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Matthew H. Brush
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Journal Articles
- 2022
- [j11]Nicolas Matentzoglu
, James P. Balhoff
, Susan M. Bello
, Chris Bizon
, Matthew H. Brush, Tiffany J. Callahan, Christopher G. Chute
, William D. Duncan
, Chris T. A. Evelo
, Davera Gabriel, John Graybeal
, Alasdair J. G. Gray, Benjamin M. Gyori
, Melissa A. Haendel
, Henriette Harmse, Nomi L. Harris
, Ian Harrow, Harshad Hegde, Amelia L. Hoyt
, Charles Tapley Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Köhler, Thomas Liener
, Qinqin Long
, James Malone, James A. McLaughlin
, Julie A. McMurry, Sierra A. T. Moxon, Monica C. Munoz-Torres
, David Osumi-Sutherland
, James A. Overton
, Bjoern Peters, Tim E. Putman
, Núria Queralt-Rosinach, Kent A. Shefchek, Harold Solbrig, Anne E. Thessen
, Tania Tudorache, Nicole A. Vasilevsky, Alex H. Wagner
, Christopher J. Mungall
:
A Simple Standard for Sharing Ontological Mappings (SSSOM). Database J. Biol. Databases Curation 2022(2022) (2022) - 2021
- [j10]Randi Vita
, Jie Zheng, Rebecca C. Jackson
, Damion M. Dooley
, James A. Overton, Mark A. Miller, Daniel C. Berrios
, Richard H. Scheuermann
, Yongqun He
, Hande Küçük-McGinty, Mathias Brochhausen, Aisyah Yu Lin, Sagar B. Jain, Marcus C. Chibucos
, John Judkins, Michelle G. Giglio, Irene Y. Feng, Gully Burns
, Matthew H. Brush, Bjoern Peters, Christian J. Stoeckert Jr.:
Standardization of assay representation in the Ontology for Biomedical Investigations. Database J. Biol. Databases Curation 2021 (2021) - 2020
- [j9]Kent A. Shefchek
, Nomi L. Harris, Michael A. Gargano, Nicolas Matentzoglu
, Deepak R. Unni
, Matthew H. Brush, Dan Keith, Tom Conlin, Nicole A. Vasilevsky
, Xingmin Aaron Zhang, James P. Balhoff
, Larry Babb, Susan M. Bello, Hannah Blau, Yvonne M. Bradford, Seth Carbon, Leigh Carmody
, Lauren E. Chan, Valentina Cipriani, Alayne Cuzick
, Maria G. Della Rocca, Nathan A. Dunn, Shahim Essaid, Petra Fey, Christian A. Grove, Jean-Philippe F. Gourdine, Ada Hamosh, Midori A. Harris, Ingo Helbig, Maureen E. Hoatlin, Marcin P. Joachimiak
, Simon Jupp
, Kenneth B. Lett, Suzanna E. Lewis, Craig McNamara, Zoë May Pendlington
, Clare Pilgrim
, Tim E. Putman
, Vida Ravanmehr, Justin T. Reese, Erin Rooney Riggs, Sofia M. C. Robb, Paola Roncaglia
, James Seager
, Erik Segerdell
, Morgan Similuk, Andrea L. Storm, Courtney Thaxon, Anne E. Thessen, Julius O. B. Jacobsen, Julie A. McMurry, Tudor Groza
, Sebastian Köhler
, Damian Smedley, Peter N. Robinson
, Christopher J. Mungall, Melissa A. Haendel
, Monica C. Munoz-Torres
, David Osumi-Sutherland
:
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res. 48(Database-Issue): D704-D715 (2020) - 2019
- [j8]Jean-Philippe F. Gourdine
, Matthew H. Brush, Nicole A. Vasilevsky
, Kent A. Shefchek, Sebastian Köhler, Nicolas Matentzoglu
, Monica C. Munoz-Torres, Julie A. McMurry, Xingmin Aaron Zhang, Peter N. Robinson, Melissa A. Haendel
:
Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery. Database J. Biol. Databases Curation 2019: baz114 (2019) - 2017
- [j7]Violeta Ilik
, Michael Conlon, Graham Triggs
, Marijane White, Muhammad Javed, Matthew H. Brush, Karen Gutzman
, Shahim Essaid, Paul Friedman, Simon Porter, Martin Szomszor, Melissa Anne Haendel
, David Eichmann, Kristi L. Holmes:
