Difference between revisions of "Publication"
From Marcotte Lab
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== 2013 == | == 2013 == | ||
− | + | <ol> | |
+ | <li value="129"> {{Paper | ||
|title=Prediction of gene-phenotype associations in humans, mice, and plants using phenologs | |title=Prediction of gene-phenotype associations in humans, mice, and plants using phenologs | ||
|authors=Woods JO, Singh-Blom UM, Laurent JM, McGary KL, Marcotte EM | |authors=Woods JO, Singh-Blom UM, Laurent JM, McGary KL, Marcotte EM | ||
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|pub_year=2013 | |pub_year=2013 | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="128"> {{Paper | ||
|title=Prediction and validation of gene-disease associations using methods inspired by social network analyses | |title=Prediction and validation of gene-disease associations using methods inspired by social network analyses | ||
|authors=Singh-Blom UM, Natarajan N, Tewari A, Woods JO, Dhillon IS, Marcotte EM | |authors=Singh-Blom UM, Natarajan N, Tewari A, Woods JO, Dhillon IS, Marcotte EM | ||
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|comment=[http://www.marcottelab.org/paper-pdfs/PLoSOne_Catapult_2013_Supplement.pdf Supplement] | |comment=[http://www.marcottelab.org/paper-pdfs/PLoSOne_Catapult_2013_Supplement.pdf Supplement] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="127"> {{Paper | ||
|title=The proteomic response to mutants of the ''Escherichia coli'' RNA degradosome | |title=The proteomic response to mutants of the ''Escherichia coli'' RNA degradosome | ||
|authors=Zhou L, Zhang AB, Wang R, Marcotte EM, Vogel C | |authors=Zhou L, Zhang AB, Wang R, Marcotte EM, Vogel C | ||
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|pub_year=2013 | |pub_year=2013 | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="126"> {{Paper | ||
|title=Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response | |title=Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response | ||
|authors=Wine Y, Boutz DR, Lavinder JJ, Miklos AE, Hughes RA, Hoi KH, Jung ST, Horton AP, Murrin EM, Ellington AD, Marcotte EM, Georgiou G | |authors=Wine Y, Boutz DR, Lavinder JJ, Miklos AE, Hughes RA, Hoi KH, Jung ST, Horton AP, Murrin EM, Ellington AD, Marcotte EM, Georgiou G | ||
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|link=http://www.pnas.org/content/early/2013/02/01/1213737110.abstract | |link=http://www.pnas.org/content/early/2013/02/01/1213737110.abstract | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="125"> {{Paper | ||
|title=Transiently transfected purine biosynthetic enzymes form stress bodies | |title=Transiently transfected purine biosynthetic enzymes form stress bodies | ||
|authors=Zhao A, Tsechansky M, Swaminathan J, Cook L, Ellington AD, Marcotte EM | |authors=Zhao A, Tsechansky M, Swaminathan J, Cook L, Ellington AD, Marcotte EM | ||
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|pub_year=2013 | |pub_year=2013 | ||
}} | }} | ||
+ | </li> | ||
+ | </ol> | ||
== 2012 == | == 2012 == | ||
− | + | <ol> | |
+ | <li value="124"> {{Paper | ||
|title=RIDDLE: Reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network | |title=RIDDLE: Reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network | ||
|authors=Wang PI, Hwang S, Kincaid RP, Sullivan CS, Lee I, Marcotte EM | |authors=Wang PI, Hwang S, Kincaid RP, Sullivan CS, Lee I, Marcotte EM | ||
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|pub_year=2012 | |pub_year=2012 | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="123"> {{Paper | ||
|title=The role of Pseudomonas aeruginosa peptidoglycan-associated outer membrane proteins in vesicle formation | |title=The role of Pseudomonas aeruginosa peptidoglycan-associated outer membrane proteins in vesicle formation | ||
|authors=Wessel AK, Liew J, Kwon T, Marcotte EM, Whiteley M | |authors=Wessel AK, Liew J, Kwon T, Marcotte EM, Whiteley M | ||
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|comment=[http://www.marcottelab.org/index.php/PSEAE_oprF.2012 Supplemental data] | |comment=[http://www.marcottelab.org/index.php/PSEAE_oprF.2012 Supplemental data] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="122"> {{Paper | ||
|title=Flaws in evaluation schemes for pair-input computational predictions | |title=Flaws in evaluation schemes for pair-input computational predictions | ||
|authors=Park Y, Marcotte EM | |authors=Park Y, Marcotte EM | ||
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|pub_year=2012 | |pub_year=2012 | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="121"> {{Paper | ||
|title=Census of Human Soluble Protein Complexes | |title=Census of Human Soluble Protein Complexes | ||
|authors=Havugimana PC, Hart GT, Nepusz T, Yang H, Turinsky AL, Li Z, Wang P, Boutz DR, Fong V, Babu M, Craig SA, Hu P, Phanse S, Wan C, Vlasblom J, Dar V, Bezginov A, Wu GC, Wodak SJ, Tillier ERM, Paccanaro A, Marcotte EM, Emili A | |authors=Havugimana PC, Hart GT, Nepusz T, Yang H, Turinsky AL, Li Z, Wang P, Boutz DR, Fong V, Babu M, Craig SA, Hu P, Phanse S, Wan C, Vlasblom J, Dar V, Bezginov A, Wu GC, Wodak SJ, Tillier ERM, Paccanaro A, Marcotte EM, Emili A | ||
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|pub_year=2012 | |pub_year=2012 | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="120"> {{Paper | ||
|title=Id2a functions to limit Notch pathway activity and thereby influence retinoblast proliferation to differentiation of retinoblasts during zebrafish retinogenesis | |title=Id2a functions to limit Notch pathway activity and thereby influence retinoblast proliferation to differentiation of retinoblasts during zebrafish retinogenesis | ||
|authors=Uribe RA, Kwon T, Marcotte EM, Gross JM | |authors=Uribe RA, Kwon T, Marcotte EM, Gross JM | ||
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|pub_year=2012 | |pub_year=2012 | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="119"> {{Paper | ||
|title=Evolutionarily Repurposed Networks Reveal the Well-Known Antifungal Drug Thiabendazole to Be a Novel Vascular Disrupting Agent | |title=Evolutionarily Repurposed Networks Reveal the Well-Known Antifungal Drug Thiabendazole to Be a Novel Vascular Disrupting Agent | ||
|authors=Cha HJ, Byrom M, Mead PE, Ellington AD, Wallingford JB, Marcotte EM | |authors=Cha HJ, Byrom M, Mead PE, Ellington AD, Wallingford JB, Marcotte EM | ||
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|comment=[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001379#s4 Supplemental Material] [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001380 Synopsis] [http://www.nytimes.com/2012/08/21/health/research/clues-to-fighting-cancer-are-found-in-the-genes-of-yeast.html NY Times] [http://publications.nigms.nih.gov/multimedia/repurposing-genes-drugs.html NIGMS video] | |comment=[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001379#s4 Supplemental Material] [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001380 Synopsis] [http://www.nytimes.com/2012/08/21/health/research/clues-to-fighting-cancer-are-found-in-the-genes-of-yeast.html NY Times] [http://publications.nigms.nih.gov/multimedia/repurposing-genes-drugs.html NIGMS video] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="118"> {{Paper | ||
|title=Dynamic Reorganization of Metabolic Enzymes into Intracellular Bodies | |title=Dynamic Reorganization of Metabolic Enzymes into Intracellular Bodies | ||
|authors=O'Connell JD, Zhao A, Ellington AD, Marcotte EM | |authors=O'Connell JD, Zhao A, Ellington AD, Marcotte EM | ||
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|pub_year=2012 | |pub_year=2012 | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="117"> {{Paper | ||
|title=Insights into the regulation of protein abundance from proteomic and transcriptomic analyses | |title=Insights into the regulation of protein abundance from proteomic and transcriptomic analyses | ||
|authors=Vogel C, Marcotte EM | |authors=Vogel C, Marcotte EM | ||
Line 149: | Line 164: | ||
|pub_year=2012 | |pub_year=2012 | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="116"> {{Paper | ||
|title=Proteomic and protein interaction network analysis of human T lymphocytes during cell-cycle entry | |title=Proteomic and protein interaction network analysis of human T lymphocytes during cell-cycle entry | ||
|authors=Orr SJ, Boutz DR, Wang R, Chronis C, Lea NC, Thayaparan T, Hamilton E, Milewicz H, Blanc E, Mufti GJ, Marcotte EM, Thomas NSB | |authors=Orr SJ, Boutz DR, Wang R, Chronis C, Lea NC, Thayaparan T, Hamilton E, Milewicz H, Blanc E, Mufti GJ, Marcotte EM, Thomas NSB | ||
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|pub_year=2012 | |pub_year=2012 | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="115"> {{Paper | ||
|title=RFX2 is broadly required for ciliogenesis during vertebrate development | |title=RFX2 is broadly required for ciliogenesis during vertebrate development | ||
|authors=Chung M-I, Peyrot S, LeBoeuf S, Park TJ, McGary KL, Marcotte EM, Wallingford JB | |authors=Chung M-I, Peyrot S, LeBoeuf S, Park TJ, McGary KL, Marcotte EM, Wallingford JB | ||
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|comment=[http://www.marcottelab.org/paper-pdfs/DevelopmentalBiology_RFX2_2011_SOM.pdf Supplement] | |comment=[http://www.marcottelab.org/paper-pdfs/DevelopmentalBiology_RFX2_2011_SOM.pdf Supplement] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="114"> {{Paper | ||
|title=Label-free quantitation using weighted spectral counting | |title=Label-free quantitation using weighted spectral counting | ||
|authors=Vogel C, Marcotte EM | |authors=Vogel C, Marcotte EM | ||
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|pdf=MethodsMolBioProteomics_VogelMarcotte_2012.pdf | |pdf=MethodsMolBioProteomics_VogelMarcotte_2012.pdf | ||
}} | }} | ||
+ | </li> | ||
+ | </ol> | ||
== 2011 == | == 2011 == | ||
− | + | <ol> | |
+ | <li value="113"> {{Paper | ||
|title=Genetic dissection of the biotic stress response using a genome-scale gene network for rice | |title=Genetic dissection of the biotic stress response using a genome-scale gene network for rice | ||
|authors=Lee I, Seo Y-S, Coltrane D, Hwang S, Oha T, Marcotte EM, Ronald PC | |authors=Lee I, Seo Y-S, Coltrane D, Hwang S, Oha T, Marcotte EM, Ronald PC | ||
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|comment=[http://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1110384108/-/DCSupplemental Supplement] | |comment=[http://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1110384108/-/DCSupplemental Supplement] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="112"> {{Paper | ||
|title=Predicting gene-disease associations using multiple species data | |title=Predicting gene-disease associations using multiple species data | ||
|authors=Natarajan N, Blom UM, Tewari A, Woods JO, Dhillon IS, Marcotte EM | |authors=Natarajan N, Blom UM, Tewari A, Woods JO, Dhillon IS, Marcotte EM | ||
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|volume=TR-11-37 | |volume=TR-11-37 | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="111"> {{Paper | ||
|title=Global protein expression regulation under oxidative stress | |title=Global protein expression regulation under oxidative stress | ||
