Eilbeck, Karen , MSc, PhD

Research Interests

  • Biomedical Informatics
  • Genomics
  • Genetic Variant Analysis
  • Genome Annotation
  • Knowledge Representation
  • Ontology

Languages

  • English

Academic Information

  • Departments: Biomedical Informatics - Professor

Academic Office Information

  • 801-585-9934
  • Biomedical Informatics
    421 Wakara Way, Room: Suite 140
    Salt Lake City, UT 84108

Academic Bio

Dr. Karen Eilbeck earned both her MSc degree in Bioinformatics and her PhD in Biochemistry at the University of Manchester in England. She did postdoctoral training in the Department of Computer Science also at the University of Manchester. She is currently a Professor in the University of Utah’s Biomedical Informatics Department.

Her expertise is in understanding and accessing biological data in order to understand diseases better. Her research involves the annotation of biological sequence, in particular genome sequence. Genomic annotation is the process of adding further knowledge to the raw sequence data, such as the location of genes, the functions of the gene products, and the positions of known mutations. Dr. Eilbeck also maintains the Sequence Ontology, an open-source project for organizing and naming the parts of genomic sequence and the relationships between these parts. This project has unified the vocabulary used to annotate genomes, enabling computational exploration of data from many sources. It forms the terminology used by many genome software programs and model organism communities.

Recently she has helped coordinate an effort to standardize the terminology and metadata needed to describe sequence variants with regards to a reference genome, and has provided a dataset of 10 standardized whole genomes for analysis and benchmarking. This work is relevant to areas of medicine such as genetic testing and whole genome analysis.

Dr. Eilbeck joined the department in 2010 as an Assistant Professor and is also an Adjunct Assistant Professor in the University’s Department of Human Genetics. Prior to moving to Utah, she was a scientist at Celera Genomics, and the Berkeley Drosophila Genome Project at UC Berkeley. She has also been a member of the Gene Ontology Consortium for several years.

More information about Dr. Eilbeck can be found at: http://eilbeck-lab.topaz.genetics.utah.edu

Google Scholar: http://scholar.google.com/citations?hl=en&user=ccf6djEAAAAJ

Research Statement

Quality control of genomic annotations; Management and analysis of personal genomics data; Ontology development to structure biological, genomic and phenotypic data

Education History

Type School Degree
Postdoctoral Training University of Manchester, Department of Computer Science, Genome Information Management System
Bioinformatics
Postdoctoral Training
Doctoral Training University of Manchester
Biochemistry
Ph.D.
Graduate Training University of Manchester
Bioinformatics
M.Sc.
Undergraduate University of Salford
Biological & Biochemical Sciences
B.Sc.

Global Impact

Education History

Type School Degree Country
Postdoctoral Training University of Manchester, Department of Computer Science, Genome Information Management System
Bioinformatics
Postdoctoral Training United Kingdom
Doctoral Training University of Manchester
Biochemistry
Ph.D. United Kingdom
Graduate Training University of Manchester
Bioinformatics
M.Sc. United Kingdom
Undergraduate University of Salford
Biological & Biochemical Sciences
B.Sc. United Kingdom

