Publication

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2008

  Hannay K, Marcotte EM, Vogel C. Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation. BMC Genomics 2008, 9:609.

PDF of pre-print

  Braisted JC, Kuntumalla S, Vogel C, Marcotte EM, Rodrigues AR, Wang R, Huang S-T, Ferlanti ES, Saeed AI, Fleischmann RD, Peterson SN, Pieper R. The APEX Quantitative Proteomics Tool: Generating protein quantitation estimates from LC-MS/MS proteomics results. BMC Bioinformatics 2008, in press.
  Narayanaswamy R, Moradi EK, Niu W, Hart GT, Davis M, McGary KL, Ellington AD, Marcotte EM. Systematic Definition of Protein Constituents along the Major Polarization Axis Reveals an Adaptive Reuse of the Polarization Machinery in Pheromone-Treated Budding Yeast. J Proteome Res. 2008, in press.

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  Kim WK, Marcotte, EM. Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence. PLoS Computational Biology 2008, 4(11): e1000232.

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  Prince JT, Marcotte, EM. mspire: Mass spectrometry proteomics in Ruby. Bioinformatics 2008, in press.

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  Vogel C, Marcotte EM. Calculating absolute protein abundance from mass spectrometry based protein expression data. Nature Protocols 2008, 3:1444-1451.

PDF | Supplement

  Niu W, Li Z, Zhan W, Iyer VR, Marcotte, EM. Mechanisms of cell cycle control revealed by a systematic and quantitative overexpression screen in S. cerevisiae. PLoS Genetics 2008, 4(7): e1000120.

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  Zhao J, Niu W, Marcotte EM, Lambowitz AM. The intracellular localization of a group II intron-encoded reverse transcriptase and other proteins is affected by polyphosphate. PLoS Biology 2008, 6(6): e150.

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  Lee I, Marcotte EM. Integrating Functional Genomics Data. in Methods in Molecular Biology: Bioinformatics, Vol. II, Structure, Function and Applications, Keith, J. M., ed., Humana Press (2008)

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  Kim WK, Krumpelman C, Marcotte EM. Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy. Genome Biology 2008 9:S5.

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  Pena-Castillo L, et al. A critical assessment of M. musculus gene function prediction using integrated genomic evidence. Genome Biology 2008 9:S2.

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  Ramani AK, Li Z, Hart GT, Carlson MW, Boutz DR, Marcotte EM. A map of human protein interactions derived from co-expression of human mRNAs and their orthologs. Mol Syst Biol. 2008 4:180. Epub 2008 Apr 15.

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  White J, Li Z, Sardana R, Bujnicki JM, Marcotte EM, Johnson AW. Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of Pre-40S subunits. Mol Cell Biol. 2008 28(10):3151-61. Epub 2008 Mar 10.

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  Wang R, Marcotte EM. The Proteomic Response of Mycobacterium smegmatis to Anti-Tuberculosis Drugs Suggests Targeted Pathways. J Proteome Res. 2008 Feb 15

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  Lee I, Lehner B, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans Nature Genetics 2008 40(2):181-8

PDF | Supplement | Supplemental web site

2007

  McGary KL, Lee I, Marcotte EM. Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes. Genome Biology 2007 8(12):R258

PDF | Supplemental web site

  Lee I, Li Z, Marcotte EM. An Improved, Bias-Reduced Probabilistic Functional Gene Network of Baker's Yeast, Saccharomyces cerevisiae. PLoS ONE 2007 2(10):e988

PDF | Supplemental web site

  Marcotte EM. Primer: How do shotgun proteomics algorithms identify proteins? Nature Biotechnology 2007 25(7):755-757

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  Hart GT, Lee I, Marcotte EM. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. BMC Bioinformatics 2007 8(1):236

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  Carlson MW, Iyer VR, Marcotte EM. Quantitative gene expression identifies appropriate cell line models for individual cervical cancer pathways. BMC Genomics 2007 8(1):117

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  Lu P, Vogel C, Wang R, Yao X, Marcotte EM. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nature Biotechnology 2007 25(1):117-124.

PDF | Supplement | Supplemental Data (zipped folder) | News & Views 1 | 2 | 3

  Lu, P., Rangan, A., Chan, S. Y., Appling, D. R., Hoffman, D. W., & Marcotte, E. M. Global metabolic changes following loss of a feedback loop reveal dynamic steady states of the yeast metabolome. Metabolic Engineering 2007 Jan;9(1):8-20. Epub 2006 Jun 30

PDF | Supplemental File 1 | 2 | 3

2006

  Hart GT, Ramani AK, Marcotte, EM. How complete are current yeast and human protein-interaction networks? Genome Biology 2006 7(11):120.1 - 120.9.

