Shailesh V. Date, Ph.D.
Chief Executive Officer
Global Viral
shailesh.date AT globalviral.org
Postdoctoral Research: University of Pennsylvania School of Medicine
Ph.D. (Mol. Biology), University of Texas, Austin
Research focus: Complex systems in Biology; Ecology & Evolution; Infectious Diseases & Public Health
Other appointments:
- Assoc. Professor (Adjunct), Dept. of Epidemiology and Biostatistics, UCSF
- Professor of Biology (Adjunct), SF State University
Research Overview
We focus on dissecting components, interactions and controls within complex systems, particularly in biology. We use computational and systems frameworks to answer questions in both classical and translational microbiology. Areas include:
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Computational microbiology: Modeling of evolutionary processes, properties of biological systems, origins of complexity in biology
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Classical microbiology: Microbial associations, novel forms, origins of biosynthetic pathways, signatures of life (exobiology)
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Translational microbiology: Pediatric health in urban environments, host-pathogen interactions, epidemiological modeling/profiling of geographical areas
The group works under the auspices of the new program in Information, Complexity and Synthetic Biology (ICS), and we are in the midst of developing several new projects in pediatric ID.
Group members:
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Jessica Lee : Denitrification, population level heterogeneity, complex systems
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Jean-Marie Volland (co-supervised by Tanja Woyke, JGI): Microbial associations, microscopy
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Tomas Tyml (co-supervised by Tanja Woyke, JGI): Microbial associations, giant viruses
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Matt Koehler (co-supervised by Ken Williford, JPL): Origins of life, prebiotic chemistry, origins of metabolic pathways
Bio
Shailesh holds a Ph.D. in Molecular Biology from the University of Texas at Austin. His thesis work in Edward Marcotte's lab focused on using computational functional genomics methods to reconstruct networks of physically and functionally interacting proteins on genome-wide scales. He was a postdoc with David Roos and Chris Stoeckert at the University of Pennsylvania's School of Medicine, where he developed computational tools to dissect the biology of ampicomplexan parasites, including the malarial parasite Plasmodium falciparum. Prior to joining Global Viral, he spent nearly 7 years as a scientist at Genentech, Inc., with joint appointments in the Departments of Bioinformatics & Computational Biology and Infectious Disease (ID). At Genentech, he was responsible for building ID R&D pipelines and for facilitating informatics-based ID research.
Selected Publications
(click the Pubmed button for a full, updated list)
Morisaki JH, Smith PA, Date SV, et al. A Putative Bacterial ABC Transporter Circumvents the Essentiality of Signal Peptidase. MBio. 2016 Sep 6;7(5). pii: e00412-16.
Date SV*, Modrusan Z*, Lawrence M*, et al. Global gene expression of methicillin-resistant Staphylococcus aureus USA300 during human and mouse infection. J Infect Dis. 2014 May 15;209(10):1542-50. (* equal contributors).
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
Lee I, Date SV, Adai AT and Marcotte EM. A Probabilistic functional network of yeast genes. Science. 2004 Nov 26;306(5701):1555-8.
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 rated by the Faculty of 1000 as a ‘Must Read’ at the time.
Book Chapters
Date SV and Peregrín-Alvarez JM (2008) Phylogenetic profiling. Methods Mol Biol.; 453:201-16.
Date SV (2008) The Rosetta stone method. Methods Mol Biol.; 453:169-80.
Date SV (2007) Estimating protein function using protein-protein relationships. Methods Mol Biol.; 408:109-27.
Date SV and Chen GG. (2007) Interaction networks of proteins. Encyclopedia of Life Sciences (ELS). John Wiley and Sons Limited, Chichester, West Sussex, PO19 8SQ.
This chapter was also published in:
Date SV and Chen GG. (2008) Interaction networks of proteins. Handbook Of Proteins: Structure, Function, and Methods. Ed. Mike Cox and George Phillips. John Wiley and Sons Limited, Chichester, West Sussex, PO19 8SQ.