|authors=Vogel C, Silva GM, Marcotte EM | |authors=Vogel C, Silva GM, Marcotte EM | ||
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|comment=[http://www.mcponline.org/content/early/2011/09/20/mcp.M111.009217/suppl/DC1 Supplement] | |comment=[http://www.mcponline.org/content/early/2011/09/20/mcp.M111.009217/suppl/DC1 Supplement] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="110"> {{Paper | ||
|title=Revisiting the negative example sampling problem for predicting protein-protein interactions | |title=Revisiting the negative example sampling problem for predicting protein-protein interactions | ||
|authors=Park Y, Marcotte EM | |authors=Park Y, Marcotte EM | ||
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|comment=[http://www.marcottelab.org/PPINegativeDataSampling/ Supplemental Data] | |comment=[http://www.marcottelab.org/PPINegativeDataSampling/ Supplemental Data] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="109"> {{Paper | ||
|title=Systematic prediction of gene function using a probabilistic functional gene network for Arabidopsis thaliana | |title=Systematic prediction of gene function using a probabilistic functional gene network for Arabidopsis thaliana | ||
|authors=Hwang S, Rhee SY, Marcotte EM, Lee I | |authors=Hwang S, Rhee SY, Marcotte EM, Lee I | ||
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|link=http://dx.doi.org/10.1038/nprot.2011.372 | |link=http://dx.doi.org/10.1038/nprot.2011.372 | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="108"> {{Paper | ||
|title=Prioritizing candidate disease genes by network-based boosting of genome-wide association data | |title=Prioritizing candidate disease genes by network-based boosting of genome-wide association data | ||
|authors=Lee I, Blom M, Wang PI, Shim JE, Marcotte EM | |authors=Lee I, Blom M, Wang PI, Shim JE, Marcotte EM | ||
Line 256: | Line 282: | ||
|comment=[http://www.marcottelab.org/paper-pdfs/GenomeResearch_HumanNet_2011_SOM.pdf Supplement] [http://www.functionalnet.org/humannet/ HumanNet web site] | |comment=[http://www.marcottelab.org/paper-pdfs/GenomeResearch_HumanNet_2011_SOM.pdf Supplement] [http://www.functionalnet.org/humannet/ HumanNet web site] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="107"> {{Paper | ||
|title=MSblender: a probabilistic approach for integrating peptide identifications from multiple database search engines | |title=MSblender: a probabilistic approach for integrating peptide identifications from multiple database search engines | ||
|authors=Kwon T, Choi H, Vogel C, Nesvizhskii AI, Marcotte EM | |authors=Kwon T, Choi H, Vogel C, Nesvizhskii AI, Marcotte EM | ||
Line 268: | Line 295: | ||
|comment=Supplemental Figures [http://www.marcottelab.org/paper-pdfs/JProteomeResearch_MSBlender_2011_S1.pdf 1] [http://www.marcottelab.org/paper-pdfs/JProteomeResearch_MSBlender_2011_S2.pdf 2] [http://www.marcottelab.org/paper-pdfs/JProteomeResearch_MSBlender_2011_S3.pdf 3] [http://www.marcottelab.org/paper-pdfs/JProteomeResearch_MSBlender_2011_S4.pdf 4] [http://www.marcottelab.org/index.php/MSblender Supporting web site] | |comment=Supplemental Figures [http://www.marcottelab.org/paper-pdfs/JProteomeResearch_MSBlender_2011_S1.pdf 1] [http://www.marcottelab.org/paper-pdfs/JProteomeResearch_MSBlender_2011_S2.pdf 2] [http://www.marcottelab.org/paper-pdfs/JProteomeResearch_MSBlender_2011_S3.pdf 3] [http://www.marcottelab.org/paper-pdfs/JProteomeResearch_MSBlender_2011_S4.pdf 4] [http://www.marcottelab.org/index.php/MSblender Supporting web site] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="106"> {{Paper | ||
|title=A two-tiered approach identifies a network of cancer and liver diseases related genes regulated by miR-122 | |title=A two-tiered approach identifies a network of cancer and liver diseases related genes regulated by miR-122 | ||
|authors=Boutz DR, Collins P, Suresh U, Lu M, Ramírez CM, Fernández-Hernando C, Huang Y, de Sousa Abreu R, Le SY, Shapiro BA, Liu AM, Luk JM, Aldred SF, Trinklein N, Marcotte EM, Penalva LO | |authors=Boutz DR, Collins P, Suresh U, Lu M, Ramírez CM, Fernández-Hernando C, Huang Y, de Sousa Abreu R, Le SY, Shapiro BA, Liu AM, Luk JM, Aldred SF, Trinklein N, Marcotte EM, Penalva LO | ||
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|link=http://www.jbc.org/content/early/2011/03/14/jbc.M110.196451 | |link=http://www.jbc.org/content/early/2011/03/14/jbc.M110.196451 | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="105"> {{Paper | ||
|title=High-throughput immunofluorescence microscopy using yeast spheroplast microarrays | |title=High-throughput immunofluorescence microscopy using yeast spheroplast microarrays | ||
|authors=Niu W, Hart GT, Marcotte EM | |authors=Niu W, Hart GT, Marcotte EM | ||
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|pdf=MethodsMolBioCellBasedMicroarrays_Niu_2010.pdf | |pdf=MethodsMolBioCellBasedMicroarrays_Niu_2010.pdf | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="104"> {{Paper | ||
|title=A role for central spindle proteins in cilia structure and function | |title=A role for central spindle proteins in cilia structure and function | ||
|authors=Smith KR, Kieserman EK, Wang PI, Basten SG, Giles RH, Marcotte EM, Wallingford JB | |authors=Smith KR, Kieserman EK, Wang PI, Basten SG, Giles RH, Marcotte EM, Wallingford JB | ||
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|link=http://dx.doi.org/10.1002/cm.20498 | |link=http://dx.doi.org/10.1002/cm.20498 | ||
}} | }} | ||
+ | </li> | ||
+ | </ol> | ||
== 2010 == | == 2010 == | ||
+ | <ol> | ||
− | + | <li value="103"> {{Paper | |
|title=Parallel evolution in <i>Pseudomonas aeruginosa</i> over 39,000 generations <i>in vivo</i> | |title=Parallel evolution in <i>Pseudomonas aeruginosa</i> over 39,000 generations <i>in vivo</i> | ||
|authors=Huse HK, Kwon T, Zlosnik JEA, Speert DP, Marcotte EM, Whiteley M | |authors=Huse HK, Kwon T, Zlosnik JEA, Speert DP, Marcotte EM, Whiteley M | ||
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|comment=[http://www.sciencenews.org/view/generic/id/63939/title/To_researchers%E2%80%99_surprise,_one_Pseudomonas_infection_is_much_like_the_next ScienceNews] [http://www.marcottelab.org/index.php/PSEAE_CF.2010 Supplement] | |comment=[http://www.sciencenews.org/view/generic/id/63939/title/To_researchers%E2%80%99_surprise,_one_Pseudomonas_infection_is_much_like_the_next ScienceNews] [http://www.marcottelab.org/index.php/PSEAE_CF.2010 Supplement] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="102"> {{Paper | ||
|title=Characterising and predicting haploinsufficiency in the human genome | |title=Characterising and predicting haploinsufficiency in the human genome | ||
|authors=Huang N, Lee I, Marcotte EM, Hurles M | |authors=Huang N, Lee I, Marcotte EM, Hurles M | ||
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|pubmed=20976243 | |pubmed=20976243 | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="101"> {{Paper | ||
|title=Protein abundances are more conserved than mRNA abundances across diverse taxa | |title=Protein abundances are more conserved than mRNA abundances across diverse taxa | ||
|authors=Laurent J, Vogel C, Kwon T, Craig SA, Boutz DR, Huse HK, Nozue K, Walia H, Whiteley M, Ronald PC, Marcotte EM | |authors=Laurent J, Vogel C, Kwon T, Craig SA, Boutz DR, Huse HK, Nozue K, Walia H, Whiteley M, Ronald PC, Marcotte EM | ||
Line 338: | Line 373: | ||
|comment=[http://www.marcottelab.org/paper-pdfs/MProteomics_ProteinVersusRNAConservation_2010_Supplement.zip Supplement] | |comment=[http://www.marcottelab.org/paper-pdfs/MProteomics_ProteinVersusRNAConservation_2010_Supplement.zip Supplement] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="100"> {{Paper | ||
|title=It's the machine that matters: predicting gene function and phenotype from protein networks | |title=It's the machine that matters: predicting gene function and phenotype from protein networks | ||
|authors=Wang PI, Marcotte EM | |authors=Wang PI, Marcotte EM | ||
Line 349: | Line 385: | ||
|page=2277-89 | |page=2277-89 | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="99"> {{Paper | ||
|title=Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line | |title=Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line | ||
|authors=Vogel C, de Sousa Abreu R, Ko D, Le S-Y, Shapiro BA, Burns SC, Sandhu D, Boutz DR, Marcotte EM, Penalva LO | |authors=Vogel C, de Sousa Abreu R, Ko D, Le S-Y, Shapiro BA, Burns SC, Sandhu D, Boutz DR, Marcotte EM, Penalva LO | ||
Line 361: | Line 398: | ||
|comment=[http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_Supplement.pdf Supplement] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_S1.xls Supplemental Data (Excel format)] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_Fig2SourceData.txt Fig 2 source data] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_Fig2SourceData.txt Fig 3A source data] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_Fig2SourceData.txt Fig 3B source data] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_NewsAndViews.pdf News and Views] | |comment=[http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_Supplement.pdf Supplement] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_S1.xls Supplemental Data (Excel format)] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_Fig2SourceData.txt Fig 2 source data] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_Fig2SourceData.txt Fig 3A source data] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_Fig2SourceData.txt Fig 3B source data] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_NewsAndViews.pdf News and Views] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="98"> {{Paper | ||
|title=Defining the pathway of cytoplasmic maturation of the 60S ribosomal subunit | |title=Defining the pathway of cytoplasmic maturation of the 60S ribosomal subunit | ||
|authors=Lo K-Y, Li Z, Bussiere C, Bresson S, Marcotte EM, Johnson AW | |authors=Lo K-Y, Li Z, Bussiere C, Bresson S, Marcotte EM, Johnson AW | ||
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|comment=[http://www.marcottelab.org/paper-pdfs/MolecularCell_60SBiogenesis_2010_Supplement.pdf Supplement] | |comment=[http://www.marcottelab.org/paper-pdfs/MolecularCell_60SBiogenesis_2010_Supplement.pdf Supplement] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="97"> {{Paper | ||
|title=Predicting genetic modifier loci using functional gene networks | |title=Predicting genetic modifier loci using functional gene networks | ||
|authors=Lee I, Lehner B, Vavouri T, Shin J, Fraser AG, Marcotte EM | |authors=Lee I, Lehner B, Vavouri T, Shin J, Fraser AG, Marcotte EM | ||
Line 385: | Line 424: | ||
|comment=[http://www.marcottelab.org/paper-pdfs/GenomeResearch_GeneticModifiers_2010_SOM.pdf Supplement] [http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg2836.html Nature Reviews Genetics] | |comment=[http://www.marcottelab.org/paper-pdfs/GenomeResearch_GeneticModifiers_2010_SOM.pdf Supplement] [http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg2836.html Nature Reviews Genetics] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="96"> {{Paper | ||
|title=Systematic discovery of nonobvious human disease models through orthologous phenotypes | |title=Systematic discovery of nonobvious human disease models through orthologous phenotypes | ||
