Medical College of Wisconsin
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Mary E. Shimoyama PhD

Mary E. Shimoyama PhD

Associate Professor

Institution: Medical College of Wisconsin
Department: Biomedical Engineering
Program: Biomedical Engineering Program

Member of the Cardiovascular Center
Member of the Genomic Sciences and Precision Medicine Center (GSPMC)


Research Experience

  • Genomics
  • Informatics
  • Knowledge Bases
  • Medical Informatics
  • Medical Informatics Applications
  • Medical Informatics Computing
  • Terminology
  • Terminology as Topic
  • Ontologies
  • Bioinformatics
  • Data Standards
  • Software development
  • Data Mining
  • Data Visualization
  • Methodologies and Techniques

  • Automatic Data Processing
  • Data Collection
  • Data Display
  • Data Interpretation, Statistical
  • Database
  • Database Management Systems
  • Databases as Topic
  • Databases, Genetic
  • Databases, Nucleic Acid
  • Genomics
  • Hospital Records
  • Informatics
  • Information Storage and Retrieval
  • Integrated Advanced Information Management Systems
  • Knowledge Bases
  • Medical Informatics
  • Medical Informatics Applications
  • Medical Informatics Computing
  • Molecular Sequence Data
  • Terminology
  • Unified Medical Language System
  • Leadership Positions

  • Steering Committee Member for the Doctoral Program in Biomedical and Health Informatics at the University of Wisconsin-Milwaukee
  • Co-Director of Doctoral Program in Biomedical and Health Informatics University of Milwaukee- Wisconsin
  • Co-Director of Bioinformatics Graduate Program, Marquette University and Medical College of Wisconsin
  • Vice Chair of Research and Clinical Affairs
  • Publications (70)

  • Alliance of Genome Resources Portal: unified model organism research platform. (Alliance of Genome Resources Consortium ) Nucleic Acids Res 2019 Sep 25 PMID: 31552413 09/26/2019    
  • Rat Genome Databases, Repositories, and Tools. (Laulederkind SJF, Hayman GT, Wang SJ, Hoffman MJ, Smith JR, Bolton ER, De Pons J, Tutaj MA, Tutaj M, Thota J, Dwinell MR, Shimoyama M) Methods Mol Biol 2019;2018:71-96 PMID: 31228152 SCOPUS ID: 2-s2.0-85068143710 06/23/2019    
  • Predicting instances of pathway ontology classes for pathway integration. (Wang LL, Thomas Hayman G, Smith JR, Tutaj M, Shimoyama ME, Gennari JH) J Biomed Semantics 2019 06 13;10(1):11 PMID: 31196182 PMCID: PMC6567466 SCOPUS ID: 2-s2.0-85067289748 06/15/2019    
  • Quantitative phenotype analysis to identify, validate and compare rat disease models. (Zhao Y, Smith JR, Wang SJ, Dwinell MR, Shimoyama M) Database (Oxford) 2019 01 01;2019 PMID: 30938777 PMCID: PMC6444380 SCOPUS ID: 2-s2.0-85064202973 04/03/2019    
  • Integrated curation and data mining for disease and phenotype models at the Rat Genome Database. (Wang SJ, Laulederkind SJF, Zhao Y, Hayman GT, Smith JR, Tutaj M, Thota J, Tutaj MA, Hoffman MJ, Bolton ER, De Pons J, Dwinell MR, Shimoyama M) Database (Oxford) 2019 01 01;2019 PMID: 30753478 PMCID: PMC6369425 SCOPUS ID: 2-s2.0-85061482732 02/13/2019    
  • RNAcentral: a hub of information for non-coding RNA sequences. (The RNAcentral Consortium) Nucleic Acids Res 2019 01 08;47(D1):D1250-D1251 PMID: 30535383 PMCID: PMC6323998 12/12/2018       2 Citations
