Etienne Marcotte, Ph.D. - Publications

2013 Physics Princeton University, Princeton, NJ 
statistical mechanics and soft condensed matter theory

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Year Citation  Score
2014 Timoshevskii V, Hu Y, Marcotte É, Guo H. Quantum transport modeling of the symmetric Fe/FeO0.5/MgO magnetic tunnel junction: the effects of correlations in the buffer layer. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 26: 015002. PMID 24263207 DOI: 10.1088/0953-8984/26/1/015002  1
2013 Kallus Y, Marcotte É, Torquato S. Jammed lattice sphere packings. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 88: 062151. PMID 24483429 DOI: 10.1103/PhysRevE.88.062151  1
2013 Marcotte É, Torquato S. Efficient linear programming algorithm to generate the densest lattice sphere packings. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 87: 063303. PMID 23848802 DOI: 10.1103/PhysRevE.87.063303  1
2013 Marcotte É, Stillinger FH, Torquato S. Nonequilibrium static growing length scales in supercooled liquids on approaching the glass transition. The Journal of Chemical Physics. 138: 12A508. PMID 23556759 DOI: 10.1063/1.4769422  1
2013 Marcotte É, Stillinger FH, Torquato S. Communication: Designed diamond ground state via optimized isotropic monotonic pair potentials. The Journal of Chemical Physics. 138: 061101. PMID 23425451 DOI: 10.1063/1.4790634  1
2013 Marcotte E, Distasio RA, Stillinger FH, Torquato S. Designer spin systems via inverse statistical mechanics. II. Ground-state enumeration and classification Physical Review B - Condensed Matter and Materials Physics. 88. DOI: 10.1103/PhysRevB.88.184432  1
2013 Martis S, Marcotte E, Stillinger FH, Torquato S. Exotic Ground States of Directional Pair Potentials via Collective-Density Variables Journal of Statistical Physics. 150: 414-431. DOI: 10.1007/s10955-012-0619-2  1
2011 Marcotte É, Stillinger FH, Torquato S. Unusual ground states via monotonic convex pair potentials. The Journal of Chemical Physics. 134: 164105. PMID 21528948 DOI: 10.1063/1.3576141  1
2011 Marcotte E, Stillinger FH, Torquato S. Optimized monotonic convex pair potentials stabilize low-coordinated crystals Soft Matter. 7: 2332-2335. DOI: 10.1039/c0sm01205j  1
Low-probability matches
2008 Lee I, Lehner B, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. Nature Genetics. 40: 181-8. PMID 18223650 DOI: 10.1038/ng.2007.70  0.04
2016 Marcotte EL, Thomopoulos TP, Infante-Rivard C, Clavel J, Petridou ET, Schüz J, Ezzat S, Dockerty JD, Metayer C, Magnani C, Scheurer ME, Mueller BA, Mora AM, Wesseling C, Skalkidou A, et al. Caesarean delivery and risk of childhood leukaemia: a pooled analysis from the Childhood Leukemia International Consortium (CLIC). The Lancet. Haematology. 3: e176-85. PMID 27063976 DOI: 10.1016/S2352-3026(16)00002-8  0.01
2016 Robotham SA, Horton AP, Cannon JR, Cotham VC, Marcotte EM, Brodbelt JS. UVnovo: A De Novo Sequencing Algorithm Using Single Series of Fragment Ions via Chromophore Tagging and 351 nm Ultraviolet Photodissociation Mass Spectrometry. Analytical Chemistry. PMID 26938041 DOI: 10.1021/acs.analchem.6b00261  0.01
2016 Phanse S, Wan C, Borgeson B, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, ... Marcotte EM, et al. Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes. Data in Brief. 6: 715-21. PMID 26870755 DOI: 10.1016/j.dib.2015.11.062  0.04
2015 Poldrack RA, Laumann TO, Koyejo O, Gregory B, Hover A, Chen MY, Gorgolewski KJ, Luci J, Joo SJ, Boyd RL, Hunicke-Smith S, Simpson ZB, Caven T, Sochat V, Shine JM, ... Marcotte EM, et al. Long-term neural and physiological phenotyping of a single human. Nature Communications. 6: 8885. PMID 26648521 DOI: 10.1038/ncomms9885  0.01
2015 Hwang S, Kim E, Lee I, Marcotte EM. Systematic comparison of variant calling pipelines using gold standard personal exome variants. Scientific Reports. 5: 17875. PMID 26639839 DOI: 10.1038/srep17875  0.04
2015 Kim E, Hwang S, Kim H, Shim H, Kang B, Yang S, Shim JH, Shin SY, Marcotte EM, Lee I. MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates. Nucleic Acids Research. PMID 26527726 DOI: 10.1093/nar/gkv1155  0.01
2015 Murray JL, Kwon T, Marcotte EM, Whiteley M. Intrinsic Antimicrobial Resistance Determinants in the Superbug Pseudomonas aeruginosa. Mbio. 6. PMID 26507235 DOI: 10.1128/mBio.01603-15  0.01
