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Items: 1 to 50 of 166

1.

HumanNet v2: human gene networks for disease research.

Hwang S, Kim CY, Yang S, Kim E, Hart T, Marcotte EM, Lee I.

Nucleic Acids Res. 2018 Nov 10. doi: 10.1093/nar/gky1126. [Epub ahead of print]

PMID:
30418591
2.

Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures.

Swaminathan J, Boulgakov AA, Hernandez ET, Bardo AM, Bachman JL, Marotta J, Johnson AM, Anslyn EV, Marcotte EM.

Nat Biotechnol. 2018 Oct 22. doi: 10.1038/nbt.4278. [Epub ahead of print]

PMID:
30346938
3.

A highly parallel strategy for storage of digital information in living cells.

Akhmetov A, Ellington AD, Marcotte EM.

BMC Biotechnol. 2018 Oct 17;18(1):64. doi: 10.1186/s12896-018-0476-4.

4.

Photography Coupled with Self-Propagating Chemical Cascades: Differentiation and Quantitation of G- and V-Nerve Agent Mimics via Chromaticity.

Sun X, Boulgakov AA, Smith LN, Metola P, Marcotte EM, Anslyn EV.

ACS Cent Sci. 2018 Jul 25;4(7):854-861. doi: 10.1021/acscentsci.8b00193. Epub 2018 Jun 27.

5.

Classification of Single Particles from Human Cell Extract Reveals Distinct Structures.

Verbeke EJ, Mallam AL, Drew K, Marcotte EM, Taylor DW.

Cell Rep. 2018 Jul 3;24(1):259-268.e3. doi: 10.1016/j.celrep.2018.06.022.

6.

Single-step Precision Genome Editing in Yeast Using CRISPR-Cas9.

Akhmetov A, Laurent JM, Gollihar J, Gardner EC, Garge RK, Ellington AD, Kachroo AH, Marcotte EM.

Bio Protoc. 2018 Mar 20;8(6). pii: e2765. doi: 10.21769/BioProtoc.2765.

7.

Paternal chromosome loss and metabolic crisis contribute to hybrid inviability in Xenopus.

Gibeaux R, Acker R, Kitaoka M, Georgiou G, van Kruijsbergen I, Ford B, Marcotte EM, Nomura DK, Kwon T, Veenstra GJC, Heald R.

Nature. 2018 Jan 18;553(7688):337-341. doi: 10.1038/nature25188. Epub 2018 Jan 10.

8.

Protein localization screening in vivo reveals novel regulators of multiciliated cell development and function.

Tu F, Sedzinski J, Ma Y, Marcotte EM, Wallingford JB.

J Cell Sci. 2018 Jan 29;131(3). pii: jcs206565. doi: 10.1242/jcs.206565.

9.

Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets.

Drew K, Müller CL, Bonneau R, Marcotte EM.

PLoS Comput Biol. 2017 Oct 12;13(10):e1005625. doi: 10.1371/journal.pcbi.1005625. eCollection 2017 Oct.

10.

Solution-phase and solid-phase sequential, selective modification of side chains in KDYWEC and KDYWE as models for usage in single-molecule protein sequencing.

Hernandez ET, Swaminathan J, Marcotte EM, Anslyn EV.

New J Chem. 2017 Jan 21;41(2):462-469. doi: 10.1039/C6NJ02932A. Epub 2016 Nov 18.

11.

Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial infection.

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.

Nat Microbiol. 2017 Nov;2(11):1493-1499. doi: 10.1038/s41564-017-0021-6. Epub 2017 Sep 18.

12.

Systematic bacterialization of yeast genes identifies a near-universally swappable pathway.

Kachroo AH, Laurent JM, Akhmetov A, Szilagyi-Jones M, McWhite CD, Zhao A, Marcotte EM.

Elife. 2017 Jun 29;6. pii: e25093. doi: 10.7554/eLife.25093.

13.

Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes.

Drew K, Lee C, Huizar RL, Tu F, Borgeson B, McWhite CD, Ma Y, Wallingford JB, Marcotte EM.

Mol Syst Biol. 2017 Jun 8;13(6):932. doi: 10.15252/msb.20167490.

14.

Systems-wide Studies Uncover Commander, a Multiprotein Complex Essential to Human Development.

Mallam AL, Marcotte EM.

