Edward M Marcotte

Edward M Marcotte

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Edward M Marcotte

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Bringing Microscopy-By-Sequencing into View.

Trends Biotechnol 2020 Feb 12;38(2):154-162. Epub 2019 Aug 12.

Center for Systems and Synthetic Biology, Institute of Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tibtech.2019.06.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6943198PMC
February 2020

Separating distinct structures of multiple macromolecular assemblies from cryo-EM projections.

J Struct Biol 2020 Jan 11;209(1):107416. Epub 2019 Nov 11.

Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jsb.2019.107416DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6952565PMC
January 2020

Synthesis of Carboxy ATTO 647N Using Redox Cycling for Xanthone Access.

Org Lett 2020 Jan 11;22(2):381-385. Epub 2019 Dec 11.

Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States.

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http://dx.doi.org/10.1021/acs.orglett.9b03981DOI Listing
January 2020

Ancestral reconstruction of protein interaction networks.

PLoS Comput Biol 2019 10 28;15(10):e1007396. Epub 2019 Oct 28.

Center for Systems and Synthetic Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1007396DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6837550PMC
October 2019

Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes.

Cell Rep 2019 Oct;29(5):1351-1368.e5

Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.09.060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6873818PMC
October 2019

HumanNet v2: human gene networks for disease research.

Nucleic Acids Res 2019 Jan;47(D1):D573-D580

Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea.

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http://dx.doi.org/10.1093/nar/gky1126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323914PMC
January 2019

A liquid-like organelle at the root of motile ciliopathy.

Elife 2018 12 18;7. Epub 2018 Dec 18.

Department of Molecular Biosciences, University of Texas, Austin, United States.

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http://dx.doi.org/10.7554/eLife.38497DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6349401PMC
December 2018

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

BMC Biotechnol 2018 10 17;18(1):64. Epub 2018 Oct 17.

Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.

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https://bmcbiotechnol.biomedcentral.com/articles/10.1186/s12
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http://dx.doi.org/10.1186/s12896-018-0476-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6191901PMC
October 2018

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

Nat Biotechnol 2018 Oct 22. Epub 2018 Oct 22.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA.

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http://www.nature.com/doifinder/10.1038/nbt.4278
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http://dx.doi.org/10.1038/nbt.4278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6482110PMC
October 2018

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

Cell Rep 2018 07;24(1):259-268.e3

Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; LIVESTRONG Cancer Institute, Dell Medical School, Austin, TX 78712, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.06.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6109231PMC
July 2018

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

ACS Cent Sci 2018 Jul 27;4(7):854-861. Epub 2018 Jun 27.

Department of Chemistry, Center for Systems and Synthetic Biology/Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, and Advanced Research Initiative, University of Texas at Austin, Austin, Texas 78712, United States.

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http://pubs.acs.org/doi/10.1021/acscentsci.8b00193
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http://dx.doi.org/10.1021/acscentsci.8b00193DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6062830PMC
July 2018

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

Bio Protoc 2018 Mar;8(6)

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA.

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http://dx.doi.org/10.21769/BioProtoc.2765DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5951413PMC
March 2018

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

J Cell Sci 2018 01 29;131(3). Epub 2018 Jan 29.

Dept. of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA

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http://jcs.biologists.org/lookup/doi/10.1242/jcs.206565
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http://dx.doi.org/10.1242/jcs.206565DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5826043PMC
January 2018

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

PLoS Comput Biol 2017 Oct 12;13(10):e1005625. Epub 2017 Oct 12.

Center for Systems and Synthetic Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005625DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5638211PMC
October 2017

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

Mol Plant 2017 08 24;10(8):1133-1136. Epub 2017 Apr 24.

Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea. Electronic address:

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http://dx.doi.org/10.1016/j.molp.2017.04.006DOI Listing
August 2017

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

Nucleic Acids Res 2017 07;45(W1):W154-W161

Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea.

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http://dx.doi.org/10.1093/nar/gkx284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5793838PMC
July 2017

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

Mol Syst Biol 2017 06 8;13(6):932. Epub 2017 Jun 8.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5488662PMC
http://dx.doi.org/10.15252/msb.20167490DOI Listing
June 2017

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

Elife 2017 06 29;6. Epub 2017 Jun 29.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, United States.

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http://dx.doi.org/10.7554/eLife.25093DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5536947PMC
June 2017

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

Cell Syst 2017 05;4(5):483-494

Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2017.04.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5541947PMC
May 2017

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

BMC Genomics 2017 04 17;18(1):301. Epub 2017 Apr 17.

Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA.

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http://dx.doi.org/10.1186/s12864-017-3676-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5392934PMC
April 2017

Predictability of Genetic Interactions from Functional Gene Modules.

G3 (Bethesda) 2017 02 9;7(2):617-624. Epub 2017 Feb 9.

Center for Systems and Synthetic Biology, The University of Texas at Austin, Texas 78712

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http://dx.doi.org/10.1534/g3.116.035915DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5295606PMC
February 2017

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

mBio 2017 01 17;8(1). Epub 2017 Jan 17.

Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, LaMontagne Center for Infectious Disease, University of Texas at Austin, Austin, Texas, USA

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http://dx.doi.org/10.1128/mBio.01864-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5241396PMC
January 2017

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

Nat Commun 2016 12 21;7:13838. Epub 2016 Dec 21.

Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA.

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http://dx.doi.org/10.1038/ncomms13838DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5187582PMC
December 2016

Genome evolution in the allotetraploid frog Xenopus laevis.

Nature 2016 10;538(7625):336-343

University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA.

