Bioinformatics concerns the development of computer databases and algorithms for learning, managing and processing biological information. Currently we are focusing on extracting structured information such as protein names and relationships from biological documents using natural language learning for information extraction.

By mining over 750,000 Medline abstracts for human protein interactions and integrating the results with existing databases, we have developed a fairly comprehensive database of 31,609 known human protein interactions. The resulting database is accessible though a web interface at Human Gene ID-SERVE

Discriminative Structure and Parameter Learning for Markov Logic Networks 2008
Tuyen N. Huynh and Raymond J. Mooney, In Proceedings of the 25th International Conference on Machine Learning (ICML), Helsinki, Finland, July 2008.
MARLEDA: Effective Distribution Estimation Through Markov Random Fields 2007
Matthew Alden, PhD Thesis, Department of Computer Sciences, the University of Texas at Austin. Also Technical Report AI07-349.
Integrating Co-occurrence Statistics with Information Extraction for Robust Retrieval of Protein Interactions from Medline 2006
Razvan Bunescu, Raymond Mooney, Arun Ramani and Edward Marcotte, In Proceedings of the HLT-NAACL Workshop on Linking Natural Language Processing and Biology (BioNLP'06), pp. 49-56, New York, NY, June 2006.
Comparative Experiments on Learning Information Extractors for Proteins and their Interactions 2005
Razvan Bunescu, Ruifang Ge, Rohit J. Kate, Edward M. Marcotte, Raymond J. Mooney, Arun Kumar Ramani, and Yuk Wah Wong, Artificial Intelligence in Medicine (special issue on Summarization and Information Extraction from Medical Documents), 2 (2005), pp. 139-155.
Consolidating the Set of Known Human Protein-Protein Interactions in Preparation for Large-Scale Mapping of the Human Interactome 2005
A.K. Ramani, R.C. Bunescu, Raymond J. Mooney and E.M. Marcotte, Genome Biology, Vol. 6, 5 (2005), pp. r40.
Using Biomedical Literature Mining to Consolidate the Set of Known Human Protein-Protein Interactions 2005
A. Ramani, E. Marcotte, R. Bunescu and Raymond J. Mooney, In Proceedings of the ISMB/ACL-05 Workshop of the BioLINK SIG: Linking Literature, Information and Knowledge for Biology, Detroit, MI, June 2005.
Collective Information Extraction with Relational Markov Networks 2004
Razvan Bunescu and Raymond J. Mooney, In Proceedings of the 42nd Annual Meeting of the Association for Computational Linguistics (ACL-04), pp. 439-446, Barcelona, Spain, July 2004.
Relational Markov Networks for Collective Information Extraction 2004
Razvan Bunescu and Raymond J. Mooney, In Proceedings of the ICML-04 Workshop on Statistical Relational Learning and its Connections to Other Fields, Banff, Alberta, July 2004.
Learning to Extract Proteins and their Interactions from Medline Abstracts 2003
Razvan Bunescu, Ruifang Ge, Rohit J. Kate, Raymond J. Mooney, Yuk Wah Wong, Edward M. Marcotte, and Arun Kumar Ramani, In Proceedings of the ICML-03 Workshop on Machine Learning in Bioinformatics, pp. 46-53, Washington, DC, August 2003.
Extracting Gene and Protein Names from Biomedical Abstracts 2002
Razvan Bunescu, Ruifang Ge, Raymond J. Mooney, Edward Marcotte, and Arun Kumar Ramani, unpublished. Unpublished Technical Note.