  • The Gene Ontology Resource: 20 years and still GOing strong. (The Gene Ontology Consortium) Nucleic Acids Res 2019 Jan 08;47(D1):D330-D338 PMID: 30395331 PMCID: PMC6323945 SCOPUS ID: 2-s2.0-85059799086 11/06/2018       65 Citations
  • RNAcentral: a hub of information for non-coding RNA sequences. (The RNAcentral Consortium ) Nucleic Acids Res 2019 Jan 08;47(D1):D221-D229 PMID: 30395267 PMCID: PMC6324050 SCOPUS ID: 2-s2.0-85058455914 11/06/2018       3 Citations
  • A Primer for the Rat Genome Database (RGD). (Laulederkind SJF, Hayman GT, Wang SJ, Smith JR, Petri V, Hoffman MJ, De Pons J, Tutaj MA, Ghiasvand O, Tutaj M, Thota J, Dwinell MR, Shimoyama M) Methods Mol Biol 2018;1757:163-209 PMID: 29761460 PMCID: PMC6487669 SCOPUS ID: 2-s2.0-85047123695 05/16/2018       1 Citation
  • Disease Ontology: improving and unifying disease annotations across species. (Bello SM, Shimoyama M, Mitraka E, Laulederkind SJF, Smith CL, Eppig JT, Schriml LM) Dis Model Mech 2018 03 12;11(3) PMID: 29590633 PMCID: PMC5897730 SCOPUS ID: 2-s2.0-85045050282 03/29/2018       10 Citations
  • Genetics and Genomics in Clinical Practice: The Views of Wisconsin Physicians. (McCauley MP, Marcus RK, Strong KA, Visotcky AM, Shimoyama ME, Derse AR) WMJ 2017 Jun;116(2):69-74 PMID: 29323820 SCOPUS ID: 2-s2.0-85026317737 01/13/2018       2 Citations
  • Rat Genome and Model Resources. (Shimoyama M, Smith JR, Bryda E, Kuramoto T, Saba L, Dwinell M) ILAR J 2017 07 01;58(1):42-58 PMID: 28838068 PMCID: PMC6057551 SCOPUS ID: 2-s2.0-85028342548 08/26/2017       6 Citations
  • Successful Application of Whole Genome Sequencing in a Medical Genetics Clinic. (Bick D, Fraser PC, Gutzeit MF, Harris JM, Hambuch TM, Helbling DC, Jacob HJ, Kersten JN, Leuthner SR, May T, North PE, Prisco SZ, Schuler BA, Shimoyama M, Strong KA, Van Why SK, Veith R, Verbsky J, Weborg AM Jr, Wilk BM, Willoughby RE Jr, Worthey EA, Dimmock DP) J Pediatr Genet 2017 Jun;6(2):61-76 PMID: 28496993 PMCID: PMC5423809 05/13/2017    
  • Expansion of the Gene Ontology knowledgebase and resources. (The Gene Ontology Consortium) Nucleic Acids Res 2017 01 04;45(D1):D331-D338 PMID: 27899567 PMCID: PMC5210579 SCOPUS ID: 2-s2.0-85016166168 12/03/2016       561 Citations
  • Exploring human disease using the Rat Genome Database. (Shimoyama M, Laulederkind SJ, De Pons J, Nigam R, Smith JR, Tutaj M, Petri V, Hayman GT, Wang SJ, Ghiasvand O, Thota J, Dwinell MR) Dis Model Mech 2016 10 01;9(10):1089-1095 PMID: 27736745 PMCID: PMC5087824 SCOPUS ID: 2-s2.0-84993949779 10/14/2016       12 Citations
  • Disease, Models, Variants and Altered Pathways-Journeying RGD Through the Magnifying Glass. (Petri V, Hayman GT, Tutaj M, Smith JR, Laulederkind S, Wang SJ, Nigam R, De Pons J, Shimoyama M, Dwinell MR) Comput Struct Biotechnol J 2016;14:35-48 PMID: 27602200 PMCID: PMC4700298 SCOPUS ID: 2-s2.0-84961710673 09/08/2016    
  • Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database. (Wang SJ, Laulederkind SJ, Hayman GT, Petri V, Smith JR, Tutaj M, Nigam R, Dwinell MR, Shimoyama M) Physiol Genomics 2016 08 01;48(8):589-600 PMID: 27287925 PMCID: PMC5005459 SCOPUS ID: 2-s2.0-84983740999 06/12/2016       1 Citation