Selected Publications

Journal Article

  1. Zastrow DB, Baudet H, Shen W, Thomas A, Si Y, Weaver MA, Lager AM, Liu J, Mangels R, Dwight SS, Wright MW, Dobrowolski SF, Eilbeck K, Enns GM, Feigenbaum A, Lichter-Konecki U, Lyon E, Pasquali M, Watson M, Blau N, Steiner RD, Craigen WJ, Mao R (2018 Nov). Unique aspects of sequence variant interpretation for inborn errors of metabolism (IEM): The ClinGen IEM Working Group and the Phenylalanine Hydroxylase Gene. Hum Mutat, 39(11), 1569-1580.
  2. Henrie A, Hemphill SE, Ruiz-Schultz N, Cushman B, DiStefano MT, Azzariti D, Harrison SM, Rehm HL, Eilbeck K (2018 May 23). ClinVar miner: Demonstrating utility of a web-based tool for viewing and filtering clinvar data.LID - 10.1002/humu.23555 [doi]. (Epub ahead of print) Hum Mutat.
  3. Flygare S, Hernandez EJ, Phan L, Moore B, Li M, Fejes A, Hu H, Eilbeck K, Huff C, Jorde L, G Reese M, Yandell M (2018 Feb 20). The VAAST Variant Prioritizer (VVP): ultrafast, easy to use whole genome variant prioritization tool. BMC Bioinformatics, 19(1), 57.
  4. Schlaberg R, Ampofo K, Tardif KD, Stockmann C, Simmon KE, Hymas W, Flygare S, Kennedy B, Blaschke A, Eilbeck K, Yandell M, McCullers JA, Williams DJ, Edwards K, Arnold SR, Bramley A, Jain S, Pavia AT (2017 Sep 15). Human Bocavirus Capsid Messenger RNA Detection in Children With Pneumonia. J Infect Dis, 216(6), 688-696.
  5. Lubin IM, Aziz N, Babb LJ, Ballinger D, Bisht H, Church DM, Cordes S, Eilbeck K, Hyland F, Kalman L, Landrum M, Lockhart ER, Maglott D, Marth G, Pfeifer JD, Rehm HL, Roy S, Tezak Z, Truty R, Ullman-Cullere M, Voelkerding KV, Worthey EA, Zaranek AW, Zook JM (2017 May). Principles and Recommendations for Standardizing the Use of the Next-Generation Sequencing Variant File in Clinical Settings. J Mol Diagn, 19(3), 417-426.
  6. Schlaberg R, Queen K, Simmon K, Tardif K, Stockmann C, Flygare S, Kennedy B, Voelkerding K, Bramley A, Zhang J, Eilbeck K, Yandell M, Jain S, Pavia AT, Tong S, Ampofo K (2017 Mar 25). Viral Pathogen Detection by Metagenomics and Pan Viral Group PCR in Children with Pneumonia Lacking Identifiable Etiology.LID - 10.1093/infdis/jix148 [doi]. (Epub ahead of print) J Infect Dis.
  7. Huang J, Eilbeck K, Smith B, Blake JA, Dou D, Huang W, Natale DA, Ruttenberg A, Huan J, Zimmermann MT, Jiang G, Lin Y, Wu B, Strachan HJ, de Silva N, Kasukurthi MV, Jha VK, He Y, Zhang S, Wang X, Liu Z, Borchert GM, Tan M (2016). The development of non-coding RNA ontology. Int J Data Min Bioinform, 15(3), 214-232.
  8. Huang J, Eilbeck K, Smith B, Blake JA, Dou D, Huang W, Natale DA, Ruttenberg A, Huan J, Zimmermann MT, Jiang G, Lin Y, Wu B, Strachan HJ, He Y, Zhang S, Wang X, Liu Z, Borchert GM, Tan M (2016). The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology. Journal of Biomedical Semantics, 7, 24.
  9. Huang J, Gutierrez F, Strachan HJ, Dou D, Huang W, Smith B, Blake JA, Eilbeck K, Natale DA, Lin Y, Wu B, Silva Nd, Wang X, Liu Z, Borchert GM, Tan M, Ruttenberg A (2016). OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data. Journal of Biomedical Semantics, 7, 25.
  10. Flygare S, Simmon K, Miller C, Qiao Y, Kennedy B, Di Sera T, Graf EH, Tardif KD, Kapusta A, Rynearson S, Stockmann C, Queen K, Tong S, Voelkerding KV, Blaschke A, Byington CL, Jain S, Pavia A, Ampofo K, Eilbeck K, Marth G, Yandell M, Schlaberg R (2016). Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling. Genome Biology, 17(1), 111.
  11. Aziz A, Kawamoto K, Eilbeck K, Williams MS, Freimuth RR, Hoffman MA, Rasmussen LV, Overby CL, Shirts BH, Hoffman JM, Welch BM (2016 Jan 15). The genomic CDS sandbox: An assessment among domain experts.LID - S1532-0464(15)00299-3 [pii]LID - 10.1016/j.jbi.2015.12.019 [doi]. (Epub ahead of print) J Biomed Inform.
  12. Graf EH, Simmon KE, Tardif KD, Hymas W, Flygare S, Eilbeck K, Yandell M, Schlaberg R (2016 Apr). Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR Panel. J Clin Microbiol, 54(4), 1000-7.
  13. Thibault JC, Roe DR, Eilbeck K, Cheatham Iii TE, Facelli JC (2015 Sep 21). Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology. SAR QSAR Environ Res, 1-17.
  14. JC Thibault, DR Roe, K Eilbeck, TE Cheatham III amp JC Facelli (). Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology. Special Issue: 8th International Symposium on Computational Methods in Toxicology and Pharmacology Integrating Internet Resources (CMTPI-2015). SAR QSAR Environ Res.
