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Edward Marcotte

Research Profile

Occupations

Chemicals & Drugs

Living Beings

Saccharomyces cerevisiae

Procedures

Concepts & Ideas

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Publications

TOP 3
Cuihong Wan; Dylan Bethune-Waddell; Blake Borgeson; Vincent Fong; Pierre C Havugimana; Jian Liu; Andrew Lugowski; Edward M Marcotte; Snejana Stoilova; Andrew Emili
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.
Li Zhou; Edward M Marcotte; Rong Wang; Ang B Zhang; Christine Vogel
The proteomic response to mutants of the Escherichia coli RNA degradosome.
Yariv Wine; Daniel R Boutz; Andrew D Ellington; Kam Hon Hoi; Andrew P Horton; Randall A Hughes; Sang Taek Jung; Jason J Lavinder; Edward M Marcotte; Aleksandr E Miklos; Ellen M Murrin; George Georgiou
Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response.

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All Publications

2013: Cuihong Wan; Dylan Bethune-Waddell; Blake Borgeson; Vincent Fong; Pierre C Havugimana; Jian Liu; Andrew Lugowski; Edward M Marcotte; Snejana Stoilova; Andrew Emili
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 2013;81():102-11.
2013: Li Zhou; Edward M Marcotte; Rong Wang; Ang B Zhang; Christine Vogel
The proteomic response to mutants of the Escherichia coli RNA degradosome.
Molecular bioSystems 2013;9(4):750-7.
2013: Yariv Wine; Daniel R Boutz; Andrew D Ellington; Kam Hon Hoi; Andrew P Horton; Randall A Hughes; Sang Taek Jung; Jason J Lavinder; Edward M Marcotte; Aleksandr E Miklos; Ellen M Murrin; George Georgiou
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 2013;110(8):2993-8.
2013: U Martin Singh-Blom; Ambuj Tewari; John O Woods; Inderjit S Dhillon; Nagarajan Natarajan; Edward M Marcotte
Prediction and validation of gene-disease associations using methods inspired by social network analyses.
PloS one 2013;8(5):e58977.
2013: Alice Zhao; Lindsey Cook; Andrew D Ellington; Jagannath Swaminathan; Mark Tsechansky; Edward M Marcotte
Transiently transfected purine biosynthetic enzymes form stress bodies.
PloS one 2013;8(2):e56203.
2013: Aimee K Wessel; Taejoon Kwon; Jean Liew; Edward M Marcotte; Marvin Whiteley
Role of Pseudomonas aeruginosa peptidoglycan-associated outer membrane proteins in vesicle formation.
Journal of bacteriology 2013;195(2):213-9.
2012: Yungki Park; Edward M Marcotte
Flaws in evaluation schemes for pair-input computational predictions.
Nature methods 2012;9(12):1134-6.
2012: Rosa A Uribe; Taejoon Kwon; Edward M Marcotte; Jeffrey M Gross
Id2a functions to limit Notch pathway activity and thereby influence the transition from proliferation to differentiation of retinoblasts during zebrafish retinogenesis.
Developmental biology 2012;371(2):280-92.
2012: Pierre C Havugimana; Pingzhao Hu; Zhihua Li; Edward M Marcotte; Tamás Nepusz; Alberto Paccanaro; Sadhna Phanse; Elisabeth R M Tillier; Andrei L Turinsky; James Vlasblom; Cuihong Wan; Peggy I Wang; Shoshana J Wodak; Gabriel C Wu; Haixuan Yang; Mohan Babu; Alexandr Bezginov; Daniel R Boutz; Gregory W Clark; Stephanie A Craig; Vaqaar-un-Nisa Dar; Vincent Fong; G Traver Hart; Andrew Emili
A census of human soluble protein complexes.
Cell 2012;150(5):1068-81.
2012: Mei-I Chung; Sarah LeBoeuf; Edward M Marcotte; Kriston L McGary; Tae Joo Park; Sara M Peyrot; John B Wallingford
RFX2 is broadly required for ciliogenesis during vertebrate development.
Developmental biology 2012;363(1):155-65.
2012: Hye Ji Cha; Andrew D Ellington; Paul E Mead; John B Wallingford; Michelle Byrom; Edward M Marcotte
Evolutionarily repurposed networks reveal the well-known antifungal drug thiabendazole to be a novel vascular disrupting agent.
PLoS biology 2012;10(8):e1001379.
2012: Stephen J Orr; Thivyan Thayaparan; Rong Wang; Eric Blanc; Daniel R Boutz; Constantinos Chronis; Emma Hamilton; Nicholas C Lea; Edward M Marcotte; Hanna Milewicz; Ghulam J Mufti; N Shaun B Thomas