2015 Laurent JM, Young JH, Kachroo AH, Marcotte EM. Efforts to make and apply humanized yeast. Briefings in Functional Genomics. PMID 26462863 DOI: 10.1093/bfgp/elv041  0.04
2015 Wan C, Borgeson B, Phanse S, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, ... Marcotte EM, et al. Panorama of ancient metazoan macromolecular complexes. Nature. 525: 339-44. PMID 26344197 DOI: 10.1038/nature14877  0.04
2015 McWhite CD, Liebeskind BJ, Marcotte EM. Applications of comparative evolution to human disease genetics. Current Opinion in Genetics & Development. 35: 16-24. PMID 26338499 DOI: 10.1016/j.gde.2015.08.004  0.01
2015 Houser JR, Barnhart C, Boutz DR, Carroll SM, Dasgupta A, Michener JK, Needham BD, Papoulas O, Sridhara V, Sydykova DK, Marx CJ, Trent MS, Barrick JE, Marcotte EM, Wilke CO. Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation. Plos Computational Biology. 11: e1004400. PMID 26275208 DOI: 10.1371/journal.pcbi.1004400  0.01
2015 Kachroo AH, Laurent JM, Yellman CM, Meyer AG, Wilke CO, Marcotte EM. Evolution. Systematic humanization of yeast genes reveals conserved functions and genetic modularity. Science (New York, N.Y.). 348: 921-5. PMID 25999509 DOI: 10.1126/science.aaa0769  0.04
2015 Lee I, Kim E, Marcotte EM. Modes of interaction between individuals dominate the topologies of real world networks. Plos One. 10: e0121248. PMID 25793969 DOI: 10.1371/journal.pone.0121248  0.04
2015 Swaminathan J, Boulgakov AA, Marcotte EM. A theoretical justification for single molecule peptide sequencing. Plos Computational Biology. 11: e1004080. PMID 25714988 DOI: 10.1371/journal.pcbi.1004080  0.04
2015 Sardana R, Liu X, Granneman S, Zhu J, Gill M, Papoulas O, Marcotte EM, Tollervey D, Correll CC, Johnson AW. The DEAH-box helicase Dhr1 dissociates U3 from the pre-rRNA to promote formation of the central pseudoknot. Plos Biology. 13: e1002083. PMID 25710520 DOI: 10.1371/journal.pbio.1002083  0.04
2015 Brown KA, Yang X, Schipper D, Hall JW, DePue LJ, Gnanam AJ, Arambula JF, Jones JN, Swaminathan J, Dieye Y, Vadivelu J, Chandler DJ, Marcotte EM, Sessler JL, Ehrlich LI, et al. A self-assembling lanthanide molecular nanoparticle for optical imaging. Dalton Transactions (Cambridge, England : 2003). 44: 2667-75. PMID 25512085 DOI: 10.1039/c4dt02646b  0.01
2015 Spector LG, Pankratz N, Marcotte EL. Genetic and nongenetic risk factors for childhood cancer. Pediatric Clinics of North America. 62: 11-25. PMID 25435109 DOI: 10.1016/j.pcl.2014.09.013  0.01
2015 Houser JR, Barnhart C, Boutz DR, Carroll SM, Dasgupta A, Michener JK, Needham BD, Papoulas O, Sridhara V, Sydykova DK, Marx CJ, Trent MS, Barrick JE, Marcotte EM, Wilke CO. Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation Plos Computational Biology. 11. DOI: 10.1371/journal.pcbi.1004400  0.04
2015 McWhite CD, Liebeskind BJ, Marcotte EM. Applications of comparative evolution to human disease genetics Current Opinion in Genetics and Development. 35: 16-24. DOI: 10.1016/j.gde.2015.08.004  0.04
2014 Kwon T, Chung MI, Gupta R, Baker JC, Wallingford JB, Marcotte EM. Identifying direct targets of transcription factor Rfx2 that coordinate ciliogenesis and cell movement. Genomics Data. 2: 192-194. PMID 25419512 DOI: 10.1016/j.gdata.2014.06.015  0.04
2014 Marcotte E, Dubé P, Drolet P, Mitchell A, Frenette S, Leblanc G, Leclerc YE, Sideris L. Hyperthermic intraperitoneal chemotherapy with oxaliplatin as treatment for peritoneal carcinomatosis arising from the appendix and pseudomyxoma peritonei: a survival analysis. World Journal of Surgical Oncology. 12: 332. PMID 25380618 DOI: 10.1186/1477-7819-12-332  0.01
2014 Jones RA, Gnanam AJ, Arambula JF, Jones JN, Swaminathan J, Yang X, Schipper D, Hall JW, DePue LJ, Dieye Y, Vadivelu J, Chandler DJ, Marcotte EM, Sessler JL, Ehrlich LI, et al. Lanthanide nano-drums: a new class of molecular nanoparticles for potential biomedical applications. Faraday Discussions. 175: 241-55. PMID 25284181 DOI: 10.1039/c4fd00117f  0.04
2014 Almouzni G, Altucci L, Amati B, Ashley N, Baulcombe D, Beaujean N, Bock C, Bongcam-Rudloff E, Bousquet J, Braun S, Bressac-de Paillerets B, Bussemakers M, Clarke L, Conesa A, Estivill X, ... ... Marcotte E, et al. Relationship between genome and epigenome--challenges and requirements for future research. Bmc Genomics. 15: 487. PMID 24942464 DOI: 10.1186/1471-2164-15-487  0.01
