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Edward Marcotte

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Edward Marcotte is a professor of biochemistry at The University of Texas at Austin, working in genetics, proteomics, and bioinformatics.[1] Marcotte is an example of a computational biologist who also relies on experiments to validate bioinformatics-based predictions.[2]

Education and positions

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Marcotte's undergraduate education was at The University of Texas at Austin, where he received a B.S. in microbiology in 1990. He received his Ph.D. in biochemistry from The University of Texas at Austin in 1995, and did his postdoctoral work both at UT Austin and at University of California, Los Angeles with Professor David Eisenberg. Marcotte has been a professor at UT Austin since 2001.[citation needed]

Research

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Marcotte's major research contributions are in the areas of bioinformatics, proteomics, systems biology, and synthetic biology.

Bioinformatics and systems biology

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In early work, Marcotte and colleagues created the first genome-scale map of functional links among proteins in any complex organism (the yeast Saccharomyces cerevisiae), an approach that allowed them to predict the function to more than half of all uncharacterized yeast proteins.[3] Marcotte also developed several methods of identifying functional interactions between proteins, including phylogenetic profiling,[4][5][6] Rosetta Stone gene fusion,[7] mRNA coexpression,[3] and mirror tree[8] approaches.

In 2010, Marcotte and colleagues identified an algorithm for identifying cases of deep homology based on phenotype.[1][9]

Proteomics

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In the field of proteomics, Marcotte's contributions include developing early versions of the human protein interaction network[10][11] and mapping of >7,000 human protein interactions.[12] Marcotte and colleagues developed the spotted cell microarray technique for high-throughput measurement of protein expression, subcellular location, and function,[11][13][14][15] developed algorithms for analyzing mass spectrometry data,[16][17][18][19] started an open access database for mass spectrometry proteomics data,[20] and developed the APEX method for absolute protein quantification on a proteome-wide scale.[21][22] Using APEX, Marcotte and colleagues demonstrated that protein abundance in a lower eukaryote is predominantly determined by mRNA levels, while human protein abundances are determined roughly equally by transcriptional and post-transcriptional regulation.[23]

