condit C, Gupta A, Larson SD, Li Y, Ozyurt B, Stagg A, Martone ME, Marenco L, Miller PL, Wang R, Shepherd GM. SciCrunch: A cooperative and collaborative data and resource discovery platform for scientific communities Ceur Workshop Proceedings. 1327: 102-103.  1
2013 Gupta A, Condit C, Grethe JS, Bandrowski A, Qian X, Martone ME. Semantic query reformulation - The NIF experience Acm International Conference Proceeding Series. DOI: 10.1145/2484838.2484839  1
2012 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. International Review of Neurobiology. 103: 39-68. PMID 23195120 DOI: 10.1016/B978-0-12-388408-4.00003-4  1
2012 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. Frontiers in Genetics. 3: 111. PMID 22737162 DOI: 10.3389/fgene.2012.00111  1
2012 Bandrowski AE, Cachat J, Li Y, Müller HM, Sternberg PW, Ciccarese P, Clark T, Marenco L, Wang R, Astakhov V, Grethe JS, Martone ME. A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework. Database : the Journal of Biological Databases and Curation. 2012: bas005. PMID 22434839 DOI: 10.1093/database/bas005  1
2012 Gadde S, Aucoin N, Grethe JS, Keator DB, Marcus DS, Pieper S. XCEDE: an extensible schema for biomedical data. Neuroinformatics. 10: 19-32. PMID 21479735 DOI: 10.1007/s12021-011-9119-9  1
2012 Imam FT, Larson S, Bandrowski A, Grethe JS, Gupta A, Martone ME. Maturation of neuroscience information framework: An ontology driven information system for neuroscience Frontiers in Artificial Intelligence and Applications. 239: 15-28. DOI: 10.3233/978-1-61499-084-0-15  1
2012 Astakhov V, Bandrowski A, Gupta A, Kulungowski AW, Grethe JS, Bouwer J, Molina T, Rowley V, Penticoff S, Terada M, Wong W, Hakozaki H, Kwon O, Martone ME, Ellisman M. Prototype of Kepler processing workflows for microscopy and neuroinformatics Procedia Computer Science. 9: 1595-1603. DOI: 10.1016/j.procs.2012.04.175  1
2011 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. Standards in Genomic Sciences. 4: 286-92. PMID 21677865 DOI: 10.4056/sigs.1344279  1
2011 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 Research. 39: D546-51. PMID 21045053 DOI: 10.1093/nar/gkq1102  1
2011 Mungall CJ, Anderson D, Bandrowski A, Canada B, Chatyr-Aryamontri A, Cheng K, Conn PM, Dolinski K, Ellisman M, Eppig J, Grethe JS, Kemnitz J, Iadonato S, Larson SD, Magness C, et al. An ontology-based approach to linking model organisms and resources to human diseases Ceur Workshop Proceedings. 833: 263-265.  1
2011 Imam FT, Larson SD, Grethe JS, Gupta A, Bandrowski A, Martone ME. NIFSTD and neurolex: A comprehensive neuroscience ontology development based on multiple biomedical ontologies and community involvement Ceur Workshop Proceedings. 833: 349-356.  1
2010 Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Soldatova LN, Stoeckert CJ, Turner JA, et al. Modeling biomedical experimental processes with OBI. Journal of Biomedical Semantics. 1: S7. PMID 20626927 DOI: 10.1186/2041-1480-1-S1-S7  1
2010 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. 8: 231-49. PMID 20567938 DOI: 10.1007/s12021-010-9078-6  1
2010 Altintas I, Lin AW, Chen J, Churas C, Gujral M, Sun S, Li W, Manansala R, Sedova M, Grethe JS, Ellisman M. CAMERA 2.0: A data-centric metagenomics community infrastructure driven by scientific workflows Proceedings - 2010 6th World Congress On Services, Services-1 2010. 352-359. DOI: 10.1109/SERVICES.2010.89  1
2010 Altintas I, Chen J, Sedova M, Gupta A, Sun S, Lin AW, Gujral M, Anand MK, Li W, Grethe JS, Ellisman M. Extending the data model for data-centric metagenomics analysis using scientific workflows in CAMERA Proceedings - 6th Ieee International Conference On E-Science Workshops, E-Sciencew 2010. 49-56. DOI: 10.1109/eScienceW.2010.18  1
2009 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. Frontiers in Neuroinformatics. 3: 30. PMID 19826494 DOI: 10.3389/neuro.11.030.2009  1
2009 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 in Molecular Biology (Clifton, N.J.). 569: 33-53. PMID 19623485 DOI: 10.1007/978-1-59745-524-4_3  1
2009 Kennedy DN, Haselgrove C, Buccigrossi R, Grethe J. Software development for neuroimaging: Promoting community access and best practices through NITRC Proceedings - 2009 Ieee International Symposium On Biomedical Imaging: From Nano to Macro, Isbi 2009. 1146-1149. DOI: 10.1109/ISBI.2009.5193260  1
2009 Young L, Tu SW, Tennakoon L, Vismer D, Astakhov V, Gupta A, Grethe JS, Martone ME, Das AK, McAuliffe MJ. Ontology driven data integration for autism research Proceedings - Ieee Symposium On Computer-Based Medical Systems. DOI: 10.1109/CBMS.2009.5255362  1
