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2020 – today
- 2020
[j26]Ranjana Kishore, Valerio Arnaboldi
, Ceri E. Van Slyke, Juancarlos Chan, Robert S. Nash, Jose-Maria Urbano, Mary E. Dolan, Stacia R. Engel, Mary Shimoyama, Paul W. Sternberg, The Alliance of Genome Resources:
Automated generation of gene summaries at the Alliance of Genome Resources. Database J. Biol. Databases Curation 2020 (2020)- [j25]Julie Agapite, Laurent-Philippe Albou, Suzi A. Aleksander, Joanna Argasinska, Valerio Arnaboldi, Helen Attrill, Susan M. Bello, Judith A. Blake, Olin Blodgett, Yvonne M. Bradford, Carol J. Bult, Scott Cain, Brian R. Calvi, Seth Carbon, Juancarlos Chan, Wen J. Chen, J. Michael Cherry, Jae-Hyoung Cho, Karen R. Christie, Madeline A. Crosby, Jeff de Pons, Mary E. Dolan, Gilberto dos Santos, Barbara Dunn, Nathan A. Dunn, Anne E. Eagle, Dustin Ebert, Stacia R. Engel, David Fashena, Ken Frazer, Sibyl Gao, Felix Gondwe, Joshua L. Goodman, L. Sian Gramates, Christian A. Grove, Todd W. Harris, Marie-Claire Harrison, Douglas G. Howe, Kevin L. Howe, Sagar Jha, James A. Kadin, Thomas C. Kaufman, Patrick Kalita, Kalpana Karra, Ranjana Kishore, Stanley J. F. Laulederkind, Raymond Y. N. Lee, Kevin A. MacPherson, Steven J. Marygold, Beverley Matthews, Gillian H. Millburn, Stuart R. Miyasato, Sierra A. T. Moxon, Hans-Michael Müller, Christopher J. Mungall, Anushya Muruganujan, Tremayne Mushayahama, Robert S. Nash, Patrick Ng, Michael Paulini, Norbert Perrimon, Christian Pich, Daniela Raciti, Joel E. Richardson, Matthew Russell, Susan Russo Gelbart, Leyla Ruzicka, Kevin Schaper, Mary Shimoyama, Matt Simison, Cynthia L. Smith, David R. Shaw, Ajay Shrivatsav, Marek S. Skrzypek, Jennifer R. Smith, Paul W. Sternberg, Christopher J. Tabone, Paul D. Thomas, Jyothi Thota, Sabrina Toro, Monika Tomczuk, Marek Tutaj, Monika Tutaj, Jose-Maria Urbano, Kimberly Van Auken, Ceri E. Van Slyke, Shur-Jen Wang, Shuai Weng, Monte Westerfield, Gary Williams, Edith D. Wong, Adam Wright, Karen Yook:
Alliance of Genome Resources Portal: unified model organism research platform. Nucleic Acids Res. 48(Database-Issue): D650-D658 (2020) - [j24]Jennifer R. Smith, G. Thomas Hayman, Shur-Jen Wang, Stanley J. F. Laulederkind, Matthew J. Hoffman, Mary L. Kaldunski, Monika Tutaj, Jyothi Thota, Harika S. Nalabolu, Santoshi L. R. Ellanki, Marek Tutaj, Jeffrey DePons, Anne E. Kwitek, Melinda R. Dwinell, Mary Shimoyama:
The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform. Nucleic Acids Res. 48(Database-Issue): D731-D742 (2020)
2010 – 2019
- 2019
- [j23]Shur-Jen Wang, Stanley J. F. Laulederkind, Yiqing Zhao, G. Thomas Hayman, Jennifer R. Smith, Monika Tutaj, Jyothi Thota, Marek Tutaj, Matthew J. Hoffman, Elizabeth R. Bolton, Jeffrey DePons, Melinda R. Dwinell, Mary Shimoyama:
Integrated curation and data mining for disease and phenotype models at the Rat Genome Database. Database J. Biol. Databases Curation 2019: baz014 (2019) - [j22]Yiqing Zhao, Jennifer R. Smith, Shur-Jen Wang, Melinda R. Dwinell, Mary Shimoyama:
Quantitative phenotype analysis to identify, validate and compare rat disease models. Database J. Biol. Databases Curation 2019: baz037 (2019) - [j21]Lucy Lu Wang, G. Thomas Hayman, Jennifer R. Smith, Monika Tutaj, Mary Shimoyama, John H. Gennari:
Predicting instances of pathway ontology classes for pathway integration. J. Biomed. Semant. 10(1): 11:1-11:11 (2019) - [c11]Cagatay Dursun, Naoki Shimoyama, Mary Shimoyama, Michael Schläppi, Serdar Bozdag:
PhenoGeneRanker: A Tool for Gene Prioritization Using Complete Multiplex Heterogeneous Networks. BCB 2019: 279-288 - 2018
- [c10]Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Elizabeth R. Bolton, Jennifer R. Smith, Marek Tutaj, Jeff de Pons, Mary Shimoyama, Melinda R. Dwinell:
Adapting Disease Vocabularies for Curation at the Rat Genome Database. ICBO 2018 - 2017
- [c9]Omid Ghiasvand, Mary Shimoyama:
Novel Unsupervised Named Entity Recognition Used in Text Annotation Tool (OntoMate) At Rat Genome Database. BCB 2017: 590 - 2016
- [j20]G. Thomas Hayman, Stanley J. F. Laulederkind, Jennifer R. Smith, Shur-Jen Wang, Victoria Petri, Rajni Nigam, Marek Tutaj, Jeff de Pons, Melinda R. Dwinell, Mary Shimoyama:
The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database. Database J. Biol. Databases Curation 2016 (2016) - [j19]Mary Shimoyama, Jennifer R. Smith, Jeff de Pons, Marek Tutaj, Pawjai Khampang, Wenzhou Hong, Christy B. Erbe, Garth D. Ehrlich, Lauren O. Bakaletz, Joseph E. Kerschner:
The Chinchilla Research Resource Database: resource for an otolaryngology disease model. Database J. Biol. Databases Curation 2016 (2016) - [c8]Mary Shimoyama, Stanley J. F. Laulederkind, Jeff de Pons, Marek Tutaj, Victoria Petri, G. Thomas Hayman, Shur-Jen Wang, Rajni Nigam, Jennifer R. Smith, Jyothi Thota, Omid Ghiasvand, Melinda R. Dwinell:
Disease Connections at RGD. AMIA 2016 - [c7]Omid Ghiasvand, Mary Shimoyama:
Introducing a Text Annotation Tool (OntoMate), Assisting Curation at Rat Genome Database. BCB 2016: 465 - 2015
- [j18]Weisong Liu, Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Rajni Nigam, Jennifer R. Smith, Jeff de Pons, Melinda R. Dwinell, Mary Shimoyama:
OntoMate: a text-mining tool aiding curation at the Rat Genome Database. Database J. Biol. Databases Curation 2015 (2015) - [j17]Shur-Jen Wang, Stanley J. F. Laulederkind, G. Thomas Hayman, Victoria Petri, Weisong Liu, Jennifer R. Smith, Rajni Nigam, Melinda R. Dwinell, Mary Shimoyama:
PhenoMiner: a quantitative phenotype database for the laboratory rat, Rattus norvegicus. Application in hypertension and renal disease. Database J. Biol. Databases Curation 2015 (2015) - [j16]Mary Shimoyama, Jeff de Pons, G. Thomas Hayman, Stanley J. F. Laulederkind, Weisong Liu, Rajni Nigam, Victoria Petri, Jennifer R. Smith, Marek Tutaj, Shur-Jen Wang, Elizabeth A. Worthey, Melinda R. Dwinell, Howard J. Jacob:
The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease. Nucleic Acids Res. 43(Database-Issue): 743-750 (2015) - 2014
