Difference between revisions of "Publication"

Revision as of 12:07, 4 August 2009

2009

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
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
Marcotte EM, Tsechansky M, Disorder, promiscuity, and toxic partnerships, Cell, 138(1):16-18 (2009) PubMed Link PDF
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
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 PDF Supplemental methods Supplemental Dataset Table S1 Table S2 Table S3
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 PDF Supplemental methods
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 PDF
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 PDF
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 PDF

2008

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 PDF Supplemental Notes Supplemental Data
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 PDF
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 PDF
Prince JT, Marcotte EM, mspire: mass spectrometry proteomics in Ruby, Bioinformatics, 24(23):2796-7 (2008) PubMed Link PDF
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 PDF Supplement
Lee I, Marcotte EM, Integrating functional genomics data, Methods Mol Biol, 453:267-78. (2008) PubMed Link PDF
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 PDF Supplement
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 PDF
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 PDF
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 PDF
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 PDF
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 PDF
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 PDF
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 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 Biol, 8(12):R258. (2007) PubMed Link 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, 2(10):e988 (2007) PubMed Link PDF Supplemental Web Site
Marcotte EM, How do shotgun proteomics algorithms identify proteins?, Nat Biotechnol, 25(7):755-7 (2007) PubMed Link PDF
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 PDF
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 PDF Supplement Supplemental Data (zipped folder) News & Views 1 News & Views 2 News & Views 3
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 PDF Supplemental File 1 Supplemental File 2 Supplemental File 3
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 PDF

2006

Hart GT, Ramani AK, Marcotte EM., How complete are current yeast and human protein-interaction networks?, Genome Biol., 7(11):120 (2006) PubMed Link PDF Additional Data File 1
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 PDF
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 PDF
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 PDF Supplement Supplemental Table 1 Supplemental Table 2 Supplemental Table 3 Supplemental Table 4
Lee I, Narayanaswamy R, Marcotte EM, Bioinformatic prediction of yeast gene function, Yeast Gene Analysis, Stansfield, I., ed., Elsevier Press: (2006) PubMed PDF
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 PDF

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, 438(7067):441-2 (2005) PubMed Link PDF the Science Daily press release Nature 2005 Gallery "First Glimpse" Nature feature on the iGEM competition featuring a bacterial portrait UT press release New York Times feature
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 PDF
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 PDF
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 PDF
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 PDF
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 PDF
Date SV, Marcotte EM, Protein function prediction using the Protein Link Explorer (PLEX), Bioinformatics, 21(10):2558-9 (2005) PubMed Link PDF Supplemental Web Site

2004

Lee I, Date SV, Adai AT, Marcotte EM, A probabilistic functional network of yeast genes., Science, 306(5701):1555-8 (2004) PubMed PDF Supplemental methods README for supplemental data files Summary of all linkages in the final network (FinalNet) Fifty five clusters representing yeast functional modules at top level of hierarchy. Same as above but 627 clusters chosen at the level of the hierarchy with the best modularity (See explanation in supplemental methods). Three dimensional network layout of the 18 major gene clusters (representing functional modules) out of the 54 top level clusters. (VRML viewer is required) Same as above but with the 564 major clusters from the 627 cluster set. (VRML viewer is required)
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) PubMed PDF
Fraser AG, Marcotte EM, Development through the eyes of functional genomics, Curr Opin Genet Dev., 14(4):336-42 (2004) PubMed Link PDF
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) PubMed Link PDF
Adai AT, Date SV, Wieland S, Marcotte EM, LGL: Creating a Map of Protein Function with an Algorithm for Visualizing Very Large Biological Networks, J Mol Biol, 340(1):179-90 (2004) PubMed Link PDF Supplemental Web Site Sourceforge Site
Fraser AG, Marcotte EM, A probabilistic view of gene function, Nature Genetics, 559-64:179-90 (2004) PubMed Link PDF
Marcotte EM, Practical computational approaches to infer protein function, Biosilico, 2:24-29 (2004) PubMed PDF
Prince JT, Carlson MW, Wang R, Lu P, Marcotte EM, The need for a public proteomics repository, Nature Biotechnology, 22(4):471-472 (2004) PubMed Link Supplemental Web Site
Date SV, Marcotte EM, Response to McDermott and Samudrala: Enhanced functional information from predicted protein networks, TRENDS in Biotechnology, 22(2):62-63 (2004) PubMed Link PDF

