Difference between revisions of "Publication"

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(Created page with '2008 Hannay K, Marcotte EM, Vogel C. Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation. BMC Genomics 2008, 9:609. PDF of pre-pri...')
 
(2020)
 
(540 intermediate revisions by 3 users not shown)
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2008
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== 2020 ==
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<ol>
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<li value="214"> {{Paper
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|title=Systematic Identification of Protein Phosphorylation-Mediated Interactions
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|authors=Floyd BM, Drew K, Marcotte EM
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|journal=bioRxiv
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|pub_year=2020
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|volume=Posted September 19
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|page=
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|link=https://doi.org/10.1101/2020.09.18.304121
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|pubmed=
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}}
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<li value="213"> {{Paper
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|title=hu.MAP 2.0: Integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies
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|authors=Drew K, Wallingford JB, Marcotte EM
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|journal=bioRxiv
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|pub_year=2020
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|volume=Posted September 16
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|page=
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|link=https://doi.org/10.1101/2020.09.15.298216
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|pubmed=
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}}
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<li value="212"> {{Paper
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|title=Antifungal benzimidazoles disrupt vasculature by targeting one of nine β-tubulins
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|authors=Garge RK, Cha HJ, Lee, C, Gollihar JD, Kachroo AH, Wallingford JB, Marcotte EM
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|journal=bioRxiv
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|pub_year=2020
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|volume=Posted September 15
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|page=
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|link=https://doi.org/10.1101/2020.09.15.298828
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|pubmed=
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}}
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<li value="211"> {{Paper
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|title=Twinfilin1 controls lamellipodial protrusive activity and actin turnover during vertebrate gastrulation
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|authors=Devitt C, Lee C, Cox R, Papoulas O, Alvarado J, Marcotte EM, Wallingford JB
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|journal=bioRxiv
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|pub_year=2020
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|volume=Posted September 3
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|page=
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|link=https://doi.org/10.1101/2020.09.03.281659
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|pubmed=
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}}
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<li value="210"> {{Paper
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|title=Next-Generation TLC: A Quantitative Platform for Parallel Spotting and Imaging
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|authors=Boulgakov AA, Moor SR, Jo HH, Metola P, Joyce LA, Marcotte EM, Welch CJ, Anslyn EV
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|journal=J Org Chem
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|pub_year=2020
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|volume=85(15)
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|page=9447–9453
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|link=https://doi.org/10.1021/acs.joc.0c00349
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|comment=[[File:JOC-TLCCover2020.jpg||100px|right]]
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|pubmed=32559382
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}}
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<li value="209"> {{Paper
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|title=Systematic humanization of the yeast cytoskeleton discerns functionally replaceable from divergent human genes
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|authors=Garge RK, Laurent JM, Kachroo AH, Marcotte EM
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|journal=Genetics
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|pub_year=2020
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|volume=215(4)
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|pubmed=32522745
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|page=1153-1169
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|comment=[https://doi.org/10.1101/2019.12.16.878751 bioRxiv preprint] Deposited December 17, 2019 [[File:GeneticsHumanizedYeastCover2020.jpg||100px|right]]
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}}
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<li value="208"> {{Paper
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|title=Humanization of yeast genes with multiple human orthologs reveals principles of functional divergence between paralogs
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|authors=Laurent J, Garge RK, Teufel AI, Wilke CO, Kachroo AH, Marcotte EM
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|journal=PLoS Biology
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|pub_year=2020
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|volume=18(5)
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|page=e3000627
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|link=https://doi.org/10.1371/journal.pbio.3000627
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|pubmed=32421706
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|comment=[https://www.biorxiv.org/content/10.1101/668335v1 bioRxiv preprint] (deposited June 13, 2019)
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}}
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<li value="207"> {{Paper
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|title=Functional partitioning of a liquid-like organelle during assembly of axonemal dyneins
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|authors=Lee C, Cox RM, Papoulas O, Horani A, Drew K, Devitt CC, Brody SL, Marcotte EM, Wallingford JB
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|journal=eLife
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|pub_year=2020
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|volume=9
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|pubmed=
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|page=e58662
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|link=https://doi.org/10.7554/eLife.58662
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|comment=[https://doi.org/10.1101/2020.04.21.052837 bioRxiv preprint] (deposited April 21, 2020)
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}}
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<li value="206"> {{Paper
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|title=A pan-plant protein complex map reveals deep conservation and novel assemblies
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|authors=McWhite CD, Papoulas O, Drew K, Cox RM, June V, Dong OX, Kwon T, Wan C, Salmi ML, Roux, SJ Jr., Browning KS, Chen ZJ, Ronald PC, Marcotte EM
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|journal=Cell
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|pub_year=2020
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|volume=181(2)
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|pubmed=32191846
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|page=460-474.e14
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|comment=[https://doi.org/10.1101/815837 bioRxiv preprint] (deposited October 24, 2019)
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|link=https://doi.org/10.1016/j.cell.2020.02.049
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|pdf=Cell_PlantComplexes_2020.pdf
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}}
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<li value="205"> {{Paper
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|title=Structural Biology in the Multi-Omics Era
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|authors=McCafferty C, Verbeke EJ, Marcotte EM, Taylor DW
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|journal=Journal of Chemical Information and Modeling
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|pub_year=2020
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|volume=60(5)
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|pubmed=32129623
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|page=2424-2429
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|link=https://doi.org/10.1021/acs.jcim.9b01164
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|comment=[[File:JCIMShotgunEMCover2020.jpg||100px|right]]
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|pdf=JChemInfModel_Structural-Omics_2020.pdf
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}}
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<li value="204"> {{Paper
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|title=Abundances of transcripts, proteins, and metabolites in the cell cycle of budding yeast reveals coordinate control of lipid metabolism
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|authors=Blank HM, Papoulas O, Maitra N, Garge RK, Kennedy BK, Schilling B, Marcotte EM, Polymenis M
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|journal=Molecular Biology of the Cell
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|pub_year=2020
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|volume=Published online 4 Mar
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|pubmed=32129706
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|page=
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|link=https://www.molbiolcell.org/doi/abs/10.1091/mbc.E19-12-0708
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|comment=[https://doi.org/10.1101/2019.12.17.880252 bioRxiv preprint] (deposited Dec 18, 2019)
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|pdf=MolBiolCell_YeastCellCycle_2020.pdf
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}}
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<li value="203"> {{Paper
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|title=A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating
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|authors=Drew K, Lee C, Cox RM, Dang V, Devitt CC, Papoulas O, Huizar RL, Marcotte EM, Wallingford JB
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|journal=Developmental Biology
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|pub_year=2020
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|volume=467(1-2)
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|comment=[https://doi.org/10.1101/2020.02.26.966754 bioRxiv preprint] (deposited Feb 27, 2020)
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|link=https://www.sciencedirect.com/science/article/abs/pii/S0012160620302293
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|pubmed=32898505
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|page=108-117
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}}
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</li>
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<li value="202"> {{Paper
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|title=Mapping functional protein neighborhoods in the mouse brain
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|authors=Liebeskind BJ, Young RL, Halling DB, Aldrich RW, Marcotte EM
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|journal=bioRxiv
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|pub_year=2020
 +
|volume=Posted January 27
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|link=https://doi.org/10.1101/2020.01.26.920447
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|pubmed=
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|page=
 +
}}
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</li>
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<li value="201"> {{Paper
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|title= Solid-phase peptide capture and release for bulk and single-molecule proteomics
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|authors=Howard CJ, Floyd Bm, Bardo AM, Swaminathan J, Marcotte EM, Anslyn EV
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|journal=ACS Chemical Biology
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|pub_year=2020
 +
|volume=15(6)
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|link=https://doi.org/10.1021/acschembio.0c00040
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|comment=[https://doi.org/10.1101/2020.01.13.904540 bioRxiv preprint] (deposited January 14, 2020)
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|pubmed=32363853
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|page=1401-1407
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}}
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</li>
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<li value="200"> {{Paper
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|title=Separating distinct structures of multiple macromolecular assemblies from cryo-EM projections
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|authors=Verbeke E, Zhou Y, Horton AP, Mallam AL, Taylor DW, Marcotte EM
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|journal=Journal of Structural Biology
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|pub_year=2020
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|volume=209(1)
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|link=https://doi.org/10.1016/j.jsb.2019.107416
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|pubmed=31726096
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|page=107416
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|pdf=JStructBiol_SLICEM_2019.pdf
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|link=https://doi.org/10.1016/j.jsb.2019.107416
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|comment=[https://github.com/marcottelab/SLICEM SLICEM code on Github] [https://www.biorxiv.org/content/10.1101/611566v1 bioRxiv preprint] (deposited Apr 20, 2019)
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}}
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<li value="199"> {{Paper
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|title=Synthesis of Carboxy ATTO 647N Using Redox Cycling for Xanthone Access
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|authors=Bachman JL, Pavlich CI, Boley AJ, Marcotte EM, Anslyn EV
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|journal=Org Lett
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|pub_year=2020
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|volume=22(2)
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|link=https://doi.org/10.1021/acs.orglett.9b03981
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|pubmed=31825225
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|page=381-385
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|pdf=OrganicLetters_Atto647N_2019.pdf
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|link=https://pubs.acs.org/doi/10.1021/acs.orglett.9b03981
 +
}}
 +
</li>
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</ol>
  
  Hannay K, Marcotte EM, Vogel C. Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation. BMC Genomics 2008, 9:609.
+
== 2019 ==
PDF of pre-print
+
<ol>
 +
<li value="198"> {{Paper
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|title=Simplified geometric representations of protein structures identify complementary interaction interfaces
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|authors=McCaffery CL, Marcotte EM, Taylor DW
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|journal=Proteins: Structure, Function, and Bioinformatics
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|pub_year=2020
 +
|volume=posted November 2
 +
|pubmed=33140424
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|page=1-13
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|link= https://doi.org/10.1002/prot.26020
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|comment=[https://doi.org/10.1101/2019.12.18.880575 bioRxiv preprint] (deposited Dec 23, 2019)
 +
}}
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<li value="197"> {{Paper
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|title=Systematic bromodomain protein screens identify homologous recombination and R-loop suppression pathways involved in genome integrity
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|authors=Kim JJ, Lee SY, Gong F, Battenhouse AM, Boutz DR, Bashyal A, Refvik ST, Chiang CM, Xhemalce B, Paull TT, Brodbelt JS, Marcotte EM, Miller KM
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|journal=Genes and Development
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|pub_year=2019
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|volume=33(23-24)
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|pubmed=31753913
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|page=1751-1774
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|pdf=GenesDev_Bromodomains_2019.pdf
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|link=https://doi.org/10.1101/gad.331231.119
 +
}}
 +
<li value="196"> {{Paper
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|title=Systematic discovery of endogenous human ribonucleoprotein complexes
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|authors=Mallam AL, Sae-Lee W, Schaub JM, Tu F, Battenhouse A, Jang YJ, Kim J, Finkelstein IJ, Marcotte EM, Drew K
 +
|journal=Cell Reports
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|pub_year=2019
 +
|volume=29(5)
 +
|page=P1351-1368.e5
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|pubmed=31665645
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|pdf=CellReports_DIFFRAC_2019.pdf
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|link=https://doi.org/10.1016/j.celrep.2019.09.060
 +
|comment=[https://www.biorxiv.org/content/early/2018/11/27/480061 bioRxiv preprint] (deposited Nov 27, 2018)
 +
}}
 +
<li value="195"> {{Paper
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|title=Ancestral Reconstruction of Protein Interaction Networks
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|authors=Liebeskind B, Aldrich RW, Marcotte EM
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|journal=PLoS Computational Biology
 +
|pub_year=2019
 +
|volume=15(10)
 +
|page=e1007396
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|pubmed=31658251
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|pdf=PLoSComputationalBiology_AncestralPPIs_2019.pdf
 +
|link= https://doi.org/10.1371/journal.pcbi.1007396
 +
|comment=[https://doi.org/10.1101/408773 bioRxiv preprint] (deposited September 9, 2018)
 +
}}
 +
<li value="194"> {{Paper
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|title=Advances and Applications in the Quest for Orthologs.
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|authors=Glover N, Dessimoz C, Ebersberger I, Forslund SK, Gabaldón T, Huerta-Cepas J, Martin MJ, Muffato M, Patricio M, Pereira C, Sousa da Silva A, Wang Y, Sonnhammer E, Thomas PD; Quest for Orthologs Consortium
 +
|journal=Mol Biol Evol
 +
|pub_year=2019
 +
|volume=36(10)
 +
|page=2157-2164
 +
|pdf=MolBiolEvol_QfO_2019.pdf
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|link=https://doi.org/10.1093/molbev/msz150
 +
|pubmed=31241141
 +
}}
 +
<li value="193"> {{Paper
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|title=Bringing Microscopy-By-Sequencing into View
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|authors=Boulgakov AA, Ellington AD, Marcotte EM
 +
|journal=Trends in Biotechnology
 +
|pub_year=available online 2019, published 2020
 +
|volume=38(2)
 +
|page=154-162
 +
|pubmed=31416630
 +
|pdf=TIBTech_DNAmicroscopy_2020.pdf
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|link=https://doi.org/10.1016/j.tibtech.2019.06.001
 +
|comment=[[File:TIBTechCover2020.jpg||100px|right]]
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}}
 +
</li>
 +
</ol>
  
  Braisted JC, Kuntumalla S, Vogel C, Marcotte EM, Rodrigues AR, Wang R, Huang S-T, 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 2008, in press.
+
== 2018 ==
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<ol>
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<li value="192"> {{Paper
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|title=Paternal chromosome loss and metabolic crisis contribute to hybrid inviability in ''Xenopus''
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|authors=Gibeaux R, Acker R, Kitaoka M, Georgiou G, van Kruijsbergen I, Ford B, Marcotte EM, Nomura DK, Kwon T, Veenstra GJC, Heald R
 +
|journal=Nature
 +
|volume=553
 +
|page=337–341
 +
|pubmed=29320479
 +
|pub_year=2018
 +
|pdf=Nature_XenopusHybridInviability_2017.pdf
 +
|link=http://dx.doi.org/10.1038/nature25188
 +
}}
 +
<li value="191"> {{Paper
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|title=A liquid-like organelle at the root of motile ciliopathy
 +
|authors=Huizar RL, Lee C, Boulgakov AA, Horani A, Tu F, Marcotte EM, Brody SL, Wallingford JB
 +
|journal=eLife
 +
|pub_year=2018
 +
|comment=[https://doi.org/10.1101/213793 bioRxiv preprint (Deposited Nov 3, 2017)]
 +
|volume=7
 +
|pubmed=30561330
 +
|page=e38497
 +
|pdf=eLife_DynAPs_2018.pdf
 +
|link=https://doi.org/10.7554/eLife.38497
 +
}}
 +
<li value="190"> {{Paper
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|title=From Space to Sequence and Back Again: Iterative DNA Proximity Ligation and its Applications to DNA-Based Imaging
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|authors=Boulgakov AA, Xiong E, Bhadra S, Ellington AD, Marcotte EM
 +
|journal=bioRxiv
 +
|pub_year=2018
 +
|volume=posted November 14
 +
|page=
 +
|link=https://doi.org/10.1101/470211
 +
}}
 +
<li value="189"> {{Paper
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|title=HumanNet v2: human gene networks for disease research
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|authors=Hwang S, Kim CY, Yang S, Kim E, Hart T, Marcotte EM, Lee I
 +
|journal=Nucleic Acids Res
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|pub_year=2018,2019
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|volume=47 (D1)
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|page=D573–D580
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|pdf=NAR_HumanNet2_2018.pdf
 +
|link=https://doi.org/10.1093/nar/gky1126
 +
|pubmed=30418591
 +
}}
 +
<li value="188"> {{Paper
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|title=Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures
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|authors=Swaminathan J, Boulgakov AA, Hernandez ET, Bardo AM, Bachman JL, Marotta J, Johnson AM, Anslyn EV, Marcotte EM
 +
|journal=Nature Biotechnology
 +
|pub_year=2018
 +
|volume=36
 +
|page=1076–1082
 +
|pubmed=30346938
 +
|pdf=NatureBiotechnology_Fluorosequencing_2018.pdf
 +
|link=https://doi.org/10.1038/nbt.4278
 +
|comment=[https://rdcu.be/9Pjj Free access authors' view-only version at NBT] [http://www.marcottelab.org/paper-pdfs/NatureBiotechnology_Fluorosequencing_2018_Supplement.pdf Supplement] [http://www.marcottelab.org/paper-pdfs/NatureBiotechnology_Fluorosequencing_2018_SupplementaryTables.pdf Supplementary Tables] [https://github.com/marcottelab/FluorosequencingImageAnalysis/ github with code] [http://doi.org/10.5281/zenodo.782860 Data repository (Zenodo)] [http://www.marcottelab.org/paper-pdfs/NatureBiotechnology_Fluorosequencing_2018_NewsAndViews-CollinsAebsersold.pdf News & Views] Commentary in [https://phys.org/news/2018-10-protein-sequencing-method-biological.html Phys.org] 
 +
}}
 +
<li value="187"> {{Paper
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|title=The many nuanced evolutionary consequences of duplicated genes
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|authors=Teufel AI, Johnson MM, Laurent JM, Kachroo AH, Marcotte EM, Wilke CO
 +
|journal=Mol Bio Evol
 +
|pub_year=2018
 +
|volume=36(2)
 +
|page=304-314
 +
|pdf=MolBiolEvol_Teufel_2018.pdf
 +
|link=https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msy210
 +
|comment = [https://doi.org/10.1101/366971 bioRxiv preprint] (deposited July 10, 2018)
 +
|pubmed=30428072
 +
}}
 +
<li value="186"> {{Paper
 +
|title=Photography Coupled with Self-Propagating Chemical Cascades. The Differentiation and Quantitation of G and V Nerve Agent Mimics via Chromaticity
 +
|authors=Sun X, Boulgakov AA, Smith L, Metola P, Marcotte EM, Anslyn EV
 +
|journal=ACS Central Science
 +
|volume=4(7)
 +
|page=854-861
 +
|pubmed=30062113
 +
|pub_year=2018
 +
|pdf=ACSCentralScience_LegoNerveGas_2018.pdf
 +
|link=https://pubs.acs.org/doi/10.1021/acscentsci.8b00193
 +
}}
 +
<li value="185"> {{Paper
 +
|title=Classification of single particles from human cell extract reveals distinct structures
 +
|authors=Verbeke EJ, Mallam AL, Drew K, Marcotte EM, Taylor DW
 +
|journal=Cell Reports
 +
|volume=(24)1
 +
|page=259–268.e3
 +
|link=https://doi.org/10.1016/j.celrep.2018.06.022
 +
|pubmed=29972786
 +
|pdf=CellReports_ShotgunEM_2018.pdf
 +
|pub_year=2018
 +
|comment = [https://www.biorxiv.org/content/early/2018/01/14/247254 bioRxiv preprint] (deposited January 14 , 2018)
 +
}}
 +
<li value="184"> {{Paper
 +
|title=Single-step precision genome editing in yeast using CRISPR-Cas9   
 +
|authors= Akhmetov A, Laurent JM, Gollihar J, Gardner EC, Garge RK, Ellington AD, Kachroo AH, Marcotte EM   
 +
|journal=Bio-protocol
 +
|volume=8(6)
 +
|page=e2765
 +
|pubmed=29770349
 +
|pub_year=2018
 +
|pdf=Bio-protocol_YeastCRISPR_2018.pdf
 +
|link=http://dx.doi.org/10.21769/BioProtoc.2765
 +
}}
 +
</li>
 +
<li value="183"> {{Paper
 +
|title=Protein localization screening in vivo reveals novel regulators of multiciliated cell development and function
 +
|authors=Tu F, Sedzinski J, Ma Y, Marcotte EM, Wallingford JB
 +
|journal=J Cell Sci
 +
|volume=131 (3)
 +
|page=jcs206565
 +
|pubmed=29180514
 +
|pub_year=2018
 +
|pdf=JCellSci_CiliaScreen_2018.pdf
 +
|link=http://jcs.biologists.org/content/131/3/jcs206565
 +
|comment=[[File:JCSCiliaCover2018.jpg||100px|right]]
 +
}}
 +
</li>
 +
</ol>
  