Proteomic and protein interaction network analysis of human T lymphocytes during cell-cycle entry.
Molecular systems biology 2012;8():573.
2011: Yungki Park; Edward M Marcotte
Revisiting the negative example sampling problem for predicting protein-protein interactions.
Bioinformatics (Oxford, England) 2011;27(21):3024-8.
2011: Taejoon Kwon; Alexey I Nesvizhskii; Christine Vogel; Hyungwon Choi; Edward M Marcotte
MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines.
Journal of proteome research 2011;10(7):2949-58.
2011: Daniel R Boutz; Patrick J Collins; Uthra Suresh; Mingzhu Lu; Cristina M Ramírez; Carlos Fernández-Hernando; Yufei Huang; Shu-Yun Le; Bruce A Shapiro; Angela M Liu; John M Luk; Nathan D Trinklein; Edward M Marcotte; Raquel de Sousa Abreu; Shelley Force Aldred; Luiz Penalva
Two-tiered approach identifies a network of cancer and liver disease-related genes regulated by miR-122.
The Journal of biological chemistry 2011;286(20):18066-78.
2011: Katherine R Smith; Esther K Kieserman; Peggy I Wang; Sander G Basten; Rachel H Giles; Edward M Marcotte; John B Wallingford
A role for central spindle proteins in cilia structure and function.
Cytoskeleton (Hoboken, N.J.) 2011;68(2):112-24.
2011: Wei Niu; G Traver Hart; Edward M Marcotte
High-throughput immunofluorescence microscopy using yeast spheroplast cell-based microarrays.
Methods in molecular biology (Clifton, N.J.) 2011;706():83-95.
2010: Jon M Laurent; Christine Vogel; Taejoon Kwon; Stephanie A Craig; Daniel R Boutz; Holly K Huse; Kazunari Nozue; Harkamal Walia; Marvin Whiteley; Pamela C Ronald; Edward M Marcotte
Protein abundances are more conserved than mRNA abundances across diverse taxa.
Proteomics 2010;10(23):4209-12.
2010: Peggy I Wang; Edward M Marcotte
It's the machine that matters: Predicting gene function and phenotype from protein networks.
Journal of proteomics 2010;73(11):2277-89.
2010: Christine Vogel; Raquel de Sousa Abreu; Daijin Ko; Shu-Yun Le; Bruce A Shapiro; Suzanne C Burns; Devraj Sandhu; Daniel R Boutz; Edward M Marcotte; Luiz Penalva
Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line.
Molecular systems biology 2010;6():400.
2010: Kai-Yin Lo; Zhihua Li; Cyril Bussiere; Stefan Bresson; Edward M Marcotte; Arlen W Johnson
Defining the pathway of cytoplasmic maturation of the 60S ribosomal subunit.
Molecular cell 2010;39(2):196-208.
2010: Kriston L McGary; Tae Joo Park; John O Woods; Hye Ji Cha; John B Wallingford; Edward M Marcotte
Systematic discovery of nonobvious human disease models through orthologous phenotypes.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(14):6544-9.
2009: Raquel de Sousa Abreu; Luiz Penalva; Edward M Marcotte; Christine Vogel
Global signatures of protein and mRNA expression levels.
Molecular bioSystems 2009;5(12):1512-26.
2009: Smriti Ramakrishnan; Christine Vogel; Taejoon Kwon; Luiz Penalva; Edward M Marcotte; Daniel P Miranker
Mining gene functional networks to improve mass-spectrometry-based protein identification.
Bioinformatics (Oxford, England) 2009;25(22):2955-61.
2009: Zhihua Li; Insuk Lee; Emily Moradi; NAI-JUNG HUNG; Arlen W Johnson; Edward M Marcotte
Rational extension of the ribosome biogenesis pathway using network-guided genetics.
PLoS biology 2009;7(10):e1000213.
2009: Ryan S Gray; Philip B Abitua; Bogdan Wlodarczyk; Heather L Szabo-Rogers; Otis Blanchard; Insuk Lee; Greg S Weiss; Karen J Liu; Edward M Marcotte; John B Wallingford; Richard H Finnell
The planar cell polarity effector Fuz is essential for targeted membrane trafficking, ciliogenesis and mouse embryonic development.
Nature cell biology 2009;11(10):1225-32.
2009: Kai-Yin Lo; Zhihua Li; Feng Wang; Edward M Marcotte; Arlen W Johnson
Ribosome stalk assembly requires the dual-specificity phosphatase Yvh1 for the exchange of Mrt4 with P0.