2014 Hwang S, Kim E, Yang S, Marcotte EM, Lee I. MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network. Nucleic Acids Research. 42: W147-53. PMID 24861622 DOI: 10.1093/nar/gku434  0.04
2014 Marcotte EL, Ritz B, Cockburn M, Yu F, Heck JE. Exposure to infections and risk of leukemia in young children. Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association For Cancer Research, Cosponsored by the American Society of Preventive Oncology. 23: 1195-203. PMID 24793957 DOI: 10.1158/1055-9965.EPI-13-1330  0.01
2014 Kwon T, Huse HK, Vogel C, Whiteley M, Marcotte EM. Protein-to-mRNA ratios are conserved between Pseudomonas aeruginosa strains. Journal of Proteome Research. 13: 2370-80. PMID 24742327 DOI: 10.1021/pr4011684  0.04
2014 Boutz DR, Horton AP, Wine Y, Lavinder JJ, Georgiou G, Marcotte EM. Proteomic identification of monoclonal antibodies from serum. Analytical Chemistry. 86: 4758-66. PMID 24684310 DOI: 10.1021/ac4037679  0.04
2014 O'Connell JD, Tsechansky M, Royall A, Boutz DR, Ellington AD, Marcotte EM. A proteomic survey of widespread protein aggregation in yeast. Molecular Biosystems. 10: 851-61. PMID 24488121 DOI: 10.1039/c3mb70508k  0.04
2014 Hammerling MJ, Ellefson JW, Boutz DR, Marcotte EM, Ellington AD, Barrick JE. Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness. Nature Chemical Biology. 10: 178-80. PMID 24487692 DOI: 10.1038/nchembio.1450  0.04
2014 Lavinder JJ, Wine Y, Giesecke C, Ippolito GC, Horton AP, Lungu OI, Hoi KH, DeKosky BJ, Murrin EM, Wirth MM, Ellington AD, Dörner T, Marcotte EM, Boutz DR, Georgiou G. Identification and characterization of the constituent human serum antibodies elicited by vaccination. Proceedings of the National Academy of Sciences of the United States of America. 111: 2259-64. PMID 24469811 DOI: 10.1073/pnas.1317793111  0.04
2014 Chung MI, Kwon T, Tu F, Brooks ER, Gupta R, Meyer M, Baker JC, Marcotte EM, Wallingford JB. Coordinated genomic control of ciliogenesis and cell movement by RFX2. Elife. 3: e01439. PMID 24424412 DOI: 10.7554/eLife.01439  0.04
2014 Zhao A, Tsechansky M, Ellington AD, Marcotte EM. Revisiting and revising the purinosome. Molecular Biosystems. 10: 369-74. PMID 24413256 DOI: 10.1039/c3mb70397e  0.04
2014 Qian Y, Kachroo AH, Yellman CM, Marcotte EM, Johnson KA. Yeast cells expressing the human mitochondrial DNA polymerase reveal correlations between polymerase fidelity and human disease progression. The Journal of Biological Chemistry. 289: 5970-85. PMID 24398692 DOI: 10.1074/jbc.M113.526418  0.04
2014 Marcotte EL, Ritz B, Cockburn M, Clarke CA, Heck JE. Birth characteristics and risk of lymphoma in young children. Cancer Epidemiology. 38: 48-55. PMID 24345816 DOI: 10.1016/j.canep.2013.11.005  0.01
2014 Gerster S, Kwon T, Ludwig C, Matondo M, Vogel C, Marcotte EM, Aebersold R, Bühlmann P. Statistical approach to protein quantification. Molecular & Cellular Proteomics : McP. 13: 666-77. PMID 24255132 DOI: 10.1074/mcp.M112.025445  0.04
2013 Huse HK, Kwon T, Zlosnik JE, Speert DP, Marcotte EM, Whiteley M. Pseudomonas aeruginosa enhances production of a non-alginate exopolysaccharide during long-term colonization of the cystic fibrosis lung. Plos One. 8: e82621. PMID 24324811 DOI: 10.1371/journal.pone.0082621  0.04
2013 Li Z, Park Y, Marcotte EM. A Bacteriophage tailspike domain promotes self-cleavage of a human membrane-bound transcription factor, the myelin regulatory factor MYRF. Plos Biology. 11: e1001624. PMID 23966832 DOI: 10.1371/journal.pbio.1001624  0.04
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. 14: 203. PMID 23800157 DOI: 10.1186/1471-2105-14-203  0.04
2013 Marcotte E, Afaneh C, Pomp A, Cherqui D. Image of the month-quiz. Cystadenoma of the cystic duct. Jama Surgery. 148: 395-6. PMID 23715797 DOI: 10.1001/jamasurg.2013.317a  0.01
2013 Marcotte E, Boone C, Babu MM, Gavin AC. Network Biology editorial 2013. Molecular Biosystems. 9: 1557-8. PMID 23712464 DOI: 10.1039/c3mb90018e  0.04
2013 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: e58977. PMID 23650495 DOI: 10.1371/journal.pone.0058977  0.04