  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. 2008, in press.
+
== 2017 ==
PDF
+
<ol>
 +
<li value="182"> {{Paper
 +
|title=Solution-phase and solid-phase sequential, selective modification of side chains in KDYWEC and KDYWE as models for usage in single-molecule protein sequencing
 +
|authors=Hernandez ET, Swaminathan J, Marcotte EM , Anslyn EV
 +
|journal=New Journal of Chemistry
 +
|pubmed=
 +
|volume=41
 +
|page=462-469
 +
|link=http://dx.doi.org/10.1039/C6NJ02932A
 +
|pub_year=2017
 +
|pdf=NewJChem_PeptideLabeling_2017.pdf
 +
|comment=[[File:NJCPeptideLabelingCover2017.jpg||100px|right]]
 +
}}
 +
<li value="181"> {{Paper
 +
|title=Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets
 +
|authors=Drew K, Müller CL, Bonneau R, Marcotte EM
 +
|journal=PLoS Computational Biology
 +
|volume=13(10)
 +
|page=e1005625
 +
|pubmed=29023445
 +
|pub_year=2017
 +
|pdf=PLoSComputationalBiology-ConditionalDependencePPIs-2017.pdf
 +
|link=https://doi.org/10.1371/journal.pcbi.1005625
 +
}}
 +
<li value="180"> {{Paper
 +
|title=Metabolic crosstalk regulates ''Porphyromonas gingivalis'' colonization and virulence during oral polymicrobial infection
 +
|authors=Kuboniwa M, Houser JR, Hendrickson EL, Wang Q, Alghamdi SA, Sakanaka A, Miller DP, Hutcherson JA, Wang T, Beck DAC, Whiteley M, Amano A, Wang H, Marcotte EM, Hackett M, Lamont RJ
 +
|journal=Nature Microbiology
 +
|volume=2
 +
|page=1493–1499
 +
|pubmed=28924191
 +
|pub_year=2017
 +
|pdf=NatureMicrobiology_PolymicrobialInfection_2017.pdf
 +
|link=https://doi.org/10.1038/s41564-017-0021-6
 +
}}
 +
<li value="179"> {{Paper
 +
|title=Systematic bacterialization of yeast genes identifies a near-universally swappable pathway
 +
|authors=Kachroo AH, Laurent JM, Akhmetov A, Szilagyi-Jones M, McWhite CD, Zhao A, Marcotte EM
 +
|journal=eLife
 +
|volume=6
 +
|page=e25093
 +
|pubmed=28661399
 +
|pub_year=2017
 +
|pdf=eLife_BacterializedYeast_2017.pdf
 +
|link=https://doi.org/10.7554/eLife.25093
 +
}}
 +
<li value="178"> {{Paper
 +
|title=A highly parallel strategy for storage of digital information in living cells
 +
|authors=Akhmetov A, Ellington A, Marcotte E
 +
|journal=BMC Biotechnology
 +
|volume=18
 +
|page=64
 +
|pdf=bioRxiv_DigitalDNAStorage_2016.pdf
 +
|pub_year=2018
 +
|comment = [https://doi.org/10.1101/096792 bioRxiv preprint (deposited December 26, 2016)] [https://rdcu.be/9u6Y Open access pdf version of the article]
 +
|link=https://doi.org/10.1186/s12896-018-0476-4
 +
}}
 +
<li value="177"> {{Paper
 +
|title=Systems-wide studies uncover Commander, a multiprotein complex essential to human development
 +
|authors=Mallam A, Marcotte EM
 +
|journal=Cell Systems
 +
|volume=4
 +
|page=483-494
 +
|link=http://www.cell.com/cell-systems/abstract/S2405-4712(17)30138-2
 +
|pdf=CellSystems_Commander_2017.pdf
 +
|pub_year=2017
 +
}}
 +
<li value="176"> {{Paper
 +
|title=Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes
 +
|authors=Drew, K., Lee, C., Huizar, R. L., Tu, F., Borgeson, B., McWhite, C. D., Ma, Y., Wallingford, J. B., Marcotte, E. M.
 +
|journal=Molecular Systems Biology
 +
|page=932
 +
|volume=13
 +
|pubmed=28596423
 +
|link=http://msb.embopress.org/content/13/6/932
 +
|pdf=MolecularSystemsBiology_2017_HuMap.pdf
 +
|comment = [https://doi.org/10.1101/092361 bioRxiv preprint (deposited December 7, 2016)] [[File:MSBHuMAPCover2018.jpg||100px|right]]
 +
|pub_year=2017
 +
}}
 +
<li value="175"> {{Paper
 +
|title=GWAB: a web server for the network-based boosting of human genome-wide association data
 +
|authors=Shim JE, Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom UM, Marcotte EM, Lee I
 +
|journal=Nucleic Acids Research
 +
|pubmed=28449091
 +
|volume=89(6)
 +
|page=3747–3753
 +
|link=http://dx.doi.org/10.1093/nar/gkx284
 +
|pub_year=2017
 +
|pdf=NAR_GWAB_2017.pdf
 +
}}
 +
<li value="174"> {{Paper
 +
|title=The ''E. coli'' molecular phenotype under different growth conditions
 +
|authors=Caglar MU, Houser JR, Barnhart CS, Boutz DR, Carroll SM, Dasgupta A, Lenoir WF, Smith BL, Sridhara V, Sydykova DK, Vander Wood D, Marx CJ, Marcotte EM, Barrick JE, Wilke CO
 +
|journal=Scientific Reports
 +
|pubmed=28417974
 +
|volume=7
 +
|page=45303
 +
|link=http://dx.doi.org/10.1038/srep45303
 +
|pub_year=2017
 +
|pdf=ScientificReports_EcoliMolecularPhenotype_2017.pdf
 +
}}
 +
<li value="173"> {{Paper
 +
|title=Large-scale analysis of post-translational modifications in ''E. coli'' under glucose-limiting conditions
 +
|authors=Brown CW, Sridhara V, Boutz DR, Person MD, Marcotte EM, Barrick JE, Wilke CO
 +
|journal=BMC Genomics
 +
|pubmed=28412930
 +
|volume=18(1)
 +
|page=301
 +
|link=http://dx.doi.org/10.1186/s12864-017-3676-8
 +
|pub_year=2017
 +
|pdf=BMCGenomics_EcoliPTMs_2017.pdf
 +
}}
 +
<li value="172"> {{Paper
 +
|title=Comprehensive de novo peptide sequencing from MS/MS pairs generated through complementary collision induced dissociation and 351 nm ultraviolet photodissociation
 +
|authors=AP Horton, SA Robotham, JR Cannon, DD Holden, EM Marcotte, Brodbelt JS
 +
|journal=Analytical Chemistry
 +
|pubmed=28234449
 +
|volume=89(6)
 +
|page=3747–3753
 +
|link=http://dx.doi.org/10.1021/acs.analchem.7b00130
 +
|pub_year=2017
 +
|pdf=AnalyticalChemistry_UVnovo2_2017.pdf
 +
}}
 +
<li value="171"> {{Paper
 +
|title=WheatNet: A genome-scale functional network for hexaploid bread wheat, ''Triticum aestivum''
 +
|authors=Lee T, Hwang S, Kim CY, Shim H, Kim H, Ronald PC, Marcotte EM, Lee I
 +
|journal=Molecular Plant
 +
|pubmed=28450181
 +
|volume=S1674-2052(17)
 +
|page=30108-9
 +
|link=http://dx.doi.org/10.1016/j.molp.2017.04.006
 +
|pdf=MolPlant_WheatNet_2017.pdf
 +
|pub_year=2017
 +
|comment = [http://dx.doi.org/10.1101/105098 bioRxiv preprint (deposited February 6, 2017)]
 +
}}
 +
<li value="170"> {{Paper
 +
|title=Murine Cytomegalovirus Deubiquitinase Regulates Viral Chemokine Levels To Control Inflammation and Pathogenesis
 +
|authors=Hilterbrand AT, Boutz DR, Marcotte EM, Upton JW
 +
|journal=mBio
 +
|pubmed=28096485
 +
|volume=8
 +
|page=e01864-16
 +
|link=http://dx.doi.org/10.1128/mBio.01864-16
 +
|pub_year=2017
 +
|pdf=mBio_CMBdeubiquitinase_2017.pdf
 +
}}
 +
</li>
 +
</ol>
  
  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 2008, 4(11): e1000232.
+
== 2016 ==
PDF
+
<ol>
 +
<li value="169"> {{Paper
 +
|title=Computational Discovery of Pathway-Level Genetic Vulnerabilities in Non-Small-Cell Lung Cancer
 +
|authors=Young JH, Peyton M, Kim HS, McMillan E, Minna JD, White MA, Marcotte EM
 +
|journal=Bioinformatics
 +
|pubmed=26755624
 +
|volume=32(9)
 +
|link=http://dx.doi.org/10.1093/bioinformatics/btw010
 +
|page=1373-9
 +
|pdf=Bioinformatics_LungCancer_2016.pdf
 +
|comment = [https://bitbucket.org/youngjh/nsclc_paper Supporting code]
 +
|pub_year=2016
 +
}}
 +
<li value="168"> {{Paper
 +
|title=Molecular-level analysis of the serum antibody repertoire in young adults before and after seasonal influenza vaccination
 +
|authors=Lee J, Boutz DR, Chromikova V, Joyce MG, Vollmers C, Leung K, Horton AP, DeKosky BJ, Lee CH, Lavinder JJ, Murrin EM, Chrysostomou C, Hoi KH, Tsybovsky Y, Thomas PV, Druz A, Zhang B, Zhang Y, Wang L, Kong WP, Park D, Popova LI, Dekker CL, Davis MM, Carter CE, Ross TM, Ellington AD, Wilson PC, Marcotte EM, Mascola JR, Ippolito GC, Krammer F, Quake SR, Kwong PD, Georgiou G
 +
|journal=Nature Medicine
 +
|pubmed=27820605
 +
|volume=22(12)
 +
|page=1456-1464
 +
|pdf=NatureMedicine_FluIgGSeq_2016.pdf
 +
|link=http://dx.doi.org/10.1038/nm.4224
 +
|comment=[[File:NatureMedicineIgSeqCover2016.jpg||100px|right]]
 +
|pub_year=2016
 +
}}
 +
<li value="167"> {{Paper
 +
|title=Genome evolution in the allotetraploid frog ''Xenopus laevis''
 +
|authors=Session AM*, Uno Y*, Kwon T*, et al.
 +
|journal=Nature
 +
|pubmed=27762356
 +
|volume=538
 +
|page=336–343
 +
|pdf=Nature_XenopusGenome_2016.pdf
 +
|link=http://dx.doi.org/10.1038/nature19840
 +
|comment=[http://www.nature.com/nature/journal/v538/n7625/full/538320a.html News&Views] and [http://www.marcottelab.org/paper-pdfs/Nature_XenopusGenome_NewsAndViews_2016.pdf pdf]; [http://www.marcottelab.org/paper-pdfs/Nature_XenopusGenome_2016_SupplementIncludesFunding.pdf Supplementary Information] [[File:NatureXenopusCover2016.jpg||100px|right]]
 +
|pub_year=2016
 +
}}
 +
<li value="166"> {{Paper
 +
|title=Temporal Stability and Molecular Persistence of the Bone Marrow Plasma Cell Antibody Repertoire
 +
|authors=Wu GC, Cheung NV, Georgiou G, Marcotte EM, Ippolito GC
 +
|journal=Nature Communications
 +
|pubmed=28000661
 +
|volume=7
 +
|pdf=NatureCommunications_BoneMarrow_2016.pdf
 +
|link=http://dx.doi.org/10.1038/ncomms13838
 +
|page=13838
 +
|pub_year=2016
 +
|comment = [http://dx.doi.org/10.1101/066878 bioRxiv preprint (deposited August 2, 2016)]
 +
}}
 +
<li value="165"> {{Paper
 +
|title=The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery
 +
|authors=Toriyama M, Lee C, Taylor SP, Duran I, Cohn DH, Bruel AL, Tabler JM, Drew K, Kelly MR, Kim S, Park TJ, Braun D, Pierquin G, Biver A, Wagner K, Malfroot A, Panigrahi I, Franco B, Al-Lami HA, Yeung Y, Choi YJ; University of Washington Center for Mendelian Genomics, Duffourd Y, Faivre L, Rivière JB, Chen J, Liu KJ, Marcotte EM, Hildebrandt F, Thauvin-Robinet C, Krakow D, Jackson PK, Wallingford JB
 +
|journal=Nature Genetics
 +
|pubmed=27158779
 +
|volume=48(6)
 +
|link=http://dx.doi.org/10.1038/ng.3558
 +
|page=648-56
 +
|pub_year=2016
 +
|pdf=NatureGenetics_CPLANE_2016.pdf
 +
}}
 +
<li value="164"> {{Paper
 +
|title=Predicting Drug Synergy and Antagonism from Genetic Interaction Neighborhoods
 +
|authors=Young JH, Marcotte EM
 +
|journal=bioRxiv
 +
|pubmed=
 +
|volume=
 +
|link=http://dx.doi.org/10.1101/050567
 +
|page=deposited April 27
 +
|pub_year=2016
 +
}}
 +
<li value="163"> {{Paper
 +
|title=Predictability of Genetic Interactions from Functional Gene Modules
 +
|authors=Young JH, Marcotte EM
 +
|journal=G3
 +
|pubmed=28007839
 +
|volume=7
 +
|pdf=G3_GeneticInteractions_2017.pdf
 +
|link=http://www.g3journal.org/content/early/2016/12/19/g3.116.035915.abstract
 +
|page=617-624
 +
|pub_year=2016
 +
|comment = [http://dx.doi.org/10.1101/049627 bioRxiv preprint (deposited April 25, 2016)]
 +
}}
 +
<li value="162"> {{Paper
 +
|title=Sperm is epigenetically programmed to regulate gene transcription in embryos
 +
|authors=Teperek M, Simeone A, Gaggioli V, Miyamoto K, Allen G, Erkek S, Peters A, Kwon T, Marcotte E, Zegerman P, Bradshaw C, Gurdon J, Jullien J
 +
|journal=Genome Research
 +
|pubmed=27034506
 +
|volume=26
 +
|pdf=GenomeResearch_SpermEpigenetics_2016.pdf
 +
|page=1034-1046
 +
|link=http://dx.doi.org/10.1101/gr.201541.115
 +
|pub_year=2016
 +
}}
 +
<li value="161"> {{Paper
 +
|title=Towards Consensus Gene Ages
 +
|authors=Liebeskind BJ, McWhite CD, Marcotte EM
 +
|journal=Genome Biology and Evolution
 +
|pubmed=27259914
 +
|volume=8(6)
 +
|pdf=GenomeBiolEvol_ConsensusGeneAges_2016.pdf
 +
|link=http://dx.doi.org/10.1093/gbe/evw113
 +
|page=1812-23
 +
|comment = [http://biorxiv.org/content/early/2016/03/01/042036 bioRxiv preprint (deposited March 1)] [https://github.com/marcottelab/Gene-Ages Supporting code and datasets]
 +
|pub_year=2016
 +
}}
 +
<li value="160"> {{Paper
 +
|title=UVnovo: A de Novo Sequencing Algorithm Using Single Series of Fragment Ions via Chromophore Tagging and 351 nm Ultraviolet Photodissociation Mass Spectrometry
 +
|authors=Robotham SA, Horton AP, Cannon JR, Cotham VC, Marcotte EM, Brodbelt JS
 +
|journal=Analytical Chemistry
 +
|pubmed=26938041
 +
|volume=88(7)
 +
|pdf=AnalyticalChemistry_UVnovo_2016.pdf
 +
|link=http://pubs.acs.org/doi/abs/10.1021/acs.analchem.6b00261
 +
|page=3990-7
 +
|comment = [https://github.com/marcottelab/UVnovo Supporting code]
 +
|pub_year=2016
 +
}}
 +
</li>
 +
</ol>
  
  Prince JT, Marcotte, EM. mspire: Mass spectrometry proteomics in Ruby. Bioinformatics 2008, in press.
+
== 2015 ==
PDF
+
<ol>
 +
<li value="159"> {{Paper
 +
|title=Interrogating conserved elements of diseases using Boolean combinations of orthologous phenotypes
 +
|authors=Woods JO, Tien M, Marcotte EM
 +
|journal=bioRxiv
 +
|pub_year=2015
 +
|volume=posted April 13
 +
|page=
 +
|link=https://www.biorxiv.org/content/10.1101/017947v1
 +
}}
 +
<li value="158"> {{Paper
 +
|title=Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes
 +
|authors=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, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, R Tillier E, Wallingford JB, Parkinson J, Marcotte EM, Emili A
 +
|journal=Data in Brief
 +
|pubmed=26870755
 +
|volume=6
 +
|link=http://dx.doi.org/10.1016/j.dib.2015.11.062
 +
|page=715-21
 +
|pub_year=2015
 +
|pdf=Data_In_Brief_AnimalComplexes_2016.pdf
 +
}}
 +
<li value="157"> {{Paper
 +
|title=MouseNet v2: A database of gene networks for studying the laboratory mouse and eight other model vertebrates
 +
|authors=Kim E, Hwang S, Kim H, Shim H, Kang B, Yang S, Shim JH, Shin SY, Marcotte EM, Lee I
 +
|journal=Nucl. Acid. Res.
 +
|pubmed=26527726
 +
|volume=44(D1)
 +
|link=http://dx.doi.org/10.1093/nar/gkv1155
 +
|page=D848-54
 +
|pdf=NAR_MouseNet2_2015.pdf
 +
|pub_year=2015
 +
}}
 +
<li value="156"> {{Paper
 +
|title=Intrinsic antimicrobial resistance determinants in the 'superbug' P. aeruginosa
 +
|authors=Murray J, Kwon T, Marcotte EM, Whiteley M
 +
|journal=mBio
 +
|pubmed=26507235
 +
|volume=6(6)
 +
|link=http://dx.doi.org/10.1128/mBio.01603-15
 +
|page=e01603-15
 +
|pdf=mBio_Murray_2015.pdf
 +
|pub_year=2015
 +
}}
 +
<li value="155"> {{Paper
 +
|title=Long-term neural and physiological phenotyping of a single human
 +
|authors=Poldrack RA, Laumann T, Koyejo O, Gregory B, Hover A, Chen M-Y, Luci J, Huk A, Joo S-J, Boyd R, Hunicke-Smith S, Simpson ZB, Caven T, Sochat V, Shine JM, Gordon E, Snyder AZ, Adeyemo B, Petersen SE, Glahn D, Mckay DR, Blangero J, Frick L, Marcotte EM, Mumford JA
 +
|journal=Nature Communications
 +
|pubmed=26648521
 +
|pdf=NatureCommunications_Poldrackome_2015.pdf
 +
|volume=6
 +
|link=http://dx.doi.org/10.1038/ncomms9885
 +
|page=Article #8885
 +
|pub_year=2015
 +
}}
 +
<li value="154"> {{Paper
 +
|title=Systematic comparison of variant calling pipelines using gold standard personal exome variants
 +
|authors=Hwang S, Eiru K, Lee I, Marcotte EM
 +
|journal=Scientific Reports
 +
|pubmed=26639839
 +
|volume=5
 +
|link=http://dx.doi.org/10.1038/srep17875
 +
|comment=[http://www.marcottelab.org/paper-pdfs/VariantCallingParameterSettings.txt Example variant calling parameters] [http://www.marcottelab.org/paper-pdfs/BEDsandGoldstandardVCFs.zip Gold standard vcf and exome capture region bed files]
 +
|page=17875
 +
|pdf=ScientificReports_Variants_2015.pdf
 +
|pub_year=2015
 +
}}
 +
<li value="153"> {{Paper
 +
|title=Efforts to make and apply humanized yeast
 +
|authors=Laurent JM, Young JH, Kachroo AH, Marcotte EM
 +
|journal=Briefings in Functional Genomics
 +
|pubmed=26462863
 +
|volume=15(2)
 +
|link=http://dx.doi.org/10.1093/bfgp/elv041
 +
|page=155-63
 +
|pdf=BriefingsInFunctionalGenomics_HumanizedYeast_2015.pdf
 +
|pub_year=2015
 +
}}
 +
<li value="152"> {{Paper
 +
|title=Panorama of ancient metazoan macromolecular complexes
 +
|authors=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, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, R Tillier E, Wallingford JB, Parkinson J, Marcotte EM, Emili A
 +
|journal=Nature
 +
|pubmed=26344197
 +
|volume=525
 +
|page=339–344
 +
|link=http://dx.doi.org/10.1038/nature14877
 +
|pdf=Nature_AnimalComplexes_2015.pdf
 +
|comment=Supplementary data is available [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14877.html#supplementary-information here]. [http://metazoa.med.utoronto.ca/ Supporting web site]
 +
|pub_year=2015
 +
}}
 +
<li value="151"> {{Paper
 +
|title=Applications of comparative evolution to human disease genetics
 +
|authors=McWhite CD, Liebeskind BJ, Marcotte EM
 +
|journal=Current Opinion in Genetics & Development
 +
|pubmed=26338499
 +
|volume=35
 +
|page=16–24
 +
|link=http://dx.doi.org/10.1016/j.gde.2015.08.004
 +
|pdf=COGD_comparativeevolution_2015.pdf
 +
|comment=COGD supplies a direct link around their paywall for [http://authors.elsevier.com/a/1ReqI,LqAZ3H8k free access to the paper]
 +
|pub_year=2015
 +
}}
 +
<li value="150"> {{Paper
 +
|title=Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation
 +
|authors=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
 +
|journal=PLoS Computational Biology
 +
|pubmed=26275208
 +
|volume=11(8)
 +
|page=e1004400
 +
|link=http://dx.doi.org/10.1371/journal.pcbi.1004400
 +
|pdf=PLoSComputationalBiology_GlucoseStarvation_2015.pdf
 +
|pub_year=2015
 +
}}
 +
<li value="149"> {{Paper
 +
|title=Systematic humanization of yeast genes reveals conserved functions and genetic modularity
 +
|authors=Kachroo AH, Laurent JM, Yellman CM, Meyer AG, Wilke CO, Marcotte EM
 +
|journal=Science
 +
|pubmed=25999509
 +
|volume=348(6237)
 +
|page=921-925
 +
|link=http://www.sciencemag.org/content/348/6237/921.abstract.html
 +
|pdf=Science_HumanizedYeast_2015.pdf
 +
|comment=[http://www.marcottelab.org/paper-pdfs/Science_HumanizedYeast_2015_SupplementaryMaterials.pdf Supplement] [http://www.sciencemag.org/content/348/6237/921/suppl/DC1 Supplementary Tables and Files] Science magazine supplies a direct link around their paywall for free access to the [http://www.sciencemag.org/cgi/content/full/348/6237/921?ijkey=Bbngd7YBvhX9s&keytype=ref&siteid=sci  manuscript] and [http://www.sciencemag.org/cgi/rapidpdf/348/6237/921?ijkey=Bbngd7YBvhX9s&keytype=ref&siteid=sci pdf reprint]. Code and data for protein interaction evolution simulations are [https://github.com/wilkelab/complex_divergence_simul here]
 +
|pub_year=2015
 +
}}
 +
<li value="148"> {{Paper
 +
|title=Modes of Interaction between Individuals Dominate the Topologies of Real World Networks
 +
|authors=Lee I, Kim E, Marcotte EM
 +
|journal=PLoS One
 +
|pubmed=25793969
 +
|volume=10(3)
 +
|page=e0121248
 +
|link=http://dx.doi.org/10.1371/journal.pone.0121248
 +
|pdf=PLoSOne_NetworkTopology_2015.pdf
 +
|pub_year=2015
 +
}}
 +
<li value="147"> {{Paper
 +
|title=The DEAH-box helicase Dhr1 dissociates U3 from the pre-rRNA to promote folding the central pseudoknot
 +
|authors=Sardana R, Liu X, Granneman S, Zhu J, Gill M, Papoulas O, Marcotte EM, Tollervey D, Correll CC, Johnson AW
 +
|journal=PLoS Biology
 +
|pubmed=25710520
 +
|volume=13(2)
 +
|page=e1002083
 +
|pdf=PLoSBiology_DHR1_2015.pdf
 +
|link=http://dx.doi.org/10.1371/journal.pbio.1002083
 +
|pub_year=2015
 +
}}
 +
<li value="146"> {{Paper
 +
|title=A self-assembling lanthanide molecular nanoparticle for optical imaging
 +
|authors=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 LIR, Jones RA
 +
|journal=Dalton Transactions
 +
|pubmed=25512085
 +
|volume=44(6)
 +
|page=2667-75
 +
|pub_year=2015
 +
|link=http://dx.doi.org/10.1039/c4dt02646b
 +
|pdf=DaltonTransactions_LanthanideNanoparticle_2015.pdf
 +
}}
 +
</li>
 +
</ol>
  