|authors=McGary KL, Park TJ, Woods JO, Cha HJ, Wallingford JB, Marcotte EM | |authors=McGary KL, Park TJ, Woods JO, Cha HJ, Wallingford JB, Marcotte EM | ||
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|comment=[http://www.marcottelab.org/paper-pdfs/PNAS_Phenologs_2010_Supplement.pdf Supplement] [http://www.nature.com/news/2010/100322/full/news.2010.140.html Nature News] [http://www.the-scientist.com/blog/display/57252/ The Scientist(blog)] [http://www.nytimes.com/2010/04/27/science/27gene.html NY Times] [http://genomebiology.com/2010/11/4/116 Genome Biology] | |comment=[http://www.marcottelab.org/paper-pdfs/PNAS_Phenologs_2010_Supplement.pdf Supplement] [http://www.nature.com/news/2010/100322/full/news.2010.140.html Nature News] [http://www.the-scientist.com/blog/display/57252/ The Scientist(blog)] [http://www.nytimes.com/2010/04/27/science/27gene.html NY Times] [http://genomebiology.com/2010/11/4/116 Genome Biology] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="95"> {{Paper | ||
|title=Reducing MCM levels in human primary T cells during the G0->G1 transition causes genomic instability during the first cell cycle | |title=Reducing MCM levels in human primary T cells during the G0->G1 transition causes genomic instability during the first cell cycle | ||
|authors=Orr SJ, Gaymes T, Ladon D, Chronis C, Czepulkowski B, Wang R, Mufti GJ, Marcotte EM, Thomas NSB | |authors=Orr SJ, Gaymes T, Ladon D, Chronis C, Czepulkowski B, Wang R, Mufti GJ, Marcotte EM, Thomas NSB | ||
Line 408: | Line 449: | ||
|pubmed=20440261 | |pubmed=20440261 | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="94"> {{Paper | ||
|title=Rational association of genes with traits using a genome-scale gene network for <i>Arabidopsis thaliana</i> | |title=Rational association of genes with traits using a genome-scale gene network for <i>Arabidopsis thaliana</i> | ||
|authors=Lee I, Ambaru B, Thakkar P, Marcotte EM, Rhee SY | |authors=Lee I, Ambaru B, Thakkar P, Marcotte EM, Rhee SY | ||
Line 420: | Line 462: | ||
|comment=[http://www.marcottelab.org/paper-pdfs/NatureBiotech_AraNet_2010_supplement.pdf Supplement] [http://www.marcottelab.org/paper-pdfs/848.full.pdf Honorable Mention in the 2010 Science Visualization Challenge] [http://www.nytimes.com/slideshow/2011/02/17/science/20110217-visualize-6.html New York Times slideshow ] | |comment=[http://www.marcottelab.org/paper-pdfs/NatureBiotech_AraNet_2010_supplement.pdf Supplement] [http://www.marcottelab.org/paper-pdfs/848.full.pdf Honorable Mention in the 2010 Science Visualization Challenge] [http://www.nytimes.com/slideshow/2011/02/17/science/20110217-visualize-6.html New York Times slideshow ] | ||
}} | }} | ||
+ | </li> | ||
+ | </ol> | ||
== 2009 == | == 2009 == | ||
+ | <ol> | ||
− | + | <li value="93"> {{Paper | |
|title=Rational extension of the ribosome biogenesis pathway using network-guided genetics | |title=Rational extension of the ribosome biogenesis pathway using network-guided genetics | ||
|authors=Li Z, Lee I, Moradi E, Hung NJ, White J, Johnson AW, Marcotte EM | |authors=Li Z, Lee I, Moradi E, Hung NJ, White J, Johnson AW, Marcotte EM | ||
Line 435: | Line 480: | ||
|comment=[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000213#s5 Supplemental Figures and Tables] | |comment=[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000213#s5 Supplemental Figures and Tables] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="92"> {{Paper | ||
|title=Human cell chips: adapting DNA microarray spotting technology to cell-based imaging assays | |title=Human cell chips: adapting DNA microarray spotting technology to cell-based imaging assays | ||
|authors=Hart GT, Zhao A, Garg A, Bolusani S, Marcotte EM | |authors=Hart GT, Zhao A, Garg A, Bolusani S, Marcotte EM | ||
Line 447: | Line 493: | ||
|comment=[http://www.marcottelab.org/paper-pdfs/PLoSOne_HumanCellChips_2009_TableS1.xls Table S1] | |comment=[http://www.marcottelab.org/paper-pdfs/PLoSOne_HumanCellChips_2009_TableS1.xls Table S1] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="91"> {{Paper | ||
|title=Ribosome stalk assembly requires the dual specificity phosphatase Yvh1 for the exchange of Mrt4 with P0 | |title=Ribosome stalk assembly requires the dual specificity phosphatase Yvh1 for the exchange of Mrt4 with P0 | ||
|authors=Lo KY, Li Z, Wang F, Marcotte EM, Johnson AF | |authors=Lo KY, Li Z, Wang F, Marcotte EM, Johnson AF | ||
Line 459: | Line 506: | ||
||pdf=JCellBiol_Yvh1_2009.pdf | ||pdf=JCellBiol_Yvh1_2009.pdf | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="90"> {{Paper | ||
|title=Absolute abundance for the masses | |title=Absolute abundance for the masses | ||
|authors=Vogel C, Marcotte EM | |authors=Vogel C, Marcotte EM | ||
Line 471: | Line 519: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="89"> {{Paper | ||
|title=Global signatures of protein and mRNA expression levels | |title=Global signatures of protein and mRNA expression levels | ||
|authors=de Sousa Abreu R, Penalva LO, Marcotte EM, Vogel C | |authors=de Sousa Abreu R, Penalva LO, Marcotte EM, Vogel C | ||
Line 483: | Line 532: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="88"> {{Paper | ||
|title=The planar cell polarity effector protein Fuzzy is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development | |title=The planar cell polarity effector protein Fuzzy is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development | ||
|authors=Gray RS, Abitua PB, Wlodarczyk BJ, Blanchard O, Lee I, Weiss G, Marcotte EM, Wallingford JB, Finnell RH | |authors=Gray RS, Abitua PB, Wlodarczyk BJ, Blanchard O, Lee I, Weiss G, Marcotte EM, Wallingford JB, Finnell RH | ||
Line 495: | Line 545: | ||
|pdf=NatureCellBiology_Fuzzy_2009.pdf | |pdf=NatureCellBiology_Fuzzy_2009.pdf | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="87"> {{Paper | ||
|title=Disorder, promiscuity, and toxic partnerships | |title=Disorder, promiscuity, and toxic partnerships | ||
|authors=Marcotte EM, Tsechansky M | |authors=Marcotte EM, Tsechansky M | ||
Line 507: | Line 558: | ||
|pdf=Cell_LehnerPreview_2009.pdf | |pdf=Cell_LehnerPreview_2009.pdf | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="86"> {{Paper | ||
|title=Mining gene functional networks to improve mass-spectrometry based protein identification | |title=Mining gene functional networks to improve mass-spectrometry based protein identification | ||
|authors=Ramakrishnan SR, Vogel C, Kwon T, Penalva LO, Marcotte EM, Miranker DP | |authors=Ramakrishnan SR, Vogel C, Kwon T, Penalva LO, Marcotte EM, Miranker DP | ||
Line 519: | Line 571: | ||
|comment=[http://aug.csres.utexas.edu/msnet/ Supplemental Website] | |comment=[http://aug.csres.utexas.edu/msnet/ Supplemental Website] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="85"> {{Paper | ||
|title=Widespread reorganization of metabolic enzymes into reversible assemblies upon nutrient starvation | |title=Widespread reorganization of metabolic enzymes into reversible assemblies upon nutrient starvation | ||
|authors=Narayanaswamy R, Levy M, Tsechansky M, Stovall GM, O'Connell J, Mirrielees J, Ellington AD, Marcotte EM | |authors=Narayanaswamy R, Levy M, Tsechansky M, Stovall GM, O'Connell J, Mirrielees J, Ellington AD, Marcotte EM | ||
Line 531: | Line 584: | ||
|pdf=PNAS_punctatebodies_2009.pdf | |pdf=PNAS_punctatebodies_2009.pdf | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="84"> {{Paper | ||
|title=A Synthetic Genetic Edge Detection Program | |title=A Synthetic Genetic Edge Detection Program | ||
|authors=Tabor JJ, Salis H, Simpson ZB, Chevalier AA, Levskaya A, Marcotte EM, Voigt CA, Ellington AD | |authors=Tabor JJ, Salis H, Simpson ZB, Chevalier AA, Levskaya A, Marcotte EM, Voigt CA, Ellington AD | ||
Line 543: | Line 597: | ||
|pdf=Cell_EdgeDetector_2009.pdf | |pdf=Cell_EdgeDetector_2009.pdf | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="83"> {{Paper | ||
|title=Effects of functional bias on supervised learning of a gene network model | |title=Effects of functional bias on supervised learning of a gene network model | ||
|authors=Lee I, Marcotte EM | |authors=Lee I, Marcotte EM | ||
Line 555: | Line 610: | ||
|pdf=MethodsMolBioCompSysBio_Lee_2009_printersproofs.pdf | |pdf=MethodsMolBioCompSysBio_Lee_2009_printersproofs.pdf | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="82"> {{Paper | ||
|title=Integrating shotgun proteomics and mRNA expression data to improve protein identification | |title=Integrating shotgun proteomics and mRNA expression data to improve protein identification | ||
|authors=Ramakrishnan SR, Vogel C, Prince JT, Wang R, Li Z, Penalva LO, Myers M, Marcotte EM, Miranker DP | |authors=Ramakrishnan SR, Vogel C, Prince JT, Wang R, Li Z, Penalva LO, Myers M, Marcotte EM, Miranker DP | ||
Line 567: | Line 623: | ||
|pdf=Bioinformatics_mspresso_2009.pdf | |pdf=Bioinformatics_mspresso_2009.pdf | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="81"> {{Paper | ||
|title=Systematic definition of protein constituents along the major polarization axis reveals an adaptive reuse of the polarization machinery in pheromone-treated budding yeast. | |title=Systematic definition of protein constituents along the major polarization axis reveals an adaptive reuse of the polarization machinery in pheromone-treated budding yeast. | ||
|authors=Narayanaswamy R, Moradi EK, Niu W, Hart GT, Davis M, McGary KL, Ellington AD, Marcotte EM. | |authors=Narayanaswamy R, Moradi EK, Niu W, Hart GT, Davis M, McGary KL, Ellington AD, Marcotte EM. | ||
Line 579: | Line 636: | ||
|pdf=JProteomeResearch_Shmoo_2008.pdf | |pdf=JProteomeResearch_Shmoo_2008.pdf | ||
}} | }} | ||
+ | </li> | ||
+ | </ol> | ||
== 2008 == | == 2008 == | ||
− | + | <ol> | |
+ | <li value="80"> {{Paper | ||
|authors=Hannay K, Marcotte EM, Vogel C | |authors=Hannay K, Marcotte EM, Vogel C | ||
|title=Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation | |title=Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation | ||
Line 593: | Line 653: | ||
|comment=[http://www.marcottelab.org/paper-pdfs/BMCGenomics_Buffering_2008_SupplementalNotes.pdf Supplemental Notes] [http://www.marcottelab.org/paper-pdfs/BMCGenomics_Buffering_2008_SupplementalData.xls Supplemental Data] | |comment=[http://www.marcottelab.org/paper-pdfs/BMCGenomics_Buffering_2008_SupplementalNotes.pdf Supplemental Notes] [http://www.marcottelab.org/paper-pdfs/BMCGenomics_Buffering_2008_SupplementalData.xls Supplemental Data] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="79"> {{Paper | ||
|title=The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results | |title=The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results | ||
|authors=Braisted JC, Kuntumalla S, Vogel C, Marcotte EM, Rodrigues AR, Wang R, Huang ST, Ferlanti ES, Saeed AI, Fleischmann RD, Peterson SN, Pieper R | |authors=Braisted JC, Kuntumalla S, Vogel C, Marcotte EM, Rodrigues AR, Wang R, Huang ST, Ferlanti ES, Saeed AI, Fleischmann RD, Peterson SN, Pieper R | ||
Line 605: | Line 666: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="78"> {{Paper | ||
|title=Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence | |title=Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence | ||
|authors=Kim WK, Marcotte EM | |authors=Kim WK, Marcotte EM | ||