2008 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 ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 1220. PMID 18999211  1
2008 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 ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 1000. PMID 18999128  1
2008 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. 6: 175-94. PMID 18975148 DOI: 10.1007/s12021-008-9032-z  1
2008 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. 6: 205-17. PMID 18958629 DOI: 10.1007/s12021-008-9033-y  1
2008 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, et al. The neuroscience information framework: a data and knowledge environment for neuroscience. Neuroinformatics. 6: 149-60. PMID 18946742 DOI: 10.1007/s12021-008-9024-z  1
2008 Keator DB, Grethe JS, Marcus D, Ozyurt B, Gadde S, Murphy S, Pieper S, Greve D, Notestine R, Bockholt HJ, Papadopoulos P. A national human neuroimaging collaboratory enabled by the Biomedical Informatics Research Network (BIRN). Ieee Transactions On Information Technology in Biomedicine : a Publication of the Ieee Engineering in Medicine and Biology Society. 12: 162-72. PMID 18348946 DOI: 10.1109/TITB.2008.917893  1
2007 Lin AW, Peltier ST, Grethe JS, Ellisman MH. Case studies on the use of workflow technologies for scientific analysis: The biomedical informatics research network and the telescience project Workflows For E-Science: Scientific Workflows For Grids. 109-125. DOI: 10.1007/978-1-84628-757-2_8  1
2007 Astakhov V, Sanders B, Grethe JS, Ross E, Little D, Gupta A, Astakhova T. Semantic data integration environment for biomedical research (Ontological Framework for e-science & imaginizer) Aaai Workshop - Technical Report. 1-8.  1
2007 Astakhov V, Grethe JS, Ross E, Little D, Sanders B, Gupta A. Semantic data integration environment for biomedical research (mediator infrastructure for information integration) Aaai Workshop - Technical Report. 1-9.  1
2006 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 ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 579-83. PMID 17238407  1
2006 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. 4: 199-212. PMID 16845169 DOI: 10.1385/NI:4:2:199  1
2006 Astakhov V, Gupta A, Grethe JS, Ross E, Little D, Yilmaz A, Qian X, Santini S, Martone M, Ellisman M. Semantically based data integration environment for biomedical research Proceedings - Ieee Symposium On Computer-Based Medical Systems. 2006: 171-176. DOI: 10.1109/CBMS.2006.143  1
2005 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. Studies in Health Technology and Informatics. 112: 100-9. PMID 15923720  1
2005 Astakhov V, Gupta A, Santini S, Grethe JS. Data integration in the Biomedical Informatics Research Network (BIRN) Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science). 3615: 317-320.  1
2003 Gupta A, Ludäscher B, Grethe JS, Martone ME. Towards a formalization of disease-specific ontologies for neuroinformatics. Neural Networks : the Official Journal of the International Neural Network Society. 16: 1277-92. PMID 14622884 DOI: 10.1016/j.neunet.2003.07.008  1
2003 Turner RS, Desmurget M, Grethe J, Crutcher MD, Grafton ST. Motor subcircuits mediating the control of movement extent and speed. Journal of Neurophysiology. 90: 3958-66. PMID 12954606 DOI: 10.1152/jn.00323.2003  1
2001 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. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 356: 1323-39. PMID 11545705 DOI: 10.1098/rstb.2001.0916  1
2001 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. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 21: 2919-28. PMID 11306644  1
2000 Desmurget M, Pélisson D, Grethe JS, Alexander GE, Urquizar C, Prablanc C, Grafton ST. Functional adaptation of reactive saccades in humans: a PET study. Experimental Brain Research. 132: 243-59. PMID 10853949 DOI: 10.1007/s002210000342  1
1999 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. Neurobiology of Learning and Memory. 71: 167-93. PMID 10082638 DOI: 10.1006/nlme.1998.3872  1
1997 Braitenberg V, Heck D, Sultan F. The detection and generation of sequences as a key to cerebellar function: experiments and theory. The Behavioral and Brain Sciences. 20: 229-45; discussion 2. PMID 10096998 DOI: 10.1017/S0140525X9700143X  1
1997 Thompson RF, Bao S, Chen L, Cipriano BD, Grethe JS, Kim JJ, Thompson JK, Tracy JA, Weninger MS, Krupa DJ. Associative learning. International Review of Neurobiology. 41: 151-89. PMID 9378587  1
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