  • The Chinchilla Research Resource Database: resource for an otolaryngology disease model. (Shimoyama M, Smith JR, De Pons J, Tutaj M, Khampang P, Hong W, Erbe CB, Ehrlich GD, Bakaletz LO, Kerschner JE) Database (Oxford) 2016;2016 PMID: 27173523 PMCID: PMC4865329 SCOPUS ID: 2-s2.0-85016147668 05/14/2016       8 Citations
  • The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database. (Hayman GT, Laulederkind SJ, Smith JR, Wang SJ, Petri V, Nigam R, Tutaj M, De Pons J, Dwinell MR, Shimoyama M) Database (Oxford) 2016;2016 PMID: 27009807 PMCID: PMC4805243 SCOPUS ID: 2-s2.0-84964901900 03/25/2016       9 Citations
  • The Resource Identification Initiative: A cultural shift in publishing (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, Gonzalez-Beltran A, Garcia-Castro A, Kenall A, Kessell A, Chalmers A, de Waard A, Booty C, Mietchen D, Kavanagh D, Kennedy D, Iorns E, van Hasselt F, Murphy F, Smith J, Deck J, Schneider J, Reiser L, Sandström M, Roelandse M, Shimoyama M, Martone M, Sullivan M, Giampoala M, Haendel M, Lauruhn M, Gaudet P, von Glasow P, Fernandes P, Murray-Rust P, McQuilton P, Nigam R, Champieux R, Crook S, Shreejoy S, Calin S, Hagstrom S, Richard S, Sansone SA, Clark T, Alm T, Whetzel T) F1000Research 29 May 2015;4 SCOPUS ID: 2-s2.0-84942100983 05/29/2015    
  • 2015 Guidelines for Establishing Genetically Modified Rat Models for Cardiovascular Research. (Flister MJ, Prokop JW, Lazar J, Shimoyama M, Dwinell M, Geurts A, International Committee on Standardized Genetic Nomenclature for Mice, Rat Genome and Nomenclature Committee) J Cardiovasc Transl Res 2015 Jun;8(4):269-77 PMID: 25920443 PMCID: PMC4475456 SCOPUS ID: 2-s2.0-84931568348 04/30/2015       13 Citations
  • EHR-based phenome wide association study in pancreatic cancer. (Adamusiak T, Shimoyama M) AMIA Jt Summits Transl Sci Proc 2014;2014:9-15 PMID: 25717392 PMCID: PMC4333703 02/27/2015    
  • PhenoMiner: a quantitative phenotype database for the laboratory rat, Rattus norvegicus. Application in hypertension and renal disease. (Wang SJ, Laulederkind SJ, Hayman GT, Petri V, Liu W, Smith JR, Nigam R, Dwinell MR, Shimoyama M) Database (Oxford) 2015;2015 PMID: 25632109 PMCID: PMC4309021 SCOPUS ID: 2-s2.0-84943179091 01/30/2015       6 Citations
  • OntoMate: a text-mining tool aiding curation at the Rat Genome Database. (Liu W, Laulederkind SJ, Hayman GT, Wang SJ, Nigam R, Smith JR, De Pons J, Dwinell MR, Shimoyama M) Database (Oxford) 2015;2015 PMID: 25619558 PMCID: PMC4305386 SCOPUS ID: 2-s2.0-85051605173 01/27/2015       7 Citations
  • Next generation phenotyping using the unified medical language system. (Adamusiak T, Shimoyama N, Shimoyama M) JMIR Med Inform 2014 Mar 18;2(1):e5 PMID: 25601137 PMCID: PMC4288084 01/21/2015    
  • Gene Ontology Consortium: going forward. (Gene Ontology Consortium) Nucleic Acids Res 2015 Jan;43(Database issue):D1049-56 PMID: 25428369 PMCID: PMC4383973 SCOPUS ID: 2-s2.0-84946735654 11/28/2014       1250 Citations
  • The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease. (Shimoyama M, De Pons J, Hayman GT, Laulederkind SJ, Liu W, Nigam R, Petri V, Smith JR, Tutaj M, Wang SJ, Worthey E, Dwinell M, Jacob H) Nucleic Acids Res 2015 Jan;43(Database issue):D743-50 PMID: 25355511 PMCID: PMC4383884 SCOPUS ID: 2-s2.0-84941092929 10/31/2014       103 Citations
  • Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease. (Petri V, Hayman GT, Tutaj M, Smith JR, Laulederkind SJ, Wang SJ, Nigam R, De Pons J, Shimoyama M, Dwinell MR, Worthey EA, Jacob HJ) Hum Genomics 2014 Sep 30;8:17 PMID: 25265995 PMCID: PMC4191248 SCOPUS ID: 2-s2.0-84964312855 10/01/2014       6 Citations
  • Structural libraries of protein models for multiple species to understand evolution of the renin-angiotensin system. (Prokop JW, Petri V, Shimoyama ME, Watanabe IK, Casarini DE, Leeper TC, Bilinovich SM, Jacob HJ, Santos RA, Martins AS, Araujo FC, Reis FM, Milsted A) Gen Comp Endocrinol 2015 May 01;215:106-16 PMID: 25260253 PMCID: PMC4375088 SCOPUS ID: 2-s2.0-84939957085 09/28/2014       1 Citation
  • Matching the pace of genomic advances through the integration of genomic education into high school health education. (Zusevics KL, Strong KA, Farrell MH, Shimoyama ME) J Sch Health 2014 Jun;84(6):351-4 PMID: 24749916 SCOPUS ID: 2-s2.0-84898921934 04/23/2014    
  • The pathway ontology - updates and applications. (Petri V, Jayaraman P, Tutaj M, Hayman GT, Smith JR, De Pons J, Laulederkind SJ, Lowry TF, Nigam R, Wang SJ, Shimoyama M, Dwinell MR, Munzenmaier DH, Worthey EA, Jacob HJ) J Biomed Semantics 2014 Feb 05;5(1):7 PMID: 24499703 PMCID: PMC3922094 SCOPUS ID: 2-s2.0-84927942575 02/07/2014    
  • Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD. (Nigam R, Munzenmaier DH, Worthey EA, Dwinell MR, Shimoyama M, Jacob HJ) J Biomed Semantics 2013 Nov 22;4(1):36 PMID: 24267899 PMCID: PMC4177145 SCOPUS ID: 2-s2.0-84943184308 11/26/2013    
  • The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications. (Smith JR, Park CA, Nigam R, Laulederkind SJ, Hayman GT, Wang SJ, Lowry TF, Petri V, Pons JD, Tutaj M, Liu W, Worthey EA, Shimoyama M, Dwinell MR) J Biomed Semantics 2013 Oct 08;4(1):26 PMID: 24103152 PMCID: PMC3882879 SCOPUS ID: 2-s2.0-84978081999 10/10/2013    
  • The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species. (Park CA, Bello SM, Smith CL, Hu ZL, Munzenmaier DH, Nigam R, Smith JR, Shimoyama M, Eppig JT, Reecy JM) J Biomed Semantics 2013 Aug 09;4(1):13 PMID: 23937709 PMCID: PMC3851175 08/14/2013    
  • Rat Genome Database: a unique resource for rat, human, and mouse quantitative trait locus data. (Nigam R, Laulederkind SJ, Hayman GT, Smith JR, Wang SJ, Lowry TF, Petri V, De Pons J, Tutaj M, Liu W, Jayaraman P, Munzenmaier DH, Worthey EA, Dwinell MR, Shimoyama M, Jacob HJ) Physiol Genomics 2013 Sep 16;45(18):809-16 PMID: 23881287 PMCID: PMC3783816 SCOPUS ID: 2-s2.0-84884191657 07/25/2013       17 Citations
  • Genomics in clinical practice: lessons from the front lines. (Jacob HJ, Abrams K, Bick DP, Brodie K, Dimmock DP, Farrell M, Geurts J, Harris J, Helbling D, Joers BJ, Kliegman R, Kowalski G, Lazar J, Margolis DA, North P, Northup J, Roquemore-Goins A, Scharer G, Shimoyama M, Strong K, Taylor B, Tsaih SW, Tschannen MR, Veith RL, Wendt-Andrae J, Wilk B, Worthey EA) Sci Transl Med 2013 Jul 17;5(194):194cm5 PMID: 23863829 SCOPUS ID: 2-s2.0-84880547053 07/19/2013       61 Citations
  • Analysis of disease-associated objects at the Rat Genome Database. (Wang SJ, Laulederkind SJ, Hayman GT, Smith JR, Petri V, Lowry TF, Nigam R, Dwinell MR, Worthey EA, Munzenmaier DH, Shimoyama M, Jacob HJ) Database (Oxford) 2013;2013:bat046 PMID: 23794737 PMCID: PMC3689439 SCOPUS ID: 2-s2.0-84885941569 06/26/2013       4 Citations