2013 Zhao A, Tsechansky M, Swaminathan J, Cook L, Ellington AD, Marcotte EM. Transiently transfected purine biosynthetic enzymes form stress bodies. Plos One. 8: e56203. PMID 23405267 DOI: 10.1371/journal.pone.0056203  0.04
2013 Zhou L, Zhang AB, Wang R, Marcotte EM, Vogel C. The proteomic response to mutants of the Escherichia coli RNA degradosome. Molecular Biosystems. 9: 750-7. PMID 23403814 DOI: 10.1039/c3mb25513a  0.04
2013 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. Proceedings of the National Academy of Sciences of the United States of America. 110: 2993-8. PMID 23382245 DOI: 10.1073/pnas.1213737110  0.04
2013 Wessel AK, Liew J, Kwon T, Marcotte EM, Whiteley M. Role of Pseudomonas aeruginosa peptidoglycan-associated outer membrane proteins in vesicle formation. Journal of Bacteriology. 195: 213-9. PMID 23123904 DOI: 10.1128/JB.01253-12  0.04
2013 Rod NH, Bordelon Y, Thompson A, Marcotte E, Ritz B. Major life events and development of major depression in Parkinson's disease patients. European Journal of Neurology. 20: 663-70. PMID 23114037 DOI: 10.1111/ene.12019  0.01
2013 Wan C, Liu J, Fong V, Lugowski A, Stoilova S, Bethune-Waddell D, Borgeson B, Havugimana PC, Marcotte EM, Emili A. ComplexQuant: high-throughput computational pipeline for the global quantitative analysis of endogenous soluble protein complexes using high resolution protein HPLC and precision label-free LC/MS/MS. Journal of Proteomics. 81: 102-11. PMID 23063720 DOI: 10.1016/j.jprot.2012.10.001  0.04
2013 DiStasio RA, Marcotte É, Car R, Stillinger FH, Torquato S. Designer spin systems via inverse statistical mechanics Physical Review B. 88. DOI: 10.1103/physrevb.88.134104  0.01
2013 Brown SR, Dunkinson CE, Douma MD, Zhou J, Aston WP, Marcotte EJP, Miron M, Radcliffe T, Gallant PJ, Wilton D. A fibre-optic coupled fluorescence multiwavelength sensor for automated monitoring of bacteria culture from drinking water Optics Infobase Conference Papers 0.01
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: R125. PMID 23268829 DOI: 10.1186/gb-2012-13-12-r125  0.04
2012 Park Y, Marcotte EM. Flaws in evaluation schemes for pair-input computational predictions. Nature Methods. 9: 1134-6. PMID 23223166 DOI: 10.1038/nmeth.2259  0.04
2012 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. PMID 23057741 DOI: 10.1146/annurev-cellbio-101011-155841  0.04
2012 Uribe RA, Kwon T, Marcotte EM, Gross JM. Id2a functions to limit Notch pathway activity and thereby influence the transition from proliferation to differentiation of retinoblasts during zebrafish retinogenesis. Developmental Biology. 371: 280-92. PMID 22981606 DOI: 10.1016/j.ydbio.2012.08.032  0.04
2012 Havugimana PC, Hart GT, Nepusz T, Yang H, Turinsky AL, Li Z, Wang PI, Boutz DR, Fong V, Phanse S, Babu M, Craig SA, Hu P, Wan C, Vlasblom J, ... Marcotte EM, et al. A census of human soluble protein complexes. Cell. 150: 1068-81. PMID 22939629 DOI: 10.1016/j.cell.2012.08.011  0.04
2012 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: e1001379. PMID 22927795 DOI: 10.1371/journal.pbio.1001379  0.04
2012 Vogel C, Marcotte EM. Label-free protein quantitation using weighted spectral counting. Methods in Molecular Biology (Clifton, N.J.). 893: 321-41. PMID 22665309 DOI: 10.1007/978-1-61779-885-6_20  0.04
2012 Marcotte E, Comeau E, Meziat-Burdin A, Ménard C, Rateb G. Early migration of fully covered double-layered metallic stents for post-gastric bypass anastomotic strictures. International Journal of Surgery Case Reports. 3: 283-6. PMID 22516420 DOI: 10.1016/j.ijscr.2012.03.022  0.01
2012 Orr SJ, Boutz DR, Wang R, Chronis C, Lea NC, Thayaparan T, Hamilton E, Milewicz H, Blanc E, Mufti GJ, Marcotte EM, Thomas NS. Proteomic and protein interaction network analysis of human T lymphocytes during cell-cycle entry. Molecular Systems Biology. 8: 573. PMID 22415777 DOI: 10.1038/msb.2012.5  0.04
2012 Vogel C, Marcotte EM. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nature Reviews. Genetics. 13: 227-32. PMID 22411467 DOI: 10.1038/nrg3185  0.04
2012 Heck JE, Marcotte EL, Argos M, Parvez F, Ahmed A, Islam T, Sarwar G, Hasan R, Ahsan H, Chen Y. Betel quid chewing in rural Bangladesh: prevalence, predictors and relationship to blood pressure. International Journal of Epidemiology. 41: 462-71. PMID 22253307 DOI: 10.1093/ije/dyr191  0.01