  Vogel C, Marcotte EM. Calculating absolute protein abundance from mass spectrometry based protein expression data. Nature Protocols 2008, 3:1444-1451.
+
== 2014 ==
PDF  |  Supplement
+
<ol>
 +
<li value="145"> {{Paper
 +
|title= A theoretical justification for single molecule peptide sequencing
 +
|authors=Swaminathan J, Boulgakov AA, Marcotte EM
 +
|journal=PLoS Computational Biology
 +
|pubmed=25714988
 +
|volume=11(2)
 +
|page=e1004080
 +
|link=http://dx.doi.org/10.1371/journal.pcbi.1004080
 +
|pdf=PLoSComputationalBiology_SingleMoleculeProteomics_2015.pdf
 +
|comment=[http://dx.doi.org/10.1101/010587 bioRxiv preprint]
 +
|pub_year=2014 bioRxiv, 2015 PLoS CB
 +
}}
 +
<li value="144"> {{Paper
 +
|title=Lanthanide  nano-drums:  A  new  class  of  molecular  nanoparticles  for potential biomedical applications
 +
|authors=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 LIR, Brown KA
 +
|journal=Faraday Discussions
 +
|pubmed=25284181
 +
|volume=175
 +
|page=241-55
 +
|link=http://dx.doi.org/10.1039/C4FD00117F
 +
|pub_year=2014
 +
|pdf=FaradayDiscussions_LanthanideNanodrums_2014.pdf
 +
}}
 +
<li value="143"> {{Paper
 +
|title=Identifying direct targets of transcription factor Rfx2 that coordinate ciliogenesis and cell movement
 +
|authors=Kwon T, Chung M-I, Gupta R, Baker JC, Wallingford JB, Marcotte EM
 +
|journal=Genomics Data
 +
|pubmed=25419512
 +
|volume=2
 +
|page=192-194
 +
|link=http://www.sciencedirect.com/science/article/pii/S2213596014000488
 +
|pub_year=2014
 +
|pdf=GenomicsData_RFX2_2014.pdf
 +
}}
 +
<li value="142"> {{Paper
 +
|title=MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network
 +
|authors=Hwang S, Kim E, Yang S, Marcotte EM, Lee I
 +
|journal=Nucleic Acids Research
 +
|pubmed=24861622
 +
|volume=42(Web Server issue)
 +
|page=W147-53
 +
|link=http://dx.doi.org/10.1093/nar/gku434
 +
|pub_year=2014
 +
|pdf=NAR_MORPHIN_2014.pdf
 +
}}
 +
<li value="141"> {{Paper
 +
|title=Protein-to-mRNA ratios are conserved between <i>Pseudomonas aeruginosa</i> strains
 +
|authors=Kwon T, Huse HK, Vogel C, Whiteley M, Marcotte EM
 +
|journal=Journal of Proteome Research
 +
|pubmed=24742327
 +
|pdf=JProteomeResearch_Pseudomonas_2014.pdf
 +
|volume=13(5)
 +
|page=2370-80
 +
|link=http://pubs.acs.org/doi/abs/10.1021/pr4011684
 +
|pub_year=2014
 +
}}
 +
<li value="140"> {{Paper
 +
|title=Proteomic identification of monoclonal antibodies from serum
 +
|authors=Boutz DR, Horton AP, Wine Y, Lavinder JJ, Georgiou G, Marcotte EM
 +
|journal=Analytical Chemistry
 +
|pubmed=24684310
 +
|volume=86(10)
 +
|page=4758-66
 +
|pdf=AnalyticalChemistry_IgGProteomics_2014.pdf
 +
|link=http://pubs.acs.org/doi/abs/10.1021/ac4037679
 +
|pub_year=2014
 +
}}
 +
<li value="139"> {{Paper
 +
|title=Formation of intracellular glutamine synthetase bodies depends strongly upon cellular age and glucose availability
 +
|authors=O’Connell JD, Tsechansky M, West-Driga M, Marcotte EM
 +
|journal=PeerJ PrePrints
 +
|pubmed=
 +
|pdf=PeerJPreprints_GSBodies_2014.pdf
 +
|volume=2
 +
|page=e270v1
 +
|link=http://dx.doi.org/10.7287/peerj.preprints.270v1
 +
|pub_year=2014
 +
}}
 +
</li>
 +
<li value="138"> {{Paper
 +
|title=A proteomic survey of widespread protein aggregation in yeast
 +
|authors=O’Connell JD, Tsechansky M, Royall A, Boutz DR, Ellington AD, Marcotte EM
 +
|journal=Molecular BioSystems
 +
|pubmed=24488121
 +
|volume=10
 +
|pdf=MolecularBioSystems_Aggregates_2014.pdf
 +
|page=851-861
 +
|link=http://dx.doi.org/10.1039/C3MB70508K
 +
|pub_year=2014
 +
|comment=[http://www.marcottelab.org/paper-pdfs/MolecularBioSystems_Aggregates_2014_SupplementalTables.pdf Supplement] [http://marcottelab.org/index.php/Widespreadaggregation.2013 Supporting Datasets]
 +
}}
 +
</li>
 +
<li value="137"> {{Paper
 +
|title=Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness
 +
|authors=Hammerling MJ, Ellefson JW, Boutz DR, Marcotte EM, Ellington AD, Barrick JE
 +
|journal=Nature Chemical Biology
 +
|pubmed=24487692
 +
|volume=10(3)
 +
|link=http://www.nature.com/nchembio/journal/vaop/ncurrent/full/nchembio.1450.html
 +
|pdf=NatureChemBio_Phage_2014.pdf
 +
|comment=[http://www.marcottelab.org/paper-pdfs/NatureChemBio_Phage_2014-S1.pdf Supplement] [http://www.marcottelab.org/paper-pdfs/NatureChemBio_Phage_2014-S2.xlsx Supplemental Data 1] [http://www.marcottelab.org/paper-pdfs/NatureChemBio_Phage_2014-S3.xlsx Supplemental Data 2]
 +
|page=178-80
 +
|pub_year=2014
 +
}}
 +
</li>
 +
<li value="136"> {{Paper
 +
|title=Yeast cells expressing the human mitochondrial DNA polymerase reveal correlations between polymerase fidelity and human disease progression
 +
|authors=Qian Y, Kachroo A, Yellman CM, Marcotte EM, Johnson KA
 +
|journal=Journal of Biological Chemistry
 +
|pubmed=24398692
 +
|volume=289
 +
|pdf=JBiolChem_hPOLG_2014.pdf
 +
|page=5970-5985
 +
|link=http://dx.doi.org/10.1074/jbc.M113.526418
 +
|pub_year=2014
 +
}}
 +
</li>
 +
<li value="135"> {{Paper
 +
|title=Identification and characterization of the constituent human serum antibodies elicited by vaccination
 +
|authors=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
 +
|journal=Proc Natl Acad Sci USA
 +
|pubmed=24469811
 +
|volume=111(6)
 +
|page=2259-64
 +
|pdf=PNAS_Tetanus_2014.pdf
 +
|pub_year=2014
 +
|link=http://www.pnas.org/content/early/2014/01/23/1317793111.abstract
 +
}}
 +
</li>
 +
<li value="134"> {{Paper
 +
|title=Revisiting and revising the purinosome
 +
|authors=Zhao A, Tsechansky M, Ellington AD, Marcotte EM
 +
|journal=Molecular BioSystems
 +
|pubmed=24413256
 +
|volume=10(3)
 +
|link=http://dx.doi.org/10.1039/C3MB70397E
 +
|page=369-74
 +
|pdf=MolecularBioSystems_RevisitingPurinosome_2013.pdf
 +
|pub_year=2014
 +
}}
 +
</li>
 +
<li value="133"> {{Paper
 +
|title=Coordinated genomic control of ciliogenesis and cell movement by Rfx2
 +
|authors=Chung MI*, Kwon T*, Tu F, Brooks ER, Gupta R, Meyer M, Baker JC, Marcotte EM, Wallingford JB
 +
|journal=eLife
 +
|pubmed=24424412
 +
|pdf=eLife_RFX2_2014.pdf
 +
|volume=3
 +
|page=e01439
 +
|link=http://dx.doi.org/10.7554/eLife.01439
 +
|pub_year=2014
 +
|comment=[[ChungKwon2013_RFX2|Supplement]]
 +
}}
 +
</li>
 +
</ol>
  
  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 2008, 4(7): e1000120.
+
== 2013 ==
PDF
+
<ol>
 +
<li value="132"> {{Paper
 +
|title=Statistical approach to protein quantification
 +
|authors=Gerster S, Kwon T, Ludwig C, Matondo M, Vogel C, Marcotte E, Aebersold R, Bühlmann P
 +
|journal=Mol Cell Proteomics
 +
|pubmed=24255132
 +
|volume=13(2)
 +
|link=http://dx.doi.org/10.1074/mcp.M112.025445
 +
|pdf=MolecularCellularProteomics_Gerster_2014.pdf
 +
|page=666-77
 +
|pub_year=2014
 +
}}
 +
</li>
 +
<li value="131"> {{Paper
 +
|title=<i>Pseudomonas aeruginosa</i> enhances production of a non-alginate exopolysaccharide during long-term colonization of the cystic fibrosis lung
 +
|authors=Huse HK, Kwon T, Zlosnik JEA, Speert DP, Marcotte EM, Whiteley M
 +
|journal=PLoS One
 +
|pubmed=24324811
 +
|volume=8(12)
 +
|page=e82621
 +
|pdf=PLoSOne_PsI_2013.pdf
 +
|link=http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0082621
 +
|pub_year=2013
 +
}}
 +
</li>
 +
<li value="130"> {{Paper
 +
|title=A bacteriophage tailspike domain promotes self-cleavage of a human membrane-bound transcription factor, the myelin regulatory factor MYRF
 +
|authors=Li Z*, Park Y*, Marcotte EM
 +
|journal=PLoS Biology
 +
|pubmed=
 +
|link=http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001624
 +
|page=e1001624
 +
|volume=11(8)
 +
|pub_year=2013
 +
|pdf=PLoSBiology_MYRF_2013.pdf
 +
|comment=[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001626 Commentary]
 +
}}
 +
</li>
 +
<li value="129"> {{Paper
 +
|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
 +
|journal=BMC Bioinformatics
 +
|pubmed=23800157
 +
|page=203
 +
|volume=14
 +
|link=http://dx.doi.org/10.1186/1471-2105-14-203
 +
|pub_year=2013
 +
|pdf=BMCBioinformatics_Phenologs_2013.pdf
 +
}}
 +
</li>
 +
<li value="128"> {{Paper
 +
|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
 +
|journal=PLoS One
 +
|pubmed=
 +
|volume=8(5)
 +
|page=e58977
 +
|pub_year=2013
 +
|pubmed=23650495
 +
|pdf=PLoSOne_Catapult_2013.pdf
 +
|link=http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977
 +
|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
 +
|authors=Zhou L, Zhang AB, Wang R, Marcotte EM, Vogel C
 +
|journal=Molecular BioSystems
 +
|pubmed=
 +
|link=http://dx.doi.org/10.1039/C3MB25513A
 +
|volume=9
 +
|page=750-757
 +
|pdf=MolecularBioSystems_RNADegradosome_2013.pdf
 +
|pubmed=23403814
 +
|pub_year=2013
 +
}}
 +
</li>
 +
<li value="126"> {{Paper
 +
|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
 +
|journal=Proc Natl Acad Sci USA
 +
|pubmed=23382245
 +
|volume=110(8)
 +
|page=2993–2998
 +
|pdf=PNAS_IgGProfiling_2013.pdf
 +
|pub_year=2013
 +
|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
 +
|authors=Zhao A, Tsechansky M, Swaminathan J, Cook L, Ellington AD, Marcotte EM
 +
|journal=PLoS One
 +
|pubmed=23405267
 +
|volume=8(2)
 +
|page=e56203
 +
|pdf=PLoSOne_PurinosomeAggregation_2013.pdf
 +
|link=http://dx.plos.org/10.1371/journal.pone.0056203
 +
|pub_year=2013
 +
}}
 +
</li>
 +
</ol>
  
  Zhao J, Niu W, Marcotte EM, Lambowitz AM. The intracellular localization of a group II intron-encoded reverse transcriptase and other proteins is affected by polyphosphate. PLoS Biology 2008, 6(6): e150.
+
== 2012 ==
PDF
+
<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
 +
|authors=Wang PI, Hwang S, Kincaid RP, Sullivan CS, Lee I, Marcotte EM
 +
|journal=Genome Biology
 +
|pubmed=23268829
 +
|volume=13(12)
 +
|page=R125
 +
|link=http://genomebiology.com/2012/13/12/R125/abstract
 +
|pdf=GenomeBiology_RIDDLE_2012.pdf
 +
|pub_year=2012
 +
}}
 +
</li>
 +
<li value="123"> {{Paper
 +
|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
 +
|journal=J Bacteriol
 +
|pubmed=23123904
 +
|page=213-9
 +
|volume=195(2)
 +
|link=http://jb.asm.org/content/early/2012/10/30/JB.01253-12.abstract
 +
|pdf=JBacteriol_Wessel_2012.pdf
 +
|pub_year=2012
 +
|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
 +
|authors=Park Y, Marcotte EM
 +
|journal=Nature Methods
 +
|pubmed=23223166
 +
|pdf=NatureMethods_FlawedPPICrossValidation_2012.pdf
 +
|volume=9(12)
 +
|page=1134–1136
 +
|link=http://dx.doi.org/10.1038/nmeth.2259
 +
|comment=[http://www.marcottelab.org/paper-pdfs/NatureMethods_FlawedPPICrossValidation_2012_Supplement.pdf Supplement]
 +
|pub_year=2012
 +
}}
 +
</li>
 +
<li value="121"> {{Paper
 +
|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
 +
|journal=Cell
 +
|pubmed=22939629
 +
|volume=150
 +
|page=1068-1081
 +
|link=http://www.cell.com/abstract/S0092-8674%2812%2901006-9
 +
|pdf=Cell_HumanProteinComplexes_2012.pdf
 +
|comment=[http://human.med.utoronto.ca/ Supporting web site] [http://www.marcottelab.org/paper-pdfs/Cell_HumanProteinComplexes_2012_ResearchHighlight.pdf Research highlight]
 +
|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
 +
|authors=Uribe RA, Kwon T, Marcotte EM, Gross JM
 +
|journal=Developmental Biology
 +
|pubmed=22981606
 +
|page=280–292
 +
|volume=371
 +
|pdf=DevelopmentalBiology_Id2a_2012.pdf
 +
|link=http://www.sciencedirect.com/science/article/pii/S0012160612004915
 +
|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
 +
|authors=Cha HJ, Byrom M, Mead PE, Ellington AD, Wallingford JB, Marcotte EM
 +
|journal=PLoS Biology
 +
|pubmed=22927795
 +
|volume=10(8)
 +
|link=http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001379
 +
|pdf=PLoSBiology_TBZ_2012.pdf
 +
|page=e1001379
 +
|pub_year=2012
 +
|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 
 +
|authors=O'Connell JD, Zhao A, Ellington AD, Marcotte EM
 +
|journal=Annual Review of Cell and Developmental Biology
 +
|pubmed=23057741
 +
|volume=28
 +
|link=http://www.annualreviews.org/doi/abs/10.1146/annurev-cellbio-101011-155841
 +
|page=89-111
 +
|pub_year=2012
 +
}}
 +
</li>
 +
<li value="117"> {{Paper
 +
|title=Insights into the regulation of protein abundance from proteomic and transcriptomic analyses 
 +
|authors=Vogel C, Marcotte EM
 +
|journal=Nature Reviews Genetics
 +
|pubmed=22411467
 +
|volume=13
 +
|link=http://dx.doi.org/10.1038/nrg3185
 +
|pdf=NatureReviewsGenetics_ProteinAbundanceRegulation_2012.pdf
 +
|page=227-232
 +
|pub_year=2012
 +
}}
 +
</li>
 +
<li value="116"> {{Paper
 +
|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
 +
|journal=Molecular Systems Biology
 +
|pubmed=22415777
 +
|volume=8
 +
|pdf=MolecularSystemsBiology_TCellCycleEntry_2012.pdf
 +
|link=http://www.nature.com/msb/journal/v8/n1/full/msb20125.html
 +
|comment=[http://www.nature.com/msb/journal/v8/n1/suppinfo/msb20125_S1.html Supplement] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_TCellCycleEntry_2012_Reviews.pdf Reviewer comments]
 +
|page=573
 +
|pub_year=2012
 +
}}
 +
</li>
 +
<li value="115"> {{Paper
 +
|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
 +
|journal=Developmental Biology
 +
|pubmed=22227339
 +
|volume=363(1)
 +
|page=155-165
 +
|link=http://dx.doi.org/10.1016/j.ydbio.2011.12.029
 +
|pdf=DevelopmentalBiology_RFX2_2012.pdf
 +
|pub_year=2012
 +
|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
 +
|authors=Vogel C, Marcotte EM
 +
|journal=Methods in Molecular Biology: Quantitative Methods in Proteomics
 +
|pubmed=22665309
 +
|pub_year=2012
 +
|volume=Marcus, K., ed., Humana Press, vol. 893(3)
 +
|page=321-341
 +
|link=http://www.springerlink.com/content/ll221655443866x8/#section=1079488&page=1
 +
|pdf=MethodsMolBioProteomics_VogelMarcotte_2012.pdf
 +
}}
 +
</li>
 +
</ol>
  
