Straight-Line Drawings of Protein Interactions. - Wojciech Basalaj; Karen Eilbeck (GD, 1999)

INTERACT: An Object Oriented Protein-Protein Interaction Database. - Karen Eilbeck; Andy Brass; Norman W. Paton; Charlie Hodgman (ISMB, 1999)

Conceptual modelling of genomic information. - Norman W. Paton; Shakeel A. Khan; Andrew Hayes; Fouzia Moussouni; Andy Brass; Karen Eilbeck; Carole A. Goble; Simon J. Hubbard; Stephen G. Oliver (Bioinform., 2000)

GIMS - A Data Warehouse for Storage and Analysis of Genome Sequence and Functional Data. - Mike Cornell; Norman W. Paton; Shengli Wu 001; Carole A. Goble; Crispin J. Miller; Paul Kirby; Karen Eilbeck; Andy Brass; Andrew Hayes; Stephen G. Oliver (BIBE, 2001)

The Protein Feature Ontology: a tool for the unification of protein feature annotations. - Gabrielle A. Reeves; Karen Eilbeck; Michele Magrane; Claire O'Donovan; Luisa Montecchi-Palazzi; Midori A. Harris; Sandra E. Orchard; Rafael C. Jiménez; Andreas Prlic; Tim J. P. Hubbard; Henning Hermjakob; Janet M. Thornton (Bioinform., 2008)

Quantitative measures for the management and comparison of annotated genomes. - Karen Eilbeck; Barry Moore; Carson Holt; Mark Yandell (BMC Bioinform., 2009)

SOBA: sequence ontology bioinformatics analysis. - Barry Moore; Guozhen Fan; Karen Eilbeck (Nucleic Acids Res., 2010)

The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data. - Robert Hoehndorf; Colin R. Batchelor; Thomas Bittner; Michel Dumontier; Karen Eilbeck; Rob Knight 001; Chris Mungall; Jane S. Richardson; Jesse Stombaugh; Eric Westhof; Craig L. Zirbel; Neocles Leontis (Appl. Ontology, 2011)

Evolution of the Sequence Ontology terms and relationships. - Christopher J. Mungall; Colin R. Batchelor; Karen Eilbeck (J. Biomed. Informatics, 2011)

Using GVF for Clinical Annotation of Personal Genomes. - Barry Moore; Shawn Rynearson; Fiona Cunningham; Graham R. S. Ritchie; Karen Eilbeck (AIMM, 2012)

Efforts toward a More Consistent and Interoperable Sequence Ontology. - Michael Bada; Karen Eilbeck (ICBO, 2012)

Using KaOS Ontologies to Model Policy Requirements for a Statewide Master Person Index. - Jeffrey Duncan; Karen Eilbeck; Catherine J. Staes; Scott P. Narus; Stephen Clyde (AMIA, 2013)

Optimize Querying of LOINC® with an Ontology: Give Me the Chlamydia Tests the Epidemiologists Want Me to Use! - Karen Eilbeck; Jason R. Jacobs; Catherine J. Staes (HICSS, 2013)

Exploring the use of ontologies and automated reasoning to manage selection of reportable condition lab tests from LOINC. - Karen Eilbeck; Jason R. Jacobs; Sunanda R. McGarvey; Cynthia Vinion; Catherine J. Staes (ICBO, 2013)

Evaluation of need for ontologies to manage domain content for the Reportable Conditions Knowledge Management System. - Karen Eilbeck; Julie Lipstein; Sunanda R. McGarvey; Catherine J. Staes (AMIA, 2014)

Clinical Decision Support for Whole Genome Sequence Information Leveraging a Service-Oriented Architecture: a Prototype. - Brandon M. Welch; Salvador Loya; Karen Eilbeck; Kensaku Kawamoto (AMIA, 2014)

Technical desiderata for the integration of genomic data with clinical decision support. - Brandon M. Welch; Karen Eilbeck; Guilherme Del Fiol; Laurence J. Meyer; Kensaku Kawamoto (J. Biomed. Informatics, 2014)

A domain ontology for the Non-Coding RNA field. - Jingshan Huang; Karen Eilbeck; Judith A. Blake; Dejing Dou; Darren A. Natale; Alan Ruttenberg; Barry Smith 001; Michael T. Zimmermann; Guoqian Jiang; Yu Lin; Bin Wu 008; Yongqun He; et al. (BIBM, 2015)

A semantic approach for knowledge capture of MIcroRNA-Target gene interactions. - Jingshan Huang; Fernando Gutierrez; Dejing Dou; Judith A. Blake; Karen Eilbeck; Darren A. Natale; Barry Smith 001; Yu Lin; Xiaowei Wang; Zixing Liu; Ming Tan; Alan Ruttenberg (BIBM, 2015)

Improving the Sequence Ontology terminology for genomic variant annotation. - Fiona Cunningham; Barry Moore; Nicole Ruiz-Schultz; Graham R. S. Ritchie; Karen Eilbeck (J. Biomed. Semant., 2015)