2003

Dhillon IS, Marcotte EM, Roshan U., Diametrical clustering for identifying anti-correlated gene clusters., Bioinformatics, 19(13):1612-9 (2003) PubMed PDF
Lu P, Nakorchevskiy A, Marcotte EM., Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations., Proc Natl Acad Sci U S A., 100(18):10370-5 (2003) PubMed PDF
Date SV, Marcotte EM., Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages., Nat Biotechnol., 21(9):1055-62 (2003) PubMed PDF Fig S1 Fig S2 Table S1
Marcotte EM., Assembling a jigsaw puzzle with 20,000 parts., Genome Biol., 4(6):323. (2003) PubMed PDF
Ramani AK, Marcotte EM., Exploiting the co-evolution of interacting proteins to discover interaction specificity., J Mol Biol., 327(1):273-84. (2003) PubMed PDF Supplemental Web Site
Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, FitzHugh W, Ma LJ, Smirnov S, Purcell S, Rehman B, Elkins T, Engels R, Wang S, Nielsen CB, Butler J, Endrizzi M, Qui D, Ianakiev P, Bell-Pedersen D, Nelson MA, Werner-Washburne M, Selitrennikoff CP, Kinsey JA, Braun EL, Zelter A, Schulte U, Kothe GO, Jedd G, Mewes W, Staben C, Marcotte E, Greenberg D, Roy A, Foley K, Naylor J, Stange-Thomann N, Barrett R, Gnerre S, Kamal M, Kamvysselis M, Mauceli E, Bielke C, Rudd S, Frishman D, Krystofova S, Rasmussen C, Metzenberg RL, Perkins DD, Kroken S, Cogoni C, Macino G, Catcheside D, Li W, Pratt RJ, Osmani SA, DeSouza CP, Glass L, Orbach MJ, Berglund JA, Voelker R, Yarden O, Plamann M, Seiler S, Dunlap J, Radford A, Aramayo R, Natvig DO, Alex LA, Mannhaupt G, Ebbole DJ, Freitag M, Paulsen I, Sachs MS, Lander ES, Nusbaum C, Birren B., The genome sequence of the filamentous fungus Neurospora crassa., Nature., 422(6934):859-68. (2003) PubMed PDF
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., : (2003) PubMed PDF

2002

Mallick P, Marcotte EM, Making sense of proteomics: Using bioinformatics to discover a protein's structure, functions, and interactions, Proteins and Proteomics: A Laboratory Manual, Simpson, R. J., ed., Cold Spring Harbor Press: (2002) PubMed
Dhillon IS, Marcotte EM, 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: (2002) PubMed PDF
Marcotte EM, Predicting Protein Function and Networks on Genome-Wide Scale, Gene Regulation and Metabolism: Post-Genomic Computational Approaches, Collado-Vides, J. & Holfstadt, R., eds., MIT press: (2002) PubMed
Verjovsky Marcotte CJ, Marcotte EM, Predicting functional linkages from gene fusions with confidence, Applied Bioinformatics, 1(2):1-8 (2002) PubMed PDF

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

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
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).
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
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
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
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

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.