PDF | Additional Data File 1

  Prince, J. T. & Marcotte, E. M. Chromatographic alignment of ESI-LC-MS proteomics datasets by ordered bijective interpolated warping. Anal. Chem. 2006 78(17):6140-52.

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  Ramakrishnan SR, Mao R, Nakorchevskiy AA, Prince JT, Willard WS, Xu W, Marcotte EM, Miranker DP.: A fast coarse filtering method for peptide identification by mass spectrometry. Bioinformatics 2006 22(12):1524-31. Epub 2006 Apr 3.

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  Narayanaswamy, R., Niu, W., Scouras, A., Hart, G. T., Davies, J., Ellington, A. D., Iyer, V. R., & Marcotte, E. M.: Systematic profiling of cellular phenotypes with spotted cell microarrays reveals new pheromone response genes. Genome Biology 7, R6 (2006).

PDF | Supplement | Supplemental data files: 1 | 2 | 3 | 4

  Lee, I. Narayanaswamy, R. & Marcotte, E. M.: Bioinformatic prediction of yeast gene function. in Yeast Gene Analysis, Stansfield, I., ed., Elsevier Press (2006).

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  Eisenberg D, Marcotte E, McLachlan AD, Pellegrini M: Bioinformatic challenges for the next decade(s). Phil. Trans. R. Soc. B 2006.

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2005

  Levskaya A, Chevalier AA, Tabor JJ, Simpson ZB, Lavery LA, Levy M, Davidson EA, Scouras A, Ellington AD, Marcotte EM, Voigt CA:   Synthetic biology: engineering Escherichia coli to see light. Nature 2005, 438(7067):441-2.

PDF | Supplement | Nature Press Release | Nature Intro | iGEM story | Nature-top 10 images of 2005 | NYTimes story | UT Feature Story | UT Press Release

  Ramakrishnan SR, Mao R, Nakorchevskiy AA, Prince JT, Willard WS, Xu W, Marcotte EM, Miranker DP:   A fast coarse filtering method for protein identification by mass spectrometry. University of Texas Dept. of Computer Sciences, Technical Report TR-05-06.

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Wang R, Prince JT,  Marcotte EM: Mass spectrometry of the M. smegmatis proteome: Protein expression levels correlate with function, operons, and codon bias. Genome Res. 2005 Aug;15(8):1118-26.

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  Ramani AK, Bunescu RC, Mooney RJ, Marcotte EM:   Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biology 2005, 6:r40.

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  Razvan Bunescu, Ruifang Ge, Rohit J. Kate, Edward M. Marcotte, Raymond J. Mooney, Arun Kumar Ramani, and Yuk Wah Wong:   Comparative Experiments on Learning Information Extractors for Proteins and their Interactions.Artif Intell Med. 2005 Feb;33(2):139-55.

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  Ramani, A. K, Marcotte, E. M., Bunescu, R. C., & Mooney, R. J.: Using Biomedical Literature Mining to Consolidate the Set of Known Human Protein-Protein Interactions. Intelligent Systems in Molecular Biology-ACL Workshop (2005).

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  Date SV, Marcotte EM:   Protein function prediction using the Protein Link Explorer (PLEX). Bioinformatics. 2005 Feb 8; [Epub ahead of print].

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2004

  Lee I, Date SV, Adai AT, Marcotte EM:   A Probabilistic functional network of yeast genes. Science 306(5701):1555-8 (2004).

PDF | Supplement | Supplemental data files: README | 1 | 2 | 3 | 4 | 5

  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:   Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res. 14(11):2221-34 (2004).

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  Fraser AG, Marcotte EM:   Development through the eyes of functional genomics. Curr Opin Genet Dev. 14(4):336-42 (2004).

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  Bork P, Jensen LJ, Von Mering C, Ramani AK, Lee I, Marcotte EM:   Protein interaction networks from yeast to human.Curr Opin Struct Biol 14(3):292-9 (2004).

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  Adai AT, Date SV, Wieland S, Marcotte EM:   LGL: Creating a Map of Protein Function with an Algorithm for Visualizing Very Large Biological Networks., JMB,340(1):179-90(2004).

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  Fraser AG, Marcotte EM:   A probabilistic view of gene function., Nature Genetics, 36(6):559-64 (2004).

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  Marcotte, E. M.: Practical computational approaches to infer protein function. Biosilico, 2, 24-29 (2004).

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  John T Prince, Mark W Carlson, Rong Wang, Peng Lu & Edward M Marcotte:   The need for a public proteomics repository, Nature Biotechnology, 22, 4, 471-472 (2004).