Birth of identity: understanding changes to birth certificates and their value for identity resolution. - Jeffrey Duncan; Scott P. Narus; Stephen Clyde; Karen Eilbeck; Sidney N. Thornton; Catherine J. Staes (J. Am. Medical Informatics Assoc., 2015)

The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology. - Jingshan Huang; Karen Eilbeck; Barry Smith 001; Judith A. Blake; Dejing Dou; Weili Huang; Darren A. Natale; Alan Ruttenberg; Jun Huan; Michael T. Zimmermann; Guoqian Jiang; Yu Lin; et al. (J. Biomed. Semant., 2016)

OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data. - Jingshan Huang; Fernando Gutierrez; Harrison J. Strachan; Dejing Dou; Weili Huang; Barry Smith 001; Judith A. Blake; Karen Eilbeck; Darren A. Natale; Yu Lin; Bin Wu 008; Nisansa de Silva; et al. (J. Biomed. Semant., 2016)

The development of non-coding RNA ontology. - Jingshan Huang; Karen Eilbeck; Barry Smith 001; Judith A. Blake; Dejing Dou; Weili Huang; Darren A. Natale; Alan Ruttenberg; Jun Huan; Michael T. Zimmermann; Guoqian Jiang; Yu Lin; et al. (Int. J. Data Min. Bioinform., 2016)

The genomic CDS sandbox: An assessment among domain experts. - Ayesha Aziz; Kensaku Kawamoto; Karen Eilbeck; Marc S. Williams; Robert R. Freimuth; Mark A. Hoffman; Luke V. Rasmussen; Casey Lynnette Overby; Brian H. Shirts; James M. Hoffman; Brandon M. Welch (J. Biomed. Informatics, 2016)

Semantics-oriented data science and computational life sciences: Innovative application of semantic technologies in microRNA and lncRNA research. - Jingshan Huang; Dejing Dou; Ming Tan; Glen M. Borchert; Karen Eilbeck; Alan Ruttenberg; Ping Yang (ICCABS, 2017)

The VAAST Variant Prioritizer (VVP): ultrafast, easy to use whole genome variant prioritization tool. - Steven Flygare; Edgar Javier Hernandez; Lon Phan; Barry Moore; Man Li; Anthony P. Fejes; Hao Hu; Karen Eilbeck; Chad D. Huff; Lynn Jorde; Martin G. Reese; Mark Yandell (BMC Bioinform., 2018)

Continuous Predictive Modelling for Sepsis, Organ Failure, and In-hospital Mortality in the Intensive Care Unit. - Amber Kiser; Devin Horton; Karen Eilbeck; Samir E. AbdelRahman (AMIA, 2019)

Implementing the VMC specification to reduce ambiguity in genomic variant representation. - Michael T. Watkins; Shawn Rynearson; Alex Henrie; Karen Eilbeck (AMIA, 2019)

Utilization of BPM+ Health for the Representation of Clinical Knowledge: A Framework for the Expression and Assessment of Clinical Practice Guidelines (CPG) Utilizing Existing and Emerging Object Management Group (OMG) Standards. - Robert F. Lario; Steve Hasely; Stephen White; Karen Eilbeck; Richard Soley; Stan Huff 001; Kensaku Kawamoto (AMIA, 2020)

Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API. - Thomas Desvignes; Phillipe Loher; Karen Eilbeck; Jeffery Ma; Gianvito Urgese; Bastian Fromm; Jason Sydes; Ernesto Aparicio-Puerta; Víctor Barrera; Roderic Espín; Florian Thibord; Xavier Bofill-De Ros; et al. (Bioinform., 2020)

LocalVar: a local variant collection manager to asynchronously detect synonyms, HGVS expression changes, and variant interpretation changes from ClinVar. - Michael T. Watkins; Wendy Kohlmann; Therese Berry; Neetha Sama; Cathryn Koptiuch; Shawn Rynearson; Karen Eilbeck (AMIA, 2022)

Proposing a Novel Hybrid Short-Term Exchange Program in Biomedical and Health Informatics Education. - Thomas Engelsma; Carolin Anders; Susan J. Oudbier; Karen Eilbeck; Petra Knaup; Linda W. Peute; Matthias Ganzinger (MIE, 2023)

A method for structuring complex clinical knowledge and its representational formalisms to support composite knowledge interoperability in healthcare. - Robert F. Lario; Kensaku Kawamoto; Davide Sottara; Karen Eilbeck; Stanley M. Huff; Guilherme Del Fiol; Richard Soley; Blackford Middleton (J. Biomed. Informatics, 2023)

The Business Process Management for Healthcare (BPM+ Health) Consortium: motivation, methodology, and deliverables for enabling clinical knowledge interoperability (CKI). - Robert F. Lario; Richard Soley; Stephen White; John Butler; Guilherme Del Fiol; Karen Eilbeck; Stanley M. Huff; Kensaku Kawamoto (J. Am. Medical Informatics Assoc., 2024)