2012 Chung MI, Peyrot SM, LeBoeuf S, Park TJ, McGary KL, Marcotte EM, Wallingford JB. RFX2 is broadly required for ciliogenesis during vertebrate development. Developmental Biology. 363: 155-65. PMID 22227339 DOI: 10.1016/j.ydbio.2011.12.029  0.04
2011 Lee I, Seo YS, Coltrane D, Hwang S, Oh T, Marcotte EM, Ronald PC. Genetic dissection of the biotic stress response using a genome-scale gene network for rice. Proceedings of the National Academy of Sciences of the United States of America. 108: 18548-53. PMID 22042862 DOI: 10.1073/pnas.1110384108  0.04
2011 Vogel C, Silva GM, Marcotte EM. Protein expression regulation under oxidative stress. Molecular & Cellular Proteomics : McP. 10: M111.009217. PMID 21933953 DOI: 10.1074/mcp.M111.009217  0.04
2011 Park Y, Marcotte EM. Revisiting the negative example sampling problem for predicting protein-protein interactions. Bioinformatics (Oxford, England). 27: 3024-8. PMID 21908540 DOI: 10.1093/bioinformatics/btr514  0.04
2011 Hwang S, Rhee SY, Marcotte EM, Lee I. Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network. Nature Protocols. 6: 1429-42. PMID 21886106 DOI: 10.1038/nprot.2011.372  0.04
2011 Lee I, Blom UM, Wang PI, Shim JE, Marcotte EM. Prioritizing candidate disease genes by network-based boosting of genome-wide association data. Genome Research. 21: 1109-21. PMID 21536720 DOI: 10.1101/gr.118992.110  0.04
2011 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: 2949-58. PMID 21488652 DOI: 10.1021/pr2002116  0.04
2011 Boutz DR, Collins PJ, Suresh U, Lu M, Ramírez CM, Fernández-Hernando C, Huang Y, Abreu Rde S, Le SY, Shapiro BA, Liu AM, Luk JM, Aldred SF, Trinklein ND, Marcotte EM, et al. Two-tiered approach identifies a network of cancer and liver disease-related genes regulated by miR-122. The Journal of Biological Chemistry. 286: 18066-78. PMID 21402708 DOI: 10.1074/jbc.M110.196451  0.04
2011 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 (Hoboken, N.J.). 68: 112-24. PMID 21246755 DOI: 10.1002/cm.20498  0.04
2011 Niu W, Hart GT, Marcotte EM. High-throughput immunofluorescence microscopy using yeast spheroplast cell-based microarrays. Methods in Molecular Biology (Clifton, N.J.). 706: 83-95. PMID 21104056 DOI: 10.1007/978-1-61737-970-3_7  0.04
2010 Laurent JM, 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: 4209-12. PMID 21089048 DOI: 10.1002/pmic.201000327  0.04
2010 Huang N, Lee I, Marcotte EM, Hurles ME. Characterising and predicting haploinsufficiency in the human genome. Plos Genetics. 6: e1001154. PMID 20976243 DOI: 10.1371/journal.pgen.1001154  0.04
2010 Huse HK, Kwon T, Zlosnik JE, Speert DP, Marcotte EM, Whiteley M. Parallel evolution in Pseudomonas aeruginosa over 39,000 generations in vivo. Mbio. 1. PMID 20856824 DOI: 10.1128/mBio.00199-10  0.04
2010 Vogel C, Abreu Rde S, Ko D, Le SY, 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: 400. PMID 20739923 DOI: 10.1038/msb.2010.59  0.04
2010 Lo KY, Li Z, Bussiere C, Bresson S, Marcotte EM, Johnson AW. Defining the pathway of cytoplasmic maturation of the 60S ribosomal subunit. Molecular Cell. 39: 196-208. PMID 20670889 DOI: 10.1016/j.molcel.2010.06.018  0.04
2010 Wang PI, Marcotte EM. It's the machine that matters: Predicting gene function and phenotype from protein networks. Journal of Proteomics. 73: 2277-89. PMID 20637909 DOI: 10.1016/j.jprot.2010.07.005  0.04
2010 Lee I, Lehner B, Vavouri T, Shin J, Fraser AG, Marcotte EM. Predicting genetic modifier loci using functional gene networks. Genome Research. 20: 1143-53. PMID 20538624 DOI: 10.1101/gr.102749.109  0.04
2010 Orr SJ, Gaymes T, Ladon D, Chronis C, Czepulkowski B, Wang R, Mufti GJ, Marcotte EM, Thomas NS. Reducing MCM levels in human primary T cells during the G(0)-->G(1) transition causes genomic instability during the first cell cycle. Oncogene. 29: 3803-14. PMID 20440261 DOI: 10.1038/onc.2010.138  0.04
2010 McGary KL, Park TJ, Woods JO, Cha HJ, Wallingford JB, Marcotte EM. Systematic discovery of nonobvious human disease models through orthologous phenotypes. Proceedings of the National Academy of Sciences of the United States of America. 107: 6544-9. PMID 20308572 DOI: 10.1073/pnas.0910200107  0.04
2010 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: 149-56. PMID 20118918 DOI: 10.1038/nbt.1603  0.04