OpenVIVO: Transparency in Scholarship. Frontiers Res. Metrics Anal. 2: 12 (2017) - [j6]Christopher J. Mungall, Julie A. McMurry
, Sebastian Köhler, James P. Balhoff
, Charles D. Borromeo, Matthew H. Brush, Seth Carbon
, Tom Conlin, Nathan A. Dunn, Mark Engelstad, Erin Foster
, Jean-Philippe F. Gourdine
, Julius O. B. Jacobsen
, Dan Keith, Bryan Laraway
, Suzanna E. Lewis, Jeremy NguyenXuan, Kent A. Shefchek, Nicole A. Vasilevsky
, Zhou Yuan, Nicole L. Washington
, Harry Hochheiser, Tudor Groza
, Damian Smedley, Peter N. Robinson, Melissa A. Haendel
:
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res. 45(Database-Issue): D712-D722 (2017) - 2016
- [j5]Alexander D. Diehl
, Terrence F. Meehan
, Yvonne M. Bradford, Matthew H. Brush, Wasila M. Dahdul
, David S. Dougall, Yongqun He
, David Osumi-Sutherland
, Alan Ruttenberg, Sirarat Sarntivijai
, Ceri E. Van Slyke
, Nicole A. Vasilevsky
, Melissa A. Haendel
, Judith A. Blake
, Christopher J. Mungall:
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. J. Biomed. Semant. 7: 44 (2016) - [j4]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) - 2015
- [j3]Christopher Ochs, Yehoshua Perl, James Geller, Melissa A. Haendel, Matthew H. Brush
, Sivaram Arabandi
, Samson W. Tu:
Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network. J. Biomed. Informatics 56: 127-144 (2015) - 2014
- [j2]Sirarat Sarntivijai
, Yu Lin, Zuoshuang Xiang, Terrence F. Meehan
, Alexander D. Diehl
, Uma D. Vempati, Stephan C. Schürer, Chao Pang
, James Malone, Helen E. Parkinson
, Yue Liu, Terue Takatsuki, Kaoru Saijo, Hiroshi Masuya, Yukio Nakamura, Matthew H. Brush, Melissa A. Haendel
, Jie Zheng, Christian J. Stoeckert Jr., Bjoern Peters, Christopher J. Mungall, Thomas E. Carey
, David J. States, Brian D. Athey
, Yongqun He
:
CLO: The cell line ontology. J. Biomed. Semant. 5: 37 (2014) - 2012
- [j1]Nicole A. Vasilevsky
, Tenille Johnson, Karen Corday, Carlo Torniai, Matthew H. Brush, Erik Segerdell
, Melanie Wilson, Chris Shaffer, David Robinson, Melissa A. Haendel
:
Research resources: curating the new eagle-i discovery system. Database J. Biol. Databases Curation 2012 (2012)
Conference and Workshop Papers
- 2021
- [c11]Sierra A. T. Moxon, Harold Solbrig, Deepak R. Unni, Dazhi Jiao, Richard M. Bruskiewich, James P. Balhoff, Gaurav Vaidya, William D. Duncan, Harshad Hegde, Mark Miller, Matthew H. Brush, Nomi L. Harris, Melissa A. Haendel, Christopher J. Mungall:
The Linked Data Modeling Language (LinkML): A General-Purpose Data Modeling Framework Grounded in Machine-Readable Semantics. ICBO 2021: 148-151 - 2018
- [c10]Jean-Philippe F. Gourdine, Nicole A. Vasilevsky, Lilly Winfree, Matthew H. Brush, Melissa A. Haendel:
Expanding the Molecular Glycophenotype Ontology to include model organisms and acquired diseases. ICBO 2018 - 2017
- [c9]James P. Balhoff, Matthew H. Brush, Laura Christopherson, Sherri de Coronado, Gilberto Fragoso, Melissa A. Haendel, Christopher J. Mungall, Kimberly Robasky, Nicole A. Vasilevsky, Lawrence W. Wright:
Tailoring the NCI Thesaurus for Use in The OBO Library. ICBO 2017 - 2016
- [c8]Matthew H. Brush, Kent A. Shefchek, Melissa A. Haendel:
SEPIO: A Semantic Model for the Integration and Analysis of Scientific Evidence. ICBO/BioCreative 2016 - [c7]Marcus C. Chibucos, Suvarna Nadendla, James B. Munro, Elvira Mitraka, Dustin Olley, Nicole A. Vasilevsky, Matthew H. Brush, Michelle G. Giglio:
