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]
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]
^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. PMID12923548. S2CID1093077.
^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. CiteSeerX10.1.1.535.9650. doi:10.1126/science.285.5428.751. PMID10427000.
^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. PMID12614624.
^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. PMID16944896.
^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. PMID15085804. S2CID3220616.
^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. PMID17187058. S2CID13061107.