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
Email: svdate@pcbi.upenn.edu
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.

M. Sc.
(Botany), University of Pune, India. (1995-1997)
Specialization: Plant Biotechnology | Report: Micropropagation of Sunflower ( Helianthus annus
L.
)

B. Sc. Honors (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 (8 th Congress of
Poets, 1985)
HONORS AND ACHIEVEMENTS

Nominated Associate Member, Sigma Xi, Univ. of Pennsylvania Chapter (December 2006)

Winner, Best Poster, Open Division, Greater Philadelphia Bioinformatics Alliance Retreat, 2005.

Founding member, Student Council, International Society for Computational Biology (ISCB-SC,
2004)

Shailesh V. Date, Curriculum vitae

President, (Student) Society of Computational Biology (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
Papers
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 SV * and Stoeckert CJ. Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale. Genome Res . 2006 Apr;16(4):542-9.
*Corresponding author
Date SV and Marcotte EM. Protein function prediction using the Protein Link EXplorer (PLEX).
Bioinformatics . 2005 May 15;21(10):2558-9.
Lee I, Date SV , Adai AT and Marcotte EM. A Probabilistic functional network of yeast genes.
Science . 2004 Nov 26;306(5701):1555-8.
Baliga NS, Bonneau R, Facciotti MT, Pan M, Glusman G, Deutsch EW, Shannon P, Chiu Y, Weng
RS, Gan RR, Hung P, Date SV , Marcotte E, Hood L and Ng WV. Genome sequence of Haloarcula marismortui : a halophilic archaeon from the Dead Sea. Genome Res . 2004 Nov;14(11):2221-34.
Adai AT, Date SV , Wieland S and Marcotte EM. LGL: Creating a Map of Protein Function with an
Algorithm for Visualizing Very Large Biological Networks. JMB . 2004 Jun 25;340(1):179-90.
Date SV and Marcotte EM. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nature Biotech . 2003 Sep;21(9):1055-62.
This paper was the subject of an invited ‘Research focus’ article. See McDermott, J. &
Samudrala, R. Enhanced functional information from predicted protein networks. Trends in
Biotech . 2004 Feb;22(2):60-2.
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Shailesh V. Date, Curriculum vitae
See also Response: Date SV & Marcotte EM. Response to McDermott and Samudrala: Enhanced functional information from predicted protein networks. TRENDS in Biotech . 2004
Feb;22(2):62-63.
This paper was rated by the Faculty of 1000 as a ‘Must Read’.
Marcotte EM and Date SV.
Exploiting Big Biology: Integrating large-scale biological data for functional inference. Briefings in Bioinformatics , 2001 Dec; 2(4): 363-74.
Book chapters
Date SV and Chen GG. Interaction networks of proteins. To appear in the Encyclopedia of Life
Sciences (ELS) . John Wiley and Sons Limited, Chichester, West Sussex, PO19 8SQ.
Date SV and Chen GG. 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 SV.
The Rosetta stone Method. To appear in Methods in Molecular Biology: Bioinformatics .
Ed. Jonathan Keith, Humana Press, Totowa, NJ, USA.
Date SV and Peregrin J. Phylogenetic profiling. To appear in Methods in Molecular Biology:
Bioinformatics . Ed. Jonathan Keith, Humana Press, Totowa, NJ, USA.
Date SV.
Estimating gene function using computational methods. To appear in Methods in Molecular
Biology: Gene Function Analysis . Ed. Michael Ochs, Humana Press, Totowa, NJ, USA.
Whetzel PL, Date SV , Essien K et al. PlasmoDB: The Plasmodium Genomics and Functional
Genomics Resource”. To appear in In silico Proteomics: Functional Annotation and Comparative
Proteomics . Nova Science Publishers, INC., Hauppauge, NY, USA
Whetzel PL, Date SV , Essien K et al. PlasmoDB: the Plasmodium Genome Resource. Molecular
Approaches to Malaria . Ed. Sherman IW, American Society for Microbiology. 2005 Aug 26; 12-23.
Thesis
Date SV.
Large Scale Protein Function Prediction and Systematic Identification of Novel Cellular
Systems. Ph.D. Thesis, Supervised by Edward M. Marcotte, Ph.D
REVIEWER DUTIES
PLOS Computational Biology, Genome Biology, Bioinformatics, Theoretical Biology and Medical
Modelling, RECOMB.
TALKS
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Shailesh V. Date, Curriculum vitae
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
Date SV and Stoeckert CJ. Computational analyses of proteins, protein families and protein domains in
Plasmodium falciparum . Molecular Parasitology Meeting, Woods Hole, Massachusetts, September
2006.
Best poster award
Date SV and Stoeckert CJ. Genome-wide inference of protein function in Plasmodium falciparum using a computational model of the parasite interactome. Greater Philadelphia Bioinformatics
Alliance Retreat, October 2005.
Date SV and Stoeckert CJ. Integration of diverse functional genomics data for gene function prediction in Plasmodium falciparum . Molecular Parasitology Meeting, Woods Hole, Massachusetts, September
2005.
Date SV and Stoeckert CJ. A generalized strategy for reconstructing genome-wide functional interaction maps using a naïve Bayesian framework: An application to the P. falciparum genome.
Automated Function Prediction - Special Interest Group (AFP-SIG), 13th Annual Conference on
Intelligent Systems in Molecular Biology (ISMB), Detroit, MI, June 2005.
Stoeckert CJ, Gajria B, Milgram AJ, Iodice J, Fraunholz MJ, Labo PT, Grant GR, Whetzel PL, Li L,
Date SV , Kissinger JC, Roos DS. PlasmoDB v4.2: Enhancing access to Plasmodium genomes as a community resource. Molecular Parasitology Meeting, Woods Hole, MA, September 2004.
Date SV and Marcotte EM. Protein Interaction Networks. Third TB Structural Genomics Consortium
Retreat, Santa Fe, New Mexico, September 2002.
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Shailesh V. Date, Curriculum vitae
Date SV and Marcotte EM. Large scale protein function prediction. Second TB Structural Genomics
Consortium Retreat, Santa Fe, New Mexico, September 2001.
WORKSHOPS
Instructor
 ApiDB workshop, University of Georgia, Athens, Georgia, June 2006.
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 , University of Pennsylvania School of Medicine (Feb 2004 - present)
Mentor: Christian J. Stoeckert, Jr, Ph.D.
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, http://www.cbil.upenn.edu/RAD/php/index.php
)

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: Extension of protein-protein interaction prediction methods to multiple genomes, maintenance 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 gain familiarity with molecular biology protocols relating to tissue culture and transformation of plant cells; assist lab members in DNA extraction and electrophoresis, gel
5

Shailesh V. Date, Curriculum vitae 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.
Duties: Developed a website for the General Botany Course: Structure, Physiology and Reproduction of
Seed Plants (BOT 320/120C)
REFERENCES
Available on request.
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