  15. Duncan J, Eilbeck K, Narus SP, Clyde S, Thornton S, Staes C (). Building an Ontology for Identity Resolution in Healthcare and Public Health. OJPHI, 7(2).
  16. Cunningham F, Moore B, Ruiz-Schultz N, Ritchie GR, Eilbeck K (2015). Improving the Sequence Ontology terminology for genomic variant annotation. Journal of Biomedical Semantics, 6, 32.
  17. Baran J, Durgahee BS, Eilbeck K, Antezana E, Hoehndorf R, Dumontier M (2015). GFVO: the Genomic Feature and Variation Ontology. PeerJ, 3, e933.
  18. Dames S, Eilbeck K, Mao R (2015). A high-throughput next-generation sequencing assay for the mitochondrial genome. Methods Mol Biol, 1264, 77-88.
  19. Duncan J, Narus SP, Clyde S, Eilbeck K, Thornton S, Staes C (2015 Apr). Birth of identity: understanding changes to birth certificates and their value for identity resolution. J Am Med Inform Assoc, 22(e1), e120-9.
  20. Eilbeck KL, Lipstein J, McGarvey S, Staes CJ (2014). Evaluation of need for ontologies to manage domain content for the Reportable Conditions Knowledge Management System. AMIA Annu Symp Proc, 2014, 496-505.
  21. Welch BM, Rodriguez-Loya S, Eilbeck K, Kawamoto K (2014). Clinical decision support for whole genome sequence information leveraging a service-oriented architecture: a prototype. AMIA Annu Symp Proc, 2014, 1188-97.
  22. Welch BM, Loya SR, Eilbeck K, Kawamoto K (2014 Apr 4). A proposed clinical decision support architecture capable of supporting whole genome sequence information. Journal of Personalized Medicine, 4(2), 176-99.
  23. Welch BM, Eilbeck K, Del Fiol G, Meyer LJ, Kawamoto K (2014 Oct). Technical desiderata for the integration of genomic data with clinical decision support. J Biomed Inform, 51, 3-7.
  24. Huang J, Dang J, Borchert GM, Eilbeck K, Zhang H, Xiong M, Jiang W, Wu H, Blake JA, Natale DA, Tan M (2014). OMIT: Dynamic, Semi-Automated Ontology Development for the microRNA Domain. PLoS ONE, 9(7), e100855.
  25. Brandon M Welch, Salvador Rodriguez Loya, Karen Eilbeck and Kensaku Kawamoto (). A Proposed Clinical Decision Support Architecture Capable of Supporting Whole Genome Sequence Information. Journal of Personalized Medicine, 4(2), 176-199.
  26. Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, Dechene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D Jr, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, de Bakker PI, Duzkale H, Dworzy Ski P, Fairbrother W, Francioli L, Funke BH, Giovanni MA, Handsaker RE, Lage K, Lebo MS, Lek M, Leshchiner I, Macarthur DG, McLaughlin HM, Murray MF, Pers TH, Polak PP, Raychaudhuri S, Rehm HL, Soemedi R, Stitziel NO, Vestecka S, Supper J, Gugenmus C, Klocke B, Hahn A, Schubach M, Menzel M, Biskup S, Freisinger P, Deng M, Braun M, Perner S, Smith RJ, Andorf JL, Huang J, Ryckman K, Sheffield VC, Stone EM, Bair T, Black-Ziegelbein EA, Braun TA, Darbro B, Deluca AP, Kolbe DL, Scheetz TE, Shearer AE, Sompallae R, Wang K, Bassuk AG, Edens E, Mathews K, Moore SA, Shchelochkov OA, Trapane P, Bossler A, Campbell CA, Heusel JW, Kwitek A, Maga T, Panzer K, Wassink T, Van Daele D, Azaiez H, Booth K, Meyer N, Segal MM, Williams MS, Tromp G, White P, Corsmeier D, Fitzgerald-Butt S, Herman G, Lamb-Thrush D, McBride KL, Newsom D, Pierson CR, Rakowsky AT, Maver A, Lovre I L, Palanda I A, Peterlin B, Torkamani A, Wedell A, Huss M, Alexeyenko A, Lindvall JM, Magnusson M, Nilsson D, Stranneheim H, Taylan F, Gilissen C, Hoischen A, van Bon B, Yntema H, Nelen M, Zhang W, Sager J, Zhang L, Blair K, Kural D, Cariaso M, Lennon GG, Javed A, Agrawal S, Ng PC, Sandhu KS, Krishna S, Veeramachaneni V, Isakov O, Halperin E, Friedman E, Shomron N, Glusman G, Roach JC, Caballero J, Cox HC, Mauldin D, Ament SA, Rowen L, Richards DR, Lucas FA, Gonzalez-Garay ML, Caskey CT, Bai Y, Huang Y, Fang F, Zhang Y, Wang Z, Barrera J, Garcia-Lobo JM, Gonzalez-Lamuno D, Llorca J, Rodriguez MC, Varela I, Reese MG, De La Vega FM, Kiruluta E, Cargill M, Hart RK, Sorenson JM, Lyon GJ, Stevenson DA, Bray BE, Moore BM, Eilbeck K, Yandell M, Zhao H, Hou L, Chen X, Yan X, Chen M, Li C, Yang C, Gunel M, Li P, Kong Y, Alexander AC, Albertyn ZI, Boycott KM, Bulman DE, Gordon PM, Innes AM, Knoppers BM, Majewski J, Marshall CR, Parboosingh JS, Sawyer SL, Samuels ME, Schwartzentruber J, Kohane IS, Margulies DM (2014 Mar 25). An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biol, 15(3), R53.