Cell Syst. 2017 May 24;4(5):483-494. doi: 10.1016/j.cels.2017.04.006. Review.

15.

WheatNet: a Genome-Scale Functional Network for Hexaploid Bread Wheat, Triticum aestivum.

Lee T, Hwang S, Kim CY, Shim H, Kim H, Ronald PC, Marcotte EM, Lee I.

Mol Plant. 2017 Aug 7;10(8):1133-1136. doi: 10.1016/j.molp.2017.04.006. Epub 2017 Apr 24. No abstract available.

16.

GWAB: a web server for the network-based boosting of human genome-wide association data.

Shim JE, Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom UM, Marcotte EM, Lee I.

Nucleic Acids Res. 2017 Jul 3;45(W1):W154-W161. doi: 10.1093/nar/gkx284.

17.

The E. coli molecular phenotype under different growth conditions.

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.

Sci Rep. 2017 Apr 18;7:45303. doi: 10.1038/srep45303.

18.

Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions.

Brown CW, Sridhara V, Boutz DR, Person MD, Marcotte EM, Barrick JE, Wilke CO.

BMC Genomics. 2017 Apr 17;18(1):301. doi: 10.1186/s12864-017-3676-8.

19.

Comprehensive de Novo Peptide Sequencing from MS/MS Pairs Generated through Complementary Collision Induced Dissociation and 351 nm Ultraviolet Photodissociation.

Horton AP, Robotham SA, Cannon JR, Holden DD, Marcotte EM, Brodbelt JS.

Anal Chem. 2017 Mar 21;89(6):3747-3753. doi: 10.1021/acs.analchem.7b00130. Epub 2017 Mar 8.

20.

Murine Cytomegalovirus Deubiquitinase Regulates Viral Chemokine Levels To Control Inflammation and Pathogenesis.

Hilterbrand AT, Boutz DR, Marcotte EM, Upton JW.

MBio. 2017 Jan 17;8(1). pii: e01864-16. doi: 10.1128/mBio.01864-16.

21.

Predictability of Genetic Interactions from Functional Gene Modules.

Young JH, Marcotte EM.

G3 (Bethesda). 2017 Feb 9;7(2):617-624. doi: 10.1534/g3.116.035915.

22.

Temporal stability and molecular persistence of the bone marrow plasma cell antibody repertoire.

Wu GC, Cheung NV, Georgiou G, Marcotte EM, Ippolito GC.

Nat Commun. 2016 Dec 21;7:13838. doi: 10.1038/ncomms13838.

23.

Molecular-level analysis of the serum antibody repertoire in young adults before and after seasonal influenza vaccination.

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.

Nat Med. 2016 Dec;22(12):1456-1464. doi: 10.1038/nm.4224. Epub 2016 Nov 7.

24.

Genome evolution in the allotetraploid frog Xenopus laevis.

Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M, van Heeringen SJ, Quigley I, Heinz S, Ogino H, Ochi H, Hellsten U, Lyons JB, Simakov O, Putnam N, Stites J, Kuroki Y, Tanaka T, Michiue T, Watanabe M, Bogdanovic O, Lister R, Georgiou G, Paranjpe SS, van Kruijsbergen I, Shu S, Carlson J, Kinoshita T, Ohta Y, Mawaribuchi S, Jenkins J, Grimwood J, Schmutz J, Mitros T, Mozaffari SV, Suzuki Y, Haramoto Y, Yamamoto TS, Takagi C, Heald R, Miller K, Haudenschild C, Kitzman J, Nakayama T, Izutsu Y, Robert J, Fortriede J, Burns K, Lotay V, Karimi K, Yasuoka Y, Dichmann DS, Flajnik MF, Houston DW, Shendure J, DuPasquier L, Vize PD, Zorn AM, Ito M, Marcotte EM, Wallingford JB, Ito Y, Asashima M, Ueno N, Matsuda Y, Veenstra GJ, Fujiyama A, Harland RM, Taira M, Rokhsar DS.

Nature. 2016 Oct 20;538(7625):336-343. doi: 10.1038/nature19840.

25.

Corrigendum: The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery.

Toriyama M, Lee C, Taylor SP, Duran I, Cohn DH, Bruel AL, Tabler JM, Drew K, Kelly MR, Kim S, Park TJ, Braun DA, 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.