Difference between revisions of "Publication"

Revision as of 12:07, 4 August 2009

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+|comment=[http://www.marcottelab.org/paper-pdfs/NatureGenetics_Wormnet_2008_Supplement.pdf Supplement] [http://www.functionalnet.org/wormnet Supplemental Web Site]
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+|comment=[http://www.marcottelab.org/paper-pdfs/NatureBiotech_APEX_2007_supplement.pdf Supplement] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_APEX_2007_SupplementaryData.zip Supplemental Data (zipped folder)] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_APEX_2007_newsandviews.pdf News & Views 1] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_APEX_2007_newsandviews2.pdf News & Views 2] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_APEX_2007_newsandviews3.pdf News & Views 3]
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+|comment=[http://www.marcottelab.org/paper-pdfs/MetabolicEngineering_OneCarbonMetab_2007_SupplementalFile1.xls Supplemental File 1] [http://www.marcottelab.org/paper-pdfs/MetabolicEngineering_OneCarbonMetab_2007_SupplementalFile2.xls Supplemental File 2] [http://www.marcottelab.org/paper-pdfs/MetabolicEngineering_OneCarbonMetab_2007_SupplementalFile3.xls Supplemental File 3]
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 |pubmed=17605818
 |link=http://www.biomedcentral.com/1471-2105/8/236
+|pdf=BMCBioinformatics_YeastComplexEssentiality_2007.pdf
 |comment=
 }}
@@ Line 351: / Line 372: @@
 |pubmed=17147767
 |link=http://genomebiology.com/2006/7/11/120
-|comment=
+|pdf=GenomeBiology_HumanPPIOverview_2006.pdf
+|comment=[http://www.marcottelab.org/paper-pdfs/GenomeBiology_HumanPPIOverview_2006_AdditionalDataFile1.pdf Additional Data File 1]
 }}
 # {{Paper
@@ Line 362: / Line 384: @@
 |pubmed=16944896
 |link=http://pubs.acs.org/doi/abs/10.1021/ac0605344
+|pdf=AnalyticalChemistry_OBIWarp_2006.pdf
 |comment=
 }}
@@ Line 373: / Line 396: @@
 |pubmed=16585069
 |link=http://bioinformatics.oxfordjournals.org/cgi/content/full/22/12/1524
+|pdf=Bioinformatics_MoBIoSCoarseFilter_2006.pdf
 |comment=
 }}
@@ Line 384: / Line 408: @@
 |pubmed=16507139
 |link=http://genomebiology.com/2006/7/1/R6
-|comment=
+|pdf=GenomeBiology_CellChips_2006.pdf
+|comment=[http://www.marcottelab.org/paper-pdfs/GenomeBiology_CellChips_Supplement_2006.pdf Supplement] [http://www.marcottelab.org/paper-pdfs/NarayanaswamySupplementalTable1.xls Supplemental Table 1] [http://www.marcottelab.org/paper-pdfs/NarayanaswamySupplementalTable2.xls Supplemental Table 2] [http://www.marcottelab.org/paper-pdfs/NarayanaswamySupplementalTable3.xls Supplemental Table 3] [http://www.marcottelab.org/paper-pdfs/NarayanaswamySupplementalTable4.xls Supplemental Table 4]
 }}
 # {{Paper
@@ Line 395: / Line 420: @@
 |pubmed=
 |link=
+|pdf=LeeNarayanaswamyMarcotteManuscript.pdf
 |comment=
 }}
@@ Line 406: / Line 432: @@
 |pubmed=16524841
 |link=http://rstb.royalsocietypublishing.org/content/361/1467/525.long
+|pdf=PhilTransactionsRoyalSocB_BioinformaticChallenges_2006.pdf
 |comment=
 }}
@@ Line 420: / Line 447: @@
 |link=http://dx.doi.org/10.1038/nature04405
 |pdf=Nature_BacterialPhotography_2005.pdf
-|comment=