Line 617: | Line 679: | ||
|comment=Supporting python code: [http://www.marcottelab.org/paper-pdfs/network_growth_functions_fixed_module.py network_growth_functions_fixed_module.py] Note that this code used an older version of the igraph library (0.4.2); the latest version that we've tested (0.5.2) gives somewhat fewer large clusters than our published clusters due to changes in the function "G.community_fastgreedy()", possibly resulting from modifications to the handling of ties in the community merging process. The previous igraph library (0.4.2) is linked here: [http://www.marcottelab.org/paper-pdfs/python-igraph-0.4.2.tar.gz python-igraph-0.4.2.tar.gz] [http://www.marcottelab.org/paper-pdfs/igraph-0.4.2.tar.gz igraph-0.4.2.tar.gz] [http://www.marcottelab.org/paper-pdfs/igraph_base.py igraph_base.py] | |comment=Supporting python code: [http://www.marcottelab.org/paper-pdfs/network_growth_functions_fixed_module.py network_growth_functions_fixed_module.py] Note that this code used an older version of the igraph library (0.4.2); the latest version that we've tested (0.5.2) gives somewhat fewer large clusters than our published clusters due to changes in the function "G.community_fastgreedy()", possibly resulting from modifications to the handling of ties in the community merging process. The previous igraph library (0.4.2) is linked here: [http://www.marcottelab.org/paper-pdfs/python-igraph-0.4.2.tar.gz python-igraph-0.4.2.tar.gz] [http://www.marcottelab.org/paper-pdfs/igraph-0.4.2.tar.gz igraph-0.4.2.tar.gz] [http://www.marcottelab.org/paper-pdfs/igraph_base.py igraph_base.py] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="77"> {{Paper | ||
|title=mspire: mass spectrometry proteomics in Ruby | |title=mspire: mass spectrometry proteomics in Ruby | ||
|authors=Prince JT, Marcotte EM | |authors=Prince JT, Marcotte EM | ||
Line 629: | Line 692: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="76"> {{Paper | ||
|title=Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data | |title=Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data | ||
|authors=Vogel C, Marcotte EM | |authors=Vogel C, Marcotte EM | ||
Line 641: | Line 705: | ||
|comment=[http://www.marcottelab.org/paper-pdfs/NatureProtocols_APEX_2008_Supplement.pdf Supplement] | |comment=[http://www.marcottelab.org/paper-pdfs/NatureProtocols_APEX_2008_Supplement.pdf Supplement] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="75"> {{Paper | ||
|title=Integrating functional genomics data | |title=Integrating functional genomics data | ||
|authors=Lee I, Marcotte EM | |authors=Lee I, Marcotte EM | ||
Line 653: | Line 718: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="74"> {{Paper | ||
|title=Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy | |title=Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy | ||
|authors=Kim WK, Krumpelman C, Marcotte EM | |authors=Kim WK, Krumpelman C, Marcotte EM | ||
Line 665: | Line 731: | ||
|comment=[http://www.marcottelab.org/paper-pdfs/GenomeBiology_MouseNet_2008_Supplement.pdf Supplement] | |comment=[http://www.marcottelab.org/paper-pdfs/GenomeBiology_MouseNet_2008_Supplement.pdf Supplement] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="73"> {{Paper | ||
|title=A critical assessment of Mus musculus gene function prediction using integrated genomic evidence | |title=A critical assessment of Mus musculus gene function prediction using integrated genomic evidence | ||
|authors=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 | |authors=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 | ||
Line 677: | Line 744: | ||
|comment=[http://func.med.harvard.edu/ MouseFunc predictions] | |comment=[http://func.med.harvard.edu/ MouseFunc predictions] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="72"> {{Paper | ||
|title=Mechanisms of cell cycle control revealed by a systematic and quantitative overexpression screen in S. cerevisiae | |title=Mechanisms of cell cycle control revealed by a systematic and quantitative overexpression screen in S. cerevisiae | ||
|authors=Niu W, Li Z, Zhan W, Iyer VR, Marcotte EM | |authors=Niu W, Li Z, Zhan W, Iyer VR, Marcotte EM | ||
Line 689: | Line 757: | ||
|comment=[http://www.marcottelab.org/paper-pdfs/Niu_et_al_MORF_strains_cell_cnt_gt5000_Z_scores.xls Supplemental File of All ORF FACS Defects] | |comment=[http://www.marcottelab.org/paper-pdfs/Niu_et_al_MORF_strains_cell_cnt_gt5000_Z_scores.xls Supplemental File of All ORF FACS Defects] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="71"> {{Paper | ||
|title=Group II intron protein localization and insertion sites are affected by polyphosphate | |title=Group II intron protein localization and insertion sites are affected by polyphosphate | ||
|authors=Zhao J, Niu W, Yao J, Mohr S, Marcotte EM, Lambowitz AM | |authors=Zhao J, Niu W, Yao J, Mohr S, Marcotte EM, Lambowitz AM | ||
Line 701: | Line 770: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="70"> {{Paper | ||
|title=A map of human protein interactions derived from co-expression of human mRNAs and their orthologs | |title=A map of human protein interactions derived from co-expression of human mRNAs and their orthologs | ||
|authors=Ramani AK, Li Z, Hart GT, Carlson MW, Boutz DR, Marcotte EM | |authors=Ramani AK, Li Z, Hart GT, Carlson MW, Boutz DR, Marcotte EM | ||
Line 713: | Line 783: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="69"> {{Paper | ||
|title=Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits | |title=Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits | ||
|authors=White J, Li Z, Sardana R, Bujnicki JM, Marcotte EM, Johnson AW | |authors=White J, Li Z, Sardana R, Bujnicki JM, Marcotte EM, Johnson AW | ||
Line 725: | Line 796: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="68"> {{Paper | ||
|title=The proteomic response of Mycobacterium smegmatis to anti-tuberculosis drugs suggests targeted pathways | |title=The proteomic response of Mycobacterium smegmatis to anti-tuberculosis drugs suggests targeted pathways | ||
|authors=Wang R, Marcotte EM | |authors=Wang R, Marcotte EM | ||
Line 737: | Line 809: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="67"> {{Paper | ||
|title=A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans | |title=A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans | ||
|authors=Lee I, Lehner B, Crombie C, Wong W, Fraser AG, Marcotte EM | |authors=Lee I, Lehner B, Crombie C, Wong W, Fraser AG, Marcotte EM | ||
Line 749: | Line 822: | ||
|comment=[http://www.marcottelab.org/paper-pdfs/NatureGenetics_Wormnet_2008_Supplement.pdf Supplement] [http://www.functionalnet.org/wormnet Supplemental Web Site] | |comment=[http://www.marcottelab.org/paper-pdfs/NatureGenetics_Wormnet_2008_Supplement.pdf Supplement] [http://www.functionalnet.org/wormnet Supplemental Web Site] | ||
}} | }} | ||
+ | </li> | ||
+ | </ol> | ||
== 2007 == | == 2007 == | ||
− | + | <ol> | |
+ | <li value="66"> {{Paper | ||
|title=Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes | |title=Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes | ||
|authors=McGary KL, Lee I, Marcotte EM | |authors=McGary KL, Lee I, Marcotte EM | ||
Line 763: | Line 839: | ||
|comment=[http://www.yeastnet.org Supplemental Web Site] | |comment=[http://www.yeastnet.org Supplemental Web Site] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="65"> {{Paper | ||
|title=An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae | |title=An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae | ||
|authors=Lee I, Li Z, Marcotte EM | |authors=Lee I, Li Z, Marcotte EM | ||
Line 775: | Line 852: | ||
|comment=[http://www.yeastnet.org Supplemental Web Site] | |comment=[http://www.yeastnet.org Supplemental Web Site] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="64"> {{Paper | ||
|title=How do shotgun proteomics algorithms identify proteins? | |title=How do shotgun proteomics algorithms identify proteins? | ||
|authors=Marcotte EM | |authors=Marcotte EM | ||
Line 787: | Line 865: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="63"> {{Paper | ||
|title=Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways | |title=Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways | ||
|authors=Carlson MW, Iyer VR, Marcotte EM | |authors=Carlson MW, Iyer VR, Marcotte EM | ||
Line 799: | Line 878: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="62"> {{Paper | ||
|title=Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation | |title=Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation | ||
|authors=Lu P, Vogel C, Wang R, Yao X, Marcotte EM | |authors=Lu P, Vogel C, Wang R, Yao X, Marcotte EM | ||
Line 811: | Line 891: | ||
|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] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_APEX_NBTretrospective_2011.pdf 2011 NBT Retrospective on APEX] | |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] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_APEX_NBTretrospective_2011.pdf 2011 NBT Retrospective on APEX] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="61"> {{Paper | ||
|title=Global metabolic changes following loss of a feedback loop reveal dynamic steady states of the yeast metabolome | |title=Global metabolic changes following loss of a feedback loop reveal dynamic steady states of the yeast metabolome | ||
|authors=Lu P, Rangan A, Chan SY, Appling DR, Hoffman DW, Marcotte EM | |authors=Lu P, Rangan A, Chan SY, Appling DR, Hoffman DW, Marcotte EM | ||
Line 823: | Line 904: | ||
|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] | |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] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="60"> {{Paper | ||
|title=A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality | |title=A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality | ||
|authors=Hart GT, Lee I, Marcotte EM | |authors=Hart GT, Lee I, Marcotte EM | ||
Line 835: | Line 917: | ||
|comment= | |comment= | ||
}} | }} | ||
+ | </li> | ||
+ | </ol> | ||
== 2006 == | == 2006 == | ||
− | + | <ol> | |
+ | <li value="59"> {{Paper | ||
|title=How complete are current yeast and human protein-interaction networks? | |title=How complete are current yeast and human protein-interaction networks? | ||
|authors=Hart GT, Ramani AK, Marcotte EM. | |authors=Hart GT, Ramani AK, Marcotte EM. | ||
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|comment=[http://www.marcottelab.org/paper-pdfs/GenomeBiology_HumanPPIOverview_2006_AdditionalDataFile1.pdf Additional Data File 1] | |comment=[http://www.marcottelab.org/paper-pdfs/GenomeBiology_HumanPPIOverview_2006_AdditionalDataFile1.pdf Additional Data File 1] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="58"> {{Paper | ||
|title=Chromatographic alignment of ESI-LC-MS proteomics datasets by ordered bijective interpolated warping | |title=Chromatographic alignment of ESI-LC-MS proteomics datasets by ordered bijective interpolated warping | ||
|authors=Prince JT, Marcotte EM | |authors=Prince JT, Marcotte EM | ||
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|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="57"> {{Paper | ||
|title=A fast coarse filtering method for peptide identification by mass spectrometry | |title=A fast coarse filtering method for peptide identification by mass spectrometry | ||