  • PhenoMiner: quantitative phenotype curation at the rat genome database. (Laulederkind SJ, Liu W, Smith JR, Hayman GT, Wang SJ, Nigam R, Petri V, Lowry TF, de Pons J, Dwinell MR, Shimoyama M) Database (Oxford) 2013;2013:bat015 PMID: 23603846 PMCID: PMC3630803 SCOPUS ID: 2-s2.0-84885154580 04/23/2013       16 Citations
  • The Rat Genome Database 2013--data, tools and users. (Laulederkind SJ, Hayman GT, Wang SJ, Smith JR, Lowry TF, Nigam R, Petri V, de Pons J, Dwinell MR, Shimoyama M, Munzenmaier DH, Worthey EA, Jacob HJ) Brief Bioinform 2013 Jul;14(4):520-6 PMID: 23434633 PMCID: PMC3713714 SCOPUS ID: 2-s2.0-84888772878 02/26/2013       54 Citations
  • The updated RGD Pathway Portal utilizes increased curation efficiency and provides expanded pathway information. (Hayman GT, Jayaraman P, Petri V, Tutaj M, Liu W, De Pons J, Dwinell MR, Shimoyama M) Hum Genomics 2013 Feb 05;7:4 PMID: 23379628 PMCID: PMC3598722 SCOPUS ID: 2-s2.0-84878767208 02/06/2013       7 Citations
  • Next generation ontology browser (Adamusiak T, Shimoyama N, Tutaj M, Shimoyama M) CEUR Workshop Proceedings 2013;1060:132-133 SCOPUS ID: 2-s2.0-84922776670 01/01/2013    
  • Exploring genetic, genomic, and phenotypic data at the rat genome database. (Laulederkind SJ, Hayman GT, Wang SJ, Lowry TF, Nigam R, Petri V, Smith JR, Dwinell MR, Jacob HJ, Shimoyama M) Curr Protoc Bioinformatics 2012 Dec;Chapter 1:Unit1.14 PMID: 23255149 PMCID: PMC3555435 SCOPUS ID: 2-s2.0-84875531338 12/21/2012       10 Citations
  • Model organism databases in behavioral neuroscience. (Shimoyama M, Smith JR, Hayman GT, Petri V, Nigam R) Int Rev Neurobiol 2012;104:25-46 PMID: 23195310 SCOPUS ID: 2-s2.0-84870282747 12/01/2012    
  • Gene Ontology annotations and resources. (Gene Ontology Consortium, Blake JA, Dolan M, Drabkin H, Hill DP, Li N, Sitnikov D, Bridges S, Burgess S, Buza T, McCarthy F, Peddinti D, Pillai L, Carbon S, Dietze H, Ireland A, Lewis SE, Mungall CJ, Gaudet P, Chrisholm RL, Fey P, Kibbe WA, Basu S, Siegele DA, McIntosh BK, Renfro DP, Zweifel AE, Hu JC, Brown NH, Tweedie S, Alam-Faruque Y, Apweiler R, Auchinchloss A, Axelsen K, Bely B, Blatter M-, Bonilla C, Bouguerleret L, Boutet E, Breuza L, Bridge A, Chan WM, Chavali G, Coudert E, Dimmer E, Estreicher A, Famiglietti L, Feuermann M, Gos A, Gruaz-Gumowski N, Hieta R, Hinz C, Hulo C, Huntley R, James J, Jungo F, Keller G, Laiho K, Legge D, Lemercier P, Lieberherr D, Magrane M, Martin MJ, Masson P, Mutowo-Muellenet P, O'Donovan C, Pedruzzi I, Pichler K, Poggioli D, Porras Millán P, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Stutz A, Sundaram S, Tognolli M, Xenarios I, Foulgar R, Lomax J, Roncaglia P, Khodiyar VK, Lovering RC, Talmud PJ, Chibucos M, Giglio MG, Chang H-, Hunter S, McAnulla C, Mitchell A, Sangrador A, Stephan R, Harris MA, Oliver SG, Rutherford K, Wood V, Bahler J, Lock A, Kersey PJ, McDowall DM, Staines DM, Dwinell M, Shimoyama M, Laulederkind S, Hayman T, Wang S-, Petri V, Lowry T, D'Eustachio P, Matthews L, Balakrishnan R, Binkley G, Cherry JM, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hitz BC, Hong EL, Karra K, Miyasato SR, Nash RS, Park J, Skrzypek MS, Weng S, Wong ED, Berardini TZ, Huala E, Mi H, Thomas PD, Chan J, Kishore R, Sternberg P, Van Auken K, Howe D, Westerfield M) Nucleic Acids Res 2013 Jan;41(Database issue):D530-5 PMID: 23161678 PMCID: PMC3531070 SCOPUS ID: 2-s2.0-84874253819 11/20/2012       342 Citations