  27. Singleton MV, Guthery SL, Voelkerding KV, Chen K, Kennedy B, Margraf RL, Durtschi J, Eilbeck K, Reese MG, Jorde LB, Huff CD, Yandell M (2014 Apr 3). Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families. Am J Hum Genet, 94(4), 599-610.
  28. ORawe JA, Fang H, Rynearson S, Robison R, Kiruluta ES, Higgins G, Eilbeck K, Reese MG, Lyon GJ (2013). Integrating precision medicine in the study and clinical treatment of a severely mentally ill person. PeerJ, 1, e177.
  29. Dames S, Chou LS, Xiao Y, Wayman T, Stocks J, Singleton M, Eilbeck K, Mao R (2013 Jul). The development of next-generation sequencing assays for the mitochondrial genome and 108 nuclear genes associated with mitochondrial disorders. J Mol Diagn, 15(4), 526-34.
  30. Hoehndorf R, Batchelor C, Bittner T, Dumontier M, Eilbeck K, Knight R, Mungall CJ, Richardson JS, Stombaugh J, Westhof E, Zirbel CL, Leontis NB (). The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data. Appl Ontol, 6(1), 53-89.
  31. Mungall CJ, Batchelor C, Eilbeck K (2011 Feb). Evolution of the Sequence Ontology terms and relationships. J Biomed Inform, 44(1), 87-93.
  32. Reese MG, Moore B, Batchelor C, Salas F, Cunningham F, Marth GT, Stein L, Flicek P, Yandell M, Eilbeck K (2010). A standard variation file format for human genome sequences. Genome Biol, 11(8), R88.
  33. Moore B, Fan G, Eilbeck K (2010 Jul). SOBA: sequence ontology bioinformatics analysis. Nucleic Acids Res, 38(Web Server issue), W161-4.
  34. The Gene Ontology Consortium Tanya Z Berardini, Donghui Li, Eva Huala, Susan Bridges, Shane Burgess, Fiona McCarthy, Seth Carbon, Suzanna E Lewis, Christopher J Mungall, Amina Abdulla, Valerie Wood, Erika Feltrin, Giorgio Valle, Rex L Chisholm, Petra Fey, Pascale Gaudet, Warren Kibbe, Siddhartha Basu, Yulia Bushmanova, Karen Eilbeck, Deborah A Siegele, Brenley McIntosh, Daniel Renfro, Adrienne Zweifel, James C Hu, Michael Ashburner, Susan Tweedie, Yasmin Alam-Faruque, Rolf Apweiler, Andrea Auchinchloss, Amos Bairoch, Daniel Barrell, David Binns, Marie-Claude Blatter, Lydie Bougueleret, Emmanuel Boutet, Lionel Breuza, Alan Bridge, Paul Browne, Wei Mun Chan, Elizabeth Coudert, Louise Daugherty, Emily Dimmer, Ruth Eberhardt, Anne Estreicher, Livia Famiglietti, Serenella Ferro-Rojas, Marc Feuermann, Rebecca Foulger, Nadine Gruaz-Gumowski, Ursula Hinz, Rachael Huntley, Silvia Jimenez, Florence Jungo, Guillaume Keller, Kati Laiho, Duncan Legge, Philippe Lemercier, Damien Lieberherr, Michele Magrane, Claire ODonovan, Ivo Pedruzzi, Sylvain Poux, Catherine Rivoire, Bernd Roechert, Tony Sawford, Michel Schneider, Eleanor Stanley, Andre Stutz, Shyamala Sundaram, Michael Tognolli, Ioannis Xenarios, Midori A Harris, Jennifer I Deegan ne Clark, Amelia Ireland, Jane Lomax, Pankaj Jaiswal, Marcus Chibucos, Michelle Gwinn Giglio, Jennifer Wortman, Linda Hannick, Ramana Madupu, David Botstein, Kara Dolinski, Michael S Livstone, Rose Oughtred, Judith A Blake, Carol Bult, Alexander D Diehl, Mary Dolan, Harold Drabkin, Janan T Eppig, David P Hill, Li Ni, Martin Ringwald, Dmitry Sitnikov, Candace Collmer, Trudy Torto-Alalibo, Stan Laulederkind, Mary Shimoyama, Simon Twigger, Peter DEustachio, Lisa Matthews, Rama Balakrishnan, Gail Binkley, J Michael Cherry, Karen R Christie, Maria C Costanzo, Stacia R Engel, Dianna G Fisk, Jodi E Hirschman, Benjamin C Hitz, Eurie L Hong, Cynthia J Krieger, Stuart R Miyasato, Robert S Nash, Julie Park, Marek S Skrzypek, Shuai Weng, Edith D Wong, Martin Aslett, Juancarlos Chan, Ranjana Kishore, Paul Sternberg, Kimberly Van Auken, Varsha K Khodiyar, Ruth C Lovering, Philippa J Talmud, Doug Howe, Monte Westerfield (In Press). The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res, Jan 38(Database), D331-5.
  35. Karp DR, Marthandan N, Marsh SG, Ahn C, Arnett FC, Deluca DS, Diehl AD, Dunivin R, Eilbeck K, Feolo M, Guidry PA, Helmberg W, Lewis S, Mayes MD, Mungall C, Natale DA, Peters B, Petersdorf E, Reveille JD, Smith B, Thomson G, Waller MJ, Scheuermann RH (2010 Feb 15). Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosis. Hum Mol Genet, 19(4), 707-19.
  36. Eilbeck K, Moore B, Holt C, Yandell M (2009). Quantitative measures for the management and comparison of annotated genomes. BMC Bioinformatics, 10, 67.
