Medical College of Wisconsin
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Mary E. Shimoyama PhD

Mary E. Shimoyama PhD

Assistant Professor

Institution: Medical College of Wisconsin
Department: Surgery
Division: Cardiothoracic
Program: Research


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
  • Publications

  • 2015 Guidelines for Establishing Genetically Modified Rat Models for Cardiovascular Research. (Flister MJ, Prokop JW, Lazar J, Shimoyama M, Dwinell M, Geurts A) J Cardiovasc Transl Res 2015 Jun;8(4):269-77 PMID: 25920443 PMCID: PMC4475456
  • 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
  • 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
  • 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
  • Next generation phenotyping using the unified medical language system. (Adamusiak T, Shimoyama N, Shimoyama M) JMIR Med Inform 2014;2(1):e5 PMID: 25601137 PMCID: PMC4288084
  • Gene Ontology Consortium: going forward. (Gene Ontology Consortium) Nucleic Acids Res 2015 Jan;43(Database issue):D1049-56 PMID: 25428369 PMCID: PMC4383973
  • 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
  • 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;8:17 PMID: 25265995 PMCID: PMC4191248
  • 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 1;215:106-16 PMID: 25260253 PMCID: PMC4375088
  • 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
  • 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;5(1):7 PMID: 24499703 PMCID: PMC3922094
  • 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;4(1):36 PMID: 24267899 PMCID: PMC4177145
  • 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;4(1):26 PMID: 24103152 PMCID: PMC3882879
  • 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;4(1):13 PMID: 23937709 PMCID: PMC3851175
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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;7:4 PMID: 23379628 PMCID: PMC3598722
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • The Gene Ontology: enhancements for 2011. (Gene Ontology Consortium) Nucleic Acids Res 2012 Jan;40(Database issue):D559-64 PMID: 22102568 PMCID: PMC3245151
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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 1;33(Database issue):D485-91 PMID: 15608243 PMCID: PMC540004
  • 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
  • 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
  • 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 1;30(1):125-8 PMID: 11752273 PMCID: PMC99132
  • Last update: 06/30/2015