| 2018 | AMIA | FAIRness and Usability for Open-access Omics Data Systems. | Daniel C. Berrios, Afshin Beheshti, Sylvain Costes |
| 2018 | AMIA | NASA's GeneLab: An Integrated Omics Data Commons and Workbench. | Daniel C. Berrios, Sylvain Costes, Peter B. Tran |
| 2016 | AMIA | NASA's GeneLab: Phase I Results and Plans. | Daniel C. Berrios, Jon Welch, Homer Fogle, Michael Skidmore, Oana Marcu |
| 2015 | AMIA | GeneLab: NASA's Open Access, Collaborative Platform for Systems Biology and Space Medicine. | Daniel C. Berrios, Terri Thompson, Homer Fogle, Jon Rask, Joseph Coughlan |
| 2001 | AMIA | Information Retrieval Using UMLS-based Structured Queries. | Lawrence M. Fagan, Daniel C. Berrios, Albert Chan, Russell J. Cucina, Anupam Datta, Maulik K. Shah, Sujith Surendran |
| 2000 | AMIA | Automated indexing for full text information retrieval. | Daniel C. Berrios |
| 1999 | AMIA | Knowledge requirements for automated inference of medical textbook markup. | Daniel C. Berrios, Andrew Kehler, Lawrence M. Fagan |
| 1999 | AMIA | Automation and integration of components for generalized semantic markup of electronic medical texts. | Jonathan M. Dugan, Daniel C. Berrios, Xiaole Liu, David K. Kim, Herbert Kaizer, Lawrence M. Fagan |
| 1998 | AMIA | Automated Text Markup for Information Retrieval from an Electronic Textbook of Infectious Disease. | Daniel C. Berrios, Andrew Kehler, David K. Kim, Victor L. Yu, Lawrence M. Fagan |
| 1998 | AMIA | MYCIN II: design and implementation of a therapy reference with complex content-based indexing. | David K. Kim, Lawrence M. Fagan, Kathleen T. Jones, Daniel C. Berrios, Victor L. Yu |