2009 de Sousa Abreu R, Penalva LO, Marcotte EM, Vogel C. Global signatures of protein and mRNA expression levels. Molecular Biosystems. 5: 1512-26. PMID 20023718 DOI: 10.1039/b908315d  0.04
2009 Hart T, Zhao A, Garg A, Bolusani S, Marcotte EM. Human cell chips: adapting DNA microarray spotting technology to cell-based imaging assays. Plos One. 4: e7088. PMID 19862318 DOI: 10.1371/journal.pone.0007088  0.04
2009 Li Z, Lee I, Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational extension of the ribosome biogenesis pathway using network-guided genetics. Plos Biology. 7: e1000213. PMID 19806183 DOI: 10.1371/journal.pbio.1000213  0.04
2009 Lo KY, Li Z, Wang F, Marcotte EM, Johnson AW. Ribosome stalk assembly requires the dual-specificity phosphatase Yvh1 for the exchange of Mrt4 with P0. The Journal of Cell Biology. 186: 849-62. PMID 19797078 DOI: 10.1083/jcb.200904110  0.04
2009 Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, Lee I, Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector Fuz is essential for targeted membrane trafficking, ciliogenesis and mouse embryonic development. Nature Cell Biology. 11: 1225-32. PMID 19767740 DOI: 10.1038/ncb1966  0.04
2009 Vogel C, Marcotte EM. Absolute abundance for the masses. Nature Biotechnology. 27: 825-6. PMID 19741640 DOI: 10.1038/nbt0909-825  0.04
2009 Ramakrishnan SR, Vogel C, Kwon T, Penalva LO, Marcotte EM, Miranker DP. Mining gene functional networks to improve mass-spectrometry-based protein identification. Bioinformatics (Oxford, England). 25: 2955-61. PMID 19633097 DOI: 10.1093/bioinformatics/btp461  0.04
2009 Marcotte EM, Tsechansky M. Disorder, promiscuity, and toxic partnerships. Cell. 138: 16-8. PMID 19596229 DOI: 10.1016/j.cell.2009.06.024  0.04
2009 Tabor JJ, Salis HM, Simpson ZB, Chevalier AA, Levskaya A, Marcotte EM, Voigt CA, Ellington AD. A synthetic genetic edge detection program. Cell. 137: 1272-81. PMID 19563759 DOI: 10.1016/j.cell.2009.04.048  0.04
2009 Narayanaswamy R, Levy M, Tsechansky M, Stovall GM, O'Connell JD, Mirrielees J, Ellington AD, Marcotte EM. Widespread reorganization of metabolic enzymes into reversible assemblies upon nutrient starvation. Proceedings of the National Academy of Sciences of the United States of America. 106: 10147-52. PMID 19502427 DOI: 10.1073/pnas.0812771106  0.04
2009 Lee I, Marcotte EM. Effects of functional bias on supervised learning of a gene network model. Methods in Molecular Biology (Clifton, N.J.). 541: 463-75. PMID 19381535 DOI: 10.1007/978-1-59745-243-4_20  0.04
2009 Pepin J, Vo TT, Boutros M, Marcotte E, Dial S, Dubé S, Vasilevsky CA, McFadden N, Patino C, Labbé AC. Risk factors for mortality following emergency colectomy for fulminant Clostridium difficile infection. Diseases of the Colon and Rectum. 52: 400-5. PMID 19333038 DOI: 10.1007/DCR.0b013e31819a69aa  0.01
2009 Ramakrishnan SR, Vogel C, Prince JT, Li Z, Penalva LO, Myers M, Marcotte EM, Miranker DP, Wang R. Integrating shotgun proteomics and mRNA expression data to improve protein identification. Bioinformatics (Oxford, England). 25: 1397-403. PMID 19318424 DOI: 10.1093/bioinformatics/btp168  0.04
2009 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. Journal of Proteome Research. 8: 6-19. PMID 19053807 DOI: 10.1021/pr800524g  0.04
2008 Hannay K, Marcotte EM, Vogel C. Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation. Bmc Genomics. 9: 609. PMID 19087332 DOI: 10.1186/1471-2164-9-609  0.04
2008 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. PMID 19068132 DOI: 10.1186/1471-2105-9-529  0.04
2008 Kim WK, Marcotte EM. Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence. Plos Computational Biology. 4: e1000232. PMID 19043579 DOI: 10.1371/journal.pcbi.1000232  0.04
2008 Prince JT, Marcotte EM. mspire: mass spectrometry proteomics in Ruby. Bioinformatics (Oxford, England). 24: 2796-7. PMID 18930952 DOI: 10.1093/bioinformatics/btn513  0.04
2008 Vogel C, Marcotte EM. Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data. Nature Protocols. 3: 1444-51. PMID 18772871 DOI: 10.1038/nport.2008.132  0.04
2008 Lee I, Marcotte EM. Integrating functional genomics data. Methods in Molecular Biology (Clifton, N.J.). 453: 267-78. PMID 18712309 DOI: 10.1007/978-1-60327-429-6_14  0.04
