Mary Shimoyama

Publication Activity (10 Years)

Years Active: 2002-2020
Publications (10 Years): 13

Top Topics

Genotype Phenotype

Visualization Tools

Computational Models

Top Venues

Database J. Biol. Databases Curation

J. Biomed. Semant.

Publications

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)
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) (2020)
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) (2020)
Cagatay Dursun, Naoki Shimoyama, Mary Shimoyama, Michael Schläppi, Serdar Bozdag
PhenoGeneRanker: A Tool for Gene Prioritization Using Complete Multiplex Heterogeneous Networks. BCB (2019)
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 (2019)
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 (2019)
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) (2019)
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)
Omid Ghiasvand, Mary Shimoyama
Novel Unsupervised Named Entity Recognition Used in Text Annotation Tool (OntoMate) At Rat Genome Database. BCB (2017)
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)
Omid Ghiasvand, Mary Shimoyama
Introducing a Text Annotation Tool (OntoMate), Assisting Curation at Rat Genome Database. BCB (2016)
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)
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)
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)
Shur-Jen Wang, Stanley J. F. Laulederkind, G. Thomas Hayman, Victoria Petri, Weisong Liu, Jennifer R. Smith, Rajni Nigam, Melinda R. Dwinell, Mary Shimoyama
. Application in hypertension and renal disease. Database J. Biol. Databases Curation 2015 (2015)
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) (2015)
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 (2014)
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)
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 (2013)
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) (2013)
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 (2013)
Tomasz Adamusiak, Mary Shimoyama
Inadvertent Disclosure of Protected Health Information (PHI) in Randomly Shifted Date Elements for De-identification. AMIA (2013)
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)
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 (2013)
Tomasz Adamusiak, Naoki Shimoyama, Marek Tutaj, Mary Shimoyama
Next generation ontology browser. ICBO (2013)
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)
Nazanin Tabesh-Saleki, Mary Shimoyama, Brian E. Carlson, Christopher T. Thompson, Daniel Beard
Making Computational Models Accessible through Ontologies and Visualization Tools. AMIA (2012)
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)
Tomasz Adamusiak, Naoki Shimoyama, Alexandra Fuiks, Mary Shimoyama
Ontologies Put More Meaning into Meaningful Use. SWAT4LS (2012)
Mary Shimoyama
Gene Annotator Tool. AMIA (2012)
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)
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)
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)
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) (2009)
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) (2007)
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) (2005)
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) (2002)