Nat Genet. 2016 Jul 27;48(8):970. doi: 10.1038/ng0816-970b. No abstract available.

PMID:
27463398
26.

Towards Consensus Gene Ages.

Liebeskind BJ, McWhite CD, Marcotte EM.

Genome Biol Evol. 2016 Jun 27;8(6):1812-23. doi: 10.1093/gbe/evw113.

27.

The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery.

Toriyama M, Lee C, Taylor SP, Duran I, Cohn DH, Bruel AL, Tabler JM, Drew K, Kelly MR, Kim S, Park TJ, Braun DA, 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.

Nat Genet. 2016 Jun;48(6):648-56. doi: 10.1038/ng.3558. Epub 2016 May 9. Erratum in: Nat Genet. 2016 Jul 27;48(8):970.

28.

Sperm is epigenetically programmed to regulate gene transcription in embryos.

Teperek M, Simeone A, Gaggioli V, Miyamoto K, Allen GE, Erkek S, Kwon T, Marcotte EM, Zegerman P, Bradshaw CR, Peters AH, Gurdon JB, Jullien J.

Genome Res. 2016 Aug;26(8):1034-46. doi: 10.1101/gr.201541.115. Epub 2016 Mar 31.

29.

UVnovo: A de Novo Sequencing Algorithm Using Single Series of Fragment Ions via Chromophore Tagging and 351 nm Ultraviolet Photodissociation Mass Spectrometry.

Robotham SA, Horton AP, Cannon JR, Cotham VC, Marcotte EM, Brodbelt JS.

Anal Chem. 2016 Apr 5;88(7):3990-7. doi: 10.1021/acs.analchem.6b00261. Epub 2016 Mar 14.

30.

Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes.

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, Tillier ER, Wallingford JB, Parkinson J, Marcotte EM, Emili A.

Data Brief. 2015 Dec 12;6:715-21. doi: 10.1016/j.dib.2015.11.062. eCollection 2016 Mar.

31.

Computational discovery of pathway-level genetic vulnerabilities in non-small-cell lung cancer.

Young JH, Peyton M, Seok Kim H, McMillan E, Minna JD, White MA, Marcotte EM.

Bioinformatics. 2016 May 1;32(9):1373-9. doi: 10.1093/bioinformatics/btw010. Epub 2016 Jan 10.

32.

Long-term neural and physiological phenotyping of a single human.

Poldrack RA, Laumann TO, Koyejo O, Gregory B, Hover A, Chen MY, Gorgolewski KJ, Luci J, Joo SJ, Boyd RL, Hunicke-Smith S, Simpson ZB, Caven T, Sochat V, Shine JM, Gordon E, Snyder AZ, Adeyemo B, Petersen SE, Glahn DC, Reese Mckay D, Curran JE, Göring HH, Carless MA, Blangero J, Dougherty R, Leemans A, Handwerker DA, Frick L, Marcotte EM, Mumford JA.

Nat Commun. 2015 Dec 9;6:8885. doi: 10.1038/ncomms9885.

33.

Systematic comparison of variant calling pipelines using gold standard personal exome variants.

Hwang S, Kim E, Lee I, Marcotte EM.

Sci Rep. 2015 Dec 7;5:17875. doi: 10.1038/srep17875.

34.

MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates.

Kim E, Hwang S, Kim H, Shim H, Kang B, Yang S, Shim JH, Shin SY, Marcotte EM, Lee I.

Nucleic Acids Res. 2016 Jan 4;44(D1):D848-54. doi: 10.1093/nar/gkv1155. Epub 2015 Nov 2.

35.

Intrinsic Antimicrobial Resistance Determinants in the Superbug Pseudomonas aeruginosa.

Murray JL, Kwon T, Marcotte EM, Whiteley M.

MBio. 2015 Oct 27;6(6):e01603-15. doi: 10.1128/mBio.01603-15.

36.

Efforts to make and apply humanized yeast.

Laurent JM, Young JH, Kachroo AH, Marcotte EM.

Brief Funct Genomics. 2016 Mar;15(2):155-63. doi: 10.1093/bfgp/elv041. Epub 2015 Oct 13. Review.

37.

Panorama of ancient metazoan macromolecular complexes.

