Standardized Representations of the Literature: Combining Diverse Sources of Ribosomal Data. - Russ B. Altman; Neil F. Abernethy; Richard O. Chen (ISMB, 1997)

MHCWeb: converting a WWW database into a knowledge-based collaborative environment. - Lawrence S. Hon; Neil F. Abernethy; Vladimir Brusic; Jenny Chai; Russ B. Altman (AMIA, 1998)

Sophia: Providing Basic Knowledge Services with a Common DBMS. - Neil F. Abernethy; Russ B. Altman (KRDB, 1998)

Sophia: a flexible, Web-based knowledge server. - Neil F. Abernethy; Julie J. Wu; Micheal Hewett; Russ B. Altman (IEEE Intell. Syst., 1999)

RiboWeb: An Ontology-Based System for Collaborative Molecular Biology. - Russ B. Altman; Michael Bada; Xiaoqian J. Chai; Michelle Whirl Carrillo; Richard O. Chen; Neil F. Abernethy (IEEE Intell. Syst., 1999)

An Evaluation of Ontology Exchange Languages for Bioinformatics. - Robin McEntire; Peter D. Karp; Neil F. Abernethy; David Benton; Gregg Helt; Matt DeJongh; Robert Kent; Anthony Kosky; Suzanna Lewis; Dan Hodnett; Eric P. Neumann; Frank Olken; et al. (ISMB, 2000)

Linking information systems for HIV care and research in Kenya. - Alicia F. Guidry; Judd L. Walson; Neil F. Abernethy (IHI, 2010)

Immunization information and population data sources: the information needs of public health practitioners. - Rebecca A. Hills; Blaine Reeder; Debra Revere; William B. Lober; Neil F. Abernethy (IHI, 2010)

Timeliness and data element completeness of immunization data in Washington State in 2010: a comparison of data transfer methods. - Rebecca A. Hills; Debra Revere; Rita Altamore; Neil F. Abernethy; William B. Lober (AMIA, 2012)

Assessing the effective communication of pharmacogenomics knowledge embedded in the electronic health record for drug therapy individualization. - Casey Lynnette Overby; Emily Beth Devine; Neil F. Abernethy; Jeannine McCune; Peter Tarczy-Hornoch (AMIA, 2012)

Assessing network characteristics of cancer associated genes in metabolic and signaling networks. - Deanna Petrochilos; Neil F. Abernethy (CIBCB, 2012)

Technical desiderata for the integration of genomic data into Electronic Health Records. - Daniel R. Masys; Gail P. Jarvik; Neil F. Abernethy; Nicholas R. Anderson 001; George J. Papanicolaou; Dina N. Paltoo; Mark A. Hoffman; Isaac S. Kohane; Howard P. Levy (J. Biomed. Informatics, 2012)

Using random walks to identify cancer-associated modules in expression data. - Deanna Petrochilos; Ali Shojaie; John H. Gennari; Neil F. Abernethy (BioData Min., 2013)

Usability evaluation of pharmacogenomics clinical decision support aids and clinical knowledge resources in a computerized provider order entry system: A mixed methods approach. - Emily Beth Devine; Chia-Ju Lee; Casey Lynnette Overby; Neil F. Abernethy; Jeannine McCune; Joe W. Smith; Peter Tarczy-Hornoch (Int. J. Medical Informatics, 2014)

Visualization and analytics tools for infectious disease epidemiology: A systematic review. - Lauren N. Carroll; Alan P. Au; Landon T. Detwiler; Tsung-chieh Fu; Ian S. Painter; Neil F. Abernethy (J. Biomed. Informatics, 2014)

The SDIDS System for Integrating Global Health Surveillance Data: An Example Application to Malaria Surveillance in Uganda. - Kate Zinszer; Anya Okhmatovskaia; Arash Shaban-Nejad; Lauren N. Carroll; Neil F. Abernethy; David L. Buckeridge (AMIA, 2015)

Making pharmacogenomic-based prescribing alerts more effective: A scenario-based pilot study with physicians. - Casey Lynnette Overby; Emily Beth Devine; Neil F. Abernethy; Jeannine S. McCune; Peter Tarczy-Hornoch (J. Biomed. Informatics, 2015)

Discovering representational differences between pathway knowledge bases for pathway resource merging. - Lucy Lu Wang; John H. Gennari; Neil F. Abernethy (AMIA, 2016)

An Analysis of Differences in Biological Pathway Resources. - Lucy Lu Wang; John H. Gennari; Neil F. Abernethy (ICBO/BioCreative, 2016)

Large benefits to youth-focused HIV treatment-as-prevention efforts in generalized heterosexual populations: An agent-based simulation model. - John E. Mittler; James T. Murphy; Sarah E. Stansfield; Kathryn Peebles; Geoffrey S. Gottlieb; Neil F. Abernethy; Molly C. Reid; Steven M. Goodreau; Joshua T. Herbeck (PLoS Comput. Biol., 2019)

Detecting Reference Errors in Scientific Literature with Large Language Models. - Tianmai M. Zhang; Neil F. Abernethy (CoRR, 2024)

Rapid development of a registry to accelerate COVID-19 vaccine clinical trials. - Neil F. Abernethy; Kylie McCloskey; Meg Trahey; Laurie Rinn; Gail Broder; Michele Andrasik; Rebecca Laborde; Daniel McGhan; Scott Spendolini; Senthil Marimuthu; Adam Kanzmeier; Jayson Hanes; et al. (npj Digit. Medicine, 2025)

Reviewing Scientific Papers for Critical Problems With Reasoning LLMs: Baseline Approaches and Automatic Evaluation. - Tianmai M. Zhang; Neil F. Abernethy (CoRR, 2025)