  Lee I, Marcotte EM. Integrating Functional Genomics Data. in Methods in Molecular Biology: Bioinformatics, Vol. II, Structure, Function and Applications, Keith, J. M., ed., Humana Press (2008)
+
== 2011 ==
PDF
+
<ol>
 +
<li value="113"> {{Paper
 +
|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
 +
|journal=Proc Natl Acad Sci USA
 +
|pubmed=22042862
 +
|page=18548-18553
 +
|link=http://www.pnas.org/cgi/doi/10.1073/pnas.1110384108
 +
|pdf=PNAS_RiceNet_2011_withSupplement.pdf
 +
|pub_year=2011
 +
|volume=108(45)
 +
|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
 +
|authors=Natarajan N, Blom UM, Tewari A, Woods JO, Dhillon IS, Marcotte EM
 +
|journal=UTCS Technical Report
 +
|pubmed=
 +
|page=
 +
|pdf=TechnicalReport-PhenoNets-TR-2053.pdf
 +
|link=http://apps.cs.utexas.edu/tech_reports/ncstrl/ncstrl2html.php?what=TR%20Abstracts&when=2011#UTEXAS.CS//CS-TR-11-37
 +
|pub_year=2011
 +
|volume=TR-11-37
 +
}}
 +
</li>
 +
<li value="111"> {{Paper
 +
|title=Global protein expression regulation under oxidative stress
 +
|authors=Vogel C, Silva GM, Marcotte EM
 +
|journal=Molecular and Cellular Proteomics
 +
|pubmed=21933953
 +
|page=M111.009217
 +
|link=http://dx.doi.org/10.1074/mcp.M111.009217
 +
|pdf=MolecularCellularProteomics_OxidativeProteomics_2011.pdf
 +
|pub_year=2011
 +
|volume=10(12)
 +
|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
 +
|authors=Park Y, Marcotte EM
 +
|journal=Bioinformatics
 +
|pubmed=21908540
 +
|page=3024-3028
 +
|pub_year=2011
 +
|volume=27(21)
 +
|pdf=Bioinformatics_NegativePPISampling_2011.pdf
 +
|link=http://dx.doi.org/10.1093/bioinformatics/btr514
 +
|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 <i>Arabidopsis thaliana</i>
 +
|authors=Hwang S, Rhee SY, Marcotte EM, Lee I
 +
|journal=Nature Protocols
 +
|pubmed=21886106
 +
|pub_year=2011
 +
|volume=6
 +
|pdf=NatureProtocols_AraNet_2011.pdf
 +
|page=1429–1442
 +
|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
 +
|authors=Lee I, Blom M, Wang PI, Shim JE, Marcotte EM
 +
|journal=Genome Research
 +
|pubmed=21536720
 +
|pub_year=2011
 +
|volume=21(7)
 +
|pdf=GenomeResearch_HumanNet_2011.pdf
 +
|page=1109-21
 +
|link=http://dx.doi.org/10.1101/gr.118992.110
 +
|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
 +
|authors=Kwon T, Choi H, Vogel C, Nesvizhskii AI, Marcotte EM
 +
|journal=Journal of Proteome Research
 +
|pubmed=21488652
 +
|pub_year=2011
 +
|volume=10(7)
 +
|pdf=JProteomeResearch_MSBlender_2011.pdf
 +
|page=2949-58
 +
|link=http://pubs.acs.org/doi/abs/10.1021/pr2002116
 +
|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
 +
|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
 +
|journal=Journal of Biological Chemistry
 +
|pubmed=21402708
 +
|pub_year=2011
 +
|volume=286(20)
 +
|pdf=JBC_miR-122_2011.pdf
 +
|page=18066-78
 +
|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
 +
|authors=Niu W, Hart GT, Marcotte EM
 +
|journal=Methods in Molecular Biology: Cell-Based Microarrays
 +
|pub_year=2011
 +
|volume=Palmer, E., ed., Humana Press, vol. 706
 +
|page=83-95
 +
|pubmed=21104056
 +
|pdf=MethodsMolBioCellBasedMicroarrays_Niu_2010.pdf
 +
}}
 +
</li>
 +
<li value="104"> {{Paper
 +
|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
 +
|journal=Cytoskeleton
 +
|pubmed=21140514
 +
|pub_year=2011
 +
|volume=68(2)
 +
|pdf=Cytoskeleton_ciliamidbody_2011.pdf
 +
|page=112-24
 +
|link=http://dx.doi.org/10.1002/cm.20498
 +
}}
 +
</li>
 +
</ol>
  
  Kim WK, Krumpelman C, Marcotte EM. Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy. Genome Biology 2008 9:S5.
+
== 2010 ==
PDF  |  Supplement
+
<ol>
  
  Pena-Castillo L, et al. A critical assessment of M. musculus gene function prediction using integrated genomic evidence. Genome Biology 2008 9:S2.
+
<li value="103"> {{Paper
PDF
+
|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
 +
|journal=mBIO
 +
|pub_year=2010
 +
|volume=1(4)
 +
|pubmed=20856824
 +
|pdf=mBIO_CFPseudomonas_2010.pdf
 +
|link=http://mbio.asm.org/content/1/4/e00199-10
 +
|page=e00199-10
 +
|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
 +
|authors=Huang N, Lee I, Marcotte EM, Hurles M
 +
|journal=PLoS Genetics
 +
|pub_year=2010
 +
|volume=6(10)
 +
|pdf=PLoSGenetics_Haploinsufficiency_2010.pdf
 +
|link=http://dx.doi.org/10.1371/journal.pgen.1001154
 +
|page=e1001154
 +
|pubmed=20976243
 +
}}
 +
</li>
 +
<li value="101"> {{Paper
 +
|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
 +
|journal=Proteomics
 +
|pub_year=2010
 +
|volume=10
 +
|pubmed=21089048
 +
|pdf=Proteomics_ProteinVersusRNAConservation_2010.pdf
 +
|link=http://onlinelibrary.wiley.com/doi/10.1002/pmic.201000327/abstract
 +
|page=4209–4212
 +
|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
 +
|authors=Wang PI, Marcotte EM
 +
|journal=Journal of Proteomics
 +
|pub_year=2010
 +
|volume=73(11)
 +
|pubmed=20637909
 +
|pdf=JProteomics_GBAReview_2010.pdf
 +
|link=http://dx.doi.org/10.1016/j.jprot.2010.07.005
 +
|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
 +
|authors=Vogel C, de Sousa Abreu R, Ko D, Le S-Y, Shapiro BA, Burns SC, Sandhu D, Boutz DR, Marcotte EM, Penalva LO
 +
|journal=Molecular Systems Biology
 +
|pub_year=2010
 +
|pubmed=20739923
 +
|volume=6
 +
|page=article 400
 +
|pdf=MolecularSystemsBiology_2010_HumanProteomics.pdf
 +
|link=http://www.nature.com/msb/journal/v6/n1/full/msb201059.html
 +
|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
 +
|authors=Lo K-Y, Li Z, Bussiere C, Bresson S, Marcotte EM, Johnson AW
 +
|journal=Molecular Cell
 +
|pub_year=2010
 +
|volume=39(2)
 +
|page=196-208
 +
|pubmed=20670889
 +
|pdf=MolecularCell_60SBiogenesis_2010.pdf
 +
|link=http://www.cell.com/molecular-cell/fulltext/S1097-2765(10)00459-4
 +
|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
 +
|authors=Lee I, Lehner B, Vavouri T, Shin J, Fraser AG, Marcotte EM
 +
|journal=Genome Research
 +
|pub_year=2010
 +
|volume=20
 +
|page=1143-1153
 +
|pubmed=20538624
 +
|pdf=GenomeResearch_GeneticModifiers_2010.pdf
 +
|link=http://dx.doi.org/10.1101/gr.102749.109
 +
|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
 +
|authors=McGary KL, Park TJ, Woods JO, Cha HJ, Wallingford JB, Marcotte EM
 +
|journal=Proc Natl Acad Sci U S A
 +
|pub_year=2010
 +
|volume=107(14)
 +
|page=6544-9
 +
|pubmed=20308572
 +
|link=http://www.pnas.org/cgi/doi/10.1073/pnas.0910200107
 +
|pdf=PNAS_Phenologs_2010.pdf
 +
|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
 +
|authors=Orr SJ, Gaymes T, Ladon D, Chronis C, Czepulkowski B, Wang R, Mufti GJ, Marcotte EM, Thomas NSB
 +
|journal=Oncogene
 +
|pub_year=2010
 +
|volume=29(26)
 +
|page=3803-14
 +
|link=http://www.nature.com/onc/journal/vaop/ncurrent/abs/onc2010138a.html
 +
|pdf=Oncogene_MCM_2010.pdf
 +
|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>
 +
|authors=Lee I, Ambaru B, Thakkar P, Marcotte EM, Rhee SY
 +
|journal=Nature Biotechnology
 +
|pub_year=2010
 +
|volume=28(2)
 +
|page=149-156
 +
|pubmed=20118918
 +
|link=http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt.1603.html
 +
|pdf=NatureBiotech_AraNet_2010.pdf
 +
|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>
  
  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. 2008 4:180. Epub 2008 Apr 15.
+
== 2009 ==
PDF
+
<ol>
  
  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. 2008 28(10):3151-61. Epub 2008 Mar 10.
+
<li value="93"> {{Paper
PDF
+
|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
 +
|journal=PLoS Biology
 +
|pub_year=2009
 +
|volume=7(10)
 +
|page=e1000213
 +
|pubmed=19806183
 +
|link=http://dx.doi.org/10.1371/journal.pbio.1000213
 +
|pdf=PLoSBiology_RibosomeBiogenesis_2009.pdf
 +
|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
 +
|authors=Hart GT, Zhao A, Garg A, Bolusani S, Marcotte EM
 +
|journal=PLoS One
 +
|pub_year=2009
 +
|volume=4(10)
 +
|page=e7088
 +
|pubmed=19862318
 +
|link=http://dx.doi.org/10.1371/journal.pone.0007088
 +
|pdf=PLoSOne_HumanCellChips_2009.pdf
 +
|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
 +
|authors=Lo KY, Li Z, Wang F, Marcotte EM, Johnson AF
 +
|journal=J. Cell Biology
 +
|pub_year=2009
 +
|volume=186(6)
 +
|page=849-62
 +
|pubmed=19797078
 +
|link=http://dx.doi.org/10.1083/jcb.200904110
 +
|comment=[http://www.marcottelab.org/paper-pdfs/JCellBiol_Yvh1_2009_Supplement.pdf Supplemental material]
 +
||pdf=JCellBiol_Yvh1_2009.pdf
 +
}}
 +
</li>
 +
<li value="90"> {{Paper
 +
|title=Absolute abundance for the masses
 +
|authors=Vogel C, Marcotte EM
 +
|journal=Nature Biotechnology
 +
|pub_year=2009
 +
|volume=27(9)
 +
|page=825-6
 +
|pubmed=19741640
 +
|link=http://dx.doi.org/10.1038/nbt0909-825
 +
|pdf=NatureBiotech_MSNewsAndViews_2009.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="89"> {{Paper
 +
|title=Global signatures of protein and mRNA expression levels
 +
|authors=de Sousa Abreu R, Penalva LO, Marcotte EM, Vogel C
 +
|journal=Molecular BioSystems
 +
|pub_year=2009
 +
|volume=5
 +
|page=1512–1526
 +
|pubmed=20023718
 +
|link=http://www.rsc.org/Publishing/Journals/MB/article.asp?doi=b908315d
 +
|pdf=MolecularBioSystems_ProteinRNA_2009.pdf
 +
|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
 +
|authors=Gray RS, Abitua PB, Wlodarczyk BJ, Blanchard O, Lee I, Weiss G, Marcotte EM, Wallingford JB, Finnell RH
 +
|journal=Nature Cell Biology
 +
|pub_year=2009
 +
|volume=11(10)
 +
|page=1225-32
 +
|pubmed=19767740
 +
|link=http://dx.doi.org/10.1038/ncb1966
 +
|comment=[http://www.nature.com/ncb/journal/v11/n10/covers/index.html Journal cover--a beautiful electron micrograph by Phil Abitua] [http://www.marcottelab.org/paper-pdfs/NatureCellBiology_Fuzzy_2009_supplement.pdf Supplemental Figures] [[File:NatureCellBiologyFuzCover2009.jpg||100px|right]]
 +
|pdf=NatureCellBiology_Fuzzy_2009.pdf
 +
}}
 +
</li>
 +
<li value="87"> {{Paper
 +
|title=Disorder, promiscuity, and toxic partnerships
 +
|authors=Marcotte EM, Tsechansky M
 +
|journal=Cell
 +
|pub_year=2009
 +
|volume=138(1)
 +
|page=16-18
 +
|pubmed=19596229 
 +
|link=http://dx.doi.org/10.1016/j.cell.2009.06.024   
 +
|comment=
 +
|pdf=Cell_LehnerPreview_2009.pdf
 +
}}
 +
</li>
 +
<li value="86"> {{Paper
 +
|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
 +
|journal=Bioinformatics
 +
|pub_year=2009
 +
|volume=25(22)
 +
|page=2955-2961
 +
|pubmed=19633097
 +
|link=http://bioinformatics.oxfordjournals.org/cgi/reprint/btp461
 +
|pdf=Bioinformatics_MSNet_2009.pdf
 +
|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
 +
|authors=Narayanaswamy R, Levy M, Tsechansky M, Stovall GM, O'Connell J, Mirrielees J, Ellington AD, Marcotte EM
 +
|journal=Proc Natl Acad Sci U S A
 +
|pub_year=2009
 +
|volume=106(25)
 +
|page=10147-52
 +
|pubmed=19502427
 +
|link=http://www.pnas.org/content/106/25/10147.long
 +
|comment=[http://www.marcottelab.org/paper-pdfs/PNAS_punctatebodies_2009_Supplement.pdf Supplemental methods] [http://www.marcottelab.org/paper-pdfs/PNAS_punctatebodies_2009_SupplementalDataset.xls Supplemental Dataset] [http://www.marcottelab.org/paper-pdfs/PNAS_punctatebodies_2009_TableS1.pdf Table S1] [http://www.marcottelab.org/paper-pdfs/PNAS_punctatebodies_2009_TableS2.pdf Table S2] [http://www.marcottelab.org/paper-pdfs/PNAS_punctatebodies_2009_TableS3.pdf Table S3]
 +
|pdf=PNAS_punctatebodies_2009.pdf
 +
}}
 +
</li>
 +
<li value="84"> {{Paper
 +
|title=A synthetic genetic edge detection program
 +
|authors=Tabor JJ, Salis H, Simpson ZB, Chevalier AA, Levskaya A, Marcotte EM, Voigt CA, Ellington AD
 +
|journal=Cell
 +
|pub_year=2009
 +
|volume=137(7)
 +
|page=1272-1281
 +
|pubmed=19563759
 +
|link=http://dx.doi.org/doi:10.1016/j.cell.2009.04.048   
 +
|comment=[http://www.marcottelab.org/paper-pdfs/Cell_EdgeDetector_2009_Supplement.pdf Supplemental methods]
 +
|pdf=Cell_EdgeDetector_2009.pdf
 +
}}
 +
</li>
 +
<li value="83"> {{Paper
 +
|title=Effects of functional bias on supervised learning of a gene network model
 +
|authors=Lee I, Marcotte EM
 +
|journal=Methods Mol Biol
 +
|pub_year=2009
 +
|volume=541
 +
|page=463-75
 +
|pubmed=19381535
 +
|link=http://www.springerlink.com/content/j1726u1h54440624/
 +
|comment=
 +
|pdf=MethodsMolBioCompSysBio_Lee_2009_printersproofs.pdf
 +
}}
 +
</li>
 +
<li value="82"> {{Paper
 +
|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
 +
|journal=Bioinformatics
 +
|pub_year=2009
 +
|volume=25(11)
 +
|page=1397-403
 +
|pubmed=19318424
 +
|link=http://bioinformatics.oxfordjournals.org/cgi/content/full/25/11/1397
 +
|comment=[http://www.marcottelab.org/paper-pdfs/Bioinformatics_mspresso_2009_Supplement.pdf Supplement] [http://www.marcottelab.org/MSpresso/ Supplemental website]
 +
|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.
 +
|authors=Narayanaswamy R, Moradi EK, Niu W, Hart GT, Davis M, McGary KL, Ellington AD, Marcotte EM.
 +
|journal=J Proteome Res.
 +
|pub_year=2009
 +
|volume=8(1)
 +
|page=6-19.
 +
|pubmed=19053807
 +
|link=http://pubs.acs.org/doi/abs/10.1021/pr800524g
 +
|comment=
 +
|pdf=JProteomeResearch_Shmoo_2008.pdf
 +
}}
 +
</li>
 +
</ol>
  
  Wang R, Marcotte EM. The Proteomic Response of Mycobacterium smegmatis to Anti-Tuberculosis Drugs Suggests Targeted Pathways. J Proteome Res. 2008 Feb 15
+
== 2008 ==
PDF
+
<ol>
 +
<li value="80"> {{Paper
 +
|authors=Hannay K, Marcotte EM, Vogel C
 +
|title=Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation
 +
|journal=BMC Genomics
 +
|pub_year=2008
 +
|volume=9
 +
|page=609
 +
|pubmed=19087332
 +
|link=http://www.biomedcentral.com/1471-2164/9/609
 +
|pdf=BMCGenomics_Buffering_2008.pdf
 +
|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
 +
|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
 +
|journal=BMC Bioinformatics
 +
|pub_year=2008
 +
|volume=9
 +
|page=529.
 +
|pubmed=19068132
 +
|link=http://www.biomedcentral.com/1471-2105/9/529
 +
|pdf=BMCBioinformatics_APEXTool_2009.pdf
 +
|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
 +
|authors=Kim WK, Marcotte EM
 +
|journal=PLoS Comput Biol
 +
|pub_year=2008
 +
|volume=4(11)
 +
|page=e1000232
 +
|pubmed=19043579
 +
|link=http://dx.doi.org/10.1371/journal.pcbi.1000232
 +
|pdf=PLoSComputationalBiology_PPINetworkEvolution_2008.pdf
 +
|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
 +
|authors=Prince JT, Marcotte EM
 +
|journal=Bioinformatics
 +
|pub_year=2008
 +
|volume=24(23)
 +
|page=2796-7
 +
|pubmed=18930952
 +
|link=http://bioinformatics.oxfordjournals.org/cgi/content/full/24/23/2796
 +
|pdf=Bioinformatics_mspire_2008.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="76"> {{Paper
 +
|title=Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data
 +
|authors=Vogel C, Marcotte EM
 +
|journal=Nat Protoc
 +
|pub_year=2008
 +
|volume=3(9)
 +
|page=1444-51.
 +
|pubmed=18772871
 +
|link=http://www.nature.com/nprot/journal/v3/n9/abs/nprot.2008.132.html
 +
|pdf=NatureProtocols_APEX_2008.pdf
 +
|comment=[http://www.marcottelab.org/paper-pdfs/NatureProtocols_APEX_2008_Supplement.pdf Supplement]
 +
}}
 +
</li>
 +
<li value="75"> {{Paper
 +
|title=Integrating functional genomics data
 +
|authors=Lee I, Marcotte EM
 +
|journal=Methods Mol Biol
 +
|pub_year=2008
 +
|volume=453
 +
|page=267-78.
 +
|pubmed=18712309
 +
|link=http://www.springerlink.com/content/h21044190m77k274/
 +
|pdf=MethodsMolBioBioinformatics_LeeMarcotte_2008.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="74"> {{Paper
 +
|title=Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy
 +
|authors=Kim WK, Krumpelman C, Marcotte EM
 +
|journal=Genome Biol
 +
|pub_year=2008
 +
|volume=9 Suppl 1:
 +
|page=S5
 +
|pubmed=18613949
 +
|link=http://genomebiology.com/2008/9/S1/S5
 +
|pdf=GenomeBiology_MouseNet_2008.pdf
 +
|comment=[http://www.marcottelab.org/paper-pdfs/GenomeBiology_MouseNet_2008_Supplement.pdf Supplement]
 +
}}
 +
</li>
 +
<li value="73"> {{Paper
 +
|title=A critical assessment of <i>Mus musculus</i> 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
 +
|journal=Genome Biol
 +
|pub_year=2008
 +
|volume=9 Suppl 1
 +
|page=S2
 +
|pubmed=18613946
 +
|link=http://genomebiology.com/2008/9/S1/S2
 +
|pdf=GenomeBiology_MouseFunc_2008.pdf
 +
|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 <i>S. cerevisiae</i>
 +
|authors=Niu W, Li Z, Zhan W, Iyer VR, Marcotte EM
 +
|journal=PLoS Genet
 +
|pub_year=2008
 +
|volume=4(7)
 +
|page=e1000120
 +
|pubmed=18617996
 +
|link=http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000120
 +
|pdf=PLoSGenetics_CellCycleScreen_2008.pdf
 +
|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
 +
|authors=Zhao J, Niu W, Yao J, Mohr S, Marcotte EM, Lambowitz AM
 +
|journal=PLoS Biol
 +
|pub_year=2008
 +
|volume=6(6)
 +
|page=e150
 +
|pubmed=18593213
 +
|link=http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0060150
 +
|pdf=PLoSBiology_IntronLocalization_2008.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="70"> {{Paper
 +
|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
 +
|journal=Mol Syst Biol
 +
|pub_year=2008
 +
|volume=4
 +
|page=180
 +
|pubmed=18414481
 +
|link=http://dx.doi.org/10.1038/msb.2008.19
 +
|pdf=MolSysBiol_CCE_2008.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="69"> {{Paper
 +
|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
 +
|journal=Mol Cell Biol
 +
|pub_year=2008
 +
|volume=28(10)
 +
|page=3151-61
 +
|pubmed=18332120
 +
|link=http://mcb.asm.org/cgi/content/full/28/10/3151
 +
|pdf=MolCellBiol_Bud23_2008.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="68"> {{Paper
 +
|title=The proteomic response of <i>Mycobacterium smegmatis</i> to anti-tuberculosis drugs suggests targeted pathways
 +
|authors=Wang R, Marcotte EM
 +
|journal=J Proteome Res
 +
|pub_year=2008
 +
|volume=7(3)
 +
|page=855-65
 +
|pubmed=18275136
 +
|link=http://pubs.acs.org/doi/abs/10.1021/pr0703066
 +
|pdf=JProteomeResearch_TBDrug_2008.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="67"> {{Paper
 +
|title=A single gene network accurately predicts phenotypic effects of gene perturbation in <i>Caenorhabditis elegans</i>
 +
|authors=Lee I, Lehner B, Crombie C, Wong W, Fraser AG, Marcotte EM
 +
|journal=Nat Genet
 +
|pub_year=2008
 +
|volume=40(2)
 +
|page=181-8
 +
|pubmed=18223650
 +
|link=http://www.nature.com/ng/journal/v40/n2/abs/ng.2007.70.html
 +
|pdf=NatureGenetics_Wormnet_2008.pdf
 +
|comment=[http://www.marcottelab.org/paper-pdfs/NatureGenetics_Wormnet_2008_Supplement.pdf Supplement] [http://www.functionalnet.org/wormnet Supplemental Web Site] [[File:NatureGeneticsWormNetCover2008.jpg||100px|right]]
  