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, Tillier ER, Wallingford JB, Parkinson J, Marcotte EM, Emili A.

Nature. 2015 Sep 17;525(7569):339-44. doi: 10.1038/nature14877. Epub 2015 Sep 7.

38.

Applications of comparative evolution to human disease genetics.

McWhite CD, Liebeskind BJ, Marcotte EM.

Curr Opin Genet Dev. 2015 Dec;35:16-24. doi: 10.1016/j.gde.2015.08.004. Epub 2015 Sep 4. Review.

39.

Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation.

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.

PLoS Comput Biol. 2015 Aug 14;11(8):e1004400. doi: 10.1371/journal.pcbi.1004400. eCollection 2015 Aug.

40.

Evolution. Systematic humanization of yeast genes reveals conserved functions and genetic modularity.

Kachroo AH, Laurent JM, Yellman CM, Meyer AG, Wilke CO, Marcotte EM.

Science. 2015 May 22;348(6237):921-5. doi: 10.1126/science.aaa0769.

41.

Modes of interaction between individuals dominate the topologies of real world networks.

Lee I, Kim E, Marcotte EM.

PLoS One. 2015 Mar 20;10(3):e0121248. doi: 10.1371/journal.pone.0121248. eCollection 2015.

42.

A theoretical justification for single molecule peptide sequencing.

Swaminathan J, Boulgakov AA, Marcotte EM.

PLoS Comput Biol. 2015 Feb 25;11(2):e1004080. doi: 10.1371/journal.pcbi.1004080. eCollection 2015 Feb.

43.

The DEAH-box helicase Dhr1 dissociates U3 from the pre-rRNA to promote formation of the central pseudoknot.

Sardana R, Liu X, Granneman S, Zhu J, Gill M, Papoulas O, Marcotte EM, Tollervey D, Correll CC, Johnson AW.

PLoS Biol. 2015 Feb 24;13(2):e1002083. doi: 10.1371/journal.pbio.1002083. eCollection 2015 Feb.

44.

A self-assembling lanthanide molecular nanoparticle for optical imaging.

Brown KA, Yang X, Schipper D, Hall JW, DePue LJ, Gnanam AJ, Arambula JF, Jones JN, Swaminathan J, Dieye Y, Vadivelu J, Chandler DJ, Marcotte EM, Sessler JL, Ehrlich LI, Jones RA.

Dalton Trans. 2015 Feb 14;44(6):2667-75. doi: 10.1039/c4dt02646b.

45.

Identifying direct targets of transcription factor Rfx2 that coordinate ciliogenesis and cell movement.

Kwon T, Chung MI, Gupta R, Baker JC, Wallingford JB, Marcotte EM.

Genom Data. 2014 Dec 1;2:192-194.

46.

Lanthanide nano-drums: a new class of molecular nanoparticles for potential biomedical applications.

Jones RA, Gnanam AJ, Arambula JF, Jones JN, Swaminathan J, Yang X, Schipper D, Hall JW, DePue LJ, Dieye Y, Vadivelu J, Chandler DJ, Marcotte EM, Sessler JL, Ehrlich LI, Brown KA.

Faraday Discuss. 2014;175:241-55. doi: 10.1039/c4fd00117f.

47.

MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network.

Hwang S, Kim E, Yang S, Marcotte EM, Lee I.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W147-53. doi: 10.1093/nar/gku434. Epub 2014 May 26.

48.

Protein-to-mRNA ratios are conserved between Pseudomonas aeruginosa strains.

Kwon T, Huse HK, Vogel C, Whiteley M, Marcotte EM.

J Proteome Res. 2014 May 2;13(5):2370-80. doi: 10.1021/pr4011684. Epub 2014 Apr 17.

49.

Proteomic identification of monoclonal antibodies from serum.

Boutz DR, Horton AP, Wine Y, Lavinder JJ, Georgiou G, Marcotte EM.

Anal Chem. 2014 May 20;86(10):4758-66. doi: 10.1021/ac4037679. Epub 2014 May 1.

50.

A proteomic survey of widespread protein aggregation in yeast.

O'Connell JD, Tsechansky M, Royal A, Boutz DR, Ellington AD, Marcotte EM.

Mol Biosyst. 2014 Apr;10(4):851-861. doi: 10.1039/c3mb70508k. Epub 2014 Feb 3.

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