- [j15]Victoria Petri, Pushkala Jayaraman, Marek Tutaj, G. Thomas Hayman, Jennifer R. Smith, Jeff de Pons, Stanley J. F. Laulederkind, Timothy Lowry, Rajni Nigam, Shur-Jen Wang, Mary Shimoyama, Melinda R. Dwinell, Diane H. Munzenmaier, Elizabeth A. Worthey, Howard J. Jacob:
The pathway ontology - updates and applications. J. Biomed. Semant. 5: 7 (2014) - 2013
- [j14]Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Jennifer R. Smith, Timothy Lowry, Rajni Nigam, Victoria Petri, Jeff de Pons, Melinda R. Dwinell, Mary Shimoyama, Diane H. Munzenmaier, Elizabeth A. Worthey, Howard J. Jacob:
The Rat Genome Database 2013 - data, tools and users. Briefings Bioinform. 14(4): 520-526 (2013) - [j13]Stanley J. F. Laulederkind, Weisong Liu, Jennifer R. Smith, G. Thomas Hayman, Shur-Jen Wang, Rajni Nigam, Victoria Petri, Timothy Lowry, Jeff de Pons, Melinda R. Dwinell, Mary Shimoyama:
PhenoMiner: quantitative phenotype curation at the rat genome database. Database J. Biol. Databases Curation 2013 (2013) - [j12]Shur-Jen Wang, Stanley J. F. Laulederkind, G. Thomas Hayman, Jennifer R. Smith, Victoria Petri, Timothy Lowry, Rajni Nigam, Melinda R. Dwinell, Elizabeth A. Worthey, Diane H. Munzenmaier, Mary Shimoyama, Howard J. Jacob:
Analysis of disease-associated objects at the Rat Genome Database. Database J. Biol. Databases Curation 2013 (2013) - [j11]Carissa A. Park, Susan M. Bello, Cynthia L. Smith, Zhi-Liang Hu, Diane H. Munzenmaier, Rajni Nigam, Jennifer R. Smith, Mary Shimoyama, Janan T. Eppig, James M. Reecy:
The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species. J. Biomed. Semant. 4: 13 (2013) - [j10]Jennifer R. Smith, Carissa A. Park, Rajni Nigam, Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Timothy Lowry, Victoria Petri, Jeff de Pons, Marek Tutaj, Weisong Liu, Elizabeth A. Worthey, Mary Shimoyama, Melinda R. Dwinell:
The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications. J. Biomed. Semant. 4: 26 (2013) - [j9]Rajni Nigam, Diane H. Munzenmaier, Elizabeth A. Worthey, Melinda R. Dwinell, Mary Shimoyama, Howard J. Jacob:
Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD. J. Biomed. Semant. 4: 36 (2013) - [c6]Tomasz Adamusiak, Mary Shimoyama:
Inadvertent Disclosure of Protected Health Information (PHI) in Randomly Shifted Date Elements for De-identification. AMIA 2013 - [c5]Nazanin Tabesh-Saleki, Brian E. Carlson, Christopher T. Thompson, Maxwell Lewis Neal, Daniel L. Cook, Mary Shimoyama:
Innovative Use of Ontologies: Association of Physiological Pathways to Corresponding Computational Models and Disparate Data Types. AMIA 2013 - [c4]Tomasz Adamusiak, Naoki Shimoyama, Marek Tutaj, Mary Shimoyama:
Next generation ontology browser. ICBO 2013: 132-133 - 2012
- [j8]Stanley J. F. Laulederkind, Marek Tutaj, Mary Shimoyama, G. Thomas Hayman, Timothy Lowry, Rajni Nigam, Victoria Petri, Jennifer R. Smith, Shur-Jen Wang, Jeff de Pons, Melinda R. Dwinell, Howard J. Jacob:
Ontology searching and browsing at the Rat Genome Database. Database J. Biol. Databases Curation 2012 (2012) - [c3]Mary Shimoyama:
