Computational Biology and Informatics Laboratory @ PENN Center for Bioinformatics
 
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SHAILESH VINAYAK DATE, Ph.D.


Postdoctoral Researcher
PENN Center for Bioinformatics, Department of Genetics,
University of Pennsylvania School of Medicine
423 Guardian Drive, 1423 Blockley Hall,
Philadelphia, PA 19104
Phone: 215-746-7020 | Fax: 215-573-3111

RESEARCH INTERESTS
  • Interactome modeling: Generating high-confidence genome-scale networks of protein-protein interactions to isolate effect/tissue -specific networks, and study propagation routes of cellular stimuli.

  • Parasite systems biology and bioinformatics: Study of conserved systems in parasite genomes, host-pathogen interactions, study of complex parasite behavior (such as that exhibited during invasion) in the context of both intracellular and extra-cellular protein-protein interactions.

  • Generation of computational resources: Creation of web-accessible computational resources, databases, sequence analysis frameworks and data standardization schemas.


EDUCATION
    Ph.D., University of Texas at Austin (1998-2003)
    Thesis: Large Scale Protein Function Prediction and Systematic Identification of Novel Cellular Systems
    Supervisor: Edward M. Marcotte, Ph.D
    GPA: 3.95

    M.Sc., University of Pune (1995-1997)
    Botany (Specialization: Plant Biotechnology), The University of Pune, Pune, India
    Report: Micropropagation of Sunflower (Helianthus annus L.)
    Supervisor: J. R. Thengane, Ph.D.

    B.Sc. Honors in Botany, Fergusson College, Pune, India (1992-1995)


AWARDS
    - Shankar Subramanian Award, Systems Biology Consortium Meeting, Penn State Univ., July 24-26, 2007.
    - National Merit Scholarship, India (1996 & 1997)
    - Diploma, Federazione Italiana Arti Figurative, Italy (1986)
    - Certificate of Merit, American Junior Poetry Society, United States of America (8th Congress of Poets, 1985)


HONORS AND ACHIEVEMENTS
    - Best Poster Award, Open Category, Greater Philadelphia Bioinformatics Alliance Retreat, 2005.
    - Founding member, Student Council, International Society for Computational Biology (ISCB-SC, 2004)
    - President, Society of Computational Biology (Student society, Univ. of Texas at Austin), Spring 2001-Fall 2002
    - Nominated, Outstanding Teaching Assistant Award, Univ. of Texas at Austin (Spring 2001)
    - Commendation, Office of the Provost, and the Center for Instructional Technology, Univ. of Texas at Austin, on 'Innovative use of Instructional Technology' for the 'LINXS' project, Spring 2000
    - Member Elect, The Honor Society of Phi Kappa Phi (November 1999)
    - Elected Member, Student Teacher Committee, Dept. Of Botany, University of Pune, India, (1996-1997)
    - Elected Class Representative, Dept. of Botany, University of Pune, Pune, India (1996-1997)


PUBLICATIONS
2007
    Manuscripts in preparation:
    • Jane Carlton et al. (with LaCount D, Date SV, Stoeckert CJ, Fields S and others) The genome sequence of Plasmodium vivax.
    • Date SV, Bidaut G and Stoeckert CJ. plasmoMAP: A repository of protein-protein interaction data and data-mining tools for the malarial parasite Plasmodium falciparum.
    • Date SV, Pinney D, Stoeckert CJ and others. Comparative genomics analyses reveal functional and organizational details of apicomplexan proteomes.

2006 - 2001
    Date, S.V.* & Stoeckert, C.J., Jr. Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale. Genome Research. 2006 Apr;16(4):542-9. *Corresponding author

    Date, S.V. & Marcotte, E.M. Protein function prediction using the Protein Link EXplorer (PLEX). Bioinformatics. 2005 May 15;21(10):2558-9. Epub 2005 Feb 8.

    Lee I., Date, S.V., Adai, A.T. & Marcotte, E.M. A Probabilistic functional network of yeast genes. Science. 2004 Nov 26;306(5701):1555-8.

    Baliga, N.S., Bonneau, R., Facciotti, M.T., Pan, M., Glusman, G., Deutsch, E.W., Shannon, P., Chiu, Y., Weng, R.S., Gan, R.R., Hung, P., Date, S.V., Marcotte, E., Hood, L. & Ng, WV. Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Research. 2004 Nov;14(11):2221-34. Erratum in: Genome Res. 2004 Dec;14(12):2510.

    Adai, A.T., Date, S.V., Wieland, S. & Marcotte, E.M. LGL: Creating a Map of Protein Function with an Algorithm for Visualizing Very Large Biological Networks. Journal of Molecular Biology. 2004 Jun 25;340(1):179-90.

    Response: Shailesh V Date & Edward M Marcotte. Response to McDermott and Samudrala: Enhanced functional information from predicted protein networks. TRENDS in Biotechnology. 2004 Feb;22(2):62-63.