|authors=Ramakrishnan SR, Mao R, Nakorchevskiy AA, Prince JT, Willard WS, Xu W, Marcotte EM, Miranker DP | |authors=Ramakrishnan SR, Mao R, Nakorchevskiy AA, Prince JT, Willard WS, Xu W, Marcotte EM, Miranker DP | ||
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|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="56"> {{Paper | ||
|title=Systematic profiling of cellular phenotypes with spotted cell microarrays reveals new pheromone response genes | |title=Systematic profiling of cellular phenotypes with spotted cell microarrays reveals new pheromone response genes | ||
|authors=Narayanaswamy R, Niu W, Scouras A, Hart GT, Davies J, Ellington AD, Iyer VR, Marcotte EM | |authors=Narayanaswamy R, Niu W, Scouras A, Hart GT, Davies J, Ellington AD, Iyer VR, Marcotte EM | ||
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|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] | |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] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="55"> {{Paper | ||
|title=Bioinformatic prediction of yeast gene function | |title=Bioinformatic prediction of yeast gene function | ||
|authors=Lee I, Narayanaswamy R, Marcotte EM | |authors=Lee I, Narayanaswamy R, Marcotte EM | ||
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|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="54"> {{Paper | ||
|title=Bioinformatic challenges for the next decade(s) | |title=Bioinformatic challenges for the next decade(s) | ||
|authors=Eisenberg D, Marcotte E, McLachlan AD, Pellegrini M | |authors=Eisenberg D, Marcotte E, McLachlan AD, Pellegrini M | ||
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|comment= | |comment= | ||
}} | }} | ||
+ | </li> | ||
+ | </ol> | ||
== 2005 == | == 2005 == | ||
− | + | <ol> | |
+ | <li value="53"> {{Paper | ||
|title=Synthetic biology: Engineering ''Escherichia coli'' to see light | |title=Synthetic biology: Engineering ''Escherichia coli'' to see light | ||
|authors=Levskaya A, Chevalier AA, Tabor JJ, Simpson ZB, Lavery LA, Levy M, Davidson EA, Scouras A, Ellington AD, Marcotte EM, Voigt CA | |authors=Levskaya A, Chevalier AA, Tabor JJ, Simpson ZB, Lavery LA, Levy M, Davidson EA, Scouras A, Ellington AD, Marcotte EM, Voigt CA | ||
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|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] | |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] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="52"> {{Paper | ||
|title=A fast coarse filtering method for protein identification by mass spectrometry | |title=A fast coarse filtering method for protein identification by mass spectrometry | ||
|authors=Ramakrishnan SR, Mao R, Nakorchevskiy AA, Prince JT, Willard WS, Xu W, Marcotte EM, Miranker DP | |authors=Ramakrishnan SR, Mao R, Nakorchevskiy AA, Prince JT, Willard WS, Xu W, Marcotte EM, Miranker DP | ||
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|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="51"> {{Paper | ||
|title=Mass spectrometry of the M. smegmatis proteome: Protein expression levels correlate with function, operons, and codon bias | |title=Mass spectrometry of the M. smegmatis proteome: Protein expression levels correlate with function, operons, and codon bias | ||
|authors=Wang R, Prince JT, Marcotte EM | |authors=Wang R, Prince JT, Marcotte EM | ||
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|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="50"> {{Paper | ||
|title=Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome | |title=Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome | ||
|authors=Ramani AK, Bunescu RC, Mooney RJ, Marcotte EM | |authors=Ramani AK, Bunescu RC, Mooney RJ, Marcotte EM | ||
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|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="49"> {{Paper | ||
|title=Comparative Experiments on Learning Information Extractors for Proteins and their Interactions | |title=Comparative Experiments on Learning Information Extractors for Proteins and their Interactions | ||
|authors=Bunescu R, Ge R, Kate RJ, Marcotte EM, Mooney RJ, Ramani AK, Wong YW | |authors=Bunescu R, Ge R, Kate RJ, Marcotte EM, Mooney RJ, Ramani AK, Wong YW | ||
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|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="48"> {{Paper | ||
|title=Using Biomedical Literature Mining to Consolidate the Set of Known Human Protein-Protein Interactions | |title=Using Biomedical Literature Mining to Consolidate the Set of Known Human Protein-Protein Interactions | ||
|authors=Ramani AK, Marcotte EM, Bunescu RC, Mooney RJ | |authors=Ramani AK, Marcotte EM, Bunescu RC, Mooney RJ | ||
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|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="47"> {{Paper | ||
|title=Protein function prediction using the Protein Link Explorer (PLEX) | |title=Protein function prediction using the Protein Link Explorer (PLEX) | ||
|authors=Date SV, Marcotte EM | |authors=Date SV, Marcotte EM | ||
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|comment=[http://bioinformatics.icmb.utexas.edu/plex/plex.html Supplemental Web Site] | |comment=[http://bioinformatics.icmb.utexas.edu/plex/plex.html Supplemental Web Site] | ||
}} | }} | ||
+ | </li> | ||
+ | </ol> | ||
== 2004 == | == 2004 == | ||
− | + | <ol> | |
+ | <li value="46"> {{Paper | ||
|title=A probabilistic functional network of yeast genes | |title=A probabilistic functional network of yeast genes | ||
|authors=Lee I, Date SV, Adai AT, Marcotte EM | |authors=Lee I, Date SV, Adai AT, Marcotte EM | ||
Line 1,008: | Line 1,110: | ||
|comment=[http://www.marcottelab.org/paper-pdfs/1099511v2s.pdf Supplemental methods] [http://www.marcottelab.org/paper-pdfs/1099511v2s_list.txt Supplemental README] [http://www.marcottelab.org/paper-pdfs/1099511v2s1.zip Supplemental File 1] [http://www.marcottelab.org/paper-pdfs/1099511v2s2.txt Supplemental File 2] [http://www.marcottelab.org/paper-pdfs/1099511v2s3 Supplemental File 3] [http://www.marcottelab.org/paper-pdfs/1099511v2s4.wrl Supplemental File 4] [http://www.marcottelab.org/paper-pdfs/1099511v2s5.wrl Supplemental File 5] (Files 4 & 5 require a VRML viewer) | |comment=[http://www.marcottelab.org/paper-pdfs/1099511v2s.pdf Supplemental methods] [http://www.marcottelab.org/paper-pdfs/1099511v2s_list.txt Supplemental README] [http://www.marcottelab.org/paper-pdfs/1099511v2s1.zip Supplemental File 1] [http://www.marcottelab.org/paper-pdfs/1099511v2s2.txt Supplemental File 2] [http://www.marcottelab.org/paper-pdfs/1099511v2s3 Supplemental File 3] [http://www.marcottelab.org/paper-pdfs/1099511v2s4.wrl Supplemental File 4] [http://www.marcottelab.org/paper-pdfs/1099511v2s5.wrl Supplemental File 5] (Files 4 & 5 require a VRML viewer) | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="45"> {{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 | |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 | ||
|title=Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea | |title=Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea | ||
Line 1,018: | Line 1,121: | ||
|pdf=GenomeResearch_HaloarculumGenome.pdf | |pdf=GenomeResearch_HaloarculumGenome.pdf | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="44"> {{Paper | ||
|title=Development through the eyes of functional genomics | |title=Development through the eyes of functional genomics | ||
|authors=Fraser AG, Marcotte EM | |authors=Fraser AG, Marcotte EM | ||
Line 1,030: | Line 1,134: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="43"> {{Paper | ||
|title=Protein interaction networks from yeast to human | |title=Protein interaction networks from yeast to human | ||
|authors=Bork P, Jensen LJ, Von Mering C, Ramani AK, Lee I, Marcotte EM | |authors=Bork P, Jensen LJ, Von Mering C, Ramani AK, Lee I, Marcotte EM | ||
Line 1,042: | Line 1,147: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="42"> {{Paper | ||
|title=LGL: Creating a Map of Protein Function with an Algorithm for Visualizing Very Large Biological Networks | |title=LGL: Creating a Map of Protein Function with an Algorithm for Visualizing Very Large Biological Networks | ||
|authors=Adai AT, Date SV, Wieland S, Marcotte EM | |authors=Adai AT, Date SV, Wieland S, Marcotte EM | ||
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|comment=[http://bioinformatics.icmb.utexas.edu/lgl/index.html Supplemental Web Site] [http://sourceforge.net/projects/lgl/ Sourceforge Site] | |comment=[http://bioinformatics.icmb.utexas.edu/lgl/index.html Supplemental Web Site] [http://sourceforge.net/projects/lgl/ Sourceforge Site] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="41"> {{Paper | ||
|title=A probabilistic view of gene function | |title=A probabilistic view of gene function | ||
|authors=Fraser AG, Marcotte EM | |authors=Fraser AG, Marcotte EM | ||
Line 1,066: | Line 1,173: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="40"> {{Paper | ||
|title=Practical computational approaches to infer protein function | |title=Practical computational approaches to infer protein function | ||
|authors=Marcotte EM | |authors=Marcotte EM | ||
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|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="39"> {{Paper | ||
|title=The need for a public proteomics repository | |title=The need for a public proteomics repository | ||
|authors=Prince JT, Carlson MW, Wang R, Lu P, Marcotte EM | |authors=Prince JT, Carlson MW, Wang R, Lu P, Marcotte EM | ||
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|comment=[http://bioinformatics.icmb.utexas.edu/OPD/ Supplemental Web Site] | |comment=[http://bioinformatics.icmb.utexas.edu/OPD/ Supplemental Web Site] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="38"> {{Paper | ||
|title=Response to McDermott and Samudrala: Enhanced functional information from predicted protein networks | |title=Response to McDermott and Samudrala: Enhanced functional information from predicted protein networks | ||
|authors=Date SV, Marcotte EM | |authors=Date SV, Marcotte EM | ||
Line 1,102: | Line 1,212: | ||
|comment= | |comment= | ||
}} | }} | ||
+ | </li> | ||
+ | </ol> | ||
== 2003 == | == 2003 == | ||
− | + | <ol> | |
+ | <li value="37"> {{Paper | ||
|title=Diametrical clustering for identifying anti-correlated gene clusters | |title=Diametrical clustering for identifying anti-correlated gene clusters | ||
|authors=Dhillon IS, Marcotte EM, Roshan U | |authors=Dhillon IS, Marcotte EM, Roshan U | ||
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|pdf=diametrical.pdf | |pdf=diametrical.pdf | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="36"> {{Paper | ||
|title=Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations | |title=Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations | ||
|authors=Lu P, Nakorchevskiy A, Marcotte EM | |authors=Lu P, Nakorchevskiy A, Marcotte EM | ||
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|pdf=peng-pnas.pdf | |pdf=peng-pnas.pdf | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="35"> {{Paper | ||
|title=Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages | |title=Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages | ||