  37. Reeves GA, Eilbeck K, Magrane M, ODonovan C, Montecchi-Palazzi L, Harris MA, Orchard S, Jimenez RC, Prlic A, Hubbard TJ, Hermjakob H, Thornton JM (2008 Dec 1). The Protein Feature Ontology: a tool for the unification of protein feature annotations. Bioinformatics, 24(23), 2767-72.
  38. 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 (2007 Nov). The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol, 25(11), 1251-5.
  39. The Gene Ontology Consortium Midori A Harris, Jennifer I Deegan ne Clark, Amelia Ireland, Jane Lomax, Michael Ashburner, Susan Tweedie, Seth Carbon, Suzanna Lewis, Chris Mungall, John Day-Richter, Eilbeck K, Judith A Blake, Carol Bult, Alexander D Diehl, Mary Dolan, Harold Drabkin, Janan T Eppig, David P Hill, Li Ni, Martin Ringwald, Rama Balakrishnan, Gail Binkley, J Michael Cherry, Karen R Christie, Maria C Costanzo, Qing Dong, Stacia R Engel, Dianna G Fisk, Jodi E Hirschman, Benjamin C Hitz, Eurie L Hong, Cynthia J Krieger, Stuart R Miyasato, Robert S Nash, Julie Park, Marek S Skrzypek, Shuai Weng, Edith D Wong, Kathy K Zhu, David Botstein, Kara Dolinski, Michael S Livstone, Rose Oughtred, Tanya Berardini, Donghui Li, Seung Y Rhee, Rolf Apweiler, Daniel Barrell, Evelyn Camon, Emily Dimmer, Rachael Huntley, Nicola Mulder, Varsha K Khodiyar, Ruth C Lovering, Sue Povey, Rex Chisholm, Petra Fey, Pascale Gaudet, Warren Kibbe, Ranjana Kishore, Erich M Schwarz, Paul Sternberg, Kimberly Van Auken, Michelle Gwinn Giglio, Linda Hannick, Jennifer Wortman, Howard Jacob, Stan Laulederkind, Victoria Petri, Mary Shimoyama, Jennifer Smith, Simon Twigger, Pankaj Jaiswal, Trent Seigfried, Doug Howe, Monte Westerfield, Candace Collmer Trudy Torto-Alalibo, Erika Feltrin, Giorgio Valle, Susan Bromberg, Shane Burgess, Fiona McCarthy (11/04/2007). The Gene Ontology project in 2008. Nucleic Acids Res, 36(database issue), 440-444.
  40. Gene Ontology Consortium The current members of the GO Consortium are Midori A Harris, Jennifer I Clark, Amelia Ireland, Jane Lomax, Michael Ashburner, Russell Collins, Eilbeck K, Suzanna Lewis, Chris Mungall, John Richter, Gerald M Rubin, ShengQiang Shu, Judith A Blake, Carol J Bult, Alexander D Diehl, Mary E Dolan, Harold J Drabkin, Janan T Eppig, David P Hill, Li Ni, Martin Ringwald, Rama Balakrishnan, Gail Binkley, J Michael Cherry, Karen R Christie, Maria C Costanzo, Qing Dong, Stacia R Engel, Dianna G Fisk, Jodi E Hirschman, Benjamin C Hitz, Eurie L Hong, Christopher Lane, Stuart Miyasato, Robert Nash, Anand Sethuraman, Marek Skrzypek, Chandra L Theesfeld, Shuai Weng, Rolf Apweiler, Daniel Barrell, Evelyn Camon, Emily Dimmer, Nicola, Rex Chisholm, Petra Fey, Pascale Gaudet, Warren Kibbe, Karen Pilcher, Carol A Bastiani, Ranjana Kishore, Erich M Schwarz, Paul Sternberg, Kimberly Van Auken, Michelle Gwinn, Linda Hannick, Jennifer, Martin Aslett, Matthew Berriman, Valerie Wood, Susan Bromberg, Cindy Foote, Howard Jacob, Dean Pasko, Victoria Petri, Dorothy Reilly, Kathy Seiler, Mary Shimoyama, Jennifer Smith, Simon Twigger, Pankaj Jaiswal, Trent Seigfried, Candace Collmer, Doug Howe, Monte Westerfield (2006). The Gene Ontology (GO) project in 2006. Nucleic Acids Res, 34(databse issue), D322-D326.
  41. Eilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, Ashburner M (2005). The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol, 6(5), R44.
  42. Eilbeck K, Lewis SE (2004). Sequence ontology annotation guide. Comparative and Functional Genomics, 5(8), 642-7.
  43. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R (2004 Jan 1). The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res, 32(Database issue), D258-61.
  44. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigo R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X (2001 Feb 16). The sequence of the human genome. Science, 291(5507), 1304-51.
  45. Paton NW, Khan SA, Hayes A, Moussouni F, Brass A, Eilbeck K, Goble CA, Hubbard SJ, Oliver SG (2000 Jun). Conceptual modelling of genomic information. Bioinformatics, 16(6), 548-57.
  46. Basalaj W, Eilbeck K (1999). Straight-line drawings of protein interactions. Lect Notes Comput Sc, 1731, 259-266.
  47. Eilbeck K, Brass A, Paton N, Hodgman C (1999). INTERACT: an object oriented protein-protein interaction database. Proc Int Conf Intell Syst Mol Biol, 87-94.