The Journal of cell biology 2009;186(6):849-62.
2009: Edward M Marcotte; Mark Tsechansky
Disorder, promiscuity, and toxic partnerships.
Cell 2009;138(1):16-8.
2009: Rammohan Narayanaswamy; Matthew Levy; Mark Tsechansky; Gwendolyn M Stovall; Jeremy D O'Connell; Jennifer Mirrielees; Andrew D Ellington; Edward M Marcotte
Widespread reorganization of metabolic enzymes into reversible assemblies upon nutrient starvation.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(25):10147-52.
2009: Smriti Ramakrishnan; Christine Vogel; John T Prince; Zhihua Li; Luiz Penalva; Margaret Myers; Edward M Marcotte; Daniel P Miranker; Rong Wang
Integrating shotgun proteomics and mRNA expression data to improve protein identification.
Bioinformatics (Oxford, England) 2009;25(11):1397-403.
2009: Traver Hart; Alice Zhao; Ankit Garg; Swetha Bolusani; Edward M Marcotte
Human cell chips: adapting DNA microarray spotting technology to cell-based imaging assays.
PloS one 2009;4(10):e7088.
2009: Insuk Lee; Edward M Marcotte
Effects of functional bias on supervised learning of a gene network model.
Methods in molecular biology (Clifton, N.J.) 2009;541():463-75.
2009: Rammohan Narayanaswamy; Emily K Moradi; Wei Niu; G Traver Hart; Matthew Davis; Kriston L McGary; Andrew D Ellington; Edward M Marcotte
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 2009;8(1):6-19.
2008: John T Prince; Edward M Marcotte
mspire: mass spectrometry proteomics in Ruby.
Bioinformatics (Oxford, England) 2008;24(23):2796-7.
2008: Wan Kyu Kim; Edward M Marcotte
Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence.
PLoS computational biology 2008;4(11):e1000232.
2008: Wei Niu; Zhihua Li; Wenjing Zhan; Vishwanath R Iyer; Edward M Marcotte
Mechanisms of cell cycle control revealed by a systematic and quantitative overexpression screen in S. cerevisiae.
PLoS genetics 2008;4(7):e1000120.
2008: Junhua Zhao; Wei Niu; Jun Yao; Sabine Mohr; Edward M Marcotte; Alan M Lambowitz
Group II intron protein localization and insertion sites are affected by polyphosphate.
PLoS biology 2008;6(6):e150.
2008: Joshua White; Zhihua Li; Richa Sardana; Janusz Bujnicki; Edward M Marcotte; Arlen W Johnson
Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits.
Molecular and cellular biology 2008;28(10):3151-61.
2008: Rong Wang; Edward M Marcotte
The proteomic response of Mycobacterium smegmatis to anti-tuberculosis drugs suggests targeted pathways.
Journal of proteome research 2008;7(3):855-65.
2008: Insuk Lee; Ben Lehner; Catriona Crombie; Wendy Wong; Andrew G Fraser; Edward M Marcotte
A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans.
Nature genetics 2008;40(2):181-8.
2008: Kevin Hannay; Edward M Marcotte; Christine Vogel
Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation.
BMC genomics 2008;9():609.
2008: Christine Vogel; Edward M Marcotte
Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.
Nature protocols 2008;3(9):1444-51.
2008: Insuk Lee; Edward M Marcotte
Integrating functional genomics data.
Methods in molecular biology (Clifton, N.J.) 2008;453():267-78.
2008: Wan Kyu Kim; Chase Krumpelman; Edward M Marcotte
Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy.
Genome biology 2008;9 Suppl 1():S5.
2008: Arun K Ramani; Zhihua Li; G Traver Hart; Mark W Carlson; Daniel R Boutz; Edward M Marcotte
A map of human protein interactions derived from co-expression of human mRNAs and their orthologs.
Molecular systems biology 2008;4():180.
2007: Edward M Marcotte
How do shotgun proteomics algorithms identify proteins?
Nature biotechnology 2007;25(7):755-7.
2007: Kriston L McGary; Insuk Lee; Edward M Marcotte
Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes.
Genome biology 2007;8(12):R258.
2007: Insuk Lee; Zhihua Li; Edward M Marcotte
An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae.
PloS one 2007;2(10):e988.
2007: Mark W Carlson; Vishwanath R Iyer; Edward M Marcotte
Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways.
BMC genomics 2007;8():117.
2007: Peng Lu; Christine Vogel; Rong Wang; Xin Yao; Edward M Marcotte
Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation.
Nature biotechnology 2007;25(1):117-24.
2006: John T Prince; Edward M Marcotte
Chromatographic alignment of ESI-LC-MS proteomics data sets by ordered bijective interpolated warping.
Analytical chemistry 2006;78(17):6140-52.
2006: Smriti Ramakrishnan; Rui Mao; Aleksey A Nakorchevskiy; John T Prince; Willard S Willard; Weijia Xu; Edward M Marcotte; Daniel P Miranker
A fast coarse filtering method for peptide identification by mass spectrometry.
Bioinformatics (Oxford, England) 2006;22(12):1524-31.
2006: G Traver Hart; Arun K Ramani; Edward M Marcotte
How complete are current yeast and human protein-interaction networks?
Genome biology 2006;7(11):120.
2006: Rammohan Narayanaswamy; Wei Niu; Alexander D Scouras; G Traver Hart; Jonathan Davies; Andrew D Ellington; Vishwanath R Iyer; Edward M Marcotte
Systematic profiling of cellular phenotypes with spotted cell microarrays reveals mating-pheromone response genes.
Genome biology 2006;7(1):R6.
2005: Rong Wang; John T Prince; Edward M Marcotte
Mass spectrometry of the M. smegmatis proteome: protein expression levels correlate with function, operons, and codon bias.
Genome research 2005;15(8):1118-26.
2005: Shailesh V Date; Edward M Marcotte
Protein function prediction using the Protein Link EXplorer (PLEX).
Bioinformatics (Oxford, England) 2005;21(10):2558-9.
2005: Razvan Bunescu; Ruifang Ge; Rohit J Kate; Edward M Marcotte; Raymond J Mooney; Arun K Ramani; Yuk Wah Wong
Comparative experiments on learning information extractors for proteins and their interactions.
Artificial intelligence in medicine 2005;33(2):139-55.
2005: Arun K Ramani; Razvan C Bunescu; Raymond J Mooney; Edward M Marcotte
Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome.
Genome biology 2005;6(5):R40.
2004: Insuk Lee; Shailesh V Date; Alex T Adai; Edward M Marcotte
A probabilistic functional network of yeast genes.
Science (New York, N.Y.) 2004;306(5701):1555-8.
2004: Nitin S Baliga; Richard Bonneau; Marc T Facciotti; Min Pan; Gustavo Glusman; Eric Deutsch; Paul Shannon; Yulun Chiu; Rueyhung Sting Weng; Rueichi Richie Gan; Pingliang Hung; Shailesh V Date; Edward M Marcotte; Leroy Hood; Wailap Victor Ng
Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea.
Genome research 2004;14(11):2221-34.
2004: Alex T Adai; Shailesh V Date; Shannon Wieland; Edward M Marcotte
LGL: creating a map of protein function with an algorithm for visualizing very large biological networks.
Journal of molecular biology 2004;340(1):179-90.
2004: Peer Bork; Lars Jensen; Christian von Mering; Arun K Ramani; Insuk Lee; Edward M Marcotte
Protein interaction networks from yeast to human.
Current opinion in structural biology 2004;14(3):292-9.
2004: John T Prince; Mark W Carlson; Rong Wang; Peng Lu; Edward M Marcotte
The need for a public proteomics repository.
Nature biotechnology 2004;22(4):471-2.
2003: Peng Lu; Aleksey Nakorchevskiy; Edward M Marcotte
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 2003;100(18):10370-5.
2003: Inderjit S Dhillon; Edward M Marcotte; Usman Roshan
Diametrical clustering for identifying anti-correlated gene clusters.
Bioinformatics (Oxford, England) 2003;19(13):1612-9.
2003: Shailesh V Date; Edward M Marcotte
Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages.
Nature biotechnology 2003;21(9):1055-62.
2003: Arun K Ramani; Edward M Marcotte
Exploiting the co-evolution of interacting proteins to discover interaction specificity.
Journal of molecular biology 2003;327(1):273-84.
2003: Edward M Marcotte
Assembling a jigsaw puzzle with 20,000 parts.
Genome biology 2003;4(6):323.
2001: Edward M Marcotte
Measuring the dynamics of the proteome.
Genome research 2001;11(2):191-3.