|authors=Date SV, Marcotte EM | |authors=Date SV, Marcotte EM | ||
Line 1,135: | Line 1,250: | ||
|comment=[http://www.marcottelab.org/paper-pdfs/NatureBiotech_SystematicNewPathways_FigS1.pdf Fig S1] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_SystematicNewPathways_FigS2.gif Fig S2] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_SystematicNewPathways_TableS1.pdf Table S1] | |comment=[http://www.marcottelab.org/paper-pdfs/NatureBiotech_SystematicNewPathways_FigS1.pdf Fig S1] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_SystematicNewPathways_FigS2.gif Fig S2] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_SystematicNewPathways_TableS1.pdf Table S1] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="34"> {{Paper | ||
|title=Assembling a jigsaw puzzle with 20,000 parts | |title=Assembling a jigsaw puzzle with 20,000 parts | ||
|authors=Marcotte EM | |authors=Marcotte EM | ||
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|pdf=genome-biology.pdf | |pdf=genome-biology.pdf | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="33"> {{Paper | ||
|title=Exploiting the co-evolution of interacting proteins to discover interaction specificity | |title=Exploiting the co-evolution of interacting proteins to discover interaction specificity | ||
|authors=Ramani AK, Marcotte EM | |authors=Ramani AK, Marcotte EM | ||
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|comment=[http://orion.icmb.utexas.edu/matrix/ Supplemental Web Site] | |comment=[http://orion.icmb.utexas.edu/matrix/ Supplemental Web Site] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="32"> {{Paper | ||
|title=The genome sequence of the filamentous fungus Neurospora crassa | |title=The genome sequence of the filamentous fungus Neurospora crassa | ||
|authors=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 | |authors=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 | ||
Line 1,166: | Line 1,284: | ||
|pdf=Ncrassa.pdf | |pdf=Ncrassa.pdf | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="31"> {{Paper | ||
|authors=Bunescu R, Ge R, Kate R, Mooney R, Wong Y, Marcotte E, Ramani A | |authors=Bunescu R, Ge R, Kate R, Mooney R, Wong Y, Marcotte E, Ramani A | ||
|title=Learning to extract proteins and their interactions from Medline abstracts | |title=Learning to extract proteins and their interactions from Medline abstracts | ||
Line 1,175: | Line 1,294: | ||
|pdf=icmlws.pdf | |pdf=icmlws.pdf | ||
}} | }} | ||
+ | </li> | ||
+ | </ol> | ||
== 2002 == | == 2002 == | ||
− | + | <ol> | |
+ | <li value="30"> {{Paper | ||
|title=Making sense of proteomics: Using bioinformatics to discover a protein's structure, functions, and interactions | |title=Making sense of proteomics: Using bioinformatics to discover a protein's structure, functions, and interactions | ||
|authors=Mallick P, Marcotte EM | |authors=Mallick P, Marcotte EM | ||
Line 1,187: | Line 1,309: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="29"> {{Paper | ||
|title=Diametrical clustering for identifying anti-correlated gene clusters | |title=Diametrical clustering for identifying anti-correlated gene clusters | ||
|authors=Dhillon IS, Marcotte EM, Roshan U. | |authors=Dhillon IS, Marcotte EM, Roshan U. | ||
Line 1,199: | Line 1,322: | ||
|pdf=TechnicalReport_DiametricClustering_tr02-49.pdf | |pdf=TechnicalReport_DiametricClustering_tr02-49.pdf | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="28"> {{Paper | ||
|title=Predicting Protein Function and Networks on Genome-Wide Scale | |title=Predicting Protein Function and Networks on Genome-Wide Scale | ||
|authors=Marcotte EM | |authors=Marcotte EM | ||
Line 1,211: | Line 1,335: | ||
|pdf=Marcotte-ColladoVidesChapter-2002.pdf | |pdf=Marcotte-ColladoVidesChapter-2002.pdf | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="27"> {{Paper | ||
|title=Predicting functional linkages from gene fusions with confidence | |title=Predicting functional linkages from gene fusions with confidence | ||
|authors=Verjovsky Marcotte CJ, Marcotte EM | |authors=Verjovsky Marcotte CJ, Marcotte EM | ||
Line 1,223: | Line 1,348: | ||
|pdf=RS_statistics.pdf | |pdf=RS_statistics.pdf | ||
}} | }} | ||
+ | </li> | ||
+ | </ol> | ||
== 2001 == | == 2001 == | ||
− | + | <ol> | |
+ | <li value="26"> {{Paper | ||
|title=Exploiting Big Biology: Integrating large-scale biological data for functional inference | |title=Exploiting Big Biology: Integrating large-scale biological data for functional inference | ||
|authors=Marcotte EM, Date SV | |authors=Marcotte EM, Date SV | ||
Line 1,237: | Line 1,365: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="25"> {{Paper | ||
|title=The path not taken | |title=The path not taken | ||
|authors=Marcotte EM | |authors=Marcotte EM | ||
Line 1,249: | Line 1,378: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="24"> {{Paper | ||
|title=Measuring the Dynamics of the Proteome | |title=Measuring the Dynamics of the Proteome | ||
|authors=Marcotte EM | |authors=Marcotte EM | ||
Line 1,261: | Line 1,391: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="23"> {{Paper | ||
|title=Mining Literature for Protein Interactions | |title=Mining Literature for Protein Interactions | ||
|authors=Marcotte EM, Xenarios I, Eisenberg D | |authors=Marcotte EM, Xenarios I, Eisenberg D | ||
Line 1,273: | Line 1,404: | ||
|comment=[http://www.marcottelab.org/paper-pdfs/README README] [http://www.marcottelab.org/paper-pdfs/500_abstracts_with_PMID 500_abstracts_with_PMID] [http://www.marcottelab.org/paper-pdfs/Discriminating_words_for_interactions Discriminating_words_for_interactions] [http://www.marcottelab.org/paper-pdfs/Discriminating_words_for_interactions_edited Discriminating_words_for_interactions_edited] [http://www.marcottelab.org/paper-pdfs/score_abstracts score_abstracts Perl script] | |comment=[http://www.marcottelab.org/paper-pdfs/README README] [http://www.marcottelab.org/paper-pdfs/500_abstracts_with_PMID 500_abstracts_with_PMID] [http://www.marcottelab.org/paper-pdfs/Discriminating_words_for_interactions Discriminating_words_for_interactions] [http://www.marcottelab.org/paper-pdfs/Discriminating_words_for_interactions_edited Discriminating_words_for_interactions_edited] [http://www.marcottelab.org/paper-pdfs/score_abstracts score_abstracts Perl script] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="22"> {{Paper | ||
|title=From genome sequences to protein interactions | |title=From genome sequences to protein interactions | ||
|authors=Eisenberg D, Marcotte E, Pellegrini M, Thompson M, Xenarios I, Yeates T | |authors=Eisenberg D, Marcotte E, Pellegrini M, Thompson M, Xenarios I, Yeates T | ||
Line 1,285: | Line 1,417: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="21"> {{Paper | ||
|title=DIP: the database of interacting proteins: 2001 update | |title=DIP: the database of interacting proteins: 2001 update | ||
|authors=Xenarios I, Fernandez E, Salwinski L, Duan XJ, Thompson MJ, Marcotte EM, Eisenberg D | |authors=Xenarios I, Fernandez E, Salwinski L, Duan XJ, Thompson MJ, Marcotte EM, Eisenberg D | ||
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|comment= | |comment= | ||
}} | }} | ||
+ | </li> | ||
+ | </ol> | ||
== 2000 == | == 2000 == | ||
− | + | <ol> | |
+ | <li value="20"> {{Paper | ||
|title=Protein function in the post-genomic era | |title=Protein function in the post-genomic era | ||
|authors=Eisenberg D, Marcotte EM, Xenarios I, Yeates TO | |authors=Eisenberg D, Marcotte EM, Xenarios I, Yeates TO | ||
Line 1,311: | Line 1,447: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="19"> {{Paper | ||
|title=Localizing proteins in the cell from their phylogenetic profiles | |title=Localizing proteins in the cell from their phylogenetic profiles | ||
|authors=Marcotte EM, Xenarios I, van der Bliek A, Eisenberg D | |authors=Marcotte EM, Xenarios I, van der Bliek A, Eisenberg D | ||
Line 1,323: | Line 1,460: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="18"> {{Paper | ||
|title=Computational genetics: Finding Function by Non-Homology Methods | |title=Computational genetics: Finding Function by Non-Homology Methods | ||
|authors=Marcotte EM | |authors=Marcotte EM | ||
Line 1,335: | Line 1,473: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="17"> {{Paper | ||
|title=Characterization of a thermostable DNA glycosylase specific for U/G and T/G mismatches from the hyperthermophilic archaeon Pyrobaculum aerophilum | |title=Characterization of a thermostable DNA glycosylase specific for U/G and T/G mismatches from the hyperthermophilic archaeon Pyrobaculum aerophilum | ||
|authors=Yang H, Fitz-Gibbon S, Marcotte EM, Tai JH, Hyman EC, Miller JH | |authors=Yang H, Fitz-Gibbon S, Marcotte EM, Tai JH, Hyman EC, Miller JH | ||
Line 1,347: | Line 1,486: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="16"> {{Paper | ||
|title=Increasing the specificity of protein functional inference by the Rosetta Stone method | |title=Increasing the specificity of protein functional inference by the Rosetta Stone method | ||
|authors=Thompson M, Marcotte E, Pellegrini M, Yeates T, Eisenberg D | |authors=Thompson M, Marcotte E, Pellegrini M, Yeates T, Eisenberg D | ||
Line 1,359: | Line 1,499: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="15"> {{Paper | ||
|title=DIP: the database of interacting proteins. | |title=DIP: the database of interacting proteins. | ||
|authors=Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D | |authors=Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D | ||
Line 1,371: | Line 1,512: | ||
|comment= | |comment= | ||
}} | }} | ||
+ | </li> | ||
+ | </ol> | ||
== 1999 == | == 1999 == | ||
− | + | <ol> | |
+ | <li value="14"> {{Paper | ||
|title=A combined algorithm for genome-wide prediction of protein function | |title=A combined algorithm for genome-wide prediction of protein function | ||
|authors=Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D | |authors=Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D | ||
Line 1,385: | Line 1,529: | ||
|comment=See also Sali, A. Genomics: Functional links between proteins. Nature 402, 23-26 (1999), Boston Globe (Nov. 3, 1999), Los Angeles Times (Nov. 4, 1999). | |comment=See also Sali, A. Genomics: Functional links between proteins. Nature 402, 23-26 (1999), Boston Globe (Nov. 3, 1999), Los Angeles Times (Nov. 4, 1999). | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="13"> {{Paper | ||
|title=Detecting protein function and protein-protein interactions from genome sequences | |title=Detecting protein function and protein-protein interactions from genome sequences | ||
|authors=Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D | |authors=Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D | ||
Line 1,397: | Line 1,542: | ||
|comment=See also Doolittle, R. F. Do you dig my groove? Nature: Genetics 23, 6-8 (1999). | |comment=See also Doolittle, R. F. Do you dig my groove? Nature: Genetics 23, 6-8 (1999). | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="12"> {{Paper | ||
|title=A census of protein repeats | |title=A census of protein repeats | ||
|authors=Marcotte EM, Pellegrini M, Yeates TO, Eisenberg D | |authors=Marcotte EM, Pellegrini M, Yeates TO, Eisenberg D | ||