  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 2008 40(2):181-8
+
}}
PDF  |  Supplement  |  Supplemental web site
+
</li>
 +
</ol>
  
2007
+
== 2007 ==
 +
<ol>
 +
<li value="66"> {{Paper
 +
|title=Broad network-based predictability of <i>Saccharomyces cerevisiae</i> gene loss-of-function phenotypes
 +
|authors=McGary KL, Lee I, Marcotte EM
 +
|journal=Genome Biol
 +
|pub_year=2007
 +
|volume=8(12)
 +
|page=R258.
 +
|pubmed=18053250
 +
|link=http://genomebiology.com/2007/8/12/R258
 +
|pdf=GenomeBiology_YeastPhenoPred_2007.pdf
 +
|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, <i>Saccharomyces cerevisiae</i>
 +
|authors=Lee I, Li Z, Marcotte EM
 +
|journal=PLoS ONE
 +
|pub_year=2007
 +
|volume=2(10)
 +
|page=e988
 +
|pubmed=17912365
 +
|link=http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000988
 +
|pdf=PLOS1_YeastNet2_2007.pdf
 +
|comment=[http://www.yeastnet.org Supplemental Web Site]
 +
}}
 +
</li>
 +
<li value="64"> {{Paper
 +
|title=How do shotgun proteomics algorithms identify proteins?
 +
|authors=Marcotte EM
 +
|journal=Nat Biotechnol
 +
|pub_year=2007
 +
|volume=25(7)
 +
|page=755-7
 +
|pubmed=17621303
 +
|link=http://www.nature.com/nbt/journal/v25/n7/abs/nbt0707-755.html
 +
|pdf=NatureBiotech_ShotgunProteomicsPrimer_2007.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="63"> {{Paper
 +
|title=Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways
 +
|authors=Carlson MW, Iyer VR, Marcotte EM
 +
|journal=BMC Genomics
 +
|pub_year=2007
 +
|volume=8
 +
|page=117.
 +
|pubmed=17493265
 +
|link=http://www.biomedcentral.com/1471-2164/8/117
 +
|pdf=BMCGenomics_CervicalCancer_2007.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="62"> {{Paper
 +
|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
 +
|journal=Nat Biotechnol
 +
|pub_year=2007
 +
|volume=25(1)
 +
|page=117-24
 +
|pubmed=17187058
 +
|link=http://www.nature.com/nbt/journal/v25/n1/abs/nbt1270.html
 +
|pdf=NatureBiotech_APEX_2007.pdf
 +
|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
 +
|authors=Lu P, Rangan A, Chan SY, Appling DR, Hoffman DW, Marcotte EM
 +
|journal=Metab Eng
 +
|pub_year=2007
 +
|volume=9(1)
 +
|page=8-20
 +
|pubmed=17049899
 +
|link=http://dx.doi.org/10.1016/j.ymben.2006.06.003
 +
|pdf=MetabolicEngineering_OneCarbonMetab_2007.pdf
 +
|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
 +
|authors=Hart GT, Lee I, Marcotte EM
 +
|journal=BMC Bioinformatics
 +
|pub_year=2007
 +
|volume=8
 +
|page=236.
 +
|pubmed=17605818
 +
|link=http://www.biomedcentral.com/1471-2105/8/236
 +
|pdf=BMCBioinformatics_YeastComplexEssentiality_2007.pdf
 +
|comment=
 +
}}
 +
</li>
 +
</ol>
  
  McGary KL, Lee I, Marcotte EM. Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes. Genome Biology 2007 8(12):R258
+
== 2006 ==
PDF  | Supplemental web site
+
<ol>
 +
<li value="59"> {{Paper
 +
|title=How complete are current yeast and human protein-interaction networks?
 +
|authors=Hart GT, Ramani AK, Marcotte EM.
 +
|journal=Genome Biol.
 +
|pub_year=2006
 +
|volume=7(11)
 +
|page=120
 +
|pubmed=17147767
 +
|link=http://genomebiology.com/2006/7/11/120
 +
|pdf=GenomeBiology_HumanPPIOverview_2006.pdf
 +
|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
 +
|authors=Prince JT, Marcotte EM
 +
|journal=Anal. Chem.
 +
|pub_year=2006
 +
|volume=78(17)
 +
|page=6140-52
 +
|pubmed=16944896
 +
|link=http://pubs.acs.org/doi/abs/10.1021/ac0605344
 +
|pdf=AnalyticalChemistry_OBIWarp_2006.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="57"> {{Paper
 +
|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
 +
|journal=Bioinformatics
 +
|pub_year=2006
 +
|volume=22(12)
 +
|page=1524-31
 +
|pubmed=16585069
 +
|link=http://bioinformatics.oxfordjournals.org/cgi/content/full/22/12/1524
 +
|pdf=Bioinformatics_MoBIoSCoarseFilter_2006.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="56"> {{Paper
 +
|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
 +
|journal=Genome Biol.
 +
|pub_year=2006
 +
|volume=7(1)
 +
|page=R6
 +
|pubmed=16507139
 +
|link=http://genomebiology.com/2006/7/1/R6
 +
|pdf=GenomeBiology_CellChips_2006.pdf
 +
|comment=[http://www.marcottelab.org/paper-pdfs/GenomeBiology_CellChips_Supplement_2006.pdf Supplement] [http://www.marcottelab.org/paper-pdfs/NarayanaswamySupplementalTable1.xls Supplemental Table 1] [http://www.marcottelab.org/paper-pdfs/NarayanaswamySupplementalTable2.xls Supplemental Table 2] [http://www.marcottelab.org/paper-pdfs/NarayanaswamySupplementalTable3.xls Supplemental Table 3] [http://www.marcottelab.org/paper-pdfs/NarayanaswamySupplementalTable4.xls Supplemental Table 4]
 +
}}
 +
</li>
 +
<li value="55"> {{Paper
 +
|title=Bioinformatic prediction of yeast gene function
 +
|authors=Lee I, Narayanaswamy R, Marcotte EM
 +
|journal=Yeast Gene Analysis
 +
|pub_year=2006
 +
|volume=Stansfield, I., ed., Elsevier Press
 +
|page=
 +
|pubmed=
 +
|link=
 +
|pdf=LeeNarayanaswamyMarcotteManuscript.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="54"> {{Paper
 +
|title=Bioinformatic challenges for the next decade(s)
 +
|authors=Eisenberg D, Marcotte E, McLachlan AD, Pellegrini M
 +
|journal=Philos Trans R Soc Lond B Biol Sci.
 +
|pub_year=2006
 +
|volume=361(1467)
 +
|page=525-7
 +
|pubmed=16524841
 +
|link=http://rstb.royalsocietypublishing.org/content/361/1467/525.long
 +
|pdf=PhilTransactionsRoyalSocB_BioinformaticChallenges_2006.pdf
 +
|comment=
 +
}}
 +
</li>
 +
</ol>
  
  Lee I, Li Z, Marcotte EM. An Improved, Bias-Reduced Probabilistic Functional Gene Network of Baker's Yeast, Saccharomyces cerevisiae. PLoS ONE 2007 2(10):e988
+
== 2005 ==
PDF |  Supplemental web site
+
<ol>
 +
<li value="53"> {{Paper
 +
|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
 +
|journal=Nature
 +
|pub_year=2005
 +
|volume=438(7067)
 +
|page=441-2
 +
|pubmed=16306980 
 +
|link=http://dx.doi.org/10.1038/nature04405
 +
|pdf=Nature_BacterialPhotography_2005.pdf
 +
|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
 +
|authors=Ramakrishnan SR, Mao R, Nakorchevskiy AA, Prince JT, Willard WS, Xu W, Marcotte EM, Miranker DP
 +
|journal=University of Texas Dept. of Computer Sciences, Technical Report
 +
|pub_year=2005
 +
|volume=TR-05-06
 +
|page=
 +
|pubmed=
 +
|link=
 +
|pdf=TechnicalReport-MoBIoS-TR-05-06.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="51"> {{Paper
 +
|title=Mass spectrometry of the <i>M. smegmatis</i> proteome: Protein expression levels correlate with function, operons, and codon bias
 +
|authors=Wang R, Prince JT,  Marcotte EM
 +
|journal=Genome Res.
 +
|pub_year=2005
 +
|volume=15(8)
 +
|page=1118-26
 +
|pubmed=16077011
 +
|link=http://genome.cshlp.org/content/15/8/1118.long
 +
|pdf=rong_2005.pdf
 +
|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
 +
|authors=Ramani AK, Bunescu RC, Mooney RJ, Marcotte EM
 +
|journal=Genome Biology
 +
|pub_year=2005
 +
|volume=6(5)
 +
|page=R40
 +
|pubmed=15892868  
 +
|link=http://genomebiology.com/2005/6/5/R40
 +
|pdf=Arun-consolidate-human.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="49"> {{Paper
 +
|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
 +
|journal=Artif Intell Med.
 +
|pub_year=2005
 +
|volume=33(2)
 +
|page=139-55
 +
|pubmed=15811782  
 +
|link=http://dx.doi.org/10.1016/j.artmed.2004.07.016
 +
|pdf=bionlp-aimed-04.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="48"> {{Paper
 +
|title=Using biomedical literature mining to consolidate the set of known human protein-protein interactions
 +
|authors=Ramani AK, Marcotte EM, Bunescu RC, Mooney RJ
 +
|journal=Intelligent Systems in Molecular Biology-ACL Workshop
 +
|pub_year=2005
 +
|volume=
 +
|page=
 +
|pubmed=
 +
|link=
 +
|pdf=ISMB-ACLworkshop_LitMining_2005.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="47"> {{Paper
 +
|title=Protein function prediction using the Protein Link Explorer (PLEX)
 +
|authors=Date SV, Marcotte EM
 +
|journal=Bioinformatics
 +
|pub_year=2005
 +
|volume=21(10)
 +
|page=2558-9
 +
|pubmed=15701682 
 +
|link=http://bioinformatics.oxfordjournals.org/cgi/content/full/21/10/2558
 +
|pdf=Plex.pdf
 +
|comment=[http://bioinformatics.icmb.utexas.edu/plex/plex.html Supplemental Web Site]
 +
}}
 +
</li>
 +
</ol>
  
   Marcotte EM. Primer: How do shotgun proteomics algorithms identify proteins? Nature Biotechnology 2007 25(7):755-757
+
== 2004 ==
PDF
+
<ol>
 +
<li value="46"> {{Paper
 +
|title=A probabilistic functional network of yeast genes
 +
|authors=Lee I, Date SV, Adai AT, Marcotte EM
 +
|journal=Science
 +
|pub_year=2004
 +
|volume=306(5701)
 +
|page=1555-8
 +
|pubmed=15567862
 +
|pdf=Science_Lee_YeastNet.pdf
 +
|comment=[http://www.marcottelab.org/paper-pdfs/1099511v2s.pdf Supplemental methods] [http://www.marcottelab.org/paper-pdfs/1099511v2s_list.txt 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
 +
|title=Genome sequence of <i>Haloarcula marismortui</i>: a halophilic archaeon from the Dead Sea
 +
|journal=Genome Res.
 +
|volume=14(11)
 +
|page=2221-34
 +
|pub_year=2004
 +
|pubmed=15520287
 +
|pdf=GenomeResearch_HaloarculumGenome.pdf
 +
|comment=[[File:GenomeResearchHaloarculaCover2004.jpg||100px|right]]
 +
}}
 +
</li>
 +
<li value="44"> {{Paper
 +
|title=Development through the eyes of functional genomics
 +
|authors=Fraser AG, Marcotte EM
 +
|journal=Curr Opin Genet Dev.
 +
|pub_year=2004
 +
|volume=14(4)
 +
|page=336-42
 +
|pubmed=15261648
 +
|link=http://dx.doi.org/10.1016/j.gde.2004.06.015 
 +
|pdf=COGD_FraserMarcotte_2004.pdf 
 +
|comment=
 +
}}
 +
</li>
 +
<li value="43"> {{Paper
 +
|title=Protein interaction networks from yeast to human
 +
|authors=Bork P, Jensen LJ, Von Mering C, Ramani AK, Lee I, Marcotte EM
 +
|journal=Curr Opin Struct Biol
 +
|pub_year=2004
 +
|volume=14(3)
 +
|page=292-9
 +
|pubmed=15193308
 +
|link=http://dx.doi.org/10.1016/j.sbi.2004.05.003    
 +
|pdf=cosb-review.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="42"> {{Paper
 +
|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
 +
|journal=J Mol Biol
 +
|pub_year=2004
 +
|volume=340(1)
 +
|page=179-90
 +
|pubmed=15184029
 +
|link=http://dx.doi.org/10.1016/j.jmb.2004.04.047 
 +
|pdf=jmb-lgl.pdf 
 +
|comment=[http://bioinformatics.icmb.utexas.edu/lgl/index.html Supplemental Web Site] [http://sourceforge.net/projects/lgl/ Sourceforge Site] For more recent support of LGL, see the LGL guide by [http://clairemcwhite.github.io/lgl-guide/ Claire McWhite] and the latest updates from [http://www.opte.org/lgl/ the Opte Project]
 +
}}
 +
</li>
 +
<li value="41"> {{Paper
 +
|title=A probabilistic view of gene function
 +
|authors=Fraser AG, Marcotte EM
 +
|journal=Nature Genetics
 +
|pub_year=2004
 +
|volume=36(6)
 +
|page=559-64
 +
|pubmed=15167932
 +
|link=http://dx.doi.org/10.1038/ng1370 
 +
|pdf=ng-fraser-review.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="40"> {{Paper
 +
|title=Practical computational approaches to infer protein function
 +
|authors=Marcotte EM
 +
|journal=Biosilico
 +
|pub_year=2004
 +
|volume=2
 +
|page=24-29
 +
|pubmed=
 +
|link=   
 +
|pdf=Biosilico_Marcotte_2004_proofs.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="39"> {{Paper
 +
|title=The need for a public proteomics repository
 +
|authors=Prince JT, Carlson MW, Wang R, Lu P, Marcotte EM
 +
|journal=Nature Biotechnology
 +
|pub_year=2004
 +
|volume=22(4)
 +
|page=471-472
 +
|pubmed=15085804
 +
|link=http://dx.doi.org/10.1038/nbt0404-471
 +
|nbt-MS-review.pdf
 +
|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
 +
|authors=Date SV, Marcotte EM
 +
|journal=TRENDS in Biotechnology
 +
|pub_year=2004
 +
|volume=22(2)
 +
|page=62-63
 +
|pubmed=
 +
|link=http://dx.doi.org/10.1016/j.tibtech.2003.11.008 
 +
|pdf=trends-biotech.pdf 
 +
|comment=
 +
}}
 +
</li>
 +
</ol>
  
  Hart GT, Lee I, Marcotte EM. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. BMC Bioinformatics 2007 8(1):236
+
== 2003 ==
PDF
+
<ol>
 +
<li value="37"> {{Paper
 +
|title=Diametrical clustering for identifying anti-correlated gene clusters
 +
|authors=Dhillon IS, Marcotte EM, Roshan U
 +
|journal=Bioinformatics
 +
|pub_year=2003
 +
|volume=19(13)
 +
|pubmed=12967956
 +
|page=1612-9
 +
|pdf=diametrical.pdf
 +
}}
 +
</li>
 +
<li value="36"> {{Paper
 +
|title=Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations
 +
|authors=Lu P, Nakorchevskiy A, Marcotte EM
 +
|journal=Proc Natl Acad Sci U S A
 +
|pub_year=2003
 +
|volume=100(18)
 +
|page=10370-5
 +
|pubmed=12934019
 +
|pdf=peng-pnas.pdf
 +
|comment=[http://www.marcottelab.org/paper-pdfs/PNAS_deconvolution_2003-supplementalfiles.zip Supplemental files] (zipped folder containing executable .jar file, yeast test data and cell cycle basis vectors)
 +
}}
 +
</li>
 +
<li value="35"> {{Paper
 +
|title=Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages
 +
|authors=Date SV, Marcotte EM
 +
|journal=Nat Biotechnol.
 +
|pub_year=2003
 +
|volume=21(9)
 +
|page=1055-62
 +
|pubmed=12923548
 +
|pdf=shailesh-natbt.pdf
 +
|comment=[http://www.marcottelab.org/paper-pdfs/NatureBiotech_SystematicNewPathways_FigS1.pdf Fig S1] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_SystematicNewPathways_FigS2.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
 +
|authors=Marcotte EM
 +
|journal=Genome Biol.
 +
|pub_year=2003
 +
|volume=4(6)
 +
|page=323
 +
|pubmed=12801408
 +
|pdf=genome-biology.pdf
 +
}}
 +
</li>
 +
<li value="33"> {{Paper
 +
|title=Exploiting the co-evolution of interacting proteins to discover interaction specificity
 +
|authors=Ramani AK, Marcotte EM
 +
|journal=J Mol Biol.
 +
|pub_year=2003
 +
|volume=327(1)
 +
|page=273-84
 +
|pubmed=12614624
 +
|pdf=jmb_2003.pdf
 +
|comment=[http://orion.icmb.utexas.edu/matrix/ Supplemental Web Site]
 +
}}
 +
</li>
 +
<li value="32"> {{Paper
 +
|title=The genome sequence of the filamentous fungus <i>Neurospora crassa</i>
 +
|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
 +
|journal=Nature
 +
|pub_year=2003
 +
|volume=422(6934)
 +
|page=859-68
 +
|pubmed=12712197
 +
|pdf=Ncrassa.pdf
 +
}}
 +
</li>
 +
<li value="31"> {{Paper
 +
|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
 +
|journal=ICML Workshop
 +
|pub_year=2003
 +
|volume=
 +
|page=
 +
|pdf=icmlws.pdf
 +
}}
 +
</li>
 +
</ol>
  
  Carlson MW, Iyer VR, Marcotte EM. Quantitative gene expression identifies appropriate cell line models for individual cervical cancer pathways. BMC Genomics 2007 8(1):117
+
== 2002 ==
PDF
+
<ol>
 +
<li value="30"> {{Paper
 +
|title=Making sense of proteomics: Using bioinformatics to discover a protein's structure, functions, and interactions
 +
|authors=Mallick P, Marcotte EM
 +
|journal=Proteins and Proteomics: A Laboratory Manual
 +
|pub_year=2002
 +
|volume=Simpson RJ, ed., Cold Spring Harbor Press
 +
|page=
 +
|link=
 +
|comment=
 +
}}
 +
</li>
 +
<li value="29"> {{Paper
 +
|title=Diametrical clustering for identifying anti-correlated gene clusters
 +
|authors=Dhillon IS, Marcotte EM, Roshan U.
 +
|journal=The University of Texas at Austin, Department of Computer Sciences
 +
|pub_year=2002
 +
|volume=Technical Report TR-02-49
 +
|pubmed=
 +
|page=
 +
|link=
 +
|comment=
 +
|pdf=TechnicalReport_DiametricClustering_tr02-49.pdf
 +
}}
 +
</li>
 +
<li value="28"> {{Paper
 +
|title=Predicting protein function and networks on genome-wide scale
 +
|authors=Marcotte EM
 +
|journal=Gene Regulation and Metabolism: Post-Genomic Computational Approaches
 +
|pub_year=2002
 +
|volume=Collado-Vides J, Holfstadt R, eds., MIT press
 +
|pubmed=
 +
|page=
 +
|link=
 +
|comment=
 +
|pdf=Marcotte-ColladoVidesChapter-2002.pdf
 +
}}
 +
</li>
 +
<li value="27"> {{Paper
 +
|title=Predicting functional linkages from gene fusions with confidence
 +
|authors=Verjovsky Marcotte CJ, Marcotte EM
 +
|journal=Applied Bioinformatics
 +
|pub_year=2002
 +
|volume=1(2)
 +
|pubmed=12967956
 +
|page=1-8
 +
|link=
 +
|comment=
 +
|pdf=RS_statistics.pdf
 +
}}
 +
</li>
 +
</ol>
  
  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 2007 25(1):117-124.
+
== 2001 ==
PDF  | Supplement  | Supplemental Data (zipped folder) | News & Views 1  | | 3
+
<ol>
 +
<li value="26"> {{Paper
 +
|title=Exploiting big biology: Integrating large-scale biological data for functional inference
 +
|authors=Marcotte EM, Date SV
 +
|journal=Brief Bioinform
 +
|pub_year=2001
 +
|volume=2(4)
 +
|page=363-74
 +
|pubmed=11808748
 +
|link=
 +
|pdf=BIB_review.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="25"> {{Paper
 +
|title=The path not taken
 +
|authors=Marcotte EM
 +
|journal=Nature Biotechnology
 +
|pub_year=2001
 +
|volume=19(7)
 +
|page=626-7
 +
|pubmed=11433271
 +
|link=
 +
|pdf=path-not-taken.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="24"> {{Paper
 +
|title=Measuring the dynamics of the proteome
 +
|authors=Marcotte EM
 +
|journal=Genome Research
 +
|pub_year=2001
 +
|volume=11(2)
 +
|page=191-3
 +
|pubmed=11157781
 +
|link=
 +
|pdf=measuring-dynamics.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="23"> {{Paper
 +
|title=Mining literature for protein interactions
 +
|authors=Marcotte EM, Xenarios I, Eisenberg D
 +
|journal=Bioinformatics
 +
|pub_year=2001
 +
|volume=17(4)
 +
|page=359-63
 +
|pubmed=11301305
 +
|link=
 +
|pdf=Bioinformatics_lit_mining.pdf
 +
|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
 +
|authors=Eisenberg D, Marcotte E, Pellegrini M, Thompson M, Xenarios I, Yeates T
 +
|journal=FASEB J
 +
|pub_year=2001
 +
|volume=15
 +
|page=A724-A724
 +
|pubmed=
 +
|link=
 +
|pdf=
 +
|comment=
 +
}}
 +
</li>
 +
<li value="21"> {{Paper
 +
|title=DIP: the database of interacting proteins: 2001 update
 +
|authors=Xenarios I, Fernandez E, Salwinski L, Duan XJ, Thompson MJ, Marcotte EM, Eisenberg D
 +
|journal=Nucleic Acids Res
 +
|pub_year=2001
 +
|volume=29(1)
 +
|page=239-41
 +
|pubmed=11125102
 +
|link=
 +
|pdf=NAR_DIP_2001.pdf
 +
|comment=
 +
}}
 +
</li>
 +
</ol>
  