    Date, S.V. & Marcotte, E.M. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nature Biotechnology. 2003 Sep;21(9):1055-62. Epub 2003 Aug 17.

      This paper was the subject of an invited commentary. See McDermott, J. & Samudrala, R. Enhanced functional information from predicted protein networks. Trends in Biotechnology. 2004 Feb;22(2):60-2, Discussion.

      This paper was also discussed by the Faculty of 1000.

    Marcotte, E. M. & Date, S.V. Exploiting Big Biology: Integrating large-scale biological data for functional inference. Briefings in Bioinformatics, 2(4), 363-74 (2001).
Thesis
    Date, S.V. Large Scale Protein Function Prediction and Systematic Identification of Novel Cellular Systems. Ph.D. Thesis, Supervised by Edward M. Marcotte, Ph.D
Book chapters
  • Date, S.V. and Chen GG. Interaction networks of proteins. To appear in Encyclopedia of Life Sciences (ELS). John Wiley and Sons Limited, Chichester, West Sussex, PO19 8SQ.

  • Date, S.V. and Chen, G.G. Interaction networks of proteins. To appear in Handbook Of Proteins: Structure, Function, and Methods. Ed. Mike Cox and George Phillips. John Wiley and Sons Limited, Chichester, West Sussex, PO19 8SQ.

  • Date, S.V. The Rosetta stone Method. To appear in Methods in Molecular Biology: Bioinformatics. Ed. Jonathan Keith, Humana Press, Totowa, NJ, USA.

  • Date, S.V., Jose Peregrin, J. Phylogenetic profiling. To appear in Methods in Molecular Biology: Bioinformatics. Ed. Jonathan Keith, Humana Press, Totowa, NJ, USA.

  • Date, S.V. Estimating gene function using computational methods. To appear in Methods in Molecular Biology: Gene Function Analysis. Ed. Michael Ochs, Humana Press, Totowa, NJ, USA.

  • Patricia L. Whetzel, Shailesh V. Date, Kobby Essien, Martin J. Fraunholz, Bindu Gajria, Gregory R. Grant, John Iodice, Jessica C. Kissinger, Philip T. Labo, Arthur J. Milgram, David S. Roos and Christian J. Stoeckert Jr. PlasmoDB: The Plasmodium Genomics and Functional Genomics Resource. In silico Proteomics: Functional Annotation and Comparative Proteomics, Nova Science Publishers, INC., Hauppauge, NY, USA

  • Patricia L. Whetzel, Shailesh V. Date, Kobby Essien, Martin J. Fraunholz, Bindu Gajria, Gregory R. Grant, John Iodice, Jessica C. Kissinger, Philip T. Labo, Arthur J. Milgram, Christian J. Stoeckert, Jr., and David S. Roos. PlasmoDB: the Plasmodium Genome Resource. Molecular Approaches to Malaria. Ed. Sherman IW, American Society for Microbiology. 2005 Aug 26; 12-23.


REVIEWER DUTIES
    PLOS Computational Biology, Genome Biology, Bioinformatics, Theoretical Biology and Medical Modelling, RECOMB.


TALKS
    Shankar Subramanian Award Lecture. Discovery of new drug targets and vaccine candidates in the Plasmodium falciparum proteome using a systems biology approach, Systems Biology Consortium Meeting, July 2007.

    Computational modeling of interactomes: Tools, techniques and application to genomes of apicomplexan parasites. University of Pennsylvania School of Veterinary Medicine, May 2007.

    Computational modeling of interactomes: Tools, techniques and application to genomes of apicomplexan parasites. NIAID/NIH, May 2007.

    Computational modeling of interactomes: Tools, techniques and application to genomes of apicomplexan parasites. Wayne State School of Medicine, February 2007.

    Genome-scale inference of gene function in Plasmodium falciparum using a computational model of the parasite interactome. 4th Annual Biomedical Postdoctoral Symposium, University of Pennsylvania.

    Annotating uncharacterized genes in the Plasmodium falciparum genome. Molecular Parasitology Meeting, Woods Hole, MA, September 2004.

    Large scale protein function prediction and systematic discovery of novel cellular systems. University of Pennsylvania, November 2003.

    Large scale protein function prediction and systematic identification of novel cellular systems. National Center for Biotechnology Information (NCBI), October 2003.


CONFERENCE POSTERS
    Shailesh V. Date & Christian J. Stoeckert, Jr. Computational analyses of proteins, protein families and protein domains in Plasmodium falciparum. Molecular Parasitology Meeting, September 2006, Woods Hole, Massachusetts.

    Best poster award
    Shailesh V. Date & Christian J. Stoeckert, Jr. Genome-wide inference of protein function in Plasmodium falciparum using a computational model of the parasite interactome. Greater Philadelphia Bioinformatics Alliance Retreat, 2005.

