Shailesh Date, PhD
Associate Professor
Epidemiology & Biostatistics
School of Medicine

Dr. Date’s research primarily focuses on developing computational tools (biology, chemistry) to analyze complex biological systems, pathways and multi-input processes with the goal of identifying points of intervention. His group also studies fundamental biophysical properties of living systems, including biological associations, at various scales. Since early in his career, Dr. Date’s goal has been to develop projects that bridge academia and industry. As a postdoctoral researcher, he published the first comprehensive interactome model of the malarial parasite Plasmodium falciparum, providing a tool to the community to initiate functional investigation of the 50%+ uncharacterized genes, as well as provide a list of potential cell-surface targets. Later at Genentech, appalled at the lack of knowledge of S. aureus behavior in human hosts (even after decades of research), he published, together with his colleagues, the first transcriptomic and proteomic map of the pathogen under true infection conditions in humans. Dr. Date has won a DARPA competition for his work on developing a statistical physics model that envisions evolution (and development of complexity) at a systems level, rather than at the level of individual genes, allowing expansion into novel biochemical, morphological and physiological dimensions. Most recently, as lead senior author, he and his group described the largest bacterium known to science – Ca. Thiomargarita magnifica. This paper highlighted the many dogmatic but incorrect assumptions in the scientific community about microbial cell sizes, cell structure and the eukaryotic-prokaryotic divide. This work was shortlisted for “breakthrough of the year” by Science magazine in 2022. Dr. Date obtained his Ph.D. from the University of Texas at Austin under the supervision of Dr. Edward Marcotte, with a focus on computational molecular biology. He completed his postdoctoral work at the University of Pennsylvania’s School of Medicine, where he was jointly supervised by Drs. David Roos and Chris Stoeckert. His group has been supported by the Templeton Foundation, The Moore Foundation, DARPA and other agencies/foundations.

• De Novo Guanine Biosynthesis but Not the Riboswitch-Regulated Purine Salvage Pathway Is Required for Staphylococcus aureus Infection In Vivo.
  Journal of bacteriology 2016 Kofoed EM, Yan D, Katakam AK, Reichelt M, Lin B, Kim J, Park S, Date SV, Monk IR, Xu M, Austin CD, Maurer T, Tan MW
• Global gene expression of methicillin-resistant Staphylococcus aureus USA300 during human and mouse infection.
  The Journal of infectious diseases 2013 Date SV, Modrusan Z, Lawrence M, Morisaki JH, Toy K, Shah IM, Kim J, Park S, Xu M, Basuino L, Chan L, Zeitschel D, Chambers HF, Tan MW, Brown EJ, Diep BA, Hazenbos WL
• Identifying potential therapeutic targets of methicillin-resistant Staphylococcus aureus through in vivo proteomic analysis.
  The Journal of infectious diseases 2013 Diep BA, Phung Q, Date S, Arnott D, Bakalarski C, Xu M, Nakamura G, Swem DL, Alexander MK, Le HN, Mai TT, Tan MW, Brown EJ, Nishiyama M
• Glycan shifting on hepatitis C virus (HCV) E2 glycoprotein is a mechanism for escape from broadly neutralizing antibodies.
  Journal of molecular biology 2013 Pantua H, Diao J, Ultsch M, Hazen M, Mathieu M, McCutcheon K, Takeda K, Date S, Cheung TK, Phung Q, Hass P, Arnott D, Hongo JA, Matthews DJ, Brown A, Patel AH, Kelley RF, Eigenbrot C, Kapadia SB
• Analysis of the nucleotide sequence of the guinea pig cytomegalovirus (GPCMV) genome.
  Virology journal 2008 Schleiss MR, McGregor A, Choi KY, Date SV, Cui X, McVoy MA
• Phylogenetic profiling.
  Methods in molecular biology (Clifton, N.J.) 2008 Date SV, Peregrín-Alvarez JM
• The Rosetta stone method.
  Methods in molecular biology (Clifton, N.J.) 2008 Date SV
• Estimating protein function using protein-protein relationships.
  Methods in molecular biology (Clifton, N.J.) 2007 Date SV
• Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale.
  Genome research 2006 Date SV, Stoeckert CJ
• Protein function prediction using the Protein Link EXplorer (PLEX).
  Bioinformatics (Oxford, England) 2005 Date SV, Marcotte EM
• A probabilistic functional network of yeast genes.
  Science (New York, N.Y.) 2004 Lee I, Date SV, Adai AT, Marcotte EM
• Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea.
  Genome research 2004 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, Ng WV
• LGL: creating a map of protein function with an algorithm for visualizing very large biological networks.
  Journal of molecular biology 2004 Adai AT, Date SV, Wieland S, Marcotte EM
• Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages.
  Nature biotechnology 2003 Date SV, Marcotte EM
• Exploiting big biology: integrating large-scale biological data for function inference.
  Briefings in bioinformatics 2001 Marcotte E, Date S