  Lu, P., Rangan, A., Chan, S. Y., Appling, D. R., Hoffman, D. W., & Marcotte, E. M. Global metabolic changes following loss of a feedback loop reveal dynamic steady states of the yeast metabolome. Metabolic Engineering 2007 Jan;9(1):8-20. Epub 2006 Jun 30
+
== 2000 ==
PDF  | Supplemental File 1 | | 3
+
<ol>
 +
<li value="20"> {{Paper
 +
|title=Protein function in the post-genomic era
 +
|authors=Eisenberg D, Marcotte EM, Xenarios I, Yeates TO
 +
|journal=Nature
 +
|pub_year=2000
 +
|volume=405(6788)
 +
|page=823-6
 +
|pubmed=10866208
 +
|link=http://dx.doi.org/10.1038/35015694
 +
|pdf=Nature_Review_2000.taf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="19"> {{Paper
 +
|title=Localizing proteins in the cell from their phylogenetic profiles
 +
|authors=Marcotte EM, Xenarios I, van der Bliek A, Eisenberg D
 +
|journal=Proc Natl Acad Sci U S A.
 +
|pub_year=2000
 +
|volume=97(22)
 +
|page=12115-20
 +
|pubmed=11035803
 +
|link=http://www.pnas.org/content/97/22/12115.long
 +
|pdf=PNAS_mito_profiles.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="18"> {{Paper
 +
|title=Computational genetics: Finding function by non-homology methods
 +
|authors=Marcotte EM
 +
|journal=Curr Opin Struct Biol.
 +
|pub_year=2000
 +
|volume=10(3)
 +
|page=359-65
 +
|pubmed=10851184
 +
|link=http://dx.doi.org/10.1016/S0959-440X(00)00097-X   
 +
|pdf=cosb_compgenetics_2000.pdf
 +
|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 <i>Pyrobaculum aerophilum</i>
 +
|authors=Yang H, Fitz-Gibbon S, Marcotte EM, Tai JH, Hyman EC, Miller JH
 +
|journal=J Bacteriol.
 +
|pub_year=2000
 +
|volume=182(5)
 +
|page=1272-9
 +
|pubmed=10671447
 +
|link=http://jb.asm.org/cgi/content/full/182/5/1272?view=long&pmid=10671447
 +
|pdf=JBacti_Pyrobaculum_glycosylase.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="16"> {{Paper
 +
|title=Increasing the specificity of protein functional inference by the Rosetta Stone method
 +
|authors=Thompson M, Marcotte E, Pellegrini M, Yeates T, Eisenberg D
 +
|journal=Currents in Computational Molecular Biology
 +
|pub_year=2000
 +
|volume=Miyano S, Shamir R, Takagi T, eds., Universal Academy Press, Inc.
 +
|page=
 +
|pubmed=
 +
|link=
 +
|pdf=CurrentsinCompMolBio_Thompson_2000.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="15"> {{Paper
 +
|title=DIP: the database of interacting proteins
 +
|authors=Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D
 +
|journal=Nucleic Acids Res.
 +
|pub_year=2000
 +
|volume=28(1)
 +
|page=289-91
 +
|pubmed=10592249
 +
|link=http://nar.oxfordjournals.org/cgi/content/full/28/1/289
 +
|pdf=NAR_DIP_2000.pdf
 +
|comment=
 +
}}
 +
</li>
 +
</ol>
  
2006
+
== 1999 ==
 +
<ol>
 +
<li value="14"> {{Paper
 +
|title=A combined algorithm for genome-wide prediction of protein function
 +
|authors=Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D
 +
|journal=Nature
 +
|pub_year=1999
 +
|volume=402(6757)
 +
|page=83-6
 +
|pubmed=10573421
 +
|link=http://www.nature.com/nature/journal/v402/n6757/full/402083a0.html
 +
|pdf=nature_genomewidepred.pdf
 +
|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
 +
|authors=Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D
 +
|journal=Science
 +
|pub_year=1999
 +
|volume=285(5428)
 +
|page=751-3
 +
|pubmed=10427000
 +
|link=http://dx.doi.org/10.1126/science.285.5428.751
 +
|pdf=RS_science.pdf
 +
|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
 +
|authors=Marcotte EM, Pellegrini M, Yeates TO, Eisenberg D
 +
|journal=J Mol Biol.
 +
|pub_year=1999
 +
|volume=293(1)
 +
|page=151-60
 +
|pubmed=10512723
 +
|link=http://dx.doi.org/10.1006/jmbi.1999.3136   
 +
|pdf=JMB_Census_2000.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="11"> {{Paper
 +
|title=Assigning protein functions by comparative genome analysis: protein phylogenetic profiles
 +
|authors=Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO
 +
|journal=Proc Natl Acad Sci U S A
 +
|pub_year=1999
 +
|volume=96(8)
 +
|page=4285-8
 +
|pubmed=10200254
 +
|link=http://www.pnas.org/content/96/8/4285.long
 +
|pdf=PNAS_phylogenetic_profiles.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="10"> {{Paper
 +
|title=A fast algorithm for genome-wide analysis of proteins with repeated sequences
 +
|authors=Pellegrini M, Marcotte EM, Yeates TO
 +
|journal=Proteins: Struct. Funct. Genet.
 +
|pub_year=1999
 +
|volume=35(4)
 +
|page=440-6
 +
|pubmed=10382671
 +
|link=http://www3.interscience.wiley.com/journal/65000326/abstract?CRETRY=1&SRETRY=0
 +
|pdf=Proteins_repeats_in_proteins.pdf
 +
|comment=
 +
}}
 +
</li>
 +
</ol>
  
  Hart GT, Ramani AK, Marcotte, EM. How complete are current yeast and human protein-interaction networks? Genome Biology 2006 7(11):120.1 - 120.9.
+
== 1998 ==
PDF  | Additional Data File 1
+
<ol>
 +
<li value="9"> {{Paper
 +
|title=Chicken prion tandem repeats form a stable, protease-resistant domain
 +
|authors=Marcotte EM, Eisenberg D
 +
|journal=Biochemistry
 +
|pub_year=1998
 +
|volume=38(2)
 +
|page=667-76
 +
|pubmed=9888807
 +
|link=http://dx.doi.org/10.1021/bi981487f
 +
|pdf=chickenprion.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="8"> {{Paper
 +
|title=A look at the future of macromolecular structure determination
 +
|authors=Cascio D, Goodwill K, Marcotte E
 +
|journal=Rigaku J.
 +
|pub_year=1998
 +
|volume=15
 +
|page=1-5
 +
|pubmed=
 +
|link=
 +
|pdf=RigakuJournal_look_at_xtal_future.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="7"> {{Paper
 +
|title=Structural analysis shows five glycohydrolase families diverged from a common ancestor
 +
|authors=Robertus JD, Monzingo AF, Marcotte EM, Hart PJ
 +
|journal=J Exp Zool.
 +
|pub_year=1998
 +
|volume=282(1-2)
 +
|page=127-32
 +
|pubmed=9723170
 +
|link=http://www3.interscience.wiley.com/journal/75837/abstract
 +
|pdf=JExpZool_chitinase_evolution.pdf
 +
|comment=
 +
}}
 +
</li>
 +
</ol>
  
  Prince, J. T. & Marcotte, E. M. Chromatographic alignment of ESI-LC-MS proteomics datasets by ordered bijective interpolated warping. Anal. Chem. 2006 78(17):6140-52.
+
== Pre - 1998 ==
PDF
+
<ol>
  
  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 2006 22(12):1524-31. Epub 2006 Apr 3.
+
<li value="6"> {{Paper
PDF
+
|title=Kinetic analysis of barley chitinase
 +
|authors=Hollis T, Honda Y, Fukamizo T, Marcotte E, Day PJ, Robertus JD
 +
|journal=Arch Biochem Biophys.
 +
|pub_year=1997
 +
|volume=344(2)
 +
|page=335-42
 +
|pubmed=9264547
 +
|link=http://dx.doi.org/10.1006/abbi.1997.0225 
 +
|pdf=ArchBiochemBiophys_chitinase_kinetics.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="5"> {{Paper
 +
|title=X-ray structure of an anti-fungal chitosanase from <i>Streptomyces</i> N174
 +
|authors=Marcotte EM, Monzingo AF, Ernst SR, Brzezinski R, Robertus JD
 +
|journal=Nat Struct Biol.
 +
|pub_year=1996
 +
|volume=3(2)
 +
|page=155-62
 +
|pubmed=8564542
 +
|link=
 +
|pdf=NatureStructuralBiology_Chitosanase_1996.pdf
 +
|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
 +
|authors=Monzingo AF, Marcotte EM, Hart PJ, Robertus JD
 +
|journal=Nat Struct Biol
 +
|pub_year=1996
 +
|volume=3(2)
 +
|page=133-40
 +
|pubmed=8564539
 +
|link=
 +
|pdf=NatureStructuralBiology_ConservedCore_1996.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="3"> {{Paper
 +
|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
 +
|journal=Can. J. Bot.
 +
|pub_year=1995
 +
|volume=73 (Suppl. 1)
 +
|page=S1142-S1146
 +
|pdf=CanadianJournalOfBotany_Chitinase_1995.pdf
 +
|pubmed=
 +
|link=
 +
|comment=
 +
}}
 +
</li>
 +
<li value="2"> {{Paper
 +
|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
 +
|journal=J Cell Biol.
 +
|pub_year=1994
 +
|volume=127(5)
 +
|page=1381-94
 +
|pubmed=7962097
 +
|link=http://jcb.rupress.org/cgi/reprint/127/5/1381
 +
|pdf=JCellBiol_KimChan_Ipl2Bem2_1994.pdf
 +
|comment=
 +
}}
 +
</li>
 +
<li value="1"> {{Paper
 +
|title=Crystallization of a chitosanase from <i>Streptomyces</i> N174
 +
|authors=Marcotte E, Hart PJ, Boucher I, Brzezinski R, Robertus JD
 +
|journal=J Mol Biol
 +
|pub_year=1993
 +
|volume=232(3)
 +
|page=995-6
 +
|pubmed=8355284
 +
|link=http://dx.doi.org/10.1006/jmbi.1993.1447
 +
|pdf=JMB_chitosanase_xtal_1993.pdf
 +
|comment=
 +
}}
 +
</li>
 +
</ol>
  
  Narayanaswamy, R., Niu, W., Scouras, A., Hart, G. T., Davies, J., Ellington, A. D., Iyer, V. R., & Marcotte, E. M.: Systematic profiling of cellular phenotypes with spotted cell microarrays reveals new pheromone response genes. Genome Biology 7, R6 (2006).
+
== Patents ==
PDF  |  Supplement  |  Supplemental data files: 1  |  2  |  3  |  4
+
<ol>
 
+
<li value="14"> [https://patents.google.com/patent/WO2020023488A1/ Publication # WO 2020023488 A1] '''Single molecule sequencing identification of post-translational modifications on proteins'''. PCT filed July 23, 2018.
  Lee, I. Narayanaswamy, R. & Marcotte, E. M.: Bioinformatic prediction of yeast gene function. in Yeast Gene Analysis, Stansfield, I., ed., Elsevier Press (2006).
+
<li value="13"> [https://patents.google.com/patent/WO2020014586A1/ Publication # WO 2020014586 A1] '''Molecular neighborhood detection by oligonucleotides'''. PCT filed July 12, 2018.
PDF  
+
<li value="12"> [http://patft1.uspto.gov/netacgi/nph-Parser?Sect1=PTO1&Sect2=HITOFF&d=PALL&p=1&u=%2Fnetahtml%2FPTO%2Fsrchnum.htm&r=1&f=G&l=50&s1=10,175,249.PN.&OS=PN/10,175,249&RS=PN/10,175,249 10,175,249 B2], issued January 8, 2019. '''Proteomic identification of antibodies'''. Lavinder, Jason; Boutz, Danny; Wine, Yariv; Marcotte, Edward; Georgiou, George.
 
+
<li value="11"> [https://patents.google.com/patent/US10545153B2/ 10,545,153 B2], issued January 28, 2020. '''Single molecule peptide sequencing'''. [https://patentscope.wipo.int/search/en/detail.jsf?docId=WO2016069124 Publication # WO/2016/069124], Intl appl # PCT/US2015/050099, International filing date 15.09.2015. Marcotte, Edward; Anslyn, Eric; Ellington, Andrew; Swaminathan, Jagannath; Hernandez, Erik; Johnson, Amber; Boulgakov, Alexander; Bachman, Logan; Seifert, Helen. '''Improved single molecule sequencing'''.
  Eisenberg D, Marcotte E, McLachlan AD, Pellegrini M: Bioinformatic challenges for the next decade(s). Phil. Trans. R. Soc. B 2006.
+
<li value="10"> [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=9,625,469&OS=9,625,469&RS=9,625,469 9,625,469], issued April, 18, 2017. '''Identifying peptides at the single molecule level'''. Marcotte, Edward; Swaminathan, Jagannath; Ellington, Andrew; Anslyn, Eric. Appl # 14128247, filed 22.06.2012; publication # US20140349860, 27.11.2014. [https://www.ipo.gov.uk/p-ipsum/Case/PublicationNumber/GB2510488 UK patent GB2510499] issued April 8, 2020.
PDF 
+
<li value="9"> [http://patentscope.wipo.int/search/en/detail.jsf?docId=WO2013067308&recNum=102&maxRec=&office=&prevFilter=&sortOption=&queryString=%28+&tab=PCT+Biblio Publication # WO 2013067308 A2], '''Compositions and methods for inducing disruption of blood vasculature and for reducing angiogenesis''', PCT filed Nov 2, 2012; provisional patent # 61/555,212 filed Nov 3, 2011.</li>
 
+
<li value="8"> [https://www.google.com/patents/WO2013055867A1?cl=en&dq=Genes+involved+in+biotic+stress+response+in+plants&hl=en&sa=X&ei=1ALYUvrrDIKnkQeVtoDwCw&ved=0CEcQ6AEwAg Publication # WO 2013055867 A1], '''Genes involved in stress response in plants''', PCT filed Oct 11, 2012.</li>
2005
+
<li value="7">  [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="6">  [http://patft1.uspto.gov/netacgi/nph-Parser?Sect1=PTO1&Sect2=HITOFF&d=PALL&p=1&u=%2Fnetahtml%2FPTO%2Fsrchnum.htm&r=1&f=G&l=50&s1=9,146,241.PN.&OS=PN/9,146,241&RS=PN/9,146,241 9,146,241], issued September 29, 2015. '''Proteomic identification of antibodies'''. Lavinder, Jason; Wine, Yariv; Boutz, Danny; Marcotte, Edward; Georgiou, George. Appl # 13/684,395, filed November 23, 2012.
  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 2005, 438(7067):441-2.
+
<li value="5"> [https://patents.google.com/patent/US9090674B2/en?oq=9%2c090%2c674 9,090,674 B2], issued July 28, 2015. '''Rapid isolation of monoclonal antibodies from animals'''. Reddy, Sai; Ge, Xin; Lavinder, Jason; Boutz, Danny; Ellington, Andrew D.; Marcotte, Edward M.; Georgiou, George.  
PDF  |  Supplement  |  Nature Press Release  |  Nature Intro  |  iGEM story  |  Nature-top 10 images of 2005  |  NYTimes story  |  UT Feature Story  |  UT Press Release 
+
<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], issued May 10, 2005. '''Determining the functions and interactions of proteins by comparative analysis'''.</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], issued August 3, 2004. '''Determining protein function and interaction from genome analysis'''.</li>
  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.
+
<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], issued May 13, 2003. '''Assigning protein functions by comparative genome analysis protein phylogenetic profiles'''.</li>
PDF 
+
<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], issued October 15, 2002. '''Rosetta stone method for detecting protein function and protein-protein interactions from genome sequences'''.</li>
 
+
</ol>
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. 2005 Aug;15(8):1118-26.
+
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 2005, 6:r40.
+
PDF 
+
 
+
  Razvan Bunescu, Ruifang Ge, Rohit J. Kate, Edward M. Marcotte, Raymond J. Mooney, Arun Kumar Ramani, and Yuk Wah Wong:  Comparative Experiments on Learning Information Extractors for Proteins and their Interactions.Artif Intell Med. 2005 Feb;33(2):139-55.
+
PDF  
+
 
+
  Ramani, A. K, Marcotte, E. M., Bunescu, R. C., & Mooney, R. J.: Using Biomedical Literature Mining to Consolidate the Set of Known Human Protein-Protein Interactions. Intelligent Systems in Molecular Biology-ACL Workshop (2005).
+
PDF 
+
 
+
  Date SV, Marcotte EM:  Protein function prediction using the Protein Link Explorer (PLEX). Bioinformatics. 2005 Feb 8; [Epub ahead of print].
+
PDF 
+
 
+
2004
+
 
+
  Lee I, Date SV, Adai AT, Marcotte EM:  A Probabilistic functional network of yeast genes. Science 306(5701):1555-8 (2004).
+
PDF  |  Supplement  |  Supplemental data files: README  |  1  |  2  |  3  |  4  |  5
+
 
+
  Baliga NS, Bonneau R, Facciotti MT, Pan M, Glusman G, Deutsch EW, Shannon P, Chiu Y, Weng RS, Gan RR, Hung P, Date SV, Marcotte E, Hood L, Ng WV:  Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res. 14(11):2221-34 (2004).
+
PDF 
+
 
+
  Fraser AG, Marcotte EM:  Development through the eyes of functional genomics. Curr Opin Genet Dev. 14(4):336-42 (2004).
+
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).
+
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., JMB,340(1):179-90(2004).
+
PDF  
+
 
+
  Fraser AG, Marcotte EM:   A probabilistic view of gene function., Nature Genetics, 36(6):559-64 (2004).
+
PDF 
+
 
+
  Marcotte, E. M.: Practical computational approaches to infer protein function. Biosilico, 2, 24-29 (2004).
+
PDF 
+
 
+
  John T Prince, Mark W Carlson, Rong Wang, Peng Lu & Edward M Marcotte:  The need for a public proteomics repository, Nature Biotechnology, 22, 4, 471-472 (2004).
+
PDF 
+
 
+
  Shailesh V Date & Edward M Marcotte:  Response to McDermott and Samudrala: Enhanced functional information from predicted protein networks, TRENDS in Biotechnology , 22, 2, 62-63 (2004).
+
PDF  |  NCBI
+
 
+
2003
+
 
+
  Shailesh V Date & Edward M Marcotte:  Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages, Nature Biotechnology, 21, 9, 1055-1062 (2003).
+
PDF  |  NCBI  |  Fig S1  |  Fig S2  |  Table S1
+
 
+
  Peng Lu, Aleksey Nakorchevskiy, and Edward M. Marcotte:  Expression deconvolution: A reinterpretation of DNA microarray data reveals dynamic changes in cell populations , PNAS, 100, 18, 10370-10375 (2003).
+
PDF  |  NCBI
+
 
+
  James E. Galagan et al:  The genome sequence of the filamentous fungus Neurospora crassa, Nature, 422, 859-868 (2003).
+
PDF  |  NCBI
+
 
+
  Edward M Marcotte:  Assembling a jigsaw puzzle with 20,000 parts., Genome Biology, 2003, Vol 4. Issue 6, Article 323.
+
PDF  |  NCBI
+
 
+
  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.
+
PDF
+
 
+
  Inderjit Dhillon, Edward Marcotte, and Usman Roshan:  Diametrical Clustering for identifying anti-correlated gene clusters., Bioinformatics, 19: 1612-1619, 2003.
+
PDF  |  NCBI
+
 
+
  Ramani,A. K. & Marcotte, E. M.:  Exploiting the co-evolution of interacting proteins to discover interaction specificity, JMB, 2003; 327(1):273-284.
+
PDF  |  NCBI
+
2002
+
 
+
  Mallick, P. & Marcotte, E. M.: Making sense of proteomics: Using bioinformatics to discover a protein's structure, functions, and interactions. in Proteins and Proteomics: A Laboratory Manual, Simpson, R. J., ed., Cold Spring Harbor Press (2002).
+
 
+
  Dhillon, I. S., Marcotte, E. M. & Roshan, U.: Diametrical Clustering for identifying anti-correlated gene clusters. The University of Texas at Austin, Department of Computer Sciences. Technical Report TR-02-49. September 2002.
+
PDF  
+
 
