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2020 – today
- 2023
[j26]Nazek Queder, Vivian B. Tien, Sanu Ann Abraham, Sebastian Georg Wenzel Urchs, Karl G. Helmer, Derek Chaplin, Theo G. M. van Erp, David N. Kennedy, Jean-Baptiste Poline, Jeffrey S. Grethe, Satrajit S. Ghosh, David B. Keator:
NIDM-Terms: community-based terminology management for improved neuroimaging dataset descriptions and query. Frontiers Neuroinformatics 17 (2023)- [j25]Anita E. Bandrowski
, Mason Pairish, Peter Eckmann, Jeffrey S. Grethe, Maryann E. Martone:
The Antibody Registry: ten years of registering antibodies. Nucleic Acids Res. 51(D1): 358-367 (2023) - 2022
- [j24]Monique Surles-Zeigler, Troy Sincomb, Thomas H. Gillespie, Bernard de Bono, Jacqueline Bresnahan, Gary M. Mawe, Jeffrey S. Grethe, Susan J. Tappan, Maci L. Heal, Maryann E. Martone:
Extending and using anatomical vocabularies in the stimulating peripheral activity to relieve conditions project. Frontiers Neuroinformatics 16 (2022) - [j23]Mathew Birdsall Abrams, Jan G. Bjaalie, Samir Das, Gary F. Egan, Satrajit S. Ghosh, Wojtek James Goscinski, Jeffrey S. Grethe, Jeanette Hellgren Kotaleski, Eric Tatt Wei Ho, David N. Kennedy, Linda J. Lanyon, Trygve B. Leergaard, Helen S. Mayberg, Luciano Milanesi, Roman Moucek, Jean-Baptiste Poline, Prasun Roy, Stephen C. Strother, Tong Boon Tang, Paul H. E. Tiesinga, Thomas Wachtler, Daniel K. Wójcik, Maryann E. Martone:
A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility. Neuroinformatics 20(1): 25-36 (2022) - [j22]Mathew Birdsall Abrams, Jan G. Bjaalie, Samir Das, Gary F. Egan, Satrajit S. Ghosh, Wojtek James Goscinski, Jeffrey S. Grethe, Jeanette Hellgren Kotaleski, Eric Tatt Wei Ho, David N. Kennedy, Linda J. Lanyon, Trygve B. Leergaard, Helen S. Mayberg, Luciano Milanesi, Roman Moucek, Jean-Baptiste Poline, Prasun Roy, Stephen C. Strother, Tong Boon Tang, Paul H. E. Tiesinga, Thomas Wachtler, Daniel K. Wójcik, Maryann E. Martone:
Correction to: A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility. Neuroinformatics 20(1): 37-38 (2022) - [j21]Abel Torres-Espin, Carlos A. Almeida, Austin Chou, J. Russell Huie, Michael Chiu, Romana Vavrek, Jeff Sacramento, Michael B. Orr, John C. Gensel, Jeffrey S. Grethe, Maryann E. Martone, Karim Fouad, Adam R. Ferguson, Warren Alilain, Mark Bacon, Nicholas Batty, Michael Beattie, Jacqueline Bresnahan, Emily Burnside, Sarah Busch, Randall Carpenter, Isaac Francos Quijorna, Xiaohui Guo, Agnes Haggerty, Sarah Haroon, Jack Harris, Lyn Jakeman, Linda Jones, Naomi Kleitman, Timothy Kopper, Michael Aron Lane, Francisco Magana, David Magnuson, Ines Maldonado, Verena May, Katelyn McFarlane, Kazuhito Morioka, Martin Oudega, Philip Leo Pascual, Jean-Baptiste Poline, Ephron S. Rosenzweig, Emma Schmidt, Wolfram Tetzlaff, Lana Zholudeva:
