Difference between revisions of "Publication"

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Revision as of 17:27, 28 July 2009

Contents

2009

  1. Li Z, Lee I, Moradi E, Hung NJ, White J, Johnson AW, Marcotte EM, Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, PLoS Biology, (in press): (2009) PubMed
  2. Gray RS, Abitua PB, Wlodarczyk BJ, Blanchard O, Lee I, Weiss G, Marcotte EM, Wallingford JB, Finnell RH, The planar cell polarity effector protein Fuzzy is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, Nature Cell Biology, (in press): (2009) PubMed
  3. Marcotte EM, Tsechansky M, Disorder, promiscuity, and toxic partnerships, Cell, 138(1):16-18 (2009) PubMed Link
  4. Ramakrishnan SR, Vogel C, Kwon T, Penalva LO, Marcotte EM, Miranker DP, Mining gene functional networks to improve mass-spectrometry based protein identification, Bioinformatics, Advanced access: (2009) PubMed Link
  5. Narayanaswamy R, Levy M, Tsechansky M, Stovall GM, O'Connell J, Mirrielees J, Ellington AD, Marcotte EM, Widespread reorganization of metabolic enzymes into reversible assemblies upon nutrient starvation, Proc Natl Acad Sci U S A, 106(25):10147-52 (2009) PubMed Link
  6. Tabor JJ, Salis H, Simpson ZB, Chevalier AA, Levskaya A, Marcotte EM, Voigt CA, Ellington AD, A Synthetic Genetic Edge Detection Program, Cell, 137(7):1272-1281 (2009) PubMed Link
  7. Lee I, Marcotte EM, Effects of functional bias on supervised learning of a gene network model, Methods Mol Biol, 541:463-75 (2009) PubMed Link
  8. Ramakrishnan SR, Vogel C, Prince JT, Li Z, Penalva LO, Myers M, Marcotte EM, Miranker DP, Wang R, Integrating shotgun proteomics and mRNA expression data to improve protein identification, Bioinformatics, 25(11):1397-403 (2009) PubMed Link
  9. 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., 8(1):6-19. (2009) PubMed Link

2008

  1. Hannay K, Marcotte EM, Vogel C, Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation, BMC Genomics, 9:609 (2008) PubMed Link
  2. Braisted JC, Kuntumalla S, Vogel C, Marcotte EM, Rodrigues AR, Wang R, Huang ST, 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, 9:529. (2008) PubMed Link
  3. Kim WK, Marcotte EM, Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence, PLoS Comput Biol, 4(11):e1000232 (2008) PubMed Link
  4. Prince JT, Marcotte EM, mspire: mass spectrometry proteomics in Ruby, Bioinformatics, 24(23):2796-7 (2008) PubMed Link
  5. Vogel C, Marcotte EM, Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data, Nat Protoc, 3(9):1444-51. (2008) PubMed Link
  6. Lee I, Marcotte EM, Integrating functional genomics data, Methods Mol Biol, 453:267-78. (2008) PubMed Link
  7. Kim WK, Krumpelman C, Marcotte EM, Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy, Genome Biol, 9 Suppl 1::S5 (2008) PubMed Link
  8. Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP, A critical assessment of Mus musculus gene function prediction using integrated genomic evidence, Genome Biol, 9 Suppl 1:S2 (2008) PubMed Link
  9. 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 Genet, 4(7):e1000120 (2008) PubMed Link
  10. Zhao J, Niu W, Yao J, Mohr S, Marcotte EM, Lambowitz AM, Group II intron protein localization and insertion sites are affected by polyphosphate, PLoS Biol, 6(6):e150 (2008) PubMed Link
  11. 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, 4:180 (2008) PubMed Link
  12. 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, 28(10):3151-61 (2008) PubMed Link
  13. Wang R, Marcotte EM, The proteomic response of Mycobacterium smegmatis to anti-tuberculosis drugs suggests targeted pathways, J Proteome Res, 7(3):855-65 (2008) PubMed Link
  14. 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, Nat Genet, 40(2):181-8 (2008) PubMed Link

2007

  1. McGary KL, Lee I, Marcotte EM, Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes, Genome Biol, 8(12):R258. (2007) PubMed Link
  2. Lee I, Li Z, Marcotte EM, An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae, PLoS ONE, 2(10):e988 (2007) PubMed Link
  3. Marcotte EM, How do shotgun proteomics algorithms identify proteins?, Nat Biotechnol, 25(7):755-7 (2007) PubMed Link
  4. Carlson MW, Iyer VR, Marcotte EM, Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways, BMC Genomics, 8:117. (2007) PubMed Link
  5. Lu P, Vogel C, Wang R, Yao X, Marcotte EM, Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation, Nat Biotechnol, 25(1):117-24 (2007) PubMed Link
  6. Lu P, Rangan A, Chan SY, Appling DR, Hoffman DW, Marcotte EM, Global metabolic changes following loss of a feedback loop reveal dynamic steady states of the yeast metabolome, Metab Eng, 9(1):8-20 (2007) PubMed Link
  7. Hart GT, Lee I, Marcotte EM, A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality, BMC Bioinformatics, 8:236. (2007) PubMed Link