+
  Marcotte, E. M.: Predicting Protein Function and Networks on Genome-Wide Scale. in Gene Regulation and Metabolism: Post-Genomic Computational Approaches, Collado-Vides, J. & Holfstadt, R., eds., MIT press (2002).
+
 
+
  Verjovsky Marcotte, C. J. & Marcotte E. M:  Prediction functional linkages from gene fusions with confidence, App. Bioinform, 2002;1(2):1-8
+
PDF(submission proofs)
+
2001
+
 
+
  Marcotte, E. M. & Date, S.V:  Exploiting Big Biology: Integrating large-scale biological data for functional inference, Brief Bioinform, 2001 Dec;2(4):363-74.
+
PDF
+
 
+
  Marcotte, E. M.:  The path not taken, Nat Biotechnol., 2001 Jul;19(7):626-7.
+
PDF
+
 
+
  Marcotte, E. M.:  Measuring the Dynamics of the Proteome, Genome Res 2001 Feb;11(2):191-3.
+
PDF
+
 
+
  Marcotte, E. M., Xenarios, I. & Eisenberg, D.:  Mining Literature for Protein Interactions, Bioinformatics 2001 Apr;17(4):359-63
+
PDF |  Supplemental Files: README  |  1  |  2  |  3  |  4
+
 
+
  Eisenberg, D., Marcotte, E., Pellegrini, M., Thompson, M., Xenarios, I., Yeates, T.: From genome sequences to protein interactions. FASEB J. 15, A724-A724 (2001).
+
 
+
  Xenarios I, Fernandez E, Salwinski L, Duan XJ, Thompson MJ, Marcotte EM, Eisenberg D.: DIP: the database of interacting proteins: 2001 update, Nucleic Acids Res. 29(1):239-41 (2001)
+
PDF
+
 
+
2000
+
 
+
  Eisenberg, D., Marcotte, E. M., Xenarios, I. & Yeates, T. O.:  Protein function in the post-genomic era.  Nature 405, 823-6 (2000).
+
PDF
+
 
+
  Marcotte, E. M., Xenarios, I., van der Bliek, A. & Eisenberg, D.: Localizing proteins in the cell from their phylogenetic profiles.  Proc. Natl. Acad. Sci.  97, 12115-20 (2000).
+
PDF
+
 
+
  Marcotte, E. M.: Computational genetics: Finding Function by Non-Homology Methods. Curr. Op. Struct. Bio. 10, 359-65 (2000).
+
PDF
+
 
+
  Yang, H., Fitz-Gibbon, S., Marcotte, E. M., Tai, J. H., Hyman, E. C. & Miller, J. H.: Characterization of a thermostable DNA glycosylase specific for U/G and T/G mismatches from the hyperthermophilic archaeon Pyrobaculum aerophilum. J. Bacteriol. 182, 1272-9 (2000).
+
PDF
+
 
+
  Thompson, M., Marcotte, E., Pellegrini, M., Yeates, T. & Eisenberg, D.: Increasing the specificity of protein functional inference by the Rosetta Stone method. in Currents in Computational Molecular Biology, Miyano, S., Shamir, R. & Takagi, T.., eds., Universal Academy Press, Inc. (2000).
+
PDF
+
 
+
  Xenarios, I., Rice, D. W., Salwinski, L., Baron, M. K., Marcotte, E. M., & Eisenberg, D.: DIP: Database of Interacting Proteins, Nucleic Acids Research 28, 289-91 (2000).
+
PDF
+
 
+
1999
+
 
+
  Marcotte, E. M., Pellegrini, M., Thompson, M. J., Yeates, T. & Eisenberg, D.  A Combined Algorithm for Genome-Wide Prediction of Protein Function. Nature 402, 83-86 (1999).
+
PDF
+
This paper was the subject of an invited commentary:
+
Sali, A.  Genomics: Functional links between proteins.  Nature 402, 23-26 (1999), and was featured in the Boston Globe (Nov. 3, 1999) and the Los Angeles Times (Nov. 4, 1999).
+
 
+
  Marcotte, E. M., Pellegrini, M., Ng, H.-L., Rice, D. W., Yeates, T. O. & Eisenberg, D. Detecting Protein Function & Protein-Protein Interactions from Genome Sequences.  Science  285, 751-753 (1999).
+
PDF
+
This paper was the subject of an invited commentary:
+
Doolittle, R. F. Do you dig my groove? Nature: Genetics  23, 6-8 (1999).
+
 
+
  Marcotte, E. M., Pellegrini, M., Yeates, T. O. & Eisenberg, D. A Census of Protein Repeats. J. Molec. Biol. 293, 151-160 (1999).
+
PDF
+
 
+
  Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D. & Yeates, T. O.: Assigning protein functions by comparative genome analysis: protein phylogenetic profiles.  Proc.Natl. Acad. Sci. 96, 4285-4288 (1999).
+
PDF
+
 
+
  Pellegrini, M.,  Marcotte, E. M. & Yeates, T. O. A Fast Algorithm for Genome-Wide Analysis of Proteins with Repeated SequencesProteins: Struct. Funct. Genet.  35, 440-446 (1999).
+
PDF
+
 
+
1998
+
 
+
  Marcotte, E. M. & Eisenberg, D.  Chicken prion tandem repeats form a stable, protease resistant domain. Biochemistry  38, 667-676 (1998).
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PDF
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  Cascio, D., Goodwill, K. & Marcotte, E.  A Look at the Future of Macromolecular Structure Determination.  Rigaku J. 15, 1-5 (1998).
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PDF
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  Robertus, J. D., Monzingo, A. F., Marcotte, E. M. & Hart, P. J.: Structural Analysis Shows Five Glycohydrolase Families Diverged From a Common Ancestor. J. Exp. Zool. 282, 127-32 (1998).
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PDF
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Pre - 1998
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  Hollis, T., Honda, Y., Fukamizo, T., Marcotte, E., Day, P. J. & Robertus, J. D.: Kinetic Analysis of Barley Chitinase. Arch. Biochem. Biophys. 344, 335-342 (1997).
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PDF
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  Marcotte EM, Monzingo AF, Ernst SR, Brzezinski R, Robertus JD: X-ray structure of an anti-fungal chitosanase from streptomyces N174., Nat Struct Biol. 1996 Feb;3(2):155-62.
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This paper was the subject of an invited commentary:
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Kirby, A. J.: Illuminating the ancient retainer. Nature: Structural Biol. 3, 107-108 (1996).
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  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)
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  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).
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  Kim, Y-J., Francisco, L., Chen, G-C., Marcotte, E. & Chan, C.: Control of Cellular Morphogenesis by the Ipl2/Bem2 GTPase-activating Protein: Possible Role of Protein Phosphorylation. J. Cell. Biol. 127, 1381-1394 (1994).
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PDF
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  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)
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PDF
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PATENTS
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  # 6,892,139, Determining the functions and interactions of proteins by comparative analysis, granted May 10, 2005.
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  # 6,772,069, Determining protein function and interaction from genome analysis, granted August 3, 2004.
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  # 6,564,151, Assigning protein functions by comparative genome analysis protein phylogenetic profiles, granted May 13, 2003.
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  # 6,466,874, Rosetta stone method for detecting protein function and protein-protein interactions from genome sequences, granted October 15, 2002.
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Latest revision as of 12:49, 2 December 2020

Contents

2020

  1. Floyd BM, Drew K, Marcotte EM, Systematic Identification of Protein Phosphorylation-Mediated Interactions, bioRxiv, Posted September 19: (2020) PubMed Link
  2. Drew K, Wallingford JB, Marcotte EM, hu.MAP 2.0: Integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies, bioRxiv, Posted September 16: (2020) PubMed Link
  3. Garge RK, Cha HJ, Lee, C, Gollihar JD, Kachroo AH, Wallingford JB, Marcotte EM, Antifungal benzimidazoles disrupt vasculature by targeting one of nine β-tubulins, bioRxiv, Posted September 15: (2020) PubMed Link
  4. Devitt C, Lee C, Cox R, Papoulas O, Alvarado J, Marcotte EM, Wallingford JB, Twinfilin1 controls lamellipodial protrusive activity and actin turnover during vertebrate gastrulation, bioRxiv, Posted September 3: (2020) PubMed Link
  5. Boulgakov AA, Moor SR, Jo HH, Metola P, Joyce LA, Marcotte EM, Welch CJ, Anslyn EV, Next-Generation TLC: A Quantitative Platform for Parallel Spotting and Imaging, J Org Chem, 85(15):9447–9453 (2020) PubMed Link
    JOC-TLCCover2020.jpg
  6. Garge RK, Laurent JM, Kachroo AH, Marcotte EM, Systematic humanization of the yeast cytoskeleton discerns functionally replaceable from divergent human genes, Genetics, 215(4):1153-1169 (2020) PubMed bioRxiv preprint Deposited December 17, 2019
    GeneticsHumanizedYeastCover2020.jpg
  7. Laurent J, Garge RK, Teufel AI, Wilke CO, Kachroo AH, Marcotte EM, Humanization of yeast genes with multiple human orthologs reveals principles of functional divergence between paralogs, PLoS Biology, 18(5):e3000627 (2020) PubMed Link bioRxiv preprint (deposited June 13, 2019)
  8. Lee C, Cox RM, Papoulas O, Horani A, Drew K, Devitt CC, Brody SL, Marcotte EM, Wallingford JB, Functional partitioning of a liquid-like organelle during assembly of axonemal dyneins, eLife, 9:e58662 (2020) PubMed Link bioRxiv preprint (deposited April 21, 2020)
  9. McWhite CD, Papoulas O, Drew K, Cox RM, June V, Dong OX, Kwon T, Wan C, Salmi ML, Roux, SJ Jr., Browning KS, Chen ZJ, Ronald PC, Marcotte EM, A pan-plant protein complex map reveals deep conservation and novel assemblies, Cell, 181(2):460-474.e14 (2020) PubMed Link PDF bioRxiv preprint (deposited October 24, 2019)
  10. McCafferty C, Verbeke EJ, Marcotte EM, Taylor DW, Structural Biology in the Multi-Omics Era, Journal of Chemical Information and Modeling, 60(5):2424-2429 (2020) PubMed Link PDF
    JCIMShotgunEMCover2020.jpg
  11. Blank HM, Papoulas O, Maitra N, Garge RK, Kennedy BK, Schilling B, Marcotte EM, Polymenis M, Abundances of transcripts, proteins, and metabolites in the cell cycle of budding yeast reveals coordinate control of lipid metabolism, Molecular Biology of the Cell, Published online 4 Mar: (2020) PubMed Link PDF bioRxiv preprint (deposited Dec 18, 2019)
  12. Drew K, Lee C, Cox RM, Dang V, Devitt CC, Papoulas O, Huizar RL, Marcotte EM, Wallingford JB, A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating, Developmental Biology, 467(1-2):108-117 (2020) PubMed Link bioRxiv preprint (deposited Feb 27, 2020)
  13. Liebeskind BJ, Young RL, Halling DB, Aldrich RW, Marcotte EM, Mapping functional protein neighborhoods in the mouse brain, bioRxiv, Posted January 27: (2020) PubMed Link
  14. Howard CJ, Floyd Bm, Bardo AM, Swaminathan J, Marcotte EM, Anslyn EV, Solid-phase peptide capture and release for bulk and single-molecule proteomics, ACS Chemical Biology, 15(6):1401-1407 (2020) PubMed Link bioRxiv preprint (deposited January 14, 2020)
  15. Verbeke E, Zhou Y, Horton AP, Mallam AL, Taylor DW, Marcotte EM, Separating distinct structures of multiple macromolecular assemblies from cryo-EM projections, Journal of Structural Biology, 209(1):107416 (2020) PubMed Link PDF SLICEM code on Github bioRxiv preprint (deposited Apr 20, 2019)
  16. Bachman JL, Pavlich CI, Boley AJ, Marcotte EM, Anslyn EV, Synthesis of Carboxy ATTO 647N Using Redox Cycling for Xanthone Access, Org Lett, 22(2):381-385 (2020) PubMed Link PDF

2019

  1. McCaffery CL, Marcotte EM, Taylor DW, Simplified geometric representations of protein structures identify complementary interaction interfaces, Proteins: Structure, Function, and Bioinformatics, posted November 2:1-13 (2020) PubMed Link bioRxiv preprint (deposited Dec 23, 2019)
  2. Kim JJ, Lee SY, Gong F, Battenhouse AM, Boutz DR, Bashyal A, Refvik ST, Chiang CM, Xhemalce B, Paull TT, Brodbelt JS, Marcotte EM, Miller KM, Systematic bromodomain protein screens identify homologous recombination and R-loop suppression pathways involved in genome integrity, Genes and Development, 33(23-24):1751-1774 (2019) PubMed Link PDF
  3. Mallam AL, Sae-Lee W, Schaub JM, Tu F, Battenhouse A, Jang YJ, Kim J, Finkelstein IJ, Marcotte EM, Drew K, Systematic discovery of endogenous human ribonucleoprotein complexes, Cell Reports, 29(5):P1351-1368.e5 (2019) PubMed Link PDF bioRxiv preprint (deposited Nov 27, 2018)
  4. Liebeskind B, Aldrich RW, Marcotte EM, Ancestral Reconstruction of Protein Interaction Networks, PLoS Computational Biology, 15(10):e1007396 (2019) PubMed Link PDF bioRxiv preprint (deposited September 9, 2018)
  5. Glover N, Dessimoz C, Ebersberger I, Forslund SK, Gabaldón T, Huerta-Cepas J, Martin MJ, Muffato M, Patricio M, Pereira C, Sousa da Silva A, Wang Y, Sonnhammer E, Thomas PD; Quest for Orthologs Consortium, Advances and Applications in the Quest for Orthologs., Mol Biol Evol, 36(10):2157-2164 (2019) PubMed Link PDF
  6. Boulgakov AA, Ellington AD, Marcotte EM, Bringing Microscopy-By-Sequencing into View, Trends in Biotechnology, 38(2):154-162 (available online 2019, published 2020) PubMed Link PDF
    TIBTechCover2020.jpg

2018

  1. Gibeaux R, Acker R, Kitaoka M, Georgiou G, van Kruijsbergen I, Ford B, Marcotte EM, Nomura DK, Kwon T, Veenstra GJC, Heald R, Paternal chromosome loss and metabolic crisis contribute to hybrid inviability in Xenopus, Nature, 553:337–341 (2018) PubMed Link PDF
  2. Huizar RL, Lee C, Boulgakov AA, Horani A, Tu F, Marcotte EM, Brody SL, Wallingford JB, A liquid-like organelle at the root of motile ciliopathy, eLife, 7:e38497 (2018) PubMed Link PDF bioRxiv preprint (Deposited Nov 3, 2017)
  3. Boulgakov AA, Xiong E, Bhadra S, Ellington AD, Marcotte EM, From Space to Sequence and Back Again: Iterative DNA Proximity Ligation and its Applications to DNA-Based Imaging, bioRxiv, posted November 14: (2018) PubMed Link
  4. Hwang S, Kim CY, Yang S, Kim E, Hart T, Marcotte EM, Lee I, HumanNet v2: human gene networks for disease research, Nucleic Acids Res, 47 (D1):D573–D580 (2018,2019) PubMed Link PDF
  5. Swaminathan J, Boulgakov AA, Hernandez ET, Bardo AM, Bachman JL, Marotta J, Johnson AM, Anslyn EV, Marcotte EM, Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures, Nature Biotechnology, 36:1076–1082 (2018) PubMed Link PDF Free access authors' view-only version at NBT Supplement Supplementary Tables github with code Data repository (Zenodo) News & Views Commentary in Phys.org
  6. Teufel AI, Johnson MM, Laurent JM, Kachroo AH, Marcotte EM, Wilke CO, The many nuanced evolutionary consequences of duplicated genes, Mol Bio Evol, 36(2):304-314 (2018) PubMed Link PDF bioRxiv preprint (deposited July 10, 2018)
  7. Sun X, Boulgakov AA, Smith L, Metola P, Marcotte EM, Anslyn EV, Photography Coupled with Self-Propagating Chemical Cascades. The Differentiation and Quantitation of G and V Nerve Agent Mimics via Chromaticity, ACS Central Science, 4(7):854-861 (2018) PubMed Link PDF
  8. Verbeke EJ, Mallam AL, Drew K, Marcotte EM, Taylor DW, Classification of single particles from human cell extract reveals distinct structures, Cell Reports, (24)1:259–268.e3 (2018) PubMed Link PDF bioRxiv preprint (deposited January 14 , 2018)
  9. Akhmetov A, Laurent JM, Gollihar J, Gardner EC, Garge RK, Ellington AD, Kachroo AH, Marcotte EM, Single-step precision genome editing in yeast using CRISPR-Cas9, Bio-protocol, 8(6):e2765 (2018) PubMed Link PDF
  10. Tu F, Sedzinski J, Ma Y, Marcotte EM, Wallingford JB, Protein localization screening in vivo reveals novel regulators of multiciliated cell development and function, J Cell Sci, 131 (3):jcs206565 (2018) PubMed Link PDF
    JCSCiliaCover2018.jpg

2017

  1. Hernandez ET, Swaminathan J, Marcotte EM , Anslyn EV, Solution-phase and solid-phase sequential, selective modification of side chains in KDYWEC and KDYWE as models for usage in single-molecule protein sequencing, New Journal of Chemistry, 41:462-469 (2017) PubMed Link PDF
    NJCPeptideLabelingCover2017.jpg
  2. Drew K, Müller CL, Bonneau R, Marcotte EM, Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets, PLoS Computational Biology, 13(10):e1005625 (2017) PubMed Link PDF
  3. Kuboniwa M, Houser JR, Hendrickson EL, Wang Q, Alghamdi SA, Sakanaka A, Miller DP, Hutcherson JA, Wang T, Beck DAC, Whiteley M, Amano A, Wang H, Marcotte EM, Hackett M, Lamont RJ, Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial infection, Nature Microbiology, 2:1493–1499 (2017) PubMed Link PDF
  4. Kachroo AH, Laurent JM, Akhmetov A, Szilagyi-Jones M, McWhite CD, Zhao A, Marcotte EM, Systematic bacterialization of yeast genes identifies a near-universally swappable pathway, eLife, 6:e25093 (2017) PubMed Link PDF
  5. Akhmetov A, Ellington A, Marcotte E, A highly parallel strategy for storage of digital information in living cells, BMC Biotechnology, 18:64 (2018) PubMed Link PDF bioRxiv preprint (deposited December 26, 2016) Open access pdf version of the article
  6. Mallam A, Marcotte EM, Systems-wide studies uncover Commander, a multiprotein complex essential to human development, Cell Systems, 4:483-494 (2017) PubMed Link PDF
  7. Drew, K., Lee, C., Huizar, R. L., Tu, F., Borgeson, B., McWhite, C. D., Ma, Y., Wallingford, J. B., Marcotte, E. M., Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes, Molecular Systems Biology, 13:932 (2017) PubMed Link PDF bioRxiv preprint (deposited December 7, 2016)
    MSBHuMAPCover2018.jpg
  8. Shim JE, Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom UM, Marcotte EM, Lee I, GWAB: a web server for the network-based boosting of human genome-wide association data, Nucleic Acids Research, 89(6):3747–3753 (2017) PubMed Link PDF
  9. Caglar MU, Houser JR, Barnhart CS, Boutz DR, Carroll SM, Dasgupta A, Lenoir WF, Smith BL, Sridhara V, Sydykova DK, Vander Wood D, Marx CJ, Marcotte EM, Barrick JE, Wilke CO, The E. coli molecular phenotype under different growth conditions, Scientific Reports, 7:45303 (2017) PubMed Link PDF
  10. Brown CW, Sridhara V, Boutz DR, Person MD, Marcotte EM, Barrick JE, Wilke CO, Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions, BMC Genomics, 18(1):301 (2017) PubMed Link PDF
  11. AP Horton, SA Robotham, JR Cannon, DD Holden, EM Marcotte, Brodbelt JS, Comprehensive de novo peptide sequencing from MS/MS pairs generated through complementary collision induced dissociation and 351 nm ultraviolet photodissociation, Analytical Chemistry, 89(6):3747–3753 (2017) PubMed Link PDF
  12. Lee T, Hwang S, Kim CY, Shim H, Kim H, Ronald PC, Marcotte EM, Lee I, WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, Molecular Plant, S1674-2052(17):30108-9 (2017) PubMed Link PDF bioRxiv preprint (deposited February 6, 2017)
  13. Hilterbrand AT, Boutz DR, Marcotte EM, Upton JW, Murine Cytomegalovirus Deubiquitinase Regulates Viral Chemokine Levels To Control Inflammation and Pathogenesis, mBio, 8:e01864-16 (2017) PubMed Link PDF