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

PDF | NCBI

2003

  Shailesh V Date & Edward M Marcotte:   Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages, Nature Biotechnology, 21, 9, 1055-1062 (2003).

PDF | NCBI | Fig S1 | Fig S2 | Table S1

  Peng Lu, Aleksey Nakorchevskiy, and Edward M. Marcotte:   Expression deconvolution: A reinterpretation of DNA microarray data reveals dynamic changes in cell populations , PNAS, 100, 18, 10370-10375 (2003).

PDF | NCBI

  James E. Galagan et al:   The genome sequence of the filamentous fungus Neurospora crassa, Nature, 422, 859-868 (2003).

PDF | NCBI

  Edward M Marcotte:   Assembling a jigsaw puzzle with 20,000 parts., Genome Biology, 2003, Vol 4. Issue 6, Article 323.

PDF | NCBI

  Bunescu R, Ge R, Kate R, Mooney R, Wong Y, Marcotte E, & Ramani A:   Learning to extract proteins and their interactions from Medline abstracts. ICML Workshop 2003.

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  Inderjit Dhillon, Edward Marcotte, and Usman Roshan:   Diametrical Clustering for identifying anti-correlated gene clusters., Bioinformatics, 19: 1612-1619, 2003.

PDF | NCBI

  Ramani,A. K. & Marcotte, E. M.:   Exploiting the co-evolution of interacting proteins to discover interaction specificity, JMB, 2003; 327(1):273-284.

PDF | NCBI 2002

  Mallick, P. & Marcotte, E. M.: Making sense of proteomics: Using bioinformatics to discover a protein's structure, functions, and interactions. in Proteins and Proteomics: A Laboratory Manual, Simpson, R. J., ed., Cold Spring Harbor Press (2002).
  Dhillon, I. S., Marcotte, E. M. & Roshan, U.: Diametrical Clustering for identifying anti-correlated gene clusters. The University of Texas at Austin, Department of Computer Sciences. Technical Report TR-02-49. September 2002.

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  Marcotte, E. M.: Predicting Protein Function and Networks on Genome-Wide Scale. in Gene Regulation and Metabolism: Post-Genomic Computational Approaches, Collado-Vides, J. & Holfstadt, R., eds., MIT press (2002).
  Verjovsky Marcotte, C. J. & Marcotte E. M:   Prediction functional linkages from gene fusions with confidence, App. Bioinform, 2002;1(2):1-8

PDF(submission proofs) 2001

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

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  Marcotte, E. M.:  The path not taken, Nat Biotechnol., 2001 Jul;19(7):626-7.

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  Marcotte, E. M.:  Measuring the Dynamics of the Proteome, Genome Res 2001 Feb;11(2):191-3.

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  Marcotte, E. M., Xenarios, I. & Eisenberg, D.:  Mining Literature for Protein Interactions, Bioinformatics 2001 Apr;17(4):359-63

PDF | Supplemental Files: README | 1 | 2 | 3 | 4

  Eisenberg, D., Marcotte, E., Pellegrini, M., Thompson, M., Xenarios, I., Yeates, T.: From genome sequences to protein interactions. FASEB J. 15, A724-A724 (2001).
  Xenarios I, Fernandez E, Salwinski L, Duan XJ, Thompson MJ, Marcotte EM, Eisenberg D.: DIP: the database of interacting proteins: 2001 update, Nucleic Acids Res. 29(1):239-41 (2001)

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2000

  Eisenberg, D., Marcotte, E. M., Xenarios, I. & Yeates, T. O.:  Protein function in the post-genomic era.  Nature 405, 823-6 (2000).

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  Marcotte, E. M., Xenarios, I., van der Bliek, A. & Eisenberg, D.: Localizing proteins in the cell from their phylogenetic profiles.  Proc. Natl. Acad. Sci.  97, 12115-20 (2000).

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  Marcotte, E. M.: Computational genetics: Finding Function by Non-Homology Methods.  Curr. Op. Struct. Bio. 10, 359-65 (2000).

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  Yang, H., Fitz-Gibbon, S.,  Marcotte, E. M., Tai, J. H., Hyman, E. C. & Miller, J. H.: Characterization of a thermostable DNA glycosylase specific for U/G and T/G mismatches from the hyperthermophilic archaeon Pyrobaculum aerophilum. J. Bacteriol. 182, 1272-9 (2000).

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  Thompson, M., Marcotte, E., Pellegrini, M., Yeates, T. & Eisenberg, D.: Increasing the specificity of protein functional inference by the Rosetta Stone method. in Currents in Computational Molecular Biology, Miyano, S., Shamir, R. & Takagi, T.., eds., Universal Academy Press, Inc. (2000).