Promoting FAIR Data Through Community-driven Agile Design: the Open Data Commons for Spinal Cord Injury (odc-sci.org). Neuroinformatics 20(1): 203-219 (2022) - [j20]Jean-Baptiste Poline, David N. Kennedy, Friedrich T. Sommer, Giorgio A. Ascoli, David C. Van Essen, Adam R. Ferguson, Jeffrey S. Grethe, Michael Hawrylycz, Paul M. Thompson, Russell A. Poldrack, Satrajit S. Ghosh, David B. Keator, Thomas L. Athey, Joshua T. Vogelstein, Helen S. Mayberg, Maryann E. Martone:
Is Neuroscience FAIR? A Call for Collaborative Standardisation of Neuroscience Data. Neuroinformatics 20(2): 507-512 (2022) - [c17]Michelle G. Giglio, Suvarna Nadendla, Arthur Brady, Amanda Charbonneau, Karl Czajkowski, Jeremy Yang, Tom Gillespie, Philippe Rocca-Serra, Jeffrey S. Grethe, Raja Mazumder, Bernard de Bono, Jonathan C. Silverstein, Daniel Clark, Mark A. Musen, Owen White:
Data Harmonization through Use of Community Standards in the Common Fund Data Ecosystem. ICBO 2022: 1-7 - [i7]Ashmita Kumar, Albert Crowley, Nazek Queder, Jean-Baptiste Poline, Satrajit S. Ghosh, David N. Kennedy, Jeffrey S. Grethe, Karl G. Helmer, David B. Keator:
The Neuroimaging Data Model Linear Regression Tool (nidm_linreg): PyNIDM Project. F1000Research 11: 228 (2022) - 2021
- [j19]Chun-Nan Hsu, Chia-Hui Chang, Thamolwan Poopradubsil, Amanda Lo, Karen A. William, Ko-Wei Lin, Anita E. Bandrowski, Ibrahim Burak Özyurt, Jeffrey S. Grethe, Maryann E. Martone:
Antibody Watch: Text mining antibody specificity from the literature. PLoS Comput. Biol. 17(5) (2021) - 2020
- [j18]Ibrahim Burak Özyurt, Anita E. Bandrowski, Jeffrey S. Grethe:
Bio-AnswerFinder: a system to find answers to questions from biomedical texts. Database J. Biol. Databases Curation 2020: baz137 (2020) - [j17]Chun-Nan Hsu, Anita E. Bandrowski, Tom Gillespie, Jon Udell, Ko-Wei Lin, Ibrahim Burak Özyurt, Jeffrey S. Grethe, Maryann E. Martone:
Comparing the Use of Research Resource Identifiers and Natural Language Processing for Citation of Databases, Software, and Other Digital Artifacts. Comput. Sci. Eng. 22(2): 22-32 (2020) - [i6]Chun-Nan Hsu, Chia-Hui Chang, Thamolwan Poopradubsil, Amanda Lo, Karen A. William, Ko-Wei Lin, Anita E. Bandrowski, Ibrahim Burak Özyurt, Jeffrey S. Grethe, Maryann E. Martone:
Antibody Watch: Text Mining Antibody Specificity from the Literature. CoRR abs/2008.01937 (2020)
2010 – 2019
- 2019
- [j16]David N. Kennedy, Sanu Ann Abraham, Julianna F. Bates, Albert Crowley, Satrajit S. Ghosh, Tom Gillespie, Mathias Goncalves, Jeffrey S. Grethe, Yaroslav O. Halchenko, Michael Hanke, Christian Haselgrove, Steven M. Hodge, Dorota Jarecka, Jakub Kaczmarzyk, David B. Keator, Kyle Meyer, Maryann E. Martone, Smruti Padhy, Jean-Baptiste Poline, Nina Preuss, Troy Sincomb, Matt Travers:
Everything Matters: The ReproNim Perspective on Reproducible Neuroimaging. Frontiers Neuroinformatics 13: 1 (2019) - [c16]Ibrahim Burak Özyurt, Jeffrey S. Grethe:
Iterative Document Retrieval via Deep Learning Approaches for Biomedical Question Answering. eScience 2019: 533-538 - [i5]Anita E. Bandrowski, Tom Gillespie, Monique Surles-Zeigler, Gabrielle Pine, Jeffrey S. Grethe, Maryann E. Martone:
How BIDs and BIDs validator has informed the data aggregation needs of the Stimulating Peripheral Activity to Relieve Conditions, SPARC, consortium. RO 2019 - [i4]John D. Van Horn, Sumiko Abe, José Luis Ambite, Teresa K. Attwood, Niall Beard, Louisa Bellis, Avnish Bhattrai, Alex A. T. Bui, Gully Burns, Lily Fierro, Jonathan Gordon, Jeffrey S. Grethe, Jeana Kamdar, Xiaoyu Lei, Kristina Lerman, Annette McGrath, Nicola J. Mulder, Caroline O'Driscoll, Crystal Stewart, Sonika Tyagi:
Advancing the international data science workforce through shared training and education. F1000Research 8: 251 (2019) - 2018
- [j15]Ibrahim Burak Özyurt, Jeffrey S. Grethe:
Foundry: a message-oriented, horizontally scalable ETL system for scientific data integration and enhancement. Database J. Biol. Databases Curation 2018: bay130 (2018) - [j14]Xiaoling Chen, Anupama E. Gururaj, Ibrahim Burak Özyurt, Ruiling Liu, Ergin Soysal, Trevor Cohen, Firat Tiryaki, Yueling Li, Nansu Zong, Min Jiang, Deevakar Rogith, Mandana Salimi, Hyeon-Eui Kim, Philippe Rocca-Serra, Alejandra N. González-Beltrán, Claudiu Farcas, Todd Johnson, Ronald Margolis, George Alter, Susanna-Assunta Sansone, Ian Fore, Lucila Ohno-Machado, Jeffrey S. Grethe, Hua Xu:
DataMed - an open source discovery index for finding biomedical datasets. J. Am. Medical Informatics Assoc. 25(3): 300-308 (2018) - 2017
- [i3]Chun-Nan Hsu, Anita E. Bandrowski, Jeffrey S. Grethe, Maryann E. Martone:
Assessing value of biomedical digital repositories. PeerJ Prepr. 5: e2688 (2017) - 2016
- [j13]Anita E. Bandrowski, Matthew H. Brush, Jeffrey S. Grethe, Melissa A. Haendel, David N. Kennedy, Sean L. Hill, Patrick R. Hof, Maryann E. Martone, Maaike Pols, Serena S. Tan, Nicole L. Washington, Elena V. Zudilova-Seinstra, Nicole A. Vasilevsky:
The Resource Identification Initiative: A Cultural Shift in Publishing. Neuroinformatics 14(2): 169-182 (2016) - [c15]Jeffrey S. Grethe, Ibrahim Burak Özyurt, Hua Xu, Xiaoling Chen, Ruiling Liu, Ergin Soysal, Anupama E. Gururaj, Hyeon-Eui Kim, Trevor Cohen, Todd R. Johnson, Mandana Salimi, Saeid Pournejati, Min Jiang, Claudiu Farcas, Alejandra N. González-Beltrán, Philippe Rocca-Serra, Muhamamd F. Amith, Cui Tao, Ian Fore, Ronald Margolis, George Alter, Susanna-Assunta Sansone, Lucila Ohno-Machado:
A Scalable Dataset Indexing Infrastructure for the bioCADDIE Data Discovery System. AMIA 2016 - [c14]Hua Xu, Jeffrey S. Grethe, Xiaoling Chen, Ruiling Liu, Ergin Soysal, Anupama E. Gururaj, Yueling Li, Ibrahim Burak Özyurt, Hyeon-Eui Kim, Trevor Cohen, Todd R. Johnson, Mandana Salimi, Saeid Pournejati, Min Jiang, Claudiu Farcas, Alejandra N. González-Beltrán, Philippe Rocca-Serra, Muhamamd F. Amith, Cui Tao, Ian Fore, Ronald Margolis, George Alter, Susanna-Assunta Sansone, Lucila Ohno-Machado:
Development of DataMed, a Data Discovery Index Prototype by bioCADDIE: Laying the Groundwork for Biomedical Data Discovery. AMIA 2016 - [i2]Friedrich T. Sommer, Thomas Wachtler, Jeffrey L. Teeters, Jan Benda, Andrew P. Davison, Stephen J. Eglen, Richard C. Gerkin, Jeffrey S. Grethe, Jan Grewe, Kenneth D. Harris, Christian Johannes Kellner, Yann Le Franc, Roman Moucek, Dimiter Prodanov, Robert Pröpper, Hyrum L. Sessions, Leslie Smith, Andrey Sobolev, Adrian Stoewer, Barry Wark:
Requirements for storing electrophysiology data. CoRR abs/1605.07673 (2016) - 2015
- [i1]Anita E. Bandrowski, Matthew H. Brush, Jeffrey S. Grethe, Melissa A. Haendel, David N. Kennedy, Sean L. Hill, Patrick R. Hof, Maryann E. Martone, Maaike Pols, Serena S. Tan, Nicole L. Washington, Elena V. Zudilova-Seinstra, Nicole A. Vasilevsky:
The Resource Identification Initiative: A cultural shift in publishing. F1000Research 4: 134 (2015) - 2014
- [j12]Luis N. Marenco, Rixin Wang, Anita E. Bandrowski, Jeffrey S. Grethe, Gordon M. Shepherd, Perry L. Miller:
Extending the NIF DISCO framework to automate complex workflow: coordinating the harvest and integration of data from diverse neuroscience information resources. Frontiers Neuroinformatics 8: 58 (2014) - 2013
- [c13]Amarnath Gupta, Anita E. Bandrowski, Christopher Condit, Xufei Qian, Jeffrey S. Grethe, Maryann E. Martone:
Semantic query reformulation: the NIF experience. SSDBM 2013: 35:1-35:4 - 2012
- [j11]Anita E. Bandrowski, Jonathan Cachat, Yuling Li, Hans-Michael Müller, Paul W. Sternberg, Paolo Ciccarese, Tim Clark, Luis N. Marenco, Rixin Wang, Vadim Astakhov, Jeffrey S. Grethe, Maryann E. Martone:
A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework. Database J. Biol. Databases Curation 2012 (2012) - [j10]Syam Gadde, Nicole Aucoin, Jeffrey S. Grethe, David B. Keator, Daniel S. Marcus, Steve Pieper:
XCEDE: An Extensible Schema for Biomedical Data. Neuroinformatics 10(1): 19-32 (2012) - [c12]Fahim T. Imam, Stephen D. Larson, Anita E. Bandrowski, Jeffrey S. Grethe, Amarnath Gupta, Maryann E. Martone:
Maturation of Neuroscience Information Framework: An Ontology Driven Information System for Neuroscience. FOIS 2012: 15-28 - [c11]Vadim Astakhov, Anita E. Bandrowski, Amarnath Gupta, A. W. Kulungowski, Jeffrey S. Grethe, James Bouwer, T. Molin, V. Rowley, S. Penticoff, Masako Terada, W. Wong, Hiroyuki Hakozaki, O. Kwon, Maryann E. Martone, Mark H. Ellisman:
Prototype of Kepler Processing Workflows For Microscopy And Neuroinformatics. ICCS 2012: 1595-1603 - 2011
- [j9]Shulei Sun, Jing Chen, Weizhong Li, Ilkay Altintas, Abel W. Lin, Steven Peltier, Karen I. Stocks, Eric E. Allen, Mark H. Ellisman, Jeffrey S. Grethe, John C. Wooley:
Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Res. 39(Database-Issue): 546-551 (2011) - [c10]Fahim T. Imam, Stephen D. Larson, Jeffrey S. Grethe, Amarnath Gupta, Anita E. Bandrowski, Maryann E. Martone:
NIFSTD and NeuroLex: Comprehensive Neuroscience Ontology Development Based on Multiple Biomedical Ontologies and Community Involvement. ICBO 2011 - [c9]Chris Mungall, David Anderson, Anita E. Bandrowski, Brian A. Canada, Andrew Chatr-aryamontri, Keith C. Cheng, P. Michael Conn, Kara Dolinski, Mark H. Ellisman, Janan T. Eppig, Jeffrey S. Grethe, Joseph W. Kemnitz, Shawn Iadonato, Stephen D. Larson, Charles Magness, Maryann E. Martone, Mike Tyers, Carlo Torniai, Olga G. Troyanskaya, Judith Turner, Monte Westerfield, Melissa A. Haendel:
An Ontology-Based Approach to Linking Model Organisms and Resources to Human Diseases. ICBO 2011 - [p2]Abel W. Lin, Ilkay Altintas, Chris Churas, Madhusudan Gujral, Jeffrey S. Grethe, Mark H. Ellisman:
Case Study on the Use of REST Architectural Principles for Scientific Analysis: CAMERA - Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis. REST: From Research to Practice 2011: 319-338 - 2010
- [j8]I. Burak Özyurt, David B. Keator, Dingying Wei, Christine Fennema-Notestine, Karen R. Pease, Henry Jeremy Bockholt, Jeffrey S. Grethe:
Federated Web-accessible Clinical Data Management within an Extensible NeuroImaging Database. Neuroinformatics 8(4): 231-249 (2010) - [c8]Ilkay Altintas, Abel W. Lin, Jing Chen, Chris Churas, Madhusudan Gujral, Shulei Sun, Weizhong Li, Ramil Manansala, Mayya Sedova, Jeffrey S. Grethe, Mark H. Ellisman:
CAMERA 2.0: A Data-centric Metagenomics Community Infrastructure Driven by Scientific Workflows. SERVICES 2010: 352-359
2000 – 2009
- 2009
- [j7]David B. Keator, Dingying Wei, Syam Gadde, Henry Jeremy Bockholt, Jeffrey S. Grethe, Daniel S. Marcus, Nicole Aucoin, Ibrahim Burak Özyurt:
Derived data storage and exchange workflow for large-scale neuroimaging analyses on the BIRN grid. Frontiers Neuroinformatics 3: 30 (2009) - [c7]Lynn Young, Samson W. Tu, Lakshika Tennakoon, David Vismer, Vadim Astakhov, Amarnath Gupta, Jeffrey S. Grethe, Maryann E. Martone, Amar K. Das, Matthew J. McAuliffe:
Ontology driven data integration for autism research. CBMS 2009: 1-7 - [c6]David N. Kennedy, Christian Haselgrove, Robert Buccigrossi, Jeffrey S. Grethe:
Software Development for Neuroimaging: Promoting Community Access And Best Practices Through NITRC. ISBI 2009: 1146-1149 - 2008
- [j6]Daniel Gardner, Huda Akil, Giorgio A. Ascoli, Douglas M. Bowden, William J. Bug, Duncan E. Donohue, David H. Goldberg, Bernice Grafstein, Jeffrey S. Grethe, Amarnath Gupta, Maryam Halavi, David N. Kennedy, Luis N. Marenco, Maryann E. Martone, Perry L. Miller, Hans-Michael Müller, Adrian Robert, Gordon M. Shepherd, Paul W. Sternberg, David C. Van Essen, Robert W. Williams:
The Neuroscience Information Framework: A Data and Knowledge Environment for Neuroscience. Neuroinformatics 6(3): 149-160 (2008) - [j5]William J. Bug, Giorgio A. Ascoli, Jeffrey S. Grethe, Amarnath Gupta, Christine Fennema-Notestine, Angela R. Laird, Stephen D. Larson, Daniel L. Rubin, Gordon M. Shepherd, Jessica A. Turner, Maryann E. Martone:
The NIFSTD and BIRNLex Vocabularies: Building Comprehensive Ontologies for Neuroscience. Neuroinformatics 6(3): 175-194 (2008) - [j4]Amarnath Gupta, William J. Bug, Luis N. Marenco, Xufei Qian, Christopher Condit, Arun Rangarajan, Hans-Michael Müller, Perry L. Miller, Brian Sanders, Jeffrey S. Grethe, Vadim Astakhov, Gordon M. Shepherd, Paul W. Sternberg, Maryann E. Martone:
Federated Access to Heterogeneous Information Resources in the Neuroscience Information Framework (NIF). Neuroinformatics 6(3): 205-217 (2008) - [j3]David B. Keator, Jeffrey S. Grethe, Daniel S. Marcus, I. Burak Özyurt, Syam Gadde, Shawn N. Murphy, Steve Pieper, Douglas N. Greve, R. Notestine, Henry Jeremy Bockholt, Philip M. Papadopoulos:
A National Human Neuroimaging Collaboratory Enabled by the Biomedical Informatics Research Network (BIRN). IEEE Trans. Inf. Technol. Biomed. 12(2): 162-172 (2008) - 2007
- [p1]Abel W. Lin, Steven T. Peltier, Jeffrey S. Grethe, Mark H. Ellisman:
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 2007: 109-125 - 2006
- [j2]David B. Keator, Syam Gadde, Jeffrey S. Grethe, Derek V. Taylor, Steven G. Potkin, First Birn:
A general XML schema and SPM toolbox for storage of neuro-imaging results and anatomical labels. Neuroinformatics 4(2): 199-211 (2006) - [c5]Shawn N. Murphy, Michael Mendis, Jeffrey S. Grethe, Randy L. Gollub, David N. Kennedy, Bruce R. Rosen:
A Web Portal that Enables Collaborative Use of Advanced Medical Image Processing and Informatics Tools through the Biomedical Informatics Research Network (BIRN). AMIA 2006 - [c4]Vadim Astakhov, Amarnath Gupta, Jeffrey S. Grethe, Edward Ross, David Little, Aylin Yilmaz, Xufei Qian, Simone Santini, Maryann E. Martone, Mark H. Ellisman:
Semantically Based Data Integration Environment for Biomedical Research. CBMS 2006: 171-176 - [c3]Ron Kikinis, Tina Kapur, Martha Elizabeth Shenton, Jeffrey S. Grethe, Mark H. Ellisman:
"Big Science" and Schizophrenia. ISBI 2006: 804-805 - 2005
- [c2]Vadim Astakhov, Amarnath Gupta, Simone Santini, Jeffrey S. Grethe:
Data Integration in the Biomedical Informatics Research Network (BIRN). DILS 2005: 317-320 - [c1]Jeffrey S. Grethe, Chaitan Baru, Amarnath Gupta, Mark James, Bertram Ludäscher, Maryann E. Martone, Philip M. Papadopoulos, Steven Peltier, Arcot Rajasekar, Simone Santini, Ilya Zaslavsky, Mark H. Ellisman:
Biomedical Informatics Research Network: Building a National Collaboratory to Hasten the Derivation of New Understanding and Treatment of Disease. HealthGrid 2005: 100-109 - 2003
- [j1]Amarnath Gupta, Bertram Ludäscher, Jeffrey S. Grethe, Maryann E. Martone:
Towards a formalization of disease-specific ontologies for neuroinformatics. Neural Networks 16(9): 1277-1292 (2003)
Coauthor Index
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