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Patricia L Whetzel

TitleAsst Professor-Research
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM-BIOMED Informatics Gen Ops

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Putman TE, Schaper K, Matentzoglu N, Rubinetti VP, Alquaddoomi FS, Cox C, Caufield JH, Elsarboukh G, Gehrke S, Hegde H, Reese JT, Braun I, Bruskiewich RM, Cappelletti L, Carbon S, Caron AR, Chan LE, Chute CG, Cortes KG, De Souza V, Fontana T, Harris NL, Hartley EL, Hurwitz E, Jacobsen JOB, Krishnamurthy M, Laraway BJ, McLaughlin JA, McMurry JA, Moxon SAT, Mullen KR, O'Neil ST, Shefchek KA, Stefancsik R, Toro S, Vasilevsky NA, Walls RL, Whetzel PL, Osumi-Sutherland D, Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC. The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes?and diseases across species. Nucleic Acids Res. 2024 Jan 05; 52(D1):D938-D949. PMID: 38000386.
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    2. Sollis E, Mosaku A, Abid A, Buniello A, Cerezo M, Gil L, Groza T, G?nes O, Hall P, Hayhurst J, Ibrahim A, Ji Y, John S, Lewis E, MacArthur JAL, McMahon A, Osumi-Sutherland D, Panoutsopoulou K, Pendlington Z, Ramachandran S, Stefancsik R, Stewart J, Whetzel P, Wilson R, Hindorff L, Cunningham F, Lambert SA, Inouye M, Parkinson H, Harris LW. The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource. Nucleic Acids Res. 2023 01 06; 51(D1):D977-D985. PMID: 36350656.
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    3. MacArthur JAL, Buniello A, Harris LW, Hayhurst J, McMahon A, Sollis E, Cerezo M, Hall P, Lewis E, Whetzel PL, Bahcall OG, Barroso I, Carroll RJ, Inouye M, Manolio TA, Rich SS, Hindorff LA, Wiley K, Parkinson H. Workshop proceedings: GWAS summary statistics standards and sharing. Cell Genom. 2021 Oct 13; 1(1). PMID: 36082306.
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    4. Courtot M, Cherubin L, Faulconbridge A, Vaughan D, Green M, Richardson D, Harrison P, Whetzel PL, Parkinson H, Burdett T. BioSamples database: an updated sample metadata hub. Nucleic Acids Res. 2019 01 08; 47(D1):D1172-D1178. PMID: 30407529.
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    5. Buniello A, MacArthur JAL, Cerezo M, Harris LW, Hayhurst J, Malangone C, McMahon A, Morales J, Mountjoy E, Sollis E, Suveges D, Vrousgou O, Whetzel PL, Amode R, Guillen JA, Riat HS, Trevanion SJ, Hall P, Junkins H, Flicek P, Burdett T, Hindorff LA, Cunningham F, Parkinson H. The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res. 2019 01 08; 47(D1):D1005-D1012. PMID: 30445434.
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    6. Xin J, Mark A, Afrasiabi C, Tsueng G, Juchler M, Gopal N, Stupp GS, Putman TE, Ainscough BJ, Griffith OL, Torkamani A, Whetzel PL, Mungall CJ, Mooney SD, Su AI, Wu C. High-performance web services for querying gene and variant annotation. Genome Biol. 2016 05 06; 17(1):91. PMID: 27154141.
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    7. Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert CJ, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J. The Ontology for Biomedical Investigations. PLoS One. 2016; 11(4):e0154556. PMID: 27128319.
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    8. Whetzel PL, Grethe JS, Banks DE, Martone ME. The NIDDK Information Network: A Community Portal for Finding Data, Materials, and Tools for Researchers Studying Diabetes, Digestive, and Kidney Diseases. PLoS One. 2015; 10(9):e0136206. PMID: 26393351.
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    9. Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP, Chen YA, Chiba H, Cock PJ, Cohen KB, Constantin A, Duck G, Dumontier M, Fujisawa T, Fujiwara T, Goto N, Hoehndorf R, Igarashi Y, Itaya H, Ito M, Iwasaki W, Kala? M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, L?tteke T, Marshall MS, Mori T, Mori H, Morita M, Murakami K, Nakao M, Narimatsu H, Nishide H, Nishimura Y, Nystrom-Persson J, Ogishima S, Okamura Y, Okuda S, Oshita K, Packer NH, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin SH, Splendiani A, Strozzi F, Tadaka S, Toukach P, Uchiyama I, Umezaki M, Vos R, Whetzel PL, Yamada I, Yamasaki C, Yamashita R, York WS, Zmasek CM, Kawamoto S, Takagi T. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. J Biomed Semantics. 2014 Feb 05; 5(1):5. PMID: 24495517.
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    10. Whetzel PL. NCBO Technology: Powering semantically aware applications. J Biomed Semantics. 2013 Apr 15; 4 Suppl 1:S8. PMID: 23734708.
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    11. Maguire E, Gonz?lez-Beltr?n A, Whetzel PL, Sansone SA, Rocca-Serra P. OntoMaton: a bioportal powered ontology widget for Google Spreadsheets. Bioinformatics. 2013 Feb 15; 29(4):525-7. PMID: 23267176.
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    12. Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr; 19(2):190-5. PMID: 22081220.
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    13. Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul; 39(Web Server issue):W541-5. PMID: 21672956.
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    14. Luciano JS, Andersson B, Batchelor C, Bodenreider O, Clark T, Denney CK, Domarew C, Gambet T, Harland L, Jentzsch A, Kashyap V, Kos P, Kozlovsky J, Lebo T, Marshall SM, McCusker JP, McGuinness DL, Ogbuji C, Pichler E, Powers RL, Prud'hommeaux E, Samwald M, Schriml L, Tonellato PJ, Whetzel PL, Zhao J, Stephens S, Dumontier M. The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside. J Biomed Semantics. 2011 05 17; 2 Suppl 2:S1. PMID: 21624155.