Review

  1. Eilbeck K, Quinlan A, Yandell M (2017 Oct). Settling the score: variant prioritization and Mendelian disease. [Review]. Nat Rev Genet, 18(10), 599-612.
  2. Desvignes T, Batzel P, Berezikov E, Eilbeck K, Eppig JT, McAndrews MS, Singer A, Postlethwait JH (2015 Nov). miRNA Nomenclature: A View Incorporating Genetic Origins, Biosynthetic Pathways, and Sequence Variants. [Review]. Trends Genet, 31(11), 613-626.

Book Chapter

  1. Shale Dames, Karen Eilbeck, and Rong Mao (). A High-Throughput Next-Generation Sequencing Assay for the Mitochondrial Genome. In Weissig, Volkmar, Edeas, Marvin (Eds.) (Eds.), Mitochondrial Medicine (Methods in Molecular Biology, Vol. 1264). Humana Press.
  2. Eilbeck K (). The Sequence Ontology. In Sylvia Blago (Ed.), Encyclopedia of Systems Biology. Springer.

Conference Proceedings

  1. Reece K Hart Invitae, GA4GH, Gil Alterovitz Harvard Medical School, FHIR Genomics, Larry J Babb Sunquest, ClinGen, Karen Eilbeck University of Utah, Sequence Ontology, Robert R Freimuth Mayo Clinic, HL7 Clinical Genomics Working Group, ClinGen, Sarah E Hunt EBI, Ensembl, David Kreda Harvard Medical School, HL7 Clinical Genomics Working Group, Jennifer Lee NCBI, ClinVar, Peter N Robinson Jackson Laboratory, Human Phenotype Ontology, Shawn Rynearson University of Utah, Sequence Ontology, David Haussler UC Santa Cruz, GA4GH, Heidi Rehm Harvard Medical School, Broad Institute, ClinGen, Peter Goodhand Ontario Institute for Cancer Research, GA4GH (). A community-developed data model for representing sequence variation. Variant Detection 2017, Santiago de Compostela, Spain.
  2. Jingshan Huang, Fernando Gutierrez, Dejing Dou, Judith Blake, Karen Eilbeck, Darren Natale, Barry Smith, Yu Lin, Xiaowei Wang, Zixing Liu, Ming Tan, and Alan Ruttenberg (). A semantic approach for knowledge capture of microRNA-target gene interactions. International Conference on Bioinformatics and Biomedicine, Washington DC: IEEE.
  3. Jingshan Huang, Karen Eilbeck, Judith Blake, Dejing Dou, Darren Natale, Alan Ruttenberg, Barry Smith, Michael Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Yongqun He, Shaojie Zhang, Xiaowei Wang, He Zhang, Zixing Liu, Ming Tan (). A domain ontology for the non-coding RNA field. International Conference on Bioinformatics and Biomedicine, Washington DC: IEEE.
  4. Thibault JC, Roe DR, Eilbeck K, Cheatham TE, Facelli J C (). Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology. Computational Methods in toxicology and pharmacology integrating ineternet resources, Chios, Greece..
  5. Brandon M Welch, Salvador Rodriguez-Loya, Karen Eilbeck, Kensaku Kawamoto (). Paper: Clinical Decision Support for Whole Genome Sequence Information Leveraging a Service-Oriented Architecture: a Prototype. AMIA, Washington DC..
  6. Karen L Eilbeck, Julie Lipstein, Sunanda McGarvey, Catherine J Staes (). Evaluation of need for ontologies to manage domain content for the Reportable Conditions Knowledge Management System. AMIA, Washington DC.
  7. Karen EIlbeck, Catherine Staes, Sunanda Macgarvey (). Transforming Case Notifications through Standards and Specifications. Reportable Conditions Knowledge Management System: Delivering Reporting Specifications. Public Health Informatics Conference,, Atlanta.
  8. Karen Eilbeck, Jason Jacobs, Sunanda McGarvey, Cynthia Vinion and Catherine Staes (). Exploring the use of ontologies and automated reasoning to manage selection of reportable condition lab tests from LOINC. International Conference of Biomedical Ontology, Montreal.
  9. Karen EIlbeck, Jason Jacobs, Catherine Staes (). Optimize Querying of LOINC® with an Ontology:Give Me the Chlamydia Tests the Epidemiologists Want Me to Use! In IEEE (Ed.), 2013 46th Hawaii International Conference on System Sciences (HICSS), Computer Society Press, 2398-2407.
  10. Moore B, Rynearson S, Cunningham F, Ritchie G, Eilbeck K (). Using GVF for Clinical Annotation of Personal Genomes. In Christopher J. O. Baker , Dietrich Rebholz-Schuhmann (Eds.), Annotation, Interpretation and Management of Mutations 2012, CEUR Workshop Proceedings, 916.
  11. Bada M, Eilbeck K (). Efforts Toward a More Consistent and Interoperable Sequence Ontology. International Conference of Biomedical Ontology, Graz, Austria.
  12. Mike Bada and Karen Eilbeck (). Toward a Richer Representation of Sequence Variation in the Sequence Ontology. Annotation, Interpretation and Management of Mutations. A workshop at ECCB10.
  13. Karen Eilbeck, Chris Mungall (July 2009). Evolution of the Sequence Ontology Terms and Relationships. International Conference on Biomedical Ontology, Buffalo: Nature Preceedings.
  14. Colin Batchelor, Karen Eilbeck, Chris Mungall, Jane Richardson, Rob Knight, Jesse Stombaugh, Craig Zirbel, Eric Westhof, Neocles Leontis (July 2009). The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data. International Conference on Biomedical Ontology, Buffalo: Nature Precedings.