Gene Annotator Tool. AMIA 2012 - [c2]Nazanin Tabesh-Saleki, Mary Shimoyama, Brian E. Carlson, Christopher T. Thompson, Daniel Beard:
Making Computational Models Accessible through Ontologies and Visualization Tools. AMIA 2012 - [c1]Tomasz Adamusiak, Naoki Shimoyama, Alexandra Fuiks, Mary Shimoyama:
Ontologies Put More Meaning into Meaningful Use. SWAT4LS 2012 - 2011
- [j7]Stanley J. F. Laulederkind, Mary Shimoyama, G. Thomas Hayman, Timothy Lowry, Rajni Nigam, Victoria Petri, Jennifer R. Smith, Shur-Jen Wang, Jeff de Pons, George Kowalski, Weisong Liu, Wes Rood, Diane H. Munzenmaier, Melinda R. Dwinell, Simon N. Twigger, Howard J. Jacob:
The Rat Genome Database curation tool suite: a set of optimized software tools enabling efficient acquisition, organization, and presentation of biological data. Database J. Biol. Databases Curation 2011 (2011) - [j6]Victoria Petri, Mary Shimoyama, G. Thomas Hayman, Jennifer R. Smith, Marek Tutaj, Jeff de Pons, Melinda R. Dwinell, Diane H. Munzenmaier, Simon N. Twigger, Howard J. Jacob:
The Rat Genome Database Pathway Portal. Database J. Biol. Databases Curation 2011 (2011)
2000 – 2009
- 2009
- [j5]Melinda R. Dwinell, Elizabeth A. Worthey, Mary Shimoyama, Burcu Bakir-Gungor, Jeffrey DePons, Stanley J. F. Laulederkind, Timothy Lowry, Rajni Nigam, Victoria Petri, Jennifer R. Smith, Alexander Stoddard, Simon N. Twigger, Howard J. Jacob:
The Rat Genome Database 2009: variation, ontologies and pathways. Nucleic Acids Res. 37(Database-Issue): 744-749 (2009) - [j4]Mary Shimoyama, G. Thomas Hayman, Stanley J. F. Laulederkind, Rajni Nigam, Timothy Lowry, Victoria Petri, Jennifer R. Smith, Shur-Jen Wang, Diane H. Munzenmaier, Melinda R. Dwinell, Simon N. Twigger, Howard J. Jacob:
The Rat Genome Database Curators: Who, What, Where, Why. PLoS Comput. Biol. 5(11) (2009) - 2007
- [j3]Simon N. Twigger, Mary Shimoyama, Susan Bromberg, Anne E. Kwitek, Howard J. Jacob:
The Rat Genome Database, update 2007 - Easing the path from disease to data and back again. Nucleic Acids Res. 35(Database-Issue): 658-662 (2007) - 2005
- [j2]Norberto de la Cruz, Susan Bromberg, Dean Pasko, Mary Shimoyama, Simon N. Twigger, Jiali Chen, Chin-Fu Chen, Chunyu Fan, Cindy Foote, Gopal R. Gopinath, Glenn Harris, Aubrey Hughes, Yuan Ji, Weihong Jin, Dawei Li, Jedidiah Mathis, Natalya Nenasheva, Jeff Nie, Rajni Nigam, Victoria Petri, Dorothy Reilly, Weiye Wang, Wenhua Wu, Angela Zuniga-Meyer, Lan Zhao, Anne E. Kwitek, Peter J. Tonellato, Howard J. Jacob:
The Rat Genome Database (RGD): developments towards a phenome database. Nucleic Acids Res. 33(Database-Issue): 485-491 (2005) - 2002
- [j1]Simon N. Twigger, Jian Lu, Mary Shimoyama, Dan Chen, Dean Pasko, Hanping Long, Jessica Ginster, Chin-Fu Chen, Rajni Nigam, Anne E. Kwitek, Janan T. Eppig, Lois Maltais, Donna R. Maglott, Gregory D. Schuler, Howard J. Jacob, Peter J. Tonellato:
Rat Genome Database (RGD): mapping disease onto the genome. Nucleic Acids Res. 30(1): 125-128 (2002)
Coauthor Index
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