2008 Marcotte E, Sideris L, Drolet P, Mitchell A, Frenette S, Leblanc G, Leclerc YE, Dubé P. Hyperthermic intraperitoneal chemotherapy with oxaliplatin for peritoneal carcinomatosis arising from appendix: preliminary results of a survival analysis. Annals of Surgical Oncology. 15: 2701-8. PMID 18654822 DOI: 10.1245/s10434-008-0073-1  0.01
2008 Niu W, Li Z, Zhan W, Iyer VR, Marcotte EM. Mechanisms of cell cycle control revealed by a systematic and quantitative overexpression screen in S. cerevisiae. Plos Genetics. 4: e1000120. PMID 18617996 DOI: 10.1371/journal.pgen.1000120  0.04
2008 Kim WK, Krumpelman C, Marcotte EM. Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy. Genome Biology. 9: S5. PMID 18613949 DOI: 10.1186/gb-2008-9-s1-s5  0.04
2008 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, ... Marcotte EM, et al. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biology. 9: S2. PMID 18613946 DOI: 10.1186/gb-2008-9-s1-s2  0.04
2008 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 Biology. 6: e150. PMID 18593213 DOI: 10.1371/journal.pbio.0060150  0.04
2008 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. Molecular Systems Biology. 4: 180. PMID 18414481 DOI: 10.1038/msb.2008.19  0.04
2008 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. Molecular and Cellular Biology. 28: 3151-61. PMID 18332120 DOI: 10.1128/MCB.01674-07  0.04
2008 Wang R, Marcotte EM. The proteomic response of Mycobacterium smegmatis to anti-tuberculosis drugs suggests targeted pathways. Journal of Proteome Research. 7: 855-65. PMID 18275136 DOI: 10.1021/pr0703066  0.04
2007 McGary KL, Lee I, Marcotte EM. Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes. Genome Biology. 8: R258. PMID 18053250 DOI: 10.1186/gb-2007-8-12-r258  0.04
2007 Lee I, Li Z, Marcotte EM. An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae. Plos One. 2: e988. PMID 17912365 DOI: 10.1371/journal.pone.0000988  0.04
2007 Marcotte EM. How do shotgun proteomics algorithms identify proteins? Nature Biotechnology. 25: 755-7. PMID 17621303 DOI: 10.1038/nbt0707-755  0.04
2007 Hart GT, Lee I, Marcotte ER. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. Bmc Bioinformatics. 8: 236. PMID 17605818 DOI: 10.1186/1471-2105-8-236  0.04
2007 Carlson MW, Iyer VR, Marcotte EM. Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways. Bmc Genomics. 8: 117. PMID 17493265 DOI: 10.1186/1471-2164-8-117  0.04
2007 Lu P, Vogel C, Wang R, Yao X, Marcotte EM. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nature Biotechnology. 25: 117-24. PMID 17187058 DOI: 10.1038/nbt1270  0.04
2007 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. Metabolic Engineering. 9: 8-20. PMID 17049899 DOI: 10.1016/j.ymben.2006.06.003  0.04
2007 Lee I, Narayanaswamy R, Marcotte EM. 24 Bioinformatic Prediction of Yeast Gene Function Methods in Microbiology. 36: 597-628. DOI: 10.1016/S0580-9517(06)36024-2  0.04
2006 Hart GT, Ramani AK, Marcotte EM. How complete are current yeast and human protein-interaction networks? Genome Biology. 7: 120. PMID 17147767 DOI: 10.1186/gb-2006-7-11-120  0.04
2006 Prince JT, Marcotte EM. Chromatographic alignment of ESI-LC-MS proteomics data sets by ordered bijective interpolated warping. Analytical Chemistry. 78: 6140-52. PMID 16944896 DOI: 10.1021/ac0605344  0.04
2006 Zadra A, Desjardins S, Marcotte E. Evolutionary function of dreams: A test of the threat simulation theory in recurrent dreams. Consciousness and Cognition. 15: 450-63. PMID 16720254 DOI: 10.1016/j.concog.2005.02.002  0.01
2006 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 (Oxford, England). 22: 1524-31. PMID 16585069 DOI: 10.1093/bioinformatics/btl118  0.04
2006 Eisenberg D, Marcotte E, McLachlan AD, Pellegrini M. Bioinformatic challenges for the next decade(s). Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 361: 525-7. PMID 16524841 DOI: 10.1098/rstb.2005.1797  0.04
2006 Narayanaswamy R, Niu W, Scouras AD, Hart GT, Davies J, Ellington AD, Iyer VR, Marcotte EM. Systematic profiling of cellular phenotypes with spotted cell microarrays reveals mating-pheromone response genes. Genome Biology. 7: R6. PMID 16507139 DOI: 10.1186/gb-2006-7-1-r6  0.04
2006 MacKenzie R, Marcotte E, Paquette H. Perturbative approach to the adiabatic approximation Physical Review a - Atomic, Molecular, and Optical Physics. 73. DOI: 10.1103/PhysRevA.73.042104  0.01