Abstract

  1. Wendy W Chapman, Samir AbdelRahman, Jeff Ferraro, Brian E Chapman, Charlene Weir, Damian Borbolla, Edgar Javier Hernandez, John Hurdle, Olga Patterson, Karen Eilbeck (). Creating a New Data Science Track in a Traditional Biomedical Informatics Training Program [Abstract]. AMIA Educators Forum.
  2. Damian Borbolla and Karen EIlbeck (). When to lump and when to split: Understanding academic and professional student expectation and motivation [Abstract]. AMIA Educators forum.
  3. Alexander R Henrie, 1 Brandon Cushman, 2 Sarah Hemphill, 2 Steven Harrison, 2 Marina DiStefano, 2 Danielle Azzariti, 2 Justin Aronson, 3 Lisa M Vincent, 4 Scott R Goehringer, 5 Erin Rooney Riggs, 5 Christa Lese Martin, 5 Heidi L Rehm, 2, 6 Karen Eilbeck1 (). ClinVar Miner: Enabling deep exploration of the ClinVar archive [Abstract]. Curating the Clinical Genome.
  4. Diane B Zastrow, Heather Baudet, Cindy Si, Meredith A Weaver, Angela Lager, Kristy Lee, Wei Shen, Amanda Thomas, Jonathan S Berg, Steven F Dobrowolski, Karen Eilbeck, Gregory Enns, Annette Feigenbaum, Danuta Krotoski, Uta Lichter-Konecki, Elaine Lyon, Marzia Pasquali, William J Craigen, Rong Mao and Robert D Steiner (). Creation and Implementation of Variant Curation Workflow for the ClinGen Inborn Errors in Metabolism Working Group: Phenylalanine Hydroxylase Deficiency [Abstract]. Biocuration 2017.
  5. Nicole Ruiz-Schultz, Justin Paschall, Xing Xu, David Caplan, Carolyn ChNg, Karen Eilbeck and Reece Hart (). hgvs-eval: automated evaluation suite to access HGVS-formatting tools [Abstract]. Biocuration 2017.
  6. Dames S, Brulotte B, Pont-Kingdon G, Eilbeck K, and Mao R (). A Review of Clinical NGS Accuracy for Mitochondrial Disorders [Abstract]. ASHG.
  7. Edward Osborne, PhD, Anne J Blaschke, MD, PhD, FIDSA, FPIDS, Krow Ampofo, MD, FIDSA, FPIDS, Hillary Crandall, MD, PhD, Jarrett Killpack, BSc, Chris R Stockmann, MSc, Andrew P Farrell, PhD, Kael F Fischer, PhD, Andrew Pavia, MD, FIDSA, FSHEA, FPIDS, Karen Eilbeck, PhD, Robert Schlaberg, MD, MPH, Mark Yandell, PhD and Carrie L Byington, MD, FIDSA (). Shared genetic variants among Streptococcus pneumoniae isolates causing complicated pneumonia and empyema in children [Abstract]. IDWEEK.
  8. K Ramachandran, T M Darlington, D A Bilder, J Morgan, M Williams, A Shcheglovitov, G Schellenberg, K Eilbeck, H Coon (). Characterization of Gene Variants Involved in Synaptic Pathways in Extended Utah ASD Pedigrees [Abstract]. 2015 International Meeting for Autism Research.
  9. L Jiang, T M Darlington, A V Bakian, J Morgan, G Schellenberg, K Eilbeck, H Coon (). Penetrance and Specificity of Significant Chromatin Pathway Sequence Risk Variants in Utah Extended ASD Pedigrees [Abstract]. 2015 International Meeting for Autism Research.
  10. Robert Schlaberg, MD, Krista Queen, Keith Simmon, Keith Tardif, Chris Stockmann, Steven Flygare, Brett Kennedy, Karl Voelkerding, Anna M Bramley, Karen Eilbeck, Mark Yandell, Seema Jain, Andrew Pavia, Suxiang Tong and Krow Ampofo (). Viral Pathogen Detection by Metagenomics and Panviral PCR in Children with Pneumonia with no Identifiable Etiology: Preliminary Results from the CDC Etiology of Pneumonia in the Community (EPIC) Study [Abstract]. IDWeek.
  11. Robert Schlaberg, Krow Ampofo, Keith Tardif, Chris Stockmann, Keith Simmon, Weston Hymas, Steven Flygare, Brett Kennedy, Anne J Blaschke, Karen Eilbeck, Mark Yandell, Anna M Bramley, Seema Jain, MD, and Andrew Pavia (). Can Human Bocavirus mRNA Detection Differentiate Acute Infection from Viral Shedding? [Abstract]. IDWeek.
  12. Marc Singleton, Karen Eilbeck, Martin G Reese, Mark Yandell (). Phevor combines phenotype and genotype to expanse diagnostics beyond disease databases [Abstract]. ICCG conference.
  13. Mark Yandell, Barry Moore, Carson Holt, Marc V Singleton, Hao Hu, Scott Watkins, Brett Kennedy, Steven Flygare, Ken R Smith, Chad D Huff, Martin G Reese, Steve L Guthery, Karl V Voelkerding, Karin Chen PeterGruber, Marti Tristani-Firouzi, Karen Eilbeck, Nickola Camp, Gabor Marth and Lynn B Jorde (). The Utah Genome Project [Abstract]. Biology of genomes, CSHL.
  14. Heidi Rehm, Swaroop Aradhya, Samuel Aronson, Sherri Bale, Jonathan Berg, Lisa Brooks, Carlos Bustamante, Mike Cherry, Karen Eilbeck, James Evans, Andrew Faucett, Madhuri Hegde, Melissa Landrum, David Ledbetter, Donna Maglott, Christa Lese Martin, Danielle Metterville, David Miller, Aleksandar Milosavljevic, Robert Nussbaum, Sharon Plon, Erin Ramos, Erin Rigg, George Riley, Steve Sherry, Erik Thorland, Michael Watson, on behalf of the ClinGen Resource (). ClinGen: The Clinical Genome Resource [Abstract]. Human Variome meeting, Paris.
