| 2011 | AIME | Understanding Etiology of Complex Neurodevelopmental Disorders: Two Approaches. | Andrey Rzhetsky |
| 2011 | HPDC | A distributed look-up architecture for text mining applications using mapreduce. | Atilla Soner Balkir, Ian T. Foster, Andrey Rzhetsky |
| 2011 | SC | A distributed look-up architecture for text mining applications using MapReduce. | Atilla Soner Balkir, Ian T. Foster, Andrey Rzhetsky |
| 2010 | ICMLA | Discovering and Counting Biomedical Verbs. | Sonjia Waxmonsky, John Goldsmith, Andrey Rzhetsky |
| 2002 | AMIA | Automatic extraction of gene and protein synonyms from MEDLINE and journal articles. | Hong Yu, Vasileios Hatzivassiloglou, Carol Friedman, Andrey Rzhetsky, W. John Wilbur |
| 2002 | ISMB | Of truth and pathways: chasing bits of information through myriads of articles. | Michael Krauthammer, Pauline Kra, Ivan Iossifov, Shawn M. Gomez, George Hripcsak, Vasileios Hatzivassiloglou, Carol Friedman, Andrey Rzhetsky |
| 2002 | PSB | Towards the Prediction of Complete Protein-Protein Interaction Networks. | Shawn M. Gomez, Andrey Rzhetsky |
| 2001 | ISMB | GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles. | Carol Friedman, Pauline Kra, Hong Yu, Michael Krauthammer, Andrey Rzhetsky |
| 2001 | ISMB | Disambiguating proteins, genes, and RNA in text: a machine learning approach. | Vasileios Hatzivassiloglou, Pablo Ariel Dubou, Andrey Rzhetsky |
| 2001 | PSB | Markov Chain Monte Carlo Computation of Confidence Intervals for Substitution-Rate Variation in Proteins. | Andrey Rzhetsky, Pavel Morozov |
| 2000 | AMIA | Using BLAST, A DNA and Protein Sequence Comparison Tool, for Finding Gene and Protein Names in Journal Articles. | Michael Krauthammer, Andrey Rzhetsky, Pavel Morozov, Carol Friedman |
| 1999 | AMIA | A Knowledge Model for Analysis and Simulation of Regulatory Based on Information in Electronic Publications. | Andrey Rzhetsky, Tomohiro Koike, Sergey Kalachikov, Pauline Kra, Carol Friedman |
| 1999 | AMIA | Representing genomic knowledge in the UMLS semantic network. | Hong Yu, Carol Friedman, Andrey Rzhetsky, Pauline Kra |