PAPERS  [go to Book chapters]

2006

• Date, S.V.* and Stoeckert, C.J., Jr. Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale. Genome Res. 2006 Apr;16(4):542-9. Epub 2006 Mar 6. * Corresponding author
  PubMed | PDF | Suppl. Info [.doc] | Website

2005

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

2004

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


• 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. and Ng, WV. Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res. 2004 Nov;14(11):2221-34.
  PubMed | PDF


• Adai, A.T., Date, S.V., Wieland, S. and Marcotte, E.M. 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.
  PubMed | PDF | Website (+ suppl. info)


• RESPONSE: Shailesh V Date and Edward M Marcotte. Response to McDermott and Samudrala: Enhanced functional information from predicted protein networks. TRENDS in Biotechnology, 22(2), 62-63 (2004).
  Journal abstract | PDF

2003

• Date, S.V. and Marcotte, E.M. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat Biotechnol. 2003 Sep;21(9):1055-62. Epub 2003 Aug 17.
  PubMed | PDF | Website (+ suppl. info)
  
  
  ~ This paper was the subject of an invited commentary. See McDermott, J. and Samudrala, R. Enhanced functional information from predicted protein networks. Trends Biotechnol. 2004 Feb;22(2):60-2. Discussion (2004).
  Journal abstract
  ~ This paper was also discussed by the Faculty of 1000.
  Saved review (.txt)


• 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
  Abstract | PDF

2001

• Marcotte, E. M. and Date, S.V. Exploiting Big Biology: Integrating large-scale biological data for functional inference. Brief Bioinform. 2001 Dec;2(4):363-74.
  PubMed | PDF

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BOOK CHAPTERS  [go to Papers]

• 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.

Contributions to book chapters as part of the PlasmoDB team

• 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.