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: 441-2. PMID 16306980 DOI: 10.1038/nature04405  0.04
2005 Wang R, Prince JT, Marcotte EM. Mass spectrometry of the M. smegmatis proteome: protein expression levels correlate with function, operons, and codon bias. Genome Research. 15: 1118-26. PMID 16077011 DOI: 10.1101/gr.3994105  0.04
2005 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: R40. PMID 15892868 DOI: 10.1186/gb-2005-6-5-r40  0.04
2005 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. Artificial Intelligence in Medicine. 33: 139-55. PMID 15811782 DOI: 10.1016/j.artmed.2004.07.016  0.04
2005 Date SV, Marcotte EM. Protein function prediction using the Protein Link EXplorer (PLEX). Bioinformatics (Oxford, England). 21: 2558-9. PMID 15701682 DOI: 10.1093/bioinformatics/bti313  0.04
2004 Lee I, Date SV, Adai AT, Marcotte EM. A probabilistic functional network of yeast genes. Science (New York, N.Y.). 306: 1555-8. PMID 15567862 DOI: 10.1126/science.1099511  0.04
2004 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 Research. 14: 2221-34. PMID 15520287 DOI: 10.1101/gr.2700304  0.04
2004 Fraser AG, Marcotte EM. Development through the eyes of functional genomics. Current Opinion in Genetics & Development. 14: 336-42. PMID 15261648 DOI: 10.1016/j.gde.2004.06.015  0.04
2004 Bork P, Jensen LJ, von Mering C, Ramani AK, Lee I, Marcotte EM. Protein interaction networks from yeast to human. Current Opinion in Structural Biology. 14: 292-9. PMID 15193308 DOI: 10.1016/  0.04
2004 Adai AT, Date SV, Wieland S, Marcotte EM. LGL: creating a map of protein function with an algorithm for visualizing very large biological networks. Journal of Molecular Biology. 340: 179-90. PMID 15184029 DOI: 10.1016/j.jmb.2004.04.047  0.04
2004 Fraser AG, Marcotte EM. A probabilistic view of gene function. Nature Genetics. 36: 559-64. PMID 15167932 DOI: 10.1038/ng1370  0.04
2004 Prince JT, Carlson MW, Wang R, Lu P, Marcotte EM. The need for a public proteomics repository. Nature Biotechnology. 22: 471-2. PMID 15085804 DOI: 10.1038/nbt0404-471  0.04
2004 McDermott J, Samudrala R, Date SV, Marcotte EM. Enhanced functional information from predicted protein networks Trends in Biotechnology. 22: 60-63. PMID 14757037 DOI: 10.1016/j.tibtech.2003.11.010  0.04
2004 Marcotte EM. Practical computational approaches to inferring protein function Drug Discovery Today: Biosilico. 2: 24-29. DOI: 10.1016/S1741-8364(04)02386-8  0.04
2003 Marcotte ER, Srivastava LK, Quirion R. cDNA microarray and proteomic approaches in the study of brain diseases: focus on schizophrenia and Alzheimer's disease. Pharmacology & Therapeutics. 100: 63-74. PMID 14550505 DOI: 10.1016/S0163-7258(03)00086-X  0.01
2003 Dhillon IS, Marcotte EM, Roshan U. Diametrical clustering for identifying anti-correlated gene clusters. Bioinformatics (Oxford, England). 19: 1612-9. PMID 12967956 DOI: 10.1093/bioinformatics/btg209  0.04
2003 Lu P, Nakorchevskiy A, Marcotte EM. Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations. Proceedings of the National Academy of Sciences of the United States of America. 100: 10370-5. PMID 12934019 DOI: 10.1073/pnas.1832361100  0.04
2003 Date SV, Marcotte EM. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nature Biotechnology. 21: 1055-62. PMID 12923548 DOI: 10.1038/nbt861  0.04
2003 Marcotte EM. Assembling a jigsaw puzzle with 20,000 parts. Genome Biology. 4: 323. PMID 12801408 DOI: 10.1186/gb-2003-4-6-323  0.04
2003 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, ... Marcotte E, et al. The genome sequence of the filamentous fungus Neurospora crassa. Nature. 422: 859-68. PMID 12712197 DOI: 10.1038/nature01554  0.04
2003 Ramani AK, Marcotte EM. Exploiting the co-evolution of interacting proteins to discover interaction specificity. Journal of Molecular Biology. 327: 273-84. PMID 12614624 DOI: 10.1016/S0022-2836(03)00114-1  0.04
2003 Marcotte EJ. Doing business with Uncle Sam Hpac Heating, Piping, Airconditioning Engineering. 75: 15-18.  0.01
2002 Marcotte CJ, Marcotte EM. Predicting functional linkages from gene fusions with confidence. Applied Bioinformatics. 1: 93-100. PMID 15130848  0.04
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