Line 1,409: | Line 1,555: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="11"> {{Paper | ||
|title=Assigning protein functions by comparative genome analysis: protein phylogenetic profiles | |title=Assigning protein functions by comparative genome analysis: protein phylogenetic profiles | ||
|authors=Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO | |authors=Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO | ||
Line 1,421: | Line 1,568: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="10"> {{Paper | ||
|title=A fast algorithm for genome-wide analysis of proteins with repeated sequences | |title=A fast algorithm for genome-wide analysis of proteins with repeated sequences | ||
|authors=Pellegrini M, Marcotte EM, Yeates TO | |authors=Pellegrini M, Marcotte EM, Yeates TO | ||
Line 1,433: | Line 1,581: | ||
|comment= | |comment= | ||
}} | }} | ||
+ | </li> | ||
+ | </ol> | ||
== 1998 == | == 1998 == | ||
− | + | <ol> | |
+ | <li value="9"> {{Paper | ||
|title=Chicken prion tandem repeats form a stable, protease-resistant domain | |title=Chicken prion tandem repeats form a stable, protease-resistant domain | ||
|authors=Marcotte EM, Eisenberg D | |authors=Marcotte EM, Eisenberg D | ||
Line 1,447: | Line 1,598: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="8"> {{Paper | ||
|title=A Look at the Future of Macromolecular Structure Determination | |title=A Look at the Future of Macromolecular Structure Determination | ||
|authors=Cascio D, Goodwill K, Marcotte E | |authors=Cascio D, Goodwill K, Marcotte E | ||
Line 1,459: | Line 1,611: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="7"> {{Paper | ||
|title=Structural analysis shows five glycohydrolase families diverged from a common ancestor | |title=Structural analysis shows five glycohydrolase families diverged from a common ancestor | ||
|authors=Robertus JD, Monzingo AF, Marcotte EM, Hart PJ | |authors=Robertus JD, Monzingo AF, Marcotte EM, Hart PJ | ||
Line 1,471: | Line 1,624: | ||
|comment= | |comment= | ||
}} | }} | ||
+ | </li> | ||
+ | </ol> | ||
== Pre - 1998 == | == Pre - 1998 == | ||
+ | <ol> | ||
− | + | <li value="6"> {{Paper | |
|title=Kinetic analysis of barley chitinase | |title=Kinetic analysis of barley chitinase | ||
|authors=Hollis T, Honda Y, Fukamizo T, Marcotte E, Day PJ, Robertus JD | |authors=Hollis T, Honda Y, Fukamizo T, Marcotte E, Day PJ, Robertus JD | ||
Line 1,486: | Line 1,642: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="5"> {{Paper | ||
|title=X-ray structure of an anti-fungal chitosanase from streptomyces N174 | |title=X-ray structure of an anti-fungal chitosanase from streptomyces N174 | ||
|authors=Marcotte EM, Monzingo AF, Ernst SR, Brzezinski R, Robertus JD | |authors=Marcotte EM, Monzingo AF, Ernst SR, Brzezinski R, Robertus JD | ||
Line 1,498: | Line 1,655: | ||
|comment=[http://www.marcottelab.org/paper-pdfs/NatureStructuralBiology_ChitosanaseCommentary_1996.pdf News & Views] | |comment=[http://www.marcottelab.org/paper-pdfs/NatureStructuralBiology_ChitosanaseCommentary_1996.pdf News & Views] | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="4"> {{Paper | ||
|title=Chitinases, chitosanases, and lysozymes can be divided into procaryotic and eucaryotic families sharing a conserved core | |title=Chitinases, chitosanases, and lysozymes can be divided into procaryotic and eucaryotic families sharing a conserved core | ||
|authors=Monzingo AF, Marcotte EM, Hart PJ, Robertus JD | |authors=Monzingo AF, Marcotte EM, Hart PJ, Robertus JD | ||
Line 1,510: | Line 1,668: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="3"> {{Paper | ||
|title=The Structure of Chitinases and Prospects for Structure-Based Drug Design | |title=The Structure of Chitinases and Prospects for Structure-Based Drug Design | ||
|authors=Robertus, J. D., Hart, P. J., Monzingo, A. F., Marcotte, E. & Hollis, T | |authors=Robertus, J. D., Hart, P. J., Monzingo, A. F., Marcotte, E. & Hollis, T | ||
Line 1,521: | Line 1,680: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="2"> {{Paper | ||
|title=Control of cellular morphogenesis by the Ip12/Bem2 GTPase-activating protein: possible role of protein phosphorylation | |title=Control of cellular morphogenesis by the Ip12/Bem2 GTPase-activating protein: possible role of protein phosphorylation | ||
|authors=Kim YJ, Francisco L, Chen GC, Marcotte E, Chan CS | |authors=Kim YJ, Francisco L, Chen GC, Marcotte E, Chan CS | ||
Line 1,533: | Line 1,693: | ||
|comment= | |comment= | ||
}} | }} | ||
− | + | </li> | |
+ | <li value="1"> {{Paper | ||
|title=Crystallization of a chitosanase from Streptomyces N174 | |title=Crystallization of a chitosanase from Streptomyces N174 | ||
|authors=Marcotte E, Hart PJ, Boucher I, Brzezinski R, Robertus JD | |authors=Marcotte E, Hart PJ, Boucher I, Brzezinski R, Robertus JD | ||
Line 1,545: | Line 1,706: | ||
|comment= | |comment= | ||
}} | }} | ||
+ | </li> | ||
+ | </ol> | ||
== Patents == | == Patents == | ||
− | + | <ol> | |
− | + | <li value="6"> [http://www.freshpatents.com/-dt20120823ptan20120215458.php USPTO Application # 20120215458], Orthologous phenotypes and non-obvious human disease models, PCT filed July 13, 2010; provisional patent # 61/225,427 filed July 14, 2009.</li> | |
− | + | <li value="5"> [http://www.freshpatents.com/-dt20111222ptan20110312505.php USPTO Application # 20110312505], Rapid isolation of monoclonal antibodies from animals, filed May 17, 2011; priority over # 61/345,538 (filed May 17, 2010) and # 61/377,816 (filed August 27, 2010).</li> | |
− | + | <li value="4"> [http://patft1.uspto.gov/netacgi/nph-Parser?Sect1=PTO2&Sect2=HITOFF&p=1&u=%2Fnetahtml%2FPTO%2Fsearch-bool.html&r=1&f=G&l=50&co1=AND&d=PTXT&s1=6892139.PN.&OS=PN/6775514&RS=PN/6892139 6,892,139], Determining the functions and interactions of proteins by comparative analysis, granted May 10, 2005.</li> | |
− | + | <li value="3"> [http://patft1.uspto.gov/netacgi/nph-Parser?Sect1=PTO2&Sect2=HITOFF&p=1&u=%2Fnetahtml%2FPTO%2Fsearch-bool.html&r=1&f=G&l=50&co1=AND&d=PTXT&s1=6772069.PN.&OS=PN/6775514&RS=PN/6772069 6,772,069], Determining protein function and interaction from genome analysis, granted August 3, 2004.</li> | |
− | + | <li value="2"> [http://patft1.uspto.gov/netacgi/nph-Parser?Sect1=PTO2&Sect2=HITOFF&p=1&u=%2Fnetahtml%2FPTO%2Fsearch-bool.html&r=1&f=G&l=50&co1=AND&d=PTXT&s1=6564151.PN.&OS=PN/6775514&RS=PN/6564151 6,564,151], Assigning protein functions by comparative genome analysis protein phylogenetic profiles, granted May 13, 2003.</li> | |
+ | <li value="1"> [http://patft1.uspto.gov/netacgi/nph-Parser?Sect1=PTO2&Sect2=HITOFF&p=1&u=%2Fnetahtml%2FPTO%2Fsearch-bool.html&r=1&f=G&l=50&co1=AND&d=PTXT&s1=6466874.PN.&OS=PN/6775514&RS=PN/6466874 6,466,874], Rosetta stone method for detecting protein function and protein-protein interactions from genome sequences, granted October 15, 2002.</li> | ||
+ | </ol> |
Revision as of 11:06, 13 June 2013
Contents |
2013
- Woods JO, Singh-Blom UM, Laurent JM, McGary KL, Marcotte EM, Prediction of gene-phenotype associations in humans, mice, and plants using phenologs, BMC Bioinformatics, (in press): (2013) PubMed
- Singh-Blom UM, Natarajan N, Tewari A, Woods JO, Dhillon IS, Marcotte EM, Prediction and validation of gene-disease associations using methods inspired by social network analyses, PLoS One, 8(5):e58977 (2013) PubMed Link PDF Supplement
- Zhou L, Zhang AB, Wang R, Marcotte EM, Vogel C, The proteomic response to mutants of the Escherichia coli RNA degradosome, Molecular BioSystems, 9:750-757 (2013) PubMed Link PDF
- Wine Y, Boutz DR, Lavinder JJ, Miklos AE, Hughes RA, Hoi KH, Jung ST, Horton AP, Murrin EM, Ellington AD, Marcotte EM, Georgiou G, Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response, Proc Natl Acad Sci USA, 110(8):2993–2998 (2013) PubMed Link PDF
- Zhao A, Tsechansky M, Swaminathan J, Cook L, Ellington AD, Marcotte EM, Transiently transfected purine biosynthetic enzymes form stress bodies, PLoS One, 8(2):e56203 (2013) PubMed Link PDF
2012
- Wang PI, Hwang S, Kincaid RP, Sullivan CS, Lee I, Marcotte EM, RIDDLE: Reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network, Genome Biology, 13(12):R125 (2012) PubMed Link PDF
- Wessel AK, Liew J, Kwon T, Marcotte EM, Whiteley M, The role of Pseudomonas aeruginosa peptidoglycan-associated outer membrane proteins in vesicle formation, J Bacteriol, 195(2):213-9 (2012) PubMed Link PDF Supplemental data
- Park Y, Marcotte EM, Flaws in evaluation schemes for pair-input computational predictions, Nature Methods, 9(12):1134–1136 (2012) PubMed Link PDF Supplement
- Havugimana PC, Hart GT, Nepusz T, Yang H, Turinsky AL, Li Z, Wang P, Boutz DR, Fong V, Babu M, Craig SA, Hu P, Phanse S, Wan C, Vlasblom J, Dar V, Bezginov A, Wu GC, Wodak SJ, Tillier ERM, Paccanaro A, Marcotte EM, Emili A, Census of Human Soluble Protein Complexes, Cell, 150:1068-1081 (2012) PubMed Link PDF Supporting web site Research highlight
- Uribe RA, Kwon T, Marcotte EM, Gross JM, Id2a functions to limit Notch pathway activity and thereby influence retinoblast proliferation to differentiation of retinoblasts during zebrafish retinogenesis, Developmental Biology, 371:280–292 (2012) PubMed Link PDF
- Cha HJ, Byrom M, Mead PE, Ellington AD, Wallingford JB, Marcotte EM, Evolutionarily Repurposed Networks Reveal the Well-Known Antifungal Drug Thiabendazole to Be a Novel Vascular Disrupting Agent, PLoS Biology, 10(8):e1001379 (2012) PubMed Link PDF Supplemental Material Synopsis NY Times NIGMS video
- O'Connell JD, Zhao A, Ellington AD, Marcotte EM, Dynamic Reorganization of Metabolic Enzymes into Intracellular Bodies, Annual Review of Cell and Developmental Biology, 28:89-111 (2012) PubMed Link
- Vogel C, Marcotte EM, Insights into the regulation of protein abundance from proteomic and transcriptomic analyses, Nature Reviews Genetics, 13:227-232 (2012) PubMed Link PDF
- Orr SJ, Boutz DR, Wang R, Chronis C, Lea NC, Thayaparan T, Hamilton E, Milewicz H, Blanc E, Mufti GJ, Marcotte EM, Thomas NSB, Proteomic and protein interaction network analysis of human T lymphocytes during cell-cycle entry, Molecular Systems Biology, 8:573 (2012) PubMed Link PDF Supplement Reviewer comments
- Chung M-I, Peyrot S, LeBoeuf S, Park TJ, McGary KL, Marcotte EM, Wallingford JB, RFX2 is broadly required for ciliogenesis during vertebrate development, Developmental Biology, 363(1):155-165 (2012) PubMed Link PDF Supplement
- Vogel C, Marcotte EM, Label-free quantitation using weighted spectral counting, Methods in Molecular Biology: Quantitative Methods in Proteomics, Marcus, K., ed., Humana Press, vol. 893(3):321-341 (2012) PubMed Link PDF
2011
- Lee I, Seo Y-S, Coltrane D, Hwang S, Oha T, Marcotte EM, Ronald PC, Genetic dissection of the biotic stress response using a genome-scale gene network for rice, Proc Natl Acad Sci USA, 108(45):18548-18553 (2011) PubMed Link PDF Supplement
- Natarajan N, Blom UM, Tewari A, Woods JO, Dhillon IS, Marcotte EM, Predicting gene-disease associations using multiple species data, UTCS Technical Report, TR-11-37: (2011) PubMed Link PDF
- Vogel C, Silva GM, Marcotte EM, Global protein expression regulation under oxidative stress, Molecular and Cellular Proteomics, 10(12):M111.009217 (2011) PubMed Link PDF Supplement