+|comment=[http://www.sciencedaily.com/releases/2005/11/051123171556.htm the Science Daily press release] [http://dx.doi.org/10.1038/4381064a <i>Nature</i> 2005 Gallery "First Glimpse"] [http://dx.doi.org/10.1038/438417a <i>Nature</i> feature on the iGEM competition featuring a bacterial portrait] [http://www.utexas.edu/features/2005/bacteria/ UT press release] [http://www.nytimes.com/2005/11/24/national/24film.html New York Times feature]
 }}
-#* [http://www.sciencedaily.com/releases/2005/11/051123171556.htm the Science Daily press release]
-#* [http://dx.doi.org/10.1038/4381064a <i>Nature</i> 2005 Gallery "First Glimpse"]
-#* [http://dx.doi.org/10.1038/438417a <i>Nature</i> feature on the iGEM competition featuring a bacterial portrait]
-#* [http://www.utexas.edu/features/2005/bacteria/ UT press release]
-#* [http://www.nytimes.com/2005/11/24/national/24film.html New York Times feature]
 # {{Paper
 |title=A fast coarse filtering method for protein identification by mass spectrometry
@@ Line 436: / Line 458: @@
 |pubmed=
 |link=
+|pdf=TechnicalReport-MoBIoS-TR-05-06.pdf
 |comment=
 }}
@@ Line 447: / Line 470: @@
 |pubmed=16077011
 |link=http://genome.cshlp.org/content/15/8/1118.long
+|pdf=rong_2005.pdf
 |comment=
 }}
@@ Line 458: / Line 482: @@
 |pubmed=15892868
 |link=http://genomebiology.com/2005/6/5/R40
+|pdf=Arun-consolidate-human.pdf
 |comment=
 }}
@@ Line 469: / Line 494: @@
 |pubmed=15811782
 |link=http://dx.doi.org/10.1016/j.artmed.2004.07.016
+|pdf=bionlp-aimed-04.pdf
 |comment=
 }}
@@ Line 480: / Line 506: @@
 |pubmed=
 |link=
+|pdf=ISMB-ACLworkshop_LitMining_2005.pdf
 |comment=
 }}
@@ Line 491: / Line 518: @@
 |pubmed=15701682
 |link=http://bioinformatics.oxfordjournals.org/cgi/content/full/21/10/2558
-|comment=
+|pdf=Plex.pdf
+|comment=[http://bioinformatics.icmb.utexas.edu/plex/plex.html Supplemental Web Site]
 }}
@@ Line 504: / Line 532: @@
 |pubmed=15567862
 |pdf=Science_Lee_YeastNet.pdf
+|comment=[http://www.marcottelab.org/paper-pdfs/1099511v2s.pdf Supplemental methods] [http://www.marcottelab.org/paper-pdfs/1099511v2s_list.txt README for supplemental data files] [http://www.marcottelab.org/paper-pdfs/1099511v2s1.zip Summary of all linkages in the final network (FinalNet)] [http://www.marcottelab.org/paper-pdfs/1099511v2s2.txt Fifty five clusters representing yeast functional modules at top level of hierarchy.] [http://www.marcottelab.org/paper-pdfs/1099511v2s3 Same as above but 627 clusters chosen at the level of the hierarchy with the best modularity (See explanation in supplemental methods).] [http://www.marcottelab.org/paper-pdfs/1099511v2s4.wrl Three dimensional network layout of the 18 major gene clusters (representing functional modules) out of the 54 top level clusters.] (VRML viewer is required) [http://www.marcottelab.org/paper-pdfs/1099511v2s5.wrl Same as above but with the 564 major clusters from the 627 cluster set.] (VRML viewer is required)
 }}
-#* [http://www.marcottelab.org/paper-pdfs/1099511v2s.pdf Supplemental methods]
-#* [http://www.marcottelab.org/paper-pdfs/1099511v2s_list.txt README for supplemental data files]
-#** [http://www.marcottelab.org/paper-pdfs/1099511v2s1.zip Summary of all linkages in the final network (FinalNet)]
-#** [http://www.marcottelab.org/paper-pdfs/1099511v2s2.txt Fifty five clusters representing yeast functional modules at top level of hierarchy.]