    Shailesh V. Date & Christian J. Stoeckert, Jr. Integration of diverse functional genomics data for gene function prediction in Plasmodium falciparum Molecular Parasitology Meeting, September 2005, Woods Hole, Massachusetts.

    Shailesh V. Date & Christian J. Stoeckert, Jr. A generalized strategy for reconstructing genome-wide functional interaction maps using a naïve Bayesian framework: An application to the PP. falciparum genome. Automated Function Prediction - Special Interest Group (AFP-SIG), 13th Annual Conference on Intelligent Systems in Molecular Biology (ISMB), June 2005, Detroit, MI.

    Christian J. Stoeckert, Bindu Gajria, A. Jules Milgram, John Iodice, Martin J. Fraunholz, Philip T. Labo, Gregory R. Grant, Patricia L. Whetzel, Li Li, Shailesh V. Date, Jessica C. Kissinger, David S. Roos. PlasmoDB v4.2: Enhancing access to Plasmodium genomes as a community resource. Molecular Parasitology Meeting, September 2004, Woods Hole, MA

    Shailesh V. Date & Edward M. Marcotte. Protein Interaction Networks. Third TB Structural Genomics Consortium Retreat, September 2002, Santa Fe, New Mexico

    Shailesh V. Date & Edward M. Marcotte. Large scale protein function prediction. Second TB Structural Genomics Consortium Retreat, September 2001, Santa Fe, New Mexico



WORKSHOPS ATTENDED
    As an instructor
    ApiDB workshop, University of Georgia, Athens, Georgia, June 2006.

    As a participant
    DIMACS Workshop on Dialogue on Reverse Engineering Assessment and Methods (DREAM), September 7 - 8, 2006, NY

    Arabidopsis Molecular Genetics Course, July 1999, Cold Spring Harbor Laboratory, 1 Bungtown Rd., Cold Spring Harbor, NY 11724.


RESEARCH EXPERIENCE
    Postdoctoral Researcher, Department of Genetics, University of Pennsylvania. (Feb 2004 - present)
    Mentor: Christian J. Stoeckert, Jr.
    Focus:
    - Application of computational functional genomics methods to apicomplexan genomes for studying protein-protein interactions (with emphasis on the genome of the malarial parasite Plasmodium falciparum)
    - comparative genomics of apicomplexa and other eukaryotic and prokaryotic groups
    - development of web-based user interfaces for querying project-specific result data (see plasmoMAP http://cbil.upenn.edu/plasmoMAP, see toxoNet http://cbil.upenn.edu/~svdate/toxo)
    - development of data handler and data loader plugins for the RNA Abundance Database (RAD)
    - development of the PlasmoDB database (http://www.plasmodb.org)

    Postdoctoral Fellow, University of Texas at Austin. (Sep 2003 - Jan 2004)
    Mentor: Edward M. Marcotte, Ph.D.
    Focus: Extention of protein-protein interaction prediction methods to multiple genomes, maintainence of the PLEX database and data generation for integration studies.

    Research Assistant (RA) University of Texas at Austin. (2001 - 2003)
    Mentor: Edward Marcotte, Ph.D.
    Focus: Development and application of tools and algorithms for predicting protein-protein interactions, generating interaction networks, development of a web-based interface for querying protein-protein interactions with a back-end database (see PLEX, http://bioinformatics.icmb.utexas.edu/plex).

    Summer Trainee, National Botanical Research Institute (NBRI), Luckhnow, India. (Summer, 1996)
    Mentor: Rakesh Tuli, Ph.D.
    Focus: To become familiar with various molecular biology protocols relating to tissue culture and transformation of plant cells; assist lab members in DNA extraction and electrophoresis, gel purification, tissue culture, Biolistics and Agrobacterium-mediated transformation of Nicotiana tabacum (to achieve stable insertion of the Bt toxin gene).


TEACHING EXPERIENCE
    Instructor, 2006 ApiDB workshop, University of Georgia, Athens, GA
    Duties: As a PlasmoDB expert, guided students through queries and tools for effective use of the ApiDB group of websites (my duties were restricted to help with PlasmoDB); helped students answer specific scientific questions using available tools; presented a demo/walk-through with the help of a scientific question.

    Teaching assistantships (1998-2001): Courses included upper division Cell Biology, General Microbiology lab, Introductory Biology: Cell Biology, and Computational Biology
    Duties: Led discussion sessions; prepared and administered exams and quizzes; graded exams; interacted with students during specified hours outside a classroom setting; prepared solutions, buffers and reagents for laboratory courses; helped in preparing course materials; developed and managed course websites.

    Student partner, ~FAST Tex project (2000)
    Faculty Advisor: David Herrin, Ph.D.
    Title: Development of a Webpage for the General Botany Course: Structure, Physiology and Reproduction of Seed Plants (BOT 320/120C)


REFERENCES
    Available upon request