- Park Y, Marcotte EM, Revisiting the negative example sampling problem for predicting protein-protein interactions, Bioinformatics, 27(21):3024-3028 (2011) PubMed Link PDF Supplemental Data
- Hwang S, Rhee SY, Marcotte EM, Lee I, Systematic prediction of gene function using a probabilistic functional gene network for Arabidopsis thaliana, Nature Protocols, 6:1429–1442 (2011) PubMed Link PDF
- Lee I, Blom M, Wang PI, Shim JE, Marcotte EM, Prioritizing candidate disease genes by network-based boosting of genome-wide association data, Genome Research, 21(7):1109-21 (2011) PubMed Link PDF Supplement HumanNet web site
- Kwon T, Choi H, Vogel C, Nesvizhskii AI, Marcotte EM, MSblender: a probabilistic approach for integrating peptide identifications from multiple database search engines, Journal of Proteome Research, 10(7):2949-58 (2011) PubMed Link PDF Supplemental Figures 1 2 3 4 Supporting web site
- Boutz DR, Collins P, Suresh U, Lu M, Ramírez CM, Fernández-Hernando C, Huang Y, de Sousa Abreu R, Le SY, Shapiro BA, Liu AM, Luk JM, Aldred SF, Trinklein N, Marcotte EM, Penalva LO, A two-tiered approach identifies a network of cancer and liver diseases related genes regulated by miR-122, Journal of Biological Chemistry, 286(20):18066-78 (2011) PubMed Link PDF
- Niu W, Hart GT, Marcotte EM, High-throughput immunofluorescence microscopy using yeast spheroplast microarrays, Methods in Molecular Biology: Cell-Based Microarrays, Palmer, E., ed., Humana Press, vol. 706:83-95 (2011) PubMed PDF
- Smith KR, Kieserman EK, Wang PI, Basten SG, Giles RH, Marcotte EM, Wallingford JB, A role for central spindle proteins in cilia structure and function, Cytoskeleton, 68(2):112-24 (2011) PubMed Link PDF
2010
- Huse HK, Kwon T, Zlosnik JEA, Speert DP, Marcotte EM, Whiteley M, Parallel evolution in Pseudomonas aeruginosa over 39,000 generations in vivo, mBIO, 1(4):e00199-10 (2010) PubMed Link PDF ScienceNews Supplement
- Huang N, Lee I, Marcotte EM, Hurles M, Characterising and predicting haploinsufficiency in the human genome, PLoS Genetics, 6(10):e1001154 (2010) PubMed Link PDF
- Laurent J, Vogel C, Kwon T, Craig SA, Boutz DR, Huse HK, Nozue K, Walia H, Whiteley M, Ronald PC, Marcotte EM, Protein abundances are more conserved than mRNA abundances across diverse taxa, Proteomics, 10:4209–4212 (2010) PubMed Link PDF Supplement
- Wang PI, Marcotte EM, It's the machine that matters: predicting gene function and phenotype from protein networks, Journal of Proteomics, 73(11):2277-89 (2010) PubMed Link PDF
- Vogel C, de Sousa Abreu R, Ko D, Le S-Y, Shapiro BA, Burns SC, Sandhu D, Boutz DR, Marcotte EM, Penalva LO, Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line, Molecular Systems Biology, 6:article 400 (2010) PubMed Link PDF Supplement Supplemental Data (Excel format) Fig 2 source data Fig 3A source data Fig 3B source data News and Views
- Lo K-Y, Li Z, Bussiere C, Bresson S, Marcotte EM, Johnson AW, Defining the pathway of cytoplasmic maturation of the 60S ribosomal subunit, Molecular Cell, 39(2):196-208 (2010) PubMed Link PDF Supplement
- Lee I, Lehner B, Vavouri T, Shin J, Fraser AG, Marcotte EM, Predicting genetic modifier loci using functional gene networks, Genome Research, 20:1143-1153 (2010) PubMed Link PDF Supplement Nature Reviews Genetics
- McGary KL, Park TJ, Woods JO, Cha HJ, Wallingford JB, Marcotte EM, Systematic discovery of nonobvious human disease models through orthologous phenotypes, Proc Natl Acad Sci U S A, 107(14):6544-9 (2010) PubMed Link PDF Supplement Nature News The Scientist(blog) NY Times Genome Biology
- Orr SJ, Gaymes T, Ladon D, Chronis C, Czepulkowski B, Wang R, Mufti GJ, Marcotte EM, Thomas NSB, Reducing MCM levels in human primary T cells during the G0->G1 transition causes genomic instability during the first cell cycle, Oncogene, 29(26):3803-14 (2010) PubMed Link PDF
- Lee I, Ambaru B, Thakkar P, Marcotte EM, Rhee SY, Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana, Nature Biotechnology, 28(2):149-156 (2010) PubMed Link PDF Supplement Honorable Mention in the 2010 Science Visualization Challenge New York Times slideshow
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, 7(10):e1000213 (2009) PubMed Link PDF Supplemental Figures and Tables
- Hart GT, Zhao A, Garg A, Bolusani S, Marcotte EM, Human cell chips: adapting DNA microarray spotting technology to cell-based imaging assays, PLoS One, 4(10):e7088 (2009) PubMed Link PDF Table S1
- Lo KY, Li Z, Wang F, Marcotte EM, Johnson AF, Ribosome stalk assembly requires the dual specificity phosphatase Yvh1 for the exchange of Mrt4 with P0, J. Cell Biology, 186(6):849-62 (2009) PubMed Link PDF Supplemental material
- Vogel C, Marcotte EM, Absolute abundance for the masses, Nature Biotechnology, 27(9):825-6 (2009) PubMed Link PDF
- de Sousa Abreu R, Penalva LO, Marcotte EM, Vogel C, Global signatures of protein and mRNA expression levels, Molecular BioSystems, 5:1512–1526 (2009) PubMed Link PDF
- 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, 11(10):1225-32 (2009) PubMed Link PDF Journal cover--a beautiful electron micrograph by Phil Abitua Supplemental Figures
- 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, 25(22):2955-2961 (2009) PubMed Link PDF Supplemental Website
- 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, Wang R, Li Z, Penalva LO, Myers M, Marcotte EM, Miranker DP, Integrating shotgun proteomics and mRNA expression data to improve protein identification, Bioinformatics, 25(11):1397-403 (2009) PubMed Link PDF Supplement Supplemental website
- 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 Supporting python code: network_growth_functions_fixed_module.py Note that this code used an older version of the igraph library (0.4.2); the latest version that we've tested (0.5.2) gives somewhat fewer large clusters than our published clusters due to changes in the function "G.community_fastgreedy()", possibly resulting from modifications to the handling of ties in the community merging process. The previous igraph library (0.4.2) is linked here: python-igraph-0.4.2.tar.gz igraph-0.4.2.tar.gz igraph_base.py
- 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 MouseFunc predictions
- 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 Supplemental File of All ORF FACS Defects
- 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 2011 NBT Retrospective on APEX
- 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 Supplemental README Supplemental File 1 Supplemental File 2 Supplemental File 3 Supplemental File 4 Supplemental File 5 (Files 4 & 5 require a VRML viewer)
- 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, 36(6):559-64 (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) 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 RJ, 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 PDF
- Verjovsky Marcotte CJ, Marcotte EM, Predicting functional linkages from gene fusions with confidence, Applied Bioinformatics, 1(2):1-8 (2002) PubMed PDF
2001
- Marcotte EM, Date SV, Exploiting Big Biology: Integrating large-scale biological data for functional inference, Brief Bioinform, 2(4):363-74 (2001) PubMed PDF
- Marcotte EM, The path not taken, Nature Biotechnology, 19(7):626-7 (2001) PubMed PDF
- Marcotte EM, Measuring the Dynamics of the Proteome, Genome Research, 11(2):191-3 (2001) PubMed PDF
- Marcotte EM, Xenarios I, Eisenberg D, Mining Literature for Protein Interactions, Bioinformatics, 17(4):359-63 (2001) PubMed PDF README 500_abstracts_with_PMID Discriminating_words_for_interactions Discriminating_words_for_interactions_edited score_abstracts Perl script
- Eisenberg D, Marcotte E, Pellegrini M, Thompson M, Xenarios I, Yeates T, From genome sequences to protein interactions, FASEB J, 15:A724-A724 (2001) PubMed
- 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) PubMed PDF
2000
- Eisenberg D, Marcotte EM, Xenarios I, Yeates TO, Protein function in the post-genomic era, Nature, 405(6788):823-6 (2000) PubMed Link PDF
- Marcotte EM, Xenarios I, van der Bliek A, Eisenberg D, Localizing proteins in the cell from their phylogenetic profiles, Proc Natl Acad Sci U S A., 97(22):12115-20 (2000) PubMed Link PDF
- Marcotte EM, Computational genetics: Finding Function by Non-Homology Methods, Curr Opin Struct Biol., 10(3):359-65 (2000) PubMed Link PDF
- Yang H, Fitz-Gibbon S, Marcotte EM, Tai JH, Hyman EC, Miller JH, Characterization of a thermostable DNA glycosylase specific for U/G and T/G mismatches from the hyperthermophilic archaeon Pyrobaculum aerophilum, J Bacteriol., 182(5):1272-9 (2000) PubMed Link PDF
- Thompson M, Marcotte E, Pellegrini M, Yeates T, Eisenberg D, Increasing the specificity of protein functional inference by the Rosetta Stone method, Currents in Computational Molecular Biology, Miyano S, Shamir R, Takagi T, eds., Universal Academy Press, Inc.: (2000) PubMed PDF
- Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D, DIP: the database of interacting proteins., Nucleic Acids Res., 28(1):289-91 (2000) PubMed Link PDF
1999
- Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D, A combined algorithm for genome-wide prediction of protein function, Nature, 402(6757):83-6 (1999) PubMed Link PDF See also Sali, A. Genomics: Functional links between proteins. Nature 402, 23-26 (1999), Boston Globe (Nov. 3, 1999), Los Angeles Times (Nov. 4, 1999).
- Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D, Detecting protein function and protein-protein interactions from genome sequences, Science, 285(5428):751-3 (1999) PubMed Link PDF See also Doolittle, R. F. Do you dig my groove? Nature: Genetics 23, 6-8 (1999).
- Marcotte EM, Pellegrini M, Yeates TO, Eisenberg D, A census of protein repeats, J Mol Biol., 293(1):151-60 (1999) PubMed Link PDF
- Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO, Assigning protein functions by comparative genome analysis: protein phylogenetic profiles, Proc Natl Acad Sci U S A, 96(8):4285-8 (1999) PubMed Link PDF
- Pellegrini M, Marcotte EM, Yeates TO, A fast algorithm for genome-wide analysis of proteins with repeated sequences, Proteins: Struct. Funct. Genet., 35(4):440-6 (1999) PubMed Link PDF
1998
- Marcotte EM, Eisenberg D, Chicken prion tandem repeats form a stable, protease-resistant domain, Biochemistry, 38(2):667-76 (1998) PubMed Link PDF
- Cascio D, Goodwill K, Marcotte E, A Look at the Future of Macromolecular Structure Determination, Rigaku J., 15:1-5 (1998) PubMed PDF
- Robertus JD, Monzingo AF, Marcotte EM, Hart PJ, Structural analysis shows five glycohydrolase families diverged from a common ancestor, J Exp Zool., 282(1-2):127-32 (1998) PubMed Link PDF
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 PDF
- 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 PDF News & Views
- 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 PDF
- 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 PDF
- 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 PDF
Patents
- USPTO Application # 20120215458, Orthologous phenotypes and non-obvious human disease models, PCT filed July 13, 2010; provisional patent # 61/225,427 filed July 14, 2009.
- USPTO Application # 20110312505, Rapid isolation of monoclonal antibodies from animals, filed May 17, 2011; priority over # 61/345,538 (filed May 17, 2010) and # 61/377,816 (filed August 27, 2010).
- 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.