2016

  1. Young JH, Peyton M, Kim HS, McMillan E, Minna JD, White MA, Marcotte EM, Computational Discovery of Pathway-Level Genetic Vulnerabilities in Non-Small-Cell Lung Cancer, Bioinformatics, 32(9):1373-9 (2016) PubMed Link PDF Supporting code
  2. Lee J, Boutz DR, Chromikova V, Joyce MG, Vollmers C, Leung K, Horton AP, DeKosky BJ, Lee CH, Lavinder JJ, Murrin EM, Chrysostomou C, Hoi KH, Tsybovsky Y, Thomas PV, Druz A, Zhang B, Zhang Y, Wang L, Kong WP, Park D, Popova LI, Dekker CL, Davis MM, Carter CE, Ross TM, Ellington AD, Wilson PC, Marcotte EM, Mascola JR, Ippolito GC, Krammer F, Quake SR, Kwong PD, Georgiou G, Molecular-level analysis of the serum antibody repertoire in young adults before and after seasonal influenza vaccination, Nature Medicine, 22(12):1456-1464 (2016) PubMed Link PDF
    NatureMedicineIgSeqCover2016.jpg
  3. Session AM*, Uno Y*, Kwon T*, et al., Genome evolution in the allotetraploid frog Xenopus laevis, Nature, 538:336–343 (2016) PubMed Link PDF News&Views and pdf; Supplementary Information
    NatureXenopusCover2016.jpg
  4. Wu GC, Cheung NV, Georgiou G, Marcotte EM, Ippolito GC, Temporal Stability and Molecular Persistence of the Bone Marrow Plasma Cell Antibody Repertoire, Nature Communications, 7:13838 (2016) PubMed Link PDF bioRxiv preprint (deposited August 2, 2016)
  5. Toriyama M, Lee C, Taylor SP, Duran I, Cohn DH, Bruel AL, Tabler JM, Drew K, Kelly MR, Kim S, Park TJ, Braun D, Pierquin G, Biver A, Wagner K, Malfroot A, Panigrahi I, Franco B, Al-Lami HA, Yeung Y, Choi YJ; University of Washington Center for Mendelian Genomics, Duffourd Y, Faivre L, Rivière JB, Chen J, Liu KJ, Marcotte EM, Hildebrandt F, Thauvin-Robinet C, Krakow D, Jackson PK, Wallingford JB, The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery, Nature Genetics, 48(6):648-56 (2016) PubMed Link PDF
  6. Young JH, Marcotte EM, Predicting Drug Synergy and Antagonism from Genetic Interaction Neighborhoods, bioRxiv, :deposited April 27 (2016) PubMed Link
  7. Young JH, Marcotte EM, Predictability of Genetic Interactions from Functional Gene Modules, G3, 7:617-624 (2016) PubMed Link PDF bioRxiv preprint (deposited April 25, 2016)
  8. Teperek M, Simeone A, Gaggioli V, Miyamoto K, Allen G, Erkek S, Peters A, Kwon T, Marcotte E, Zegerman P, Bradshaw C, Gurdon J, Jullien J, Sperm is epigenetically programmed to regulate gene transcription in embryos, Genome Research, 26:1034-1046 (2016) PubMed Link PDF
  9. Liebeskind BJ, McWhite CD, Marcotte EM, Towards Consensus Gene Ages, Genome Biology and Evolution, 8(6):1812-23 (2016) PubMed Link PDF bioRxiv preprint (deposited March 1) Supporting code and datasets
  10. 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, 88(7):3990-7 (2016) PubMed Link PDF Supporting code

2015

  1. Woods JO, Tien M, Marcotte EM, Interrogating conserved elements of diseases using Boolean combinations of orthologous phenotypes, bioRxiv, posted April 13: (2015) PubMed Link
  2. 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, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, R Tillier E, Wallingford JB, Parkinson J, Marcotte EM, Emili A, Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes, Data in Brief, 6:715-21 (2015) PubMed Link PDF
  3. 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, Nucl. Acid. Res., 44(D1):D848-54 (2015) PubMed Link PDF
  4. Murray J, Kwon T, Marcotte EM, Whiteley M, Intrinsic antimicrobial resistance determinants in the 'superbug' P. aeruginosa, mBio, 6(6):e01603-15 (2015) PubMed Link PDF
  5. Poldrack RA, Laumann T, Koyejo O, Gregory B, Hover A, Chen M-Y, Luci J, Huk A, Joo S-J, Boyd R, Hunicke-Smith S, Simpson ZB, Caven T, Sochat V, Shine JM, Gordon E, Snyder AZ, Adeyemo B, Petersen SE, Glahn D, Mckay DR, Blangero J, Frick L, Marcotte EM, Mumford JA, Long-term neural and physiological phenotyping of a single human, Nature Communications, 6:Article #8885 (2015) PubMed Link PDF
  6. Hwang S, Eiru K, Lee I, Marcotte EM, Systematic comparison of variant calling pipelines using gold standard personal exome variants, Scientific Reports, 5:17875 (2015) PubMed Link PDF Example variant calling parameters Gold standard vcf and exome capture region bed files
  7. Laurent JM, Young JH, Kachroo AH, Marcotte EM, Efforts to make and apply humanized yeast, Briefings in Functional Genomics, 15(2):155-63 (2015) PubMed Link PDF
  8. 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, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, R Tillier E, Wallingford JB, Parkinson J, Marcotte EM, Emili A, Panorama of ancient metazoan macromolecular complexes, Nature, 525:339–344 (2015) PubMed Link PDF Supplementary data is available here. Supporting web site
  9. McWhite CD, Liebeskind BJ, Marcotte EM, Applications of comparative evolution to human disease genetics, Current Opinion in Genetics & Development, 35:16–24 (2015) PubMed Link PDF COGD supplies a direct link around their paywall for free access to the paper
  10. 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(8):e1004400 (2015) PubMed Link PDF
  11. Kachroo AH, Laurent JM, Yellman CM, Meyer AG, Wilke CO, Marcotte EM, Systematic humanization of yeast genes reveals conserved functions and genetic modularity, Science, 348(6237):921-925 (2015) PubMed Link PDF Supplement Supplementary Tables and Files Science magazine supplies a direct link around their paywall for free access to the manuscript and pdf reprint. Code and data for protein interaction evolution simulations are here
  12. Lee I, Kim E, Marcotte EM, Modes of Interaction between Individuals Dominate the Topologies of Real World Networks, PLoS One, 10(3):e0121248 (2015) PubMed Link PDF
  13. 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 folding the central pseudoknot, PLoS Biology, 13(2):e1002083 (2015) PubMed Link PDF
  14. 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 LIR, Jones RA, A self-assembling lanthanide molecular nanoparticle for optical imaging, Dalton Transactions, 44(6):2667-75 (2015) PubMed Link PDF

2014

  1. Swaminathan J, Boulgakov AA, Marcotte EM, A theoretical justification for single molecule peptide sequencing, PLoS Computational Biology, 11(2):e1004080 (2014 bioRxiv, 2015 PLoS CB) PubMed Link PDF bioRxiv preprint
  2. 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 LIR, Brown KA, Lanthanide nano-drums: A new class of molecular nanoparticles for potential biomedical applications, Faraday Discussions, 175:241-55 (2014) PubMed Link PDF
  3. Kwon T, Chung M-I, 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 (2014) PubMed Link PDF
  4. 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(Web Server issue):W147-53 (2014) PubMed Link PDF
  5. 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(5):2370-80 (2014) PubMed Link PDF
  6. Boutz DR, Horton AP, Wine Y, Lavinder JJ, Georgiou G, Marcotte EM, Proteomic identification of monoclonal antibodies from serum, Analytical Chemistry, 86(10):4758-66 (2014) PubMed Link PDF
  7. O’Connell JD, Tsechansky M, West-Driga M, Marcotte EM, Formation of intracellular glutamine synthetase bodies depends strongly upon cellular age and glucose availability, PeerJ PrePrints, 2:e270v1 (2014) PubMed Link PDF
  8. O’Connell JD, Tsechansky M, Royall A, Boutz DR, Ellington AD, Marcotte EM, A proteomic survey of widespread protein aggregation in yeast, Molecular BioSystems, 10:851-861 (2014) PubMed Link PDF Supplement Supporting Datasets
  9. 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(3):178-80 (2014) PubMed Link PDF Supplement Supplemental Data 1 Supplemental Data 2
  10. Qian Y, Kachroo A, Yellman CM, Marcotte EM, Johnson KA, Yeast cells expressing the human mitochondrial DNA polymerase reveal correlations between polymerase fidelity and human disease progression, Journal of Biological Chemistry, 289:5970-5985 (2014) PubMed Link PDF
  11. 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, Proc Natl Acad Sci USA, 111(6):2259-64 (2014) PubMed Link PDF
  12. Zhao A, Tsechansky M, Ellington AD, Marcotte EM, Revisiting and revising the purinosome, Molecular BioSystems, 10(3):369-74 (2014) PubMed Link PDF
  13. 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 (2014) PubMed Link PDF Supplement

2013

  1. Gerster S, Kwon T, Ludwig C, Matondo M, Vogel C, Marcotte E, Aebersold R, Bühlmann P, Statistical approach to protein quantification, Mol Cell Proteomics, 13(2):666-77 (2014) PubMed Link PDF
  2. Huse HK, Kwon T, Zlosnik JEA, 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(12):e82621 (2013) PubMed Link PDF
  3. 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(8):e1001624 (2013) PubMed Link PDF Commentary
  4. 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 (2013) PubMed Link PDF
  5. 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
  6. 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
  7. 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
  8. 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

  1. 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
  2. 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
  3. Park Y, Marcotte EM, Flaws in evaluation schemes for pair-input computational predictions, Nature Methods, 9(12):1134–1136 (2012) PubMed Link PDF Supplement
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

  1. Li Z, Lee I, Moradi E, Hung NJ, White J, Johnson AW, Marcotte EM, Rational extension of the ribosome biogenesis pathway using network-guided genetics, PLoS Biology, 7(10):e1000213 (2009) PubMed Link PDF Supplemental Figures and Tables
  2. 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
  3. 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
  4. Vogel C, Marcotte EM, Absolute abundance for the masses, Nature Biotechnology, 27(9):825-6 (2009) PubMed Link PDF
  5. 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
  6. 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
    NatureCellBiologyFuzCover2009.jpg
  7. Marcotte EM, Tsechansky M, Disorder, promiscuity, and toxic partnerships, Cell, 138(1):16-18 (2009) PubMed Link PDF
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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

  1. Hannay K, Marcotte EM, Vogel C, Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation, BMC Genomics, 9:609 (2008) PubMed Link PDF Supplemental Notes Supplemental Data
  2. Braisted JC, Kuntumalla S, Vogel C, Marcotte EM, Rodrigues AR, Wang R, Huang ST, Ferlanti ES, Saeed AI, Fleischmann RD, Peterson SN, Pieper R, The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results, BMC Bioinformatics, 9:529. (2008) PubMed Link PDF
  3. Kim WK, Marcotte EM, Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence, PLoS Comput Biol, 4(11):e1000232 (2008) PubMed Link 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
  4. Prince JT, Marcotte EM, mspire: mass spectrometry proteomics in Ruby, Bioinformatics, 24(23):2796-7 (2008) PubMed Link PDF
  5. Vogel C, Marcotte EM, Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data, Nat Protoc, 3(9):1444-51. (2008) PubMed Link PDF Supplement
  6. Lee I, Marcotte EM, Integrating functional genomics data, Methods Mol Biol, 453:267-78. (2008) PubMed Link PDF
  7. Kim WK, Krumpelman C, Marcotte EM, Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy, Genome Biol, 9 Suppl 1::S5 (2008) PubMed Link PDF Supplement
  8. Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP, A critical assessment of Mus musculus gene function prediction using integrated genomic evidence, Genome Biol, 9 Suppl 1:S2 (2008) PubMed Link PDF MouseFunc predictions
  9. Niu W, Li Z, Zhan W, Iyer VR, Marcotte EM, Mechanisms of cell cycle control revealed by a systematic and quantitative overexpression screen in S. cerevisiae, PLoS Genet, 4(7):e1000120 (2008) PubMed Link PDF Supplemental File of All ORF FACS Defects
  10. Zhao J, Niu W, Yao J, Mohr S, Marcotte EM, Lambowitz AM, Group II intron protein localization and insertion sites are affected by polyphosphate, PLoS Biol, 6(6):e150 (2008) PubMed Link PDF
  11. Ramani AK, Li Z, Hart GT, Carlson MW, Boutz DR, Marcotte EM, A map of human protein interactions derived from co-expression of human mRNAs and their orthologs, Mol Syst Biol, 4:180 (2008) PubMed Link PDF
  12. White J, Li Z, Sardana R, Bujnicki JM, Marcotte EM, Johnson AW, Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits, Mol Cell Biol, 28(10):3151-61 (2008) PubMed Link PDF
  13. Wang R, Marcotte EM, The proteomic response of Mycobacterium smegmatis to anti-tuberculosis drugs suggests targeted pathways, J Proteome Res, 7(3):855-65 (2008) PubMed Link PDF
  14. Lee I, Lehner B, Crombie C, Wong W, Fraser AG, Marcotte EM, A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans, Nat Genet, 40(2):181-8 (2008) PubMed Link PDF Supplement Supplemental Web Site
    NatureGeneticsWormNetCover2008.jpg

2007

  1. McGary KL, Lee I, Marcotte EM, Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes, Genome Biol, 8(12):R258. (2007) PubMed Link PDF Supplemental Web Site
  2. Lee I, Li Z, Marcotte EM, An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae, PLoS ONE, 2(10):e988 (2007) PubMed Link PDF Supplemental Web Site
  3. Marcotte EM, How do shotgun proteomics algorithms identify proteins?, Nat Biotechnol, 25(7):755-7 (2007) PubMed Link PDF
  4. Carlson MW, Iyer VR, Marcotte EM, Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways, BMC Genomics, 8:117. (2007) PubMed Link PDF
  5. Lu P, Vogel C, Wang R, Yao X, Marcotte EM, Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation, Nat Biotechnol, 25(1):117-24 (2007) PubMed Link PDF Supplement Supplemental Data (zipped folder) News & Views 1 News & Views 2 News & Views 3 2011 NBT Retrospective on APEX
  6. Lu P, Rangan A, Chan SY, Appling DR, Hoffman DW, Marcotte EM, Global metabolic changes following loss of a feedback loop reveal dynamic steady states of the yeast metabolome, Metab Eng, 9(1):8-20 (2007) PubMed Link PDF Supplemental File 1 Supplemental File 2 Supplemental File 3
  7. Hart GT, Lee I, Marcotte EM, A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality, BMC Bioinformatics, 8:236. (2007) PubMed Link PDF

2006

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

2005

  1. Levskaya A, Chevalier AA, Tabor JJ, Simpson ZB, Lavery LA, Levy M, Davidson EA, Scouras A, Ellington AD, Marcotte EM, Voigt CA, Synthetic biology: Engineering Escherichia coli to see light, Nature, 438(7067):441-2 (2005) PubMed Link PDF 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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

  1. 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)
  2. 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
    GenomeResearchHaloarculaCover2004.jpg
  3. Fraser AG, Marcotte EM, Development through the eyes of functional genomics, Curr Opin Genet Dev., 14(4):336-42 (2004) PubMed Link PDF
  4. 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
  5. 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 For more recent support of LGL, see the LGL guide by Claire McWhite and the latest updates from the Opte Project
  6. Fraser AG, Marcotte EM, A probabilistic view of gene function, Nature Genetics, 36(6):559-64 (2004) PubMed Link PDF
  7. Marcotte EM, Practical computational approaches to infer protein function, Biosilico, 2:24-29 (2004) PubMed PDF
  8. 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
  9. 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

  1. Dhillon IS, Marcotte EM, Roshan U, Diametrical clustering for identifying anti-correlated gene clusters, Bioinformatics, 19(13):1612-9 (2003) PubMed PDF
  2. 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 Supplemental files (zipped folder containing executable .jar file, yeast test data and cell cycle basis vectors)
  3. 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
  4. Marcotte EM, Assembling a jigsaw puzzle with 20,000 parts, Genome Biol., 4(6):323 (2003) PubMed PDF
  5. 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
  6. 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
  7. 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

  1. 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
  2. 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
  3. 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
  4. Verjovsky Marcotte CJ, Marcotte EM, Predicting functional linkages from gene fusions with confidence, Applied Bioinformatics, 1(2):1-8 (2002) PubMed PDF

2001

  1. Marcotte EM, Date SV, Exploiting big biology: Integrating large-scale biological data for functional inference, Brief Bioinform, 2(4):363-74 (2001) PubMed PDF
  2. Marcotte EM, The path not taken, Nature Biotechnology, 19(7):626-7 (2001) PubMed PDF
  3. Marcotte EM, Measuring the dynamics of the proteome, Genome Research, 11(2):191-3 (2001) PubMed PDF
  4. 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
  5. 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
  6. 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

  1. Eisenberg D, Marcotte EM, Xenarios I, Yeates TO, Protein function in the post-genomic era, Nature, 405(6788):823-6 (2000) PubMed Link PDF
  2. 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
  3. Marcotte EM, Computational genetics: Finding function by non-homology methods, Curr Opin Struct Biol., 10(3):359-65 (2000) PubMed Link PDF
  4. 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
  5. 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
  6. 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

  1. 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).
  2. 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).
  3. Marcotte EM, Pellegrini M, Yeates TO, Eisenberg D, A census of protein repeats, J Mol Biol., 293(1):151-60 (1999) PubMed Link PDF
  4. 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
  5. 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

  1. Marcotte EM, Eisenberg D, Chicken prion tandem repeats form a stable, protease-resistant domain, Biochemistry, 38(2):667-76 (1998) PubMed Link PDF
  2. Cascio D, Goodwill K, Marcotte E, A look at the future of macromolecular structure determination, Rigaku J., 15:1-5 (1998) PubMed PDF
  3. 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

  1. Hollis T, Honda Y, Fukamizo T, Marcotte E, Day PJ, Robertus JD, Kinetic analysis of barley chitinase, Arch Biochem Biophys., 344(2):335-42 (1997) PubMed Link PDF
  2. Marcotte EM, Monzingo AF, Ernst SR, Brzezinski R, Robertus JD, X-ray structure of an anti-fungal chitosanase from Streptomyces N174, Nat Struct Biol., 3(2):155-62 (1996) PubMed PDF News & Views
  3. Monzingo AF, Marcotte EM, Hart PJ, Robertus JD, Chitinases, chitosanases, and lysozymes can be divided into procaryotic and eucaryotic families sharing a conserved core, Nat Struct Biol, 3(2):133-40 (1996) PubMed PDF
  4. Robertus, J. D., Hart, P. J., Monzingo, A. F., Marcotte, E. & Hollis, T, The structure of chitinases and prospects for structure-Based drug design, Can. J. Bot., 73 (Suppl. 1):S1142-S1146 (1995) PubMed PDF
  5. Kim YJ, Francisco L, Chen GC, Marcotte E, Chan CS, Control of cellular morphogenesis by the Ip12/Bem2 GTPase-activating protein: possible role of protein phosphorylation, J Cell Biol., 127(5):1381-94 (1994) PubMed Link PDF
  6. Marcotte E, Hart PJ, Boucher I, Brzezinski R, Robertus JD, Crystallization of a chitosanase from Streptomyces N174, J Mol Biol, 232(3):995-6 (1993) PubMed Link PDF

Patents

  1. Publication # WO 2020023488 A1 Single molecule sequencing identification of post-translational modifications on proteins. PCT filed July 23, 2018.
  2. Publication # WO 2020014586 A1 Molecular neighborhood detection by oligonucleotides. PCT filed July 12, 2018.
  3. 10,175,249 B2, issued January 8, 2019. Proteomic identification of antibodies. Lavinder, Jason; Boutz, Danny; Wine, Yariv; Marcotte, Edward; Georgiou, George.
  4. 10,545,153 B2, issued January 28, 2020. Single molecule peptide sequencing. Publication # WO/2016/069124, Intl appl # PCT/US2015/050099, International filing date 15.09.2015. Marcotte, Edward; Anslyn, Eric; Ellington, Andrew; Swaminathan, Jagannath; Hernandez, Erik; Johnson, Amber; Boulgakov, Alexander; Bachman, Logan; Seifert, Helen. Improved single molecule sequencing.
  5. 9,625,469, issued April, 18, 2017. Identifying peptides at the single molecule level. Marcotte, Edward; Swaminathan, Jagannath; Ellington, Andrew; Anslyn, Eric. Appl # 14128247, filed 22.06.2012; publication # US20140349860, 27.11.2014. UK patent GB2510499 issued April 8, 2020.
  6. Publication # WO 2013067308 A2, Compositions and methods for inducing disruption of blood vasculature and for reducing angiogenesis, PCT filed Nov 2, 2012; provisional patent # 61/555,212 filed Nov 3, 2011.
  7. Publication # WO 2013055867 A1, Genes involved in stress response in plants, PCT filed Oct 11, 2012.
  8. 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.
  9. 9,146,241, issued September 29, 2015. Proteomic identification of antibodies. Lavinder, Jason; Wine, Yariv; Boutz, Danny; Marcotte, Edward; Georgiou, George. Appl # 13/684,395, filed November 23, 2012.
  10. 9,090,674 B2, issued July 28, 2015. Rapid isolation of monoclonal antibodies from animals. Reddy, Sai; Ge, Xin; Lavinder, Jason; Boutz, Danny; Ellington, Andrew D.; Marcotte, Edward M.; Georgiou, George.
  11. 6,892,139, issued May 10, 2005. Determining the functions and interactions of proteins by comparative analysis.
  12. 6,772,069, issued August 3, 2004. Determining protein function and interaction from genome analysis.
  13. 6,564,151, issued May 13, 2003. Assigning protein functions by comparative genome analysis protein phylogenetic profiles.
  14. 6,466,874, issued October 15, 2002. Rosetta stone method for detecting protein function and protein-protein interactions from genome sequences.