Supporting Database Annotations and Beyond with the Evidence & Conclusion Ontology (ECO). ICBO/BioCreative 2016 - [c6]Jean-Philippe F. Gourdine, Thomas O. Metz, David Koeller, Matthew H. Brush, Melissa A. Haendel:
Building a Molecular Glyco-phenotype Ontology to Decipher Undiagnosed Diseases. ICBO/BioCreative 2016 - [c5]Marijane White, Matthew H. Brush, Shahim Essaid, Robin Champieux, Adrienne Zell, Melissa A. Haendel, Colin Grove, Syeda Momina Tabish, David Eichmann:
Enhancing SciENcv through Semantic Research Profile Integration with the VIVO-ISF Ontology. ICBO/BioCreative 2016 - 2013
- [c4]Matthew H. Brush, Chris Mungall, Nicole L. Washington, Melissa A. Haendel:
What's in a Genotype?: An Ontological Characterization for Integration of Genetic Variation Data. ICBO 2013: 105-108 - [c3]Matthew H. Brush, Jie Zheng, Yongqun He, Sirarat Sarntivijai, Bjoern Peters, Alexander D. Diehl, Christian J. Stoeckert Jr., Melissa A. Haendel:
Alignment of Cultured Cell Modeling Across OBO Foundry Ontologies: Key Outcomes, Insights. ICBO 2013: 120 - 2011
- [c2]Matthew H. Brush, Nicole A. Vasilevsky, Carlo Torniai, Tenille Johnson, Chris Shaffer, Melissa A. Haendel:
Developing a Reagent Application Ontology within the OBO Foundry Framework. ICBO 2011 - [c1]Carlo Torniai, Matthew H. Brush, Nicole A. Vasilevsky, Erik Segerdell, Melanie Wilson, Tenille Johnson, Karen Corday, Chris Shaffer, Melissa A. Haendel:
Developing an Application Ontology for Biomedical Resource Annotation and Retrieval: Challenges and Lessons Learned. ICBO 2011
Informal and Other Publications
- 2022
- [i4]Deepak R. Unni, Sierra A. T. Moxon, Michael Bada, Matthew H. Brush, Richard M. Bruskiewich, Paul A. Clemons, Vlado Dancík, Michel Dumontier, Karamarie Fecho, Gustavo Glusman
, Jennifer J. Hadlock, Nomi L. Harris, Arpita Joshi, Tim E. Putman, Guangrong Qin, Stephen A. Ramsey, Kent A. Shefchek, Harold Solbrig, Karthik Soman, Anne E. Thessen, Melissa A. Haendel, Chris Bizon, Christopher J. Mungall:
Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science. CoRR abs/2203.13906 (2022) - 2021
- [i3]Nicolas Matentzoglu, James P. Balhoff, Susan M. Bello, Chris Bizon, Matthew H. Brush, Tiffany J. Callahan, Christopher G. Chute, William D. Duncan, Chris T. A. Evelo, Davera Gabriel, John Graybeal, Alasdair J. G. Gray, Benjamin M. Gyori, Melissa A. Haendel, Henriette Harmse, Nomi L. Harris, Ian Harrow, Harshad Hegde, Amelia L. Hoyt, Charles Tapley Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Köhler, Thomas Liener, Qinqin Long, James Malone, James A. McLaughlin, Julie A. McMurry, Sierra A. T. Moxon, Monica C. Munoz-Torres, David Osumi-Sutherland, James A. Overton, Bjoern Peters, Tim E. Putman, Núria Queralt-Rosinach, Kent A. Shefchek, Harold Solbrig, Anne E. Thessen, Tania Tudorache, Nicole A. Vasilevsky, Alex H. Wagner, Christopher J. Mungall:
A Simple Standard for Sharing Ontological Mappings (SSSOM). CoRR abs/2112.07051 (2021) - 2019
- [i2]Kristi L. Holmes
, Nicole A. Vasilevsky, Marijane White, Matthew H. Brush, Lisa O'Keefe, Karen Gutzman
, Melissa A. Haendel:
Architecting Attribution: expanding the scope of academic credit. RO 2019 - 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)
Coauthor Index
aka: Melissa Anne Haendel
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