  • Erratum: Multiscale modeling and data integration in the virtual physiological rat project (Annals of Biomedical Engineering DOI:10.1007/s10439- 012-0611-7) (Beard DA, Neal ML, Tabesh-Saleki N, Thompson CT, Bassingthwaighte JB, Shimoyama M, Carlson BE) Annals of Biomedical Engineering November 2012;40(11):2501 SCOPUS ID: 2-s2.0-84868349535 11/01/2012    
  • Erratum to: Multiscale Modeling and Data Integration in the Virtual Physiological Rat Project. (Beard DA, Neal ML, Tabesh-Saleki N, Thompson CT, Bassingthwaighte JB, Shimoyama M, Carlson BE) Ann Biomed Eng 2012 Nov;40(11):2501 PMID: 22923062 08/28/2012    
  • Multiscale modeling and data integration in the virtual physiological rat project. (Beard DA, Neal ML, Tabesh-Saleki N, Thompson CT, Bassingthwaighte JB, Shimoyama M, Carlson BE) Ann Biomed Eng 2012 Nov;40(11):2365-78 PMID: 22805979 PMCID: PMC3463790 SCOPUS ID: 2-s2.0-84868362445 07/19/2012       31 Citations
  • Three ontologies to define phenotype measurement data. (Shimoyama M, Nigam R, McIntosh LS, Nagarajan R, Rice T, Rao DC, Dwinell MR) Front Genet 2012;3:87 PMID: 22654893 PMCID: PMC3361058 SCOPUS ID: 2-s2.0-84869772444 06/02/2012    
  • Ontology searching and browsing at the Rat Genome Database. (Laulederkind SJ, Tutaj M, Shimoyama M, Hayman GT, Lowry TF, Nigam R, Petri V, Smith JR, Wang SJ, de Pons J, Dwinell MR, Jacob HJ) Database (Oxford) 2012;2012:bas016 PMID: 22434847 PMCID: PMC3308169 SCOPUS ID: 2-s2.0-84862262998 03/22/2012       15 Citations
  • Ontologies put more meaning into Meaningful Use (Adamusiak T, Shimoyama N, Fuiks A, Shimoyama M) CEUR Workshop Proceedings 2012;952 SCOPUS ID: 2-s2.0-84922754046 01/01/2012    
  • The Gene Ontology: enhancements for 2011. (Gene Ontology Consortium) Nucleic Acids Res 2012 Jan;40(Database issue):D559-64 PMID: 22102568 PMCID: PMC3245151 SCOPUS ID: 2-s2.0-84859699831 11/22/2011       168 Citations
  • A prioritization analysis of disease association by data-mining of functional annotation of human genes. (Taniya T, Tanaka S, Yamaguchi-Kabata Y, Hanaoka H, Yamasaki C, Maekawa H, Barrero RA, Lenhard B, Datta MW, Shimoyama M, Bumgarner R, Chakraborty R, Hopkinson I, Jia L, Hide W, Auffray C, Minoshima S, Imanishi T, Gojobori T) Genomics 2012 Jan;99(1):1-9 PMID: 22019378 SCOPUS ID: 2-s2.0-84855195943 10/25/2011       7 Citations
  • The Rat Genome Database pathway portal. (Petri V, Shimoyama M, Hayman GT, Smith JR, Tutaj M, de Pons J, Dwinell MR, Munzenmaier DH, Twigger SN, Jacob HJ, RGD Team) Database (Oxford) 2011;2011:bar010 PMID: 21478484 PMCID: PMC3072770 SCOPUS ID: 2-s2.0-80052334281 04/12/2011       13 Citations
  • The Rat Genome Database curation tool suite: a set of optimized software tools enabling efficient acquisition, organization, and presentation of biological data. (Laulederkind SJ, Shimoyama M, Hayman GT, Lowry TF, Nigam R, Petri V, Smith JR, Wang SJ, de Pons J, Kowalski G, Liu W, Rood W, Munzenmaier DH, Dwinell MR, Twigger SN, Jacob HJ, RGD Team) Database (Oxford) 2011;2011:bar002 PMID: 21321022 PMCID: PMC3041158 SCOPUS ID: 2-s2.0-79956225148 02/16/2011       10 Citations