  15. De La Vega FM, Kiruluta E, Reese M, Eilbeck K, Bray B, Mitchell J, Moore B, Rynearson S, Stevenson D, Yandell M (). Children's Leadership Award for the Reliable Interpretation and Appropriate Transmission of Your Genomic Information [Abstract]. Childrens Hospital Boston.
  16. Bada M, Eilbeck K (). Efforts toward a More Consistent and Interoperable Sequence Ontology [Abstract]. Internation Conference on Biomedical Ontology (ICBO).
  17. Cornell M, Paton NW, Wu S, Goble C, Miller C, Kirby P, Eilbeck K, Brass A, Oliver S (2001). GIMS -A Data Warehouse for storage and analysis of genome sequence and functional data [Abstract]. 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE).
  18. Ram Gouripeddi, Danielle Groat, Samir E AbdelRahman, Tom Cheatham, Mollie Cummins, Karen EIlbeck, Bernie LaSalle, Katherine Sward, Julio C Facelli (). Development of a Competency-based Informatics Course for Translational
    Researchers
    [Abstract]. Association for Clinical and Translational Science.
  19. Diane B Zastrow1, 2, Heather Baudet3, Cindy Si4, Amanda Thomas5, Meredith Weaver6, Wei Shen7, Jixia Liu8, Akemi Tanaka5, Rachel Mangels2, Jonathan S Berg3, Stephen F Dobrowski9, Karen Eilbeck10, Gregory Enns2, Annette Feigenbaum11, Uta Lichter-Konecki12, Elaine Lyon7, 10, Marzia Pasquali10, Nenad Blau13, Robert D Steiner14, William J Craigen15, and Rong Mao7 for the ClinGen Inborn Errors of Metabolism Working Group (). Curation of Metabolic Disease Genes: The ClinGen Inborn Errors of Metabolism Working Group and Phenylalanine Hydroxylase [Abstract]. Curating the Clinical Genome.
  20. Shawn Rynearson1, Michael Watkins2, Alex Henrie2, Karen Eilbeck2 (). Tools for managing VMC computed identifiers for variant representation [Abstract]. Curating the Clinical Genome.
  21. Thomas Desvignes2, Karen EIlbeck3, Ioannis S Vlachos4, Bastian Fromm5, Marc K Halushka6, Michael Hackenberg7, Gianvito Urgese8, Elisa Ficarra8, Shruthi Bandyadka9, Jason Sydes2, Peter Batzel2, John H Postlethwait2, Phillipe Loher10, Eric Londin10, Aristeidis G Telonis10, Isidore Rigoutsos10, Lorena Pantano1 (). miRTop: An open source community project for the development of a unified format file for miRNA data [Abstract]. BOSC.
  22. Nicole Ruiz, Justin Paschall, Xing Xu, David Caplan, Carolyn Chng, Karen Eilbeck, Reece Hart (). hgvs-eval: automated evaluation suite to assess HGVS-formatting tools [Abstract]. Curating the Clinical Genome.
  23. Karen Eilbeck1, Shawn Rynearson1, Gil Alterovitz2, Larry J Babb3, Robert R Freimuth4, Sarah E Hunt5, David Kreda6, Jennifer Lee17, Peter N Robinson8, David Haussler9, Heidi Rehm10, 11, Peter Goodhand12, Reece K Hart13 (). A community-developed data model for representing sequence variation [Abstract]. Curating the clinical genome.
  24. Reece K Hart Invitae, GA4GH, Gil Alterovitz Harvard Medical School, FHIR Genomics, Larry J Babb Sunquest, ClinGen, Karen Eilbeck University of Utah, Sequence Ontology, Robert R Freimuth Mayo Clinic, HL7 Clinical Genomics Working Group, ClinGen, Sarah E Hunt EBI, Ensembl, David Kreda Harvard Medical School, HL7 Clinical Genomics Working Group, Jennifer Lee NCBI, ClinVar, Peter N Robinson Jackson Laboratory, Human Phenotype Ontology, Shawn Rynearson University of Utah, Sequence Ontology, David Haussler UC Santa Cruz, GA4GH, Heidi Rehm Harvard Medical School, Broad Institute, ClinGen, Peter Goodhand Ontario Institute for Cancer Research, GA4GH (). A community-developed data model for representing sequence variation [Abstract]. Variant Detection 2017.
  25. Damian Borbolla, MD, MS, Charlene Weir, PhD, Brian E Chapman, PhD, Jennifer Garvin, PhD, Karen Eilbeck, PhD, Wendy W Chapman, PhD (). Training the Next Generation of Informaticians: Development and Implementation of Areas of Emphasis in a Biomedical Informatics Curriculum [Abstract]. Inspire 2017.

Report

  1. Catherine Staes, Karen Eilbeck and Sunanda McGarvey (). Findings and Recommendations: Knowledge Representation Workgroup (CDC's Reportable Conditions Knowledge management System). Atlanta: CDC.

Video/Film/CD/Web/Podcast

  1. Mitchell JA, EIlbeck K, Hurdle JF, Narus SP (). Department of Biomedical Informatics Promotional Video [Web]. Salt Lake City. Available: http://www.youtube.com/user/UofUBMI.
  2. Eilbeck K (2004). The ABCs of Bioinformatics [Web]. Science's Next Wave online magazine. Available: http://nextwave.sciencemag.org/cgi/content/full/2004/09/02/3.