-#** [http://www.marcottelab.org/paper-pdfs/1099511v2s3 Same as above but 627 clusters chosen at the level of the hierarchy with the best modularity (See explanation in supplemental methods).]
-#** [http://www.marcottelab.org/paper-pdfs/1099511v2s4.wrl Three dimensional network layout of the 18 major gene clusters (representing functional modules) out of the 54 top level clusters.] (VRML viewer is required)
-#** [http://www.marcottelab.org/paper-pdfs/1099511v2s5.wrl Same as above but with the 564 major clusters from the 627 cluster set.] (VRML viewer is required)
 # {{Paper
 |authors= 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
@@ Line 530: / Line 552: @@
 |page=336-42
 |pubmed=15261648
 |link=http://dx.doi.org/10.1016/j.gde.2004.06.015
+|pdf=COGD_FraserMarcotte_2004.pdf
 |comment=
 }}
@@ Line 542: / Line 565: @@
 |pubmed=15193308
 |link=http://dx.doi.org/10.1016/j.sbi.2004.05.003
+|pdf=cosb-review.pdf
 |comment=
 }}
@@ Line 552: / Line 576: @@
 |page=179-90
 |pubmed=15184029
 |link=http://dx.doi.org/10.1016/j.jmb.2004.04.047
-|comment=
+|pdf=jmb-lgl.pdf
+|comment=[http://bioinformatics.icmb.utexas.edu/lgl/index.html Supplemental Web Site] [http://sourceforge.net/projects/lgl/ Sourceforge Site]
 }}
 # {{Paper
@@ Line 563: / Line 588: @@
 |page=179-90
 |pubmed=15167932
 |link=http://dx.doi.org/10.1038/ng1370
+|pdf=ng-fraser-review.pdf
 |comment=
 }}
@@ Line 575: / Line 601: @@
 |pubmed=
 |link=
+|pdf=Biosilico_Marcotte_2004_proofs.pdf
 |comment=
 }}
@@ Line 586: / Line 613: @@
 |pubmed=15085804
 |link=http://dx.doi.org/10.1038/nbt0404-471
-|comment=
+|nbt-MS-review.pdf
+|comment=[http://bioinformatics.icmb.utexas.edu/OPD/ Supplemental Web Site]
 }}
 # {{Paper
@@ Line 596: / Line 624: @@
 |page=62-63
 |pubmed=
 |link=http://dx.doi.org/10.1016/j.tibtech.2003.11.008
+|pdf=trends-biotech.pdf
 |comment=
 }}
@@ Line 608: / Line 637: @@
 |volume=19(13)
 |pubmed=12967956
-|page=1612-9}}
+|page=1612-9
+|pdf=diametrical.pdf
+}}
 # {{Paper
 |title=Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations.
@@ Line 616: / Line 647: @@
 |volume=100(18)
 |page=10370-5
-|pubmed=12934019}}
+|pubmed=12934019
+|pdf=peng-pnas.pdf
+}}
 # {{Paper
 |title=Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages.
@@ Line 624: / Line 657: @@
 |volume=21(9)
 |page=1055-62
-|pubmed=12923548}}
+|pubmed=12923548
+|pdf=shailesh-natbt.pdf
+|comment=[http://www.marcottelab.org/paper-pdfs/NatureBiotech_SystematicNewPathways_FigS1.pdf Fig S1] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_SystematicNewPathways_FigS2.pdf Fig S2] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_SystematicNewPathways_TableS1.pdf Table S1]
+}}
 # {{Paper
 |title=Assembling a jigsaw puzzle with 20,000 parts.
@@ Line 632: / Line 668: @@
 |volume=4(6)
 |page=323.
-|pubmed=12801408}}
+|pubmed=12801408
+|pdf=genome-biology.pdf
+}}
 # {{Paper
 |title=Exploiting the co-evolution of interacting proteins to discover interaction specificity.
@@ Line 641: / Line 679: @@
 |page=273-84.
 |pubmed=12614624
+|pdf=jmb_2003.pdf
+|comment=[http://orion.icmb.utexas.edu/matrix/ Supplemental Web Site]
 }}
 # {{Paper
@@ Line 649: / Line 689: @@
 |volume=422(6934)
 |page=859-68.
-|pubmed=12712197}}
+|pubmed=12712197
+|pdf=Ncrassa.pdf
+}}
 # {{Paper
 |authors=Bunescu R, Ge R, Kate R, Mooney R, Wong Y, Marcotte E, Ramani A
@@ Line 657: / Line 699: @@
 |volume=
 |page=
+|pdf=icmlws.pdf
 }}