Vanathi Gopalakrishnan, Ph.D.

Welcome to my home page. Click here for my dissertation. Here is a short version of my resume.
Name Etymology: Tamil - Vaanam = "Sky" and Nadhi = "River"... Vanathi = "The Milky Way" or "The river in the sky"

Current Appointments and Teaching:

Core Faculty Member, Center for Biomedical Informatics
Associate Faculty Member, Center for Computational Biology and Bioinformatics
Secondary Faculty Appointment, Intelligent Systems Program

Fall 2004: Introduction to Bioinformatics (ISSP 2081 / BIOINF 2051) - Core course in Biomedical Informatics

Fall 2003: Introduction to Bioinformatics (ISSP 2081 / BIOINF 2051) - Core course in Biomedical Informatics

Summer 2003: Sequence Analysis Laboratory - Directed Study

Spring 2003: Bioinformatics@Pitt

Fall 2002: Introduction to Bioinformatics (ISSP 2081 / BIOINF 2051) - Core course in Biomedical Informatics

Summer 2002: Computational Biology Laboratory - Directed Study

Spring 2002: Bioinformatics Journal Club

Fall 2001: Introduction to Bioinformatics (ISSP 2080) - Core course in Biomedical Informatics

Spring 2001: Bioinformatics@Pitt

Fall 2000: Introduction to Bioinformatics (ISSP 2080) - Core course in Biomedical Informatics

Spring 2000: Introduction to Bioinformatics (ISSP 2080)

Research Interests:

Current Advisees:

Publications:

• Yan Liu, Jaime Carbonell, Peter Weigele, Vanathi Gopalakrishnan. Segmentation Conditional Random Fields: A New Approach for Protein Fold Recognition. To appear in Proceedings of The Ninth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2005).
• Vanathi Gopalakrishnan, Gary Livingston, Daniel Hennessy, Bruce Buchanan, John Rosenberg. Machine-Learning Techniques for Macromolecular Crystallization Data. Acta Cryst. (2004). D60, 1705-1716
• Xinghua Lu, Chengxiang Zhai, Vanathi Gopalakrishnan, Bruce G. Buchanan. Automatic annotation of protein motif function with Gene Ontology terms. BMC Bioinformatics. 2004, 5: 122.
• Yan Liu, Jaime Carbonell, Judith Klein-Seetharaman, Vanathi Gopalakrishnan. Comparison of Probabilistic Combination Methods for Protein Secondary Structure Predictions. Bioinformatics. 2004 Nov 22;20(17):3099-107.
• Yan Liu, Jaime Carbonell, Judith Klein-Seetharaman, Vanathi Gopalakrishnan. Context Sensitive Vocabulary And its Application in Protein Secondary Structure Prediction. Proceedings of the 27th annual ACM Conference on Research and Development in Information Retrieval (ACM SIGIR 2004), pp. 538-9. July 2004.
• Vanathi Gopalakrishnan, Eric Williams, Srikanth Ranganathan, Robert Bowser, Merit E. Cudkowic, Max Novelli, Wanda Lattazi, Andreas Gambotto, Billy W. Day. Proteomic Data Mining Challenges in Identification of Disease-Specific Biomarkers from Variable Resolution Mass Spectra. In Proceedings of SIAM Bioinformatics Workshop, Society for Industrial and Applied Mathematics International Data Mining Conference, Lake Buena Vista, FL. April 2004. pages 1- 10.
• Fan Li, Yiming Yang, Gulsum Anderson, Judith Klein-Seetharaman, Venkatesh Jitendar, Vanathi Gopalakrishnan. Constructing Genetic Networks from Microarray Data Using Recursive Ridge Regression (RRR). Biological Language Modeling Conference Proceedings, Carnegie Mellon University, November 2003.
• Yan Liu, Jaime Carbonell, Judith Klein-Seetharaman, Vanathi Gopalakrishnan. Prediction of Parallel and Antiparallel -sheets using Conditional Random Fields. Biological Language Modeling Conference Proceedings, Carnegie Mellon University, November 2003.
• Vanathi Gopalakrishnan, Bruce G. Buchanan, John M. Rosenberg. A Simple Simulator of Protein Crystallization. Journal of Applied Crystallography, volume 35, part 6, pages 727-733 (2002). Electronic Reprint. Copyright © International Union of Crystallography J. Appl. Cryst. 35, 727---733
• Chanqing Ma, Vanathi Gopalakrishnan, David Peters, Robert Ferrell. Decision-Tree Learning Based Characterization of the Global Effects of Cocaine Abuse on Gene Expression in the Rat Brain. Best Brief Report Paper presented at the Annual Advancing Pathology Imaging, Informatics and the Internet (APIII) conference, 2002 , February 2002.
• Denver Dash, Vanathi Gopalakrishnan. Modeling DNA Splice Regions by Learning Bayesian Networks. CBMI Tech Report , December 2001.
• Vanathi Gopalakrishnan, Bruce G. Buchanan, John M. Rosenberg. Intelligent Aids for Parallel Experiment Planning and Macromolecular Crystallization In the Proceedings of the Eight International Conference on Intelligent Systems for Molecular Biology, pages 171-180, La Jolla, California, 2000.
• Vanathi Gopalakrishnan. Parallel Experiment Planning: Macromolecular Crystallization Case Study. Ph.D. Thesis. University of Pittsburgh, December 1999.
• Vanathi Gopalakrishnan, Bruce Buchanan. Representing and Learning Temporal Relationships among Experimental Variables. In Proceedings of the Fifth International Workshop on Temporal Representation and Reasoning (TIME-98), pages 148-155, Sanibel Island, Florida, 1998.
• Vanathi Gopalakrishnan. Inducing design biases that characterize successful experimentation in weak-theory domains: TIPS. In Proceedings of AAAI-96 , Seattle, Washington, 1996.
• Vanathi Gopalakrishnan, Daniel Hennessy, Bruce Buchanan, Devika Subramanian, Patricia A. Wilcosz, K. Chandrasekhar, John M. Rosenberg. Preliminary Tests of Machine Learning Tools for the Analysis of Biological Macromolecular Crystallization Data. Tech Report ISL-94-17, Department of Computer Science, University of Pittsburgh.
• Daniel Hennessy, Vanathi Gopalakrishnan, Bruce G. Buchanan, Devika Subramanian, John M. Rosenberg. Induction of Rules for Biological Macromolecule Crystallization. In Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pages 179-187, Palo Alto, California, August, 1994.
• Vanathi Gopalakrishnan, Daniel Hennessy, Bruce Buchanan, Devika Subramanian. The Crystallographer's Assistant. Abstract in Proceedings of the Twelfth National Conference on Artificial Intelligence, page 1451, Seattle, Washington, August, 1994.
• Vanathi Gopalakrishnan, Dan Hennessy. The Crystallographer's Assistant. Abstract in the Proceedings of the Fourth Keck Symposium on Computational Biology, Pittsburgh, Pennsylvania, 1993.
• Vanathi Gopalakrishnan, Bruce Buchanan. Determining the Effectiveness of Using Expert Systems to Enable Rapid Response During Emergencies. In Proceedings of the World Congress on Expert Systems , pages 1983-1991, Orlando, Florida, 1991.
• Bruce Buchanan, Vanathi Gopalakrishnan. A Distributed Problem Solving Model for Emergency Response. Poster Presentation. In Proceedings of the Second IEEE Symposium on Parallel and Distributed Processing. Dallas, TX, December 1990.