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
  • Publications

  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • The Gene Ontology: enhancements for 2011. (Gene Ontology Consortium) Nucleic Acids Res 2012 Jan;40(Database issue):D559-64 PMID 22102568
  • 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
  • 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
  • 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
  • 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
  • The Gene Ontology in 2010: extensions and refinements. (Gene Ontology Consortium) Nucleic Acids Res 2010 Jan;38(Database issue):D331-5 PMID 19920128
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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