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  Xenarios, I., Rice, D. W., Salwinski, L., Baron, M. K., Marcotte, E. M., & Eisenberg, D.: DIP: Database of Interacting Proteins, Nucleic Acids Research 28, 289-91 (2000).

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1999

  Marcotte, E. M., Pellegrini, M., Thompson, M. J., Yeates, T. & Eisenberg, D.  A Combined Algorithm for Genome-Wide Prediction of Protein Function. Nature 402, 83-86 (1999).

PDF This paper was the subject of an invited commentary: Sali, A. Genomics: Functional links between proteins. Nature 402, 23-26 (1999), and was featured in the Boston Globe (Nov. 3, 1999) and the Los Angeles Times (Nov. 4, 1999).

  Marcotte, E. M., Pellegrini, M., Ng, H.-L., Rice, D. W., Yeates, T. O. & Eisenberg, D.  Detecting Protein Function & Protein-Protein Interactions from Genome Sequences.  Science  285, 751-753 (1999).

PDF This paper was the subject of an invited commentary: Doolittle, R. F. Do you dig my groove? Nature: Genetics 23, 6-8 (1999).

  Marcotte, E. M., Pellegrini, M., Yeates, T. O. & Eisenberg, D. A Census of Protein Repeats.  J. Molec. Biol. 293, 151-160 (1999).

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  Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D. & Yeates, T. O.: Assigning protein functions by comparative genome analysis: protein phylogenetic profiles.   Proc.Natl. Acad. Sci. 96, 4285-4288 (1999).

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  Pellegrini, M.,  Marcotte, E. M. & Yeates, T. O. A Fast Algorithm for Genome-Wide Analysis of Proteins with Repeated Sequences.  Proteins: Struct. Funct. Genet.  35, 440-446 (1999).

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1998

  Marcotte, E. M. & Eisenberg, D.  Chicken prion tandem repeats form a stable, protease resistant domain. Biochemistry  38, 667-676 (1998).

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  Cascio, D., Goodwill, K. &  Marcotte, E.  A Look at the Future of Macromolecular Structure Determination.  Rigaku J. 15, 1-5 (1998).

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  Robertus, J. D., Monzingo, A. F., Marcotte, E. M. & Hart, P. J.: Structural Analysis Shows Five Glycohydrolase Families Diverged From a Common Ancestor. J. Exp. Zool. 282, 127-32 (1998).

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Pre - 1998

  Hollis, T., Honda, Y., Fukamizo, T., Marcotte, E., Day, P. J. & Robertus, J. D.: Kinetic Analysis of Barley Chitinase. Arch. Biochem. Biophys. 344, 335-342 (1997).

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  Marcotte EM, Monzingo AF, Ernst SR, Brzezinski R, Robertus JD: X-ray structure of an anti-fungal chitosanase from streptomyces N174., Nat Struct Biol. 1996 Feb;3(2):155-62.

This paper was the subject of an invited commentary: Kirby, A. J.: Illuminating the ancient retainer. Nature: Structural Biol. 3, 107-108 (1996).

  Monzingo AF, Marcotte EM, Hart PJ, Robertus JD.: Chitinases, chitosanases, and lysozymes can be divided into procaryotic and eucaryotic families sharing a conserved core. Nat Struct Biol. ;3(2):133-40.(1996)
  Robertus, J. D., Hart, P. J., Monzingo, A. F., Marcotte, E. & Hollis, T.: The Structure of Chitinases and Prospects for Structure-Based Drug Design. Can. J. Bot. 73 (Suppl. 1), S1142-S1146 (1995).
  Kim, Y-J., Francisco, L., Chen, G-C., Marcotte, E. & Chan, C.: Control of Cellular Morphogenesis by the Ipl2/Bem2 GTPase-activating Protein: Possible Role of Protein Phosphorylation. J. Cell. Biol. 127, 1381-1394 (1994).

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  Marcotte E, Hart PJ, Boucher I, Brzezinski R, Robertus JD.: Crystallization of a chitosanase from Streptomyces N174. J Mol Biol.;232(3):995-6.(1993)

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PATENTS

  # 6,892,139, Determining the functions and interactions of proteins by comparative analysis, granted May 10, 2005.
  # 6,772,069, Determining protein function and interaction from genome analysis, granted August 3, 2004.
  # 6,564,151, Assigning protein functions by comparative genome analysis protein phylogenetic profiles, granted May 13, 2003.
  # 6,466,874, Rosetta stone method for detecting protein function and protein-protein interactions from genome sequences, granted October 15, 2002.