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    15. Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Karsch Mizrachi I, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C. Towards BioDBcore: a community-defined information specification for biological databases. Database (Oxford). 2011; 2011:baq027. PMID: 21205783.
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    16. Kettner C, Field D, Sansone SA, Taylor C, Aerts J, Binns N, Blake A, Britten CM, de Marco A, Fostel J, Gaudet P, Gonz?lez-Beltr?n A, Hardy N, Hellemans J, Hermjakob H, Juty N, Leebens-Mack J, Maguire E, Neumann S, Orchard S, Parkinson H, Piel W, Ranganathan S, Rocca-Serra P, Santarsiero A, Shotton D, Sterk P, Untergasser A, Whetzel PL. Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop. Stand Genomic Sci. 2010 Dec 25; 3(3):259-66. PMID: 21304730.
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    17. Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Mizrachi IK, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C. Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res. 2011 Jan; 39(Database issue):D7-10. PMID: 21097465.
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    18. Tenenbaum JD, Whetzel PL, Anderson K, Borromeo CD, Dinov ID, Gabriel D, Kirschner B, Mirel B, Morris T, Noy N, Nyulas C, Rubenson D, Saxman PR, Singh H, Whelan N, Wright Z, Athey BD, Becich MJ, Ginsburg GS, Musen MA, Smith KA, Tarantal AF, Rubin DL, Lyster P. The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research. J Biomed Inform. 2011 Feb; 44(1):137-45. PMID: 20955817.
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    19. Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL, Storey MA, Chute CG, Musen MA. BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res. 2009 Jul; 37(Web Server issue):W170-3. PMID: 19483092.
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    20. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007 Nov; 25(11):1251-5. PMID: 17989687.
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    21. Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, Degreef J, Hardy N, Hermjakob H, Hubbard SJ, Hussey P, Igra M, Jenkins H, Julian RK, Laursen K, Oliver SG, Paton NW, Sansone SA, Sarkans U, Stoeckert CJ, Taylor CF, Whetzel PL, White JA, Spellman P, Pizarro A. The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat Biotechnol. 2007 Oct; 25(10):1127-33. PMID: 17921998.
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    22. Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ, White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma A. A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics. 2006 Nov 06; 7:489. PMID: 17087822.
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    23. Whetzel PL, Parkinson H, Causton HC, Fan L, Fostel J, Fragoso G, Game L, Heiskanen M, Morrison N, Rocca-Serra P, Sansone SA, Taylor C, White J, Stoeckert CJ. The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics. 2006 Apr 01; 22(7):866-73. PMID: 16428806.
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    24. Whetzel PL, Brinkman RR, Causton HC, Fan L, Field D, Fostel J, Fragoso G, Gray T, Heiskanen M, Hernandez-Boussard T, Morrison N, Parkinson H, Rocca-Serra P, Sansone SA, Schober D, Smith B, Stevens R, Stoeckert CJ, Taylor C, White J, Wood A. Development of FuGO: an ontology for functional genomics investigations. OMICS. 2006; 10(2):199-204. PMID: 16901226.
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    25. Stoeckert C, Ball C, Brazma A, Brinkman R, Causton H, Fan L, Fostel J, Fragoso G, Heiskanen M, Holstege F, Morrison N, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Sarkans U, Sherlock G, Stevens R, Taylor C, Taylor R, Whetzel P, White J. Wrestling with SUMO and bio-ontologies. Nat Biotechnol. 2006 Jan; 24(1):21-2; author reply 23. PMID: 16404382.
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    26. Whetzel PL, Parkinson H, Stoeckert CJ. Using ontologies to annotate microarray experiments. Methods Enzymol. 2006; 411:325-39. PMID: 16939798.
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    27. Manduchi E, Grant GR, He H, Liu J, Mailman MD, Pizarro AD, Whetzel PL, Stoeckert CJ. RAD and the RAD Study-Annotator: an approach to collection, organization and exchange of all relevant information for high-throughput gene expression studies. Bioinformatics. 2004 Mar 01; 20(4):452-9. PMID: 14990441.
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    28. Bahl A, Brunk B, Crabtree J, Fraunholz MJ, Gajria B, Grant GR, Ginsburg H, Gupta D, Kissinger JC, Labo P, Li L, Mailman MD, Milgram AJ, Pearson DS, Roos DS, Schug J, Stoeckert CJ, Whetzel P. PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data. Nucleic Acids Res. 2003 Jan 01; 31(1):212-5. PMID: 12519984.
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    29. Whetzel PL, Hnatow LL, Keeler CL, Dohms JE. Transposon mutagenesis of Mycoplasma gallisepticum. Plasmid. 2003 Jan; 49(1):34-43. PMID: 12583999.
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    30. Keeler CL, Hnatow LL, Whetzel PL, Dohms JE. Cloning and characterization of a putative cytadhesin gene (mgc1) from Mycoplasma gallisepticum. Infect Immun. 1996 May; 64(5):1541-7. PMID: 8613358.
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    31. Whetzel PL, Jackwood DJ. Comparison of neutralizing epitopes among infectious bursal disease viruses using radioimmunoprecipitation. Avian Dis. 1995 Jul-Sep; 39(3):499-506. PMID: 8561733.
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    32. Dohms JE, Hnatow LL, Whetzel P, Morgan R, Keeler CL. Identification of the putative cytadhesin gene of Mycoplasma gallisepticum and its use as a DNA probe. Avian Dis. 1993 Apr-Jun; 37(2):380-8. PMID: 8363503.
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