2006

  1. Hart GT, Ramani AK, Marcotte EM., How complete are current yeast and human protein-interaction networks?, Genome Biol., 7(11):120 (2006) PubMed Link
  2. Prince JT, Marcotte EM, Chromatographic alignment of ESI-LC-MS proteomics datasets by ordered bijective interpolated warping, Anal. Chem., 78(17):6140-52 (2006) PubMed Link
  3. 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, 22(12):1524-31 (2006) PubMed Link
  4. Narayanaswamy R, Niu W, Scouras A, Hart GT, Davies J, Ellington AD, Iyer VR, Marcotte EM, Systematic profiling of cellular phenotypes with spotted cell microarrays reveals new pheromone response genes, Genome Biol., 7(1):R6 (2006) PubMed Link
  5. Lee I, Narayanaswamy R, Marcotte EM, Bioinformatic prediction of yeast gene function, Yeast Gene Analysis, Stansfield, I., ed., Elsevier Press: (2006) PubMed
  6. Eisenberg D, Marcotte E, McLachlan AD, Pellegrini M, Bioinformatic challenges for the next decade(s), Philos Trans R Soc Lond B Biol Sci., 361(1467):525-7 (2006) PubMed Link

2005

  1. 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, 438(7067):441-2 (2005) PubMed Link PDF
  1. 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: (2005) PubMed
  2. 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., 15(8):1118-26 (2005) PubMed Link
  3. 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, 6(5):R40 (2005) PubMed Link
  4. Bunescu R, Ge R, Kate RJ, Marcotte EM, Mooney RJ, Ramani AK, Wong YW, Comparative Experiments on Learning Information Extractors for Proteins and their Interactions, Artif Intell Med., 33(2):139-55 (2005) PubMed Link
  5. Ramani AK, Marcotte EM, Bunescu RC, Mooney RJ, Using Biomedical Literature Mining to Consolidate the Set of Known Human Protein-Protein Interactions, Intelligent Systems in Molecular Biology-ACL Workshop, : (2005) PubMed
  6. Date SV, Marcotte EM, Protein function prediction using the Protein Link Explorer (PLEX), Bioinformatics, 21(10):2558-9 (2005) PubMed Link

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).
  Fraser AG, Marcotte EM:   Development through the eyes of functional genomics. Curr Opin Genet Dev. 14(4):336-42 (2004).
  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).
  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).
  Fraser AG, Marcotte EM:   A probabilistic view of gene function., Nature Genetics, 36(6):559-64 (2004).
  Marcotte, E. M.: Practical computational approaches to infer protein function. Biosilico, 2, 24-29 (2004).
  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).
  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).

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).
  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).
  James E. Galagan et al:   The genome sequence of the filamentous fungus Neurospora crassa, Nature, 422, 859-868 (2003).
  Edward M Marcotte:   Assembling a jigsaw puzzle with 20,000 parts., Genome Biology, 2003, Vol 4. Issue 6, Article 323.
  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.
  Inderjit Dhillon, Edward Marcotte, and Usman Roshan:   Diametrical Clustering for identifying anti-correlated gene clusters., Bioinformatics, 19: 1612-1619, 2003.
  Ramani,A. K. & Marcotte, E. M.:   Exploiting the co-evolution of interacting proteins to discover interaction specificity, JMB, 2003; 327(1):273-284.

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.
  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

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.
  Marcotte, E. M.:  The path not taken, Nat Biotechnol., 2001 Jul;19(7):626-7.
  Marcotte, E. M.:  Measuring the Dynamics of the Proteome, Genome Res 2001 Feb;11(2):191-3.
  Marcotte, E. M., Xenarios, I. & Eisenberg, D.:  Mining Literature for Protein Interactions, Bioinformatics 2001 Apr;17(4):359-63
  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)

2000

  Eisenberg, D., Marcotte, E. M., Xenarios, I. & Yeates, T. O.:  Protein function in the post-genomic era.  Nature 405, 823-6 (2000).
  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).
  Marcotte, E. M.: Computational genetics: Finding Function by Non-Homology Methods.  Curr. Op. Struct. Bio. 10, 359-65 (2000).
  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).
  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).
  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).

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).

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).

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).
  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).
  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).

1998

  Marcotte, E. M. & Eisenberg, D.  Chicken prion tandem repeats form a stable, protease resistant domain. Biochemistry  38, 667-676 (1998).
  Cascio, D., Goodwill, K. &  Marcotte, E.  A Look at the Future of Macromolecular Structure Determination.  Rigaku J. 15, 1-5 (1998).
  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).

Pre - 1998

  1. Hollis T, Honda Y, Fukamizo T, Marcotte E, Day PJ, Robertus JD, Kinetic analysis of barley chitinase, Arch Biochem Biophys., 344(2):335-42 (1997) PubMed Link
  2. Marcotte EM, Monzingo AF, Ernst SR, Brzezinski R, Robertus JD, X-ray structure of an anti-fungal chitosanase from streptomyces N174, Nat Struct Biol., 3(2):155-62 (1996) PubMed See also: Kirby AJ, Illuminating the ancient retainer, Nature Struct Biol. 3, 107-108 (1996).
  3. 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) PubMed
  4. 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) PubMed
  5. Kim YJ, Francisco L, Chen GC, Marcotte E, Chan CS, Control of cellular morphogenesis by the Ip12/Bem2 GTPase-activating protein: possible role of protein phosphorylation, J Cell Biol., 127(5):1381-94 (1994) PubMed Link
  6. 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) PubMed Link

Patents

  1. 6,892,139, Determining the functions and interactions of proteins by comparative analysis, granted May 10, 2005.
  2. 6,772,069, Determining protein function and interaction from genome analysis, granted August 3, 2004.
  3. 6,564,151, Assigning protein functions by comparative genome analysis protein phylogenetic profiles, granted May 13, 2003.
  4. 6,466,874, Rosetta stone method for detecting protein function and protein-protein interactions from genome sequences, granted October 15, 2002.