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References

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  1. ^ a b Zimmer, Carl (April 26, 2010). "The Search for Genes Leads to Unexpected Places". The New York Times.
  2. ^ "Edward M Marcotte". People. Institute for Cellular and Molecular, Biology University of Texas at Austin. Retrieved 16 August 2016.
  3. ^ a b Marcotte, E.M.; Pellegrini, M.; Thompson, M. J.; Yeates, T.; Eisenberg, D. (1999). "A Combined Algorithm for Genome-Wide Prediction of Protein Function". Nature. 402 (6757): 83–86. Bibcode:1999Natur.402...83M. doi:10.1038/47048. PMID 10573421. S2CID 144447.
  4. ^ Pellegrini, M.; Marcotte, E. M.; Thompson, M. J.; Eisenberg, D.; Yeates, T. O. (1999). "Detecting the Components of Protein Complexes and Pathways by Comparative Genome Analysis: Protein Phylogenetic Profiles". Proc. Natl. Acad. Sci. U.S.A. 96 (8): 4285–4288. doi:10.1073/pnas.96.8.4285. PMC 16324. PMID 10200254.
  5. ^ Marcotte, Edward M.; Xenarios, Ioannis; van Der Bliek, Alexander M.; Eisenberg, David (2000). "Localizing proteins in the cell from their phylogenetic profiles". Proceedings of the National Academy of Sciences of the United States of America. 97 (22): 12115–12120. Bibcode:2000PNAS...9712115M. doi:10.1073/pnas.220399497. PMC 17303. PMID 11035803.
  6. ^ Date, S.V.; Marcotte, E. M. (2003). "Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages". Nature Biotechnology. 21 (9): 1055–1062. doi:10.1038/nbt861. PMID 12923548. S2CID 1093077.
  7. ^ Marcotte, Edward M.; Pellegrini, Matteo; Ng, Ho-Leung; Rice, Danny W.; Yeates, Todd O.; Eisenberg, David (1999). "Detecting Protein Function & Protein-Protein Interactions from Genome Sequences". Science. 285 (5428): 751–753. CiteSeerX 10.1.1.535.9650. doi:10.1126/science.285.5428.751. PMID 10427000.
  8. ^ Ramani, A.K.; Marcotte, E. M. (2003). "Exploiting the Co-evolution of Interacting Proteins to Discover Interaction Specificity". J. Mol. Biol. 327 (1): 273–284. doi:10.1016/s0022-2836(03)00114-1. PMID 12614624.
  9. ^ McGary KL; Park TJ; Woods JO; Cha HJ; Wallingford JB; Marcotte EM (April 2010). "Systematic discovery of nonobvious human disease models through orthologous phenotypes" (PDF). Proceedings of the National Academy of Sciences. 107 (14): 6544–9. Bibcode:2010PNAS..107.6544M. doi:10.1073/pnas.0910200107. PMC 2851946. PMID 20308572.
  10. ^ Ramani, A.K.; Bunescu, R. C.; Mooney, R. J.; Marcotte, E. M. (2005). "Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome". Genome Biology. 6 (5): R40.1–12. doi:10.1186/gb-2005-6-5-r40. PMC 1175952. PMID 15892868.
  11. ^ a b Narayanaswamy, R.; Niu, W.; Scouras, A.; Hart, G. T.; Davies, J.; Ellington, A. D.; Iyer, V. R.; Marcotte, E. M. (2006). "Systematic profiling of cellular phenotypes with spotted cell microarrays reveals new pheromone response genes". Genome Biology. 7 (1): R6. doi:10.1186/gb-2006-7-1-r6. PMC 1431703. PMID 16507139.
  12. ^ Ramani, A.K.; Li, Z.; Hart, G. T.; Carlson, M. W.; Boutz, D.; Marcotte, E. M. (2008). "A map of human protein interactions derived from co-expression of human mRNAs and their orthologs". Mol. Syst. Biol. 4: 180. doi:10.1038/msb.2008.19. PMC 2387231. PMID 18414481.
  13. ^ Zhao, J.; Niu, W.; Yao, J.; Mohr, S.; Marcotte, E. M.; Lambowitz, A. M. (2008). "Group II intron protein localization and insertion sites are affected by polyphosphate". PLOS Biology. 6 (6): e150. doi:10.1371/journal.pbio.0060150. PMC 2435150. PMID 18593213.
  14. ^ Narayanaswamy, R.; Moradi, E. K.; Niu, W.; Hart, G. T.; Davis, M.; McGary, K. L.; Ellington, A. D.; Marcotte, E. M. (2009). "Systematic definition of protein constituents along the major polarization axis reveals an adaptive reuse of the polarization machinery in pheromone-treated budding yeast". Journal of Proteome Research. 8 (1): 6–19. doi:10.1021/pr800524g. PMC 2651748. PMID 19053807.
  15. ^ Narayanaswamy, R.; Levy, M.; Tsechansky, M.; Stovall, G. M.; O’Connell, J.; Mirrielees, J.; Ellington, A. D.; Marcotte, E. M. (2009). "Widespread reorganization of metabolic enzymes into reversible assemblies upon nutrient starvation". Proc. Natl. Acad. Sci. U.S.A. 106 (25): 10147–52. Bibcode:2009PNAS..10610147N. doi:10.1073/pnas.0812771106. PMC 2691686. PMID 19502427.
  16. ^ Ramakrishnan, S.; Mao, R.; Nakorchevskiy, A. A.; Prince, J. T.; Willard, W. S.; Xu, W.; Marcotte, E. M.; Miranker, D. P. (2006). "A fast coarse filtering method for protein identification by mass spectrometry". Bioinformatics. 22 (12): 1524–31. doi:10.1093/bioinformatics/btl118. PMID 16585069.
  17. ^ Prince, J.T.; Marcotte, E. M. (2008). "mspire: Mass spectrometry proteomics in Ruby". Bioinformatics. 24 (23): 2796–7. doi:10.1093/bioinformatics/btn513. PMC 2639276. PMID 18930952.
  18. ^ Ramakrishnan, S.R.; Vogel, C.; Prince, J. T.; Li, Z.; Penalva, L. O.; Myers, M.; Marcotte, E. M.; Miranker, D. P. (2009). "Integrating shotgun proteomics and mRNA expression data to improve protein identification". Bioinformatics. 25 (11): 1397–1403. doi:10.1093/bioinformatics/btp168. PMC 2682515. PMID 19318424.
  19. ^ Prince, J.T.; Marcotte, E. M. (2006). "Chromatographic alignment of ESI-LC-MS proteomics datasets by ordered bijective interpolated warping". Analytical Chemistry. 78 (17): 6140–6152. doi:10.1021/ac0605344. PMID 16944896.
  20. ^ Prince, J.T.; Carlson, M. W; Wang, R.; Lu, P.; Marcotte, E. M. (2004). "The need for a public proteomics repository". Nature Biotechnology. 22 (4): 471–2. doi:10.1038/nbt0404-471. PMID 15085804. S2CID 3220616.
  21. ^ Lu, P.; Vogel, C.; Wang, R.; Yao, X.; Marcotte, E. M. (2007). "Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation". Nature Biotechnology. 25 (1): 117–20. doi:10.1038/nbt1270. PMID 17187058. S2CID 13061107.
  22. ^ Vogel, Christine; Marcotte, Edward M. (2008). "Calculating absolute and relative protein abundance from mass spectrometry based protein expression data". Nature Protocols. 3 (9): 1444–1451. doi:10.1038/nprot.2008.132. PMID 18772871. S2CID 17456044.
  23. ^ Vogel, Christine; de Sousa Abreu, Raquel; Ko, Daijin; Le, Shu‐Yun; Shapiro, Bruce A; Burns, Suzanne C; Sandhu, Devraj; Boutz, Daniel R; Marcotte, Edward M.; Penalva, Luiz O (2010). "Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line". Molecular Systems Biology. 6: 400. doi:10.1038/msb.2010.59. PMC 2947365. PMID 20739923.
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