Shailesh Date, PhD

Title(s)Associate Professor, Epidemiology & Biostatistics
SchoolSchool of Medicine
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    Collapse Education and Training
    Stanford University (Graduate School of Business), Stanford, CAIgnite Program2013Innovation & Entrepreneurship
    Univ. of Pennsylvania School of Medicine, Philadelphia, PAPostdoc2008Infectious Diseases (Comp. Bio. of Apicomplexan Parasites)
    Univ. Of Texas at Austin, Austin, TexasPh.D.2003Molecular Biology (Computational Biology)
    Univ. of Pune, Pune, IndiaM.Sc.1997Botany (Plant Biotech. as specialization)
    Fergusson College, Pune, IndiaB.Sc. (Hons)1995Botany

    Collapse Overview 
    Collapse Overview
    Dr. Shailesh Date is Chief Executive Officer of the Laboratory for Research in Complex Systems (LRC), an independent research institute that uses rigorous quantitative approaches to solve high-value problems in the sciences and the society. He is also Chief Executive Officer of Silicogenix Inc. 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.

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Synthase-selected sorting approach identifies a beta-lactone synthase in a nudibranch symbiotic bacterium. Microbiome. 2023 06 13; 11(1):130. Džunková M, La Clair JJ, Tyml T, Doud D, Schulz F, Piquer-Esteban S, Porcel Sanchis D, Osborn A, Robinson D, Louie KB, Bowen BP, Bowers RM, Lee J, Arnau V, Díaz-Villanueva W, Stepanauskas R, Gosliner T, Date SV, Northen TR, Cheng JF, Burkart MD, Woyke T. PMID: 37312139; PMCID: PMC10262491.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    2. A centimeter-long bacterium with DNA contained in metabolically active, membrane-bound organelles. Science. 2022 06 24; 376(6600):1453-1458. Volland JM, Gonzalez-Rizzo S, Gros O, Tyml T, Ivanova N, Schulz F, Goudeau D, Elisabeth NH, Nath N, Udwary D, Malmstrom RR, Guidi-Rontani C, Bolte-Kluge S, Davies KM, Jean MR, Mansot JL, Mouncey NJ, Angert ER, Woyke T, Date SV. PMID: 35737788.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    3. Examining the Relationship Between the Testate Amoeba Hyalosphenia papilio (Arcellinida, Amoebozoa) and its Associated Intracellular Microalgae Using Molecular and Microscopic Methods. Protist. 2022 02; 173(1):125853. Weiner AKM, Cullison B, Date SV, Tyml T, Volland JM, Woyke T, Katz LA, Sleith RS. PMID: 35030517; PMCID: PMC9148389.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
    4. A single-cell genome perspective on studying intracellular associations in unicellular eukaryotes. Philos Trans R Soc Lond B Biol Sci. 2019 11 25; 374(1786):20190082. Tyml T, Date SV, Woyke T. PMID: 31587647; PMCID: PMC6792452.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    5. A Putative Bacterial ABC Transporter Circumvents the Essentiality of Signal Peptidase. mBio. 2016 09 06; 7(5). Morisaki JH, Smith PA, Date SV, Kajihara KK, Truong CL, Modrusan Z, Yan D, Kang J, Xu M, Shah IM, Mintzer R, Kofoed EM, Cheung TK, Arnott D, Koehler MF, Heise CE, Brown EJ, Tan MW, Hazenbos WL. PMID: 27601569; PMCID: PMC5013292.
      View in: PubMed   Mentions: 11     Fields:    Translation:AnimalsCells
    6. De Novo Guanine Biosynthesis but Not the Riboswitch-Regulated Purine Salvage Pathway Is Required for Staphylococcus aureus Infection In Vivo. J Bacteriol. 2016 07 15; 198(14):2001-2015. 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. PMID: 27161118; PMCID: PMC4936099.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansAnimalsCells
    7. Global gene expression of methicillin-resistant Staphylococcus aureus USA300 during human and mouse infection. J Infect Dis. 2014 May 15; 209(10):1542-50. 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. PMID: 24286981.
      View in: PubMed   Mentions: 54     Fields:    Translation:HumansAnimalsCells
    8. Identifying potential therapeutic targets of methicillin-resistant Staphylococcus aureus through in vivo proteomic analysis. J Infect Dis. 2014 May 15; 209(10):1533-41. 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. PMID: 24280367; PMCID: PMC3997574.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansAnimalsCells
    9. Glycan shifting on hepatitis C virus (HCV) E2 glycoprotein is a mechanism for escape from broadly neutralizing antibodies. J Mol Biol. 2013 Jun 12; 425(11):1899-1914. 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. PMID: 23458406.
      View in: PubMed   Mentions: 81     Fields:    Translation:Cells
    10. Analysis of the nucleotide sequence of the guinea pig cytomegalovirus (GPCMV) genome. Virol J. 2008 Nov 12; 5:139. Schleiss MR, McGregor A, Choi KY, Date SV, Cui X, McVoy MA. PMID: 19014498; PMCID: PMC2614972.
      View in: PubMed   Mentions: 30     Fields:    Translation:Cells
    11. The Rosetta stone method. Methods Mol Biol. 2008; 453:169-80. Date SV. PMID: 18712302.
      View in: PubMed   Mentions: 9     Fields:    
    12. Phylogenetic profiling. Methods Mol Biol. 2008; 453:201-16. Date SV, Peregrín-Alvarez JM. PMID: 18712304.
      View in: PubMed   Mentions: 4     Fields:    
    13. Estimating protein function using protein-protein relationships. Methods Mol Biol. 2007; 408:109-27. Date SV. PMID: 18314580.
      View in: PubMed   Mentions: 7     Fields:    
    14. Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale. Genome Res. 2006 Apr; 16(4):542-9. Date SV, Stoeckert CJ. PMID: 16520460; PMCID: PMC1457034.
      View in: PubMed   Mentions: 50     Fields:    Translation:Animals
    15. Protein function prediction using the Protein Link EXplorer (PLEX). Bioinformatics. 2005 May 15; 21(10):2558-9. Date SV, Marcotte EM. PMID: 15701682.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    16. A probabilistic functional network of yeast genes. Science. 2004 Nov 26; 306(5701):1555-8. Lee I, Date SV, Adai AT, Marcotte EM. PMID: 15567862.
      View in: PubMed   Mentions: 300     Fields:    Translation:AnimalsCells
    17. Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res. 2004 Nov; 14(11):2221-34. 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. PMID: 15520287; PMCID: PMC525680.
      View in: PubMed   Mentions: 120     Fields:    Translation:Cells
    18. LGL: creating a map of protein function with an algorithm for visualizing very large biological networks. J Mol Biol. 2004 Jun 25; 340(1):179-90. Adai AT, Date SV, Wieland S, Marcotte EM. PMID: 15184029.
      View in: PubMed   Mentions: 46     Fields:    Translation:HumansCells
    19. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat Biotechnol. 2003 Sep; 21(9):1055-62. Date SV, Marcotte EM. PMID: 12923548.
      View in: PubMed   Mentions: 83     Fields:    Translation:Cells
    20. Exploiting big biology: integrating large-scale biological data for function inference. Brief Bioinform. 2001 Dec; 2(4):363-74. Marcotte E, Date S. PMID: 11808748.
      View in: PubMed   Mentions: 11     Fields:    
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