Link to Google Scolar Profile 

Journal papers

  • Jingshan Huang, Karen Eilbeck, Barry Smith, Judith A. Blake, Dejing Dou, Weili Huang, Darren A. Natale, Alan Ruttenberg, Jun Huan, Michael T. Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison J. Strachan, Yongqun He, Shaojie Zhang, Xiaowei Wang, Zixing Liu, Glen Borchert, Ming Tan. (2016) The Non-Coding RNA Ontology (NCRO): A comprehensive resource for the unification of non-coding RNA biology. Journal of Biomedical Semantics.20167:24
    DOI: 10.1186/s13326-016-0066-0
  • Aziz A, Kawamoto K, Eilbeck K, Williams MS, Freimuth RR, Hoffman MA, Rasmussen LV, Overby CL, Shirts BH, Hoffman JM, Welch BM (2016). 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.
  • Graf EH, Simmon KE, Tardif KD, Hymas W, Flygare S, Eilbeck K, Yandell M, Schlaberg R (2016). 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.
  • Thibault JC, Roe DR, Eilbeck K, Cheatham Iii TE, Facelli JC (2015). Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology. SAR QSAR Environ Res, 1-17.
  • Dames S, Eilbeck K, Mao R (2015). A high-throughput next-generation sequencing assay for the mitochondrial genome. Methods Mol Biol, 1264, 77-88.
  • Duncan J., Eilbeck K., Narus S.P., Clyde S., Thornton S., Staes C (2015). Building an Ontology for Identity Resolution in Healthcare and Public Health. OJPHI, 7(2).
  • Baran J, Durgahee BS, Eilbeck K, Antezana E, Hoehndorf R, Dumontier M (2015). GFVO: the Genomic Feature and Variation Ontology. PeerJ, 3, e933.
  • 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
  • Jeffrey Duncan, Scott P Narus, Stephen Clyde, Karen Eilbeck, Sidney Thornton, Catherine Staes.(2014)  Birth of identity: understanding changes to birth certificates and their value for identity resolution. J Am Med Inform Assoc doi:10.1136/amiajnl-2014-002774 
  • The Gene Ontology Consortium: Berardini TZ, Li D, Huala E, Bridges S, Burgess S, McCarthy F, Carbon S, Lewis SE, Mungall CJ, Abdulla A, Wood V, Feltrin E, Valle G, Chisholm RL, Fey P, Gaudet P, Kibbe W, Basu S, Bushmanova Y, Eilbeck K et al. (2010). The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 38(Database issue):D331-5.
  • Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J Goldberg, Karen Eilbeck, Amelia Ireland, Christopher J Mungall, The OBI Consortium, Neocles Leontis, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H Scheuermann, Nigam Shah, Patricia L Whetzel & Suzanna Lewis. (2007) The OBO Foundry coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology 25, 1251-1255. Published online 7th November 2007
  • Paton, N.W., Khan S., Hayes A., Moussouni F., Brass A., Eilbeck K., Goble C.A., Hubbard S., Oliver S. (2000) Conceptual Modelling of Genomic Information. Bioinformatics 16, 548-557       Also selected for inclusion in the Yearbook of Medical Informatics 2002.


Conference papers

Book Chapters

  • K Eilbeck, C Holt (2013) Sequence Ontology. Encyclopedia of Systems Biology, Springer New York: 1928-1932



  • Duncan JD, Clyde S, Narus S, Eilbeck K, Staes C (2013). Using KAoS Ontologies to Model Policy Requirements for a Statewide Master Person Index. Poster session presented at Poster presentation at: American Medical Informatics Association Annual Symposium, Washington DC..
  • Marc Singleton, Karen EIlbeck, Martin Reese, Mark Yandell (2013). Using Phevor to identify disease-genes in a single affected exome. Poster session presented at Precision Medicine: Personal Genomes & Pharmacogenomics, CSHL.
  • Nicole Ruiz, Barry Moore, Shawn Rynearson, Karen Eilbeck (2013). Using the Sequence Ontology to compare the range of variant annotations from various annotation tools. Poster session presented at Annual Biomedical Research Conference for Minority Students, Nashville.
  • Marc Singleton, Lynn Jorde, Karen Eilbeck, Mark Yandell (2013). Phevor: Using phenotype to identify disease genes in a single affected exome. Poster session presented at ASHG, Boston.
  • Dames S, Wayman T, Stocks J, Eilbeck K, Salama M, Mao R (2012). Bioinformatics optimization for the detection of low level heteroplasmy in the mitochondrial genome. Poster session presented at ASHG, Monreal.
  • Moore B , Rynearson S , Reese M , Yandell M , Eilbeck K. (2012). Annotating Clinical Impact in NGS Data. Poster session presented at Cold Spring Harbor lab, Biology of Genomes Meeting.
  • Dames S. , Wayman T. , Durtschi JD , Singleton M. , Ridge P. , Eilbeck K. , Mao R. (10/14/2011). The use of Next Generation Sequencing for the Development of Mitochondrial Disorder Clinical Assays. Poster session presented at ASHG.