BMSCE IAA

BMSCE, International Alumni Association

Vanathi Gopalakrishnan, Ph.D. Assistant Professor of Medicin

Posted by bmsceiaa on November 19, 2006

Vanathi Gopalakrishnan, Ph.D.
Assistant Professor of Medicine and Intelligent Systems
Forbes Tower, Suite 8084
Center for Biomedical Informatics
University of Pittsburgh
(412) 648-6677
vanathi@cbmi.upmc.edu
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:
Bioinformatics – Machine learning and data mining applied to clinical proteomics, gene expression analysis, macromolecular crystallization, secondary structure prediction and neuroinformatics

Current Advisees:
Doctoral students:
David Dougall – Center for Biomedical Informatics
Pinaki Mitra – Center for Biomedical Informatics
Philip Ganchev – Intelligent Systems Program
Eric Williams – Intelligent Systems Program
Jonathan Lustgarten – Center for Biomedical Informatics
Yan Liu – CMU SCS (with Prof. Jaime Carbonell)
Graduate students:
Venkatesh Jitender (co-advising with Dr. Judith-Klein Seetharaman)
Zhong Guo – CBMI and Department of Surgery, UPMC
Andrew Post, M.D. – CBMI – Doctoral Dissertation Committee Member
Changqing Ma – Interdisciplinary Biomedical Program – Doctoral Dissertation Committee Member

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-9Cool, 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.

Vanathi Gopalakrishnan

Visiting Assistant Professor

Department of Medicine, Section of Medical Informatics

Secondary appointment in the Intelligent Systems Program

University of Pittsburgh
vanathi@cs.pitt.edu

412-647-7131
http://www.cs.pitt.edu/~vanathi

GOALS

· To be involved in research, teaching and service in the fields of Computer Science, Intelligent Systems and Bioinformatics.

· To collaborate on interdisciplinary projects involving the application of existing computational tools to biological problems, as well as the creation of new tools.

· To help establish a curriculum and a world-class research program in Bioinformatics and Computational Biology.

· To apply machine learning and statistical techniques to pattern recognition and information retrieval from data.

EDUCATION

· Ph.D., Computer Science December 1999

University of Pittsburgh, PA, USA

Major Advisor: Prof. Bruce G. Buchanan

· M.S., Computer Science 1989 – 1991
University of Pittsburgh, PA, USA

· B.E., Computer Engineering & Technology 1983 – 1988
BMS College of Engineering, Bangalore, India
Passed in First Class with Distinction

RESEARCH AND PROFESSIONAL EXPERIENCE

· Bioinformatics@Pitt Spring 2001
Introduced a new colloqium type 1-credit course that aims to bring together faculty and students from diverse departments in the Schools of Medicine and Faculty of Arts and Sciences that are involved in bioinformatics related research.

· Instructor (Introduction to Bioinformatics) Spring 2000, Fall 2000
Introduced a new graduate level core course at the Center for Biomedical Informatics, University of Pittsburgh. This course aims to provide an understanding of the computational aspects of biological problems and existing methods in computational biology through case studies.

· Co-founder of Intelligent Systems Software,Inc. 1996-1998
Start-up company based in Clearwater, FL, that specializes in medical image analysis and is building

intelligent tools to assist radiologists in detection of breast cancer. ISMD has been awarded Phase I

and Phase II grants from NIH as part of the SBIR (Small Business Innovative Research) program.

· Research Assistant 1989 – 1997

Intelligent Systems Lab, Dept. of Computer Science, University of Pittsburgh

· Teaching Assistant /Instructor Sept 1993 – Dec 1993

University of Pittsburgh, Dept. of Computer Science

· Research in Computational Biology May 1992 – Sept 1992

Prof. Jude Shavlik’s Machine Learning Group, University of Wisconsin, Madison, WI

· Software Design and Implementation June 1991 – Sept 1991

Systems Modeling Corporation, Sewickley, PA

· Systems Executive May 1988 – June 1989

WIPRO Information Technology Limited, Bangalore, India

· Bachelor’s degree Projects May 1987 – May 1988

BMS College of Engineering, Bangalore, India

PUBLICATIONS

· Denver Dash, Vanathi Gopalakrishnan.Modeling DNA Splice Regions by Learning Bayesian Networks. Submitted to the Ninth International Conference on Intelligent Systems for Molecular Biology, February 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, Bruce G. Buchanan, John M. Rosenberg. A Model for Simulating Hypothetical Protein Crystallization Behaviors. Being submitted to the Journal of Computational Biology.

· Vanathi Gopalakrishnan. Parallel Experiment Planning: Macromolecular Crystallization Case Study. Ph.D. Thesis. Department of Computer Science, University of Pittsburgh, December 1999.

· Vanathi Gopalakrishnan and Bruce Buchanan. Representing and Learning Temporal Relationships among Experimental Variables, pages 148-155, In proceedings of the Fifth International Workshop on Temporal Representation and Reasoning (TIME-9Cool, 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.

· 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, Dan Hennessy, Bruce Buchanan and 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, pp. 1983-1991, Orlando, Florida, 1991.

· Bruce Buchanan, Vanathi Gopalakrishnan. A Distributed Problem Solving Model for Emergency Response, Poster Presentation, Proceedings of the Second IEEE Symposium on Parallel and Distributed Processing, Dallas, TX, December 1990.

PRESENTATIONS / INVITED TALKS

· Parallel Experiment Planning, Macromolecular Crystallization, and Computational Biology, invited seminar talk jointly sponsored by the Center for Automated Learning and Discovery and the Language Technologies Institute at the Carnegie Mellon University, Pittsburgh, September, 2000.

· Bioinformatics, invited talk at the Introduction to Medical Informatics Course, Center for Biomedical Informatics, University of Pittsburgh, September 2000.

· Intelligent Aids for Parallel Experiment Planning and Macromolecular Crystallization, presented

at the Eighth International Conference on Intelligent Systems for Molecular Biology – ISMB 2000,

La Jolla, California, August, 2000.

· Representing and Learning Temporal Relationships among Experimental Variables at the Fifth International Workshop on Temporal Representation and Reasoning (TIME-9Cool, Sanibel Island, Florida, 1998.

· Symbolic Induction of Heuristics to Aid Macromolecular Crystallization, Institute of Systems Science, National University of Singapore, July, 1995.

· Induction of Rules for Biological Macromolecule Crystallization, at the Second International Conference on Intelligent Systems for Molecular Biology, Stanford University, Palo Alto, California, August, 1994.

AWARDS

· Best Trainee Award, WIPRO Information Technology Ltd, India (1988)

· W.M. Keck Fellowship in Computational Biology (Sept 1994 – August 1995)

· Funded by a research grant from NIH for the Crystallographer’s Assistant (Sept 1995 – 1997)

· Co-investigator (20% time) on a grant from NIH for a project involving UPMC Pathology Informatics group headed by Dr. Mike Becich, researching the Molecular Reclassification of Prostate Cancer.

· Pending: Recently submitted a proposal to NIMH entitled “Genomic Analysis of Morphine Sensitization in the Rat” where I am listed as co-investigator for the data mining and bioinformatics aspects of the project. The PI is Prof. Robert E. Ferrell, an acknowledged expert in Human Genetics, affiliated with the Graduate School of Public Health, University of Pittsburgh.

REFERENCES

Prof. Bruce Buchanan, Department of Computer Science, University of Pittsburgh

Prof. John Rosenberg, Department of Biological Sciences, University of Pittsburgh

Prof. Charles Friedman, Director of the Center for Biomedical Informatics, University of Pittsburgh.

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