  • RGD: a comparative genomics platform. (Shimoyama M, Smith JR, Hayman T, Laulederkind S, Lowry T, Nigam R, Petri V, Wang SJ, Dwinell M, Jacob H, RGD Team) Hum Genomics 2011 Jan;5(2):124-9 PMID: 21296746 PMCID: PMC3222152 SCOPUS ID: 2-s2.0-79955839943 02/08/2011       23 Citations
  • The rat genome database curators: who, what, where, why. (Shimoyama M, Hayman GT, Laulederkind SJ, Nigam R, Lowry TF, Petri V, Smith JR, Wang SJ, Munzenmaier DH, Dwinell MR, Twigger SN, Jacob HJ, RGD Team) PLoS Comput Biol 2009 Nov;5(11):e1000582 PMID: 19956751 PMCID: PMC2775909 SCOPUS ID: 2-s2.0-73449141822 12/04/2009       14 Citations
  • The Gene Ontology in 2010: extensions and refinements. (Gene Ontology Consortium) Nucleic Acids Res 2010 Jan;38(Database issue):D331-5 PMID: 19920128 PMCID: PMC2808930 11/19/2009       322 Citations
  • Corrigendum to "A revised nomenclature for the human and rodent α-tubulin gene family" [Genomics 90 (2007) 285-289] (DOI:10.1016/j.ygeno.2007.04.008) (Khodiyar VK, Maltais LJ, Ruef BJ, Sneddon KMB, Smith JR, Shimoyama M, Cabral F, Dumontet C, Dutcher SK, Harvey RJ, Lafanechère L, Murray JM, Nogales E, Piquemal D, Stanchi F, Povey S, Lovering RC) Genomics April 2009;93(4):397 SCOPUS ID: 2-s2.0-62149132545 04/01/2009    
  • The Rat Genome Database 2009: variation, ontologies and pathways. (Dwinell MR, Worthey EA, Shimoyama M, Bakir-Gungor B, DePons J, Laulederkind S, Lowry T, Nigram R, Petri V, Smith J, Stoddard A, Twigger SN, Jacob HJ, RGD Team) Nucleic Acids Res 2009 Jan;37(Database issue):D744-9 PMID: 18996890 PMCID: PMC2686558 SCOPUS ID: 2-s2.0-58149194606 11/11/2008       56 Citations
  • Using multiple ontologies to integrate complex biological data. (Shimoyama M, Petri V, Pasko D, Bromberg S, Wu W, Chen J, Nenasheva N, Kwitek A, Twigger S, Jacob H) Comp Funct Genomics 2005;6(7-8):373-8 PMID: 18629202 PMCID: PMC2447497 07/17/2008    
  • The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. (Genome Information Integration Project And H-Invitational 2, Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, Sanbonmatsu R, Shiba R, Suzuki M, Takabayashi K, Takahashi A, Tamura T, Tanaka M, Tanaka S, Todokoro F, Yamaguchi K, Yamamoto N, Okido T, Mashima J, Hashizume A, Jin L, Lee KB, Lin YC, Nozaki A, Sakai K, Tada M, Miyazaki S, Makino T, Ohyanagi H, Osato N, Tanaka N, Suzuki Y, Ikeo K, Saitou N, Sugawara H, O'Donovan C, Kulikova T, Whitfield E, Halligan B, Shimoyama M, Twigger S, Yura K, Kimura K, Yasuda T, Nishikawa T, Akiyama Y, Motono C, Mukai Y, Nagasaki H, Suwa M, Horton P, Kikuno R, Ohara O, Lancet D, Eveno E, Graudens E, Imbeaud S, Debily MA, Hayashizaki Y, Amid C, Han M, Osanger A, Endo T, Thomas MA, Hirakawa M, Makalowski W, Nakao M, Kim NS, Yoo HS, De Souza SJ, Bonaldo Mde F, Niimura Y, Kuryshev V, Schupp I, Wiemann S, Bellgard M, Shionyu M, Jia L, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Zhang Q, Go M, Minoshima S, Ohtsubo M, Hanada K, Tonellato P, Isogai T, Zhang J, Lenhard B, Kim S, Chen Z, Hinz U, Estreicher A, Nakai K, Makalowska I, Hide W, Tiffin N, Wilming L, Chakraborty R, Soares MB, Chiusano ML, Suzuki Y, Auffray C, Yamaguchi-Kabata Y, Itoh T, Hishiki T, Fukuchi S, Nishikawa K, Sugano S, Nomura N, Tateno Y, Imanishi T, Gojobori T) Nucleic Acids Res 2008 Jan;36(Database issue):D793-9 PMID: 18089548 PMCID: PMC2238988 SCOPUS ID: 2-s2.0-38549163285 12/20/2007       55 Citations
  • The Gene Ontology project in 2008. (Gene Ontology Consortium) Nucleic Acids Res 2008 Jan;36(Database issue):D440-4 PMID: 17984083 PMCID: PMC2238979 SCOPUS ID: 2-s2.0-84984996500 11/07/2007       458 Citations
  • A revised nomenclature for the human and rodent alpha-tubulin gene family. (Khodiyar VK, Maltais LJ, Ruef BJ, Sneddon KM, Smith JR, Shimoyama M, Cabral F, Dumontet C, Dutcher SK, Harvey RJ, Lafanechère L, Murray JM, Nogales E, Piquemal D, Stanchi F, Povey S, Lovering RC) Genomics 2007 Aug;90(2):285-9 PMID: 17543498 SCOPUS ID: 2-s2.0-34447266385 06/05/2007       29 Citations
  • The Rat Genome Database, update 2007--easing the path from disease to data and back again. (Twigger SN, Shimoyama M, Bromberg S, Kwitek AE, Jacob HJ, RGD Team) Nucleic Acids Res 2007 Jan;35(Database issue):D658-62 PMID: 17151068 PMCID: PMC1761441 SCOPUS ID: 2-s2.0-33846111969 12/08/2006       103 Citations
  • The Gene Ontology (GO) project in 2006. (Gene Ontology Consortium) Nucleic Acids Res 2006 Jan 01;34(Database issue):D322-6 PMID: 16381878 PMCID: PMC1347384 SCOPUS ID: 2-s2.0-33644875286 12/31/2005       614 Citations
  • Tools and strategies for physiological genomics: the Rat Genome Database. (Twigger SN, Pasko D, Nie J, Shimoyama M, Bromberg S, Campbell D, Chen J, dela Cruz N, Fan C, Foote C, Harris G, Hickmann B, Ji Y, Jin W, Li D, Mathis J, Nenasheva N, Nigam R, Petri V, Reilly D, Ruotti V, Schauberger E, Seiler K, Slyper R, Smith J, Wang W, Wu W, Zhao L, Zuniga-Meyer A, Tonellato PJ, Kwitek AE, Jacob HJ) Physiol Genomics 2005 Oct 17;23(2):246-56 PMID: 16106031 PMCID: PMC4505745 SCOPUS ID: 2-s2.0-28844446021 08/18/2005       21 Citations
  • The Rat Genome Database (RGD): developments towards a phenome database. (de la Cruz N, Bromberg S, Pasko D, Shimoyama M, Twigger S, Chen J, Chen CF, Fan C, Foote C, Gopinath GR, Harris G, Hughes A, Ji Y, Jin W, Li D, Mathis J, Nenasheva N, Nie J, Nigam R, Petri V, Reilly D, Wang W, Wu W, Zuniga-Meyer A, Zhao L, Kwitek A, Tonellato P, Jacob H) Nucleic Acids Res 2005 Jan 01;33(Database issue):D485-91 PMID: 15608243 PMCID: PMC540004 SCOPUS ID: 2-s2.0-13444273396 12/21/2004       44 Citations
  • Integrative annotation of 21,037 human genes validated by full-length cDNA clones. (Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Mde F, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S) PLoS Biol 2004 Jun;2(6):e162 PMID: 15103394 PMCID: PMC393292 SCOPUS ID: 2-s2.0-4344623260 04/23/2004       262 Citations
  • Integrative genomics: in silico coupling of rat physiology and complex traits with mouse and human data. (Twigger SN, Nie J, Ruotti V, Yu J, Chen D, Li D, Mathis J, Narayanasamy V, Gopinath GR, Pasko D, Shimoyama M, De La Cruz N, Bromberg S, Kwitek AE, Jacob HJ, Tonellato PJ) Genome Res 2004 Apr;14(4):651-60 PMID: 15060006 PMCID: PMC383309 SCOPUS ID: 2-s2.0-3042536890 04/03/2004       17 Citations
  • Rat Genome Database (RGD): mapping disease onto the genome. (Twigger S, Lu J, Shimoyama M, Chen D, Pasko D, Long H, Ginster J, Chen CF, Nigam R, Kwitek A, Eppig J, Maltais L, Maglott D, Schuler G, Jacob H, Tonellato PJ) Nucleic Acids Res 2002 Jan 01;30(1):125-8 PMID: 11752273 PMCID: PMC99132 SCOPUS ID: 2-s2.0-18444394318 12/26/2001       75 Citations
  • Last update: 10/14/2019
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