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http://dx.doi.org/10.1038/nature19840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5313049PMC
October 2016

Sperm is epigenetically programmed to regulate gene transcription in embryos.

Genome Res 2016 08 31;26(8):1034-46. Epub 2016 Mar 31.

Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, United Kingdom; Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom;

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http://dx.doi.org/10.1101/gr.201541.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4971762PMC
August 2016

Towards Consensus Gene Ages.

Genome Biol Evol 2016 06 27;8(6):1812-23. Epub 2016 Jun 27.

Department of Molecular Biosciences, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin.

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http://dx.doi.org/10.1093/gbe/evw113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4943184PMC
June 2016

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

Bioinformatics 2016 05 10;32(9):1373-9. Epub 2016 Jan 10.

Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, TX, USA, Center for Systems and Synthetic Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4848405PMC
May 2016

Efforts to make and apply humanized yeast.

Brief Funct Genomics 2016 Mar 13;15(2):155-63. Epub 2015 Oct 13.

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http://dx.doi.org/10.1093/bfgp/elv041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4803062PMC
March 2016

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

PLoS One 2015 20;10(3):e0121248. Epub 2015 Mar 20.

Center for Systems and Synthetic Biology, Department of Molecular Biosciences, and Institute for Cellular and Molecular Biology, MBB 3.148BA, University of Texas at Austin, 2500 Speedway, Austin, Texas 78712-1064, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121248PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4368763PMC
February 2016

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

Nucleic Acids Res 2016 Jan 2;44(D1):D848-54. Epub 2015 Nov 2.

Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea

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http://dx.doi.org/10.1093/nar/gkv1155DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702832PMC
January 2016

Applications of comparative evolution to human disease genetics.

Curr Opin Genet Dev 2015 Dec 4;35:16-24. Epub 2015 Sep 4.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, & Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, United States. Electronic address:

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http://dx.doi.org/10.1016/j.gde.2015.08.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4947381PMC
December 2015

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

Sci Rep 2015 Dec 7;5:17875. Epub 2015 Dec 7.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, TX 78712, USA.

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http://dx.doi.org/10.1038/srep17875DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4671096PMC
December 2015

Coordinated genomic control of ciliogenesis and cell movement by RFX2.

Elife 2014 14;3:e01439. Epub 2014 Jan 14.

Department of Molecular Biosciences, University of Texas at Austin, Austin, United States.

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http://dx.doi.org/10.7554/eLife.01439DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3889689PMC
November 2015

Intrinsic Antimicrobial Resistance Determinants in the Superbug Pseudomonas aeruginosa.

mBio 2015 Oct 27;6(6):e01603-15. Epub 2015 Oct 27.

Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA Institute of Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA Center for Infectious Disease, The University of Texas at Austin, Austin, Texas, USA

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http://dx.doi.org/10.1128/mBio.01603-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4626858PMC
October 2015

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

PLoS Comput Biol 2015 08 14;11(8):e1004400. Epub 2015 Aug 14.

Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America; Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas, United States of America; Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004400DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4537216PMC
August 2015

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

Science 2015 May;348(6237):921-5

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA. Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, TX 78712, USA. Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.

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http://dx.doi.org/10.1126/science.aaa0769DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4718922PMC
May 2015

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

PLoS Biol 2015 Feb 24;13(2):e1002083. Epub 2015 Feb 24.

Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1002083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4340053PMC
February 2015

A theoretical justification for single molecule peptide sequencing.

PLoS Comput Biol 2015 Feb 25;11(2):e1004080. Epub 2015 Feb 25.

Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, United States of America; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America; Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4341059PMC
February 2015

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

Genom Data 2014 Dec;2:192-194

Department of Molecular Biosciences, University of Texas at Austin ; Center for Systems & Synthetic Biology and Institute for Cellular & Molecular Biology, University of Texas.

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http://dx.doi.org/10.1016/j.gdata.2014.06.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4236849PMC
December 2014

Pseudomonas aeruginosa enhances production of a non-alginate exopolysaccharide during long-term colonization of the cystic fibrosis lung.

PLoS One 2013 6;8(12):e82621. Epub 2013 Dec 6.

Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas, United States of America ; Institute of Cellular and Molecular Biology and Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0082621PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3855792PMC
July 2014

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

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

Department of Biotechnology, Yonsei University, Seoul, 120-749, Korea

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http://dx.doi.org/10.1093/nar/gku434DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086117PMC
July 2014

Proteomic identification of monoclonal antibodies from serum.

Anal Chem 2014 May 1;86(10):4758-66. Epub 2014 May 1.

Center for Systems & Synthetic Biology, †Institute for Cellular and Molecular Biology, ⊥Department of Biomedical Engineering, §Department of Chemical Engineering, and ∥Department of Molecular Biosciences, University of Texas at Austin , Austin, Texas 78712, United States.

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http://dx.doi.org/10.1021/ac4037679DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4033631PMC
May 2014

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

J Proteome Res 2014 May 17;13(5):2370-80. Epub 2014 Apr 17.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin , 2500 Speedway, Austin, Texas 78712, United States.

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http://dx.doi.org/10.1021/pr4011684DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4012837PMC
May 2014

A proteomic survey of widespread protein aggregation in yeast.

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

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America.

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http://dx.doi.org/10.1039/c3mb70508kDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4142438PMC
April 2014

A Bacteriophage tailspike domain promotes self-cleavage of a human membrane-bound transcription factor, the myelin regulatory factor MYRF.

PLoS Biol 2013 13;11(8):e1001624. Epub 2013 Aug 13.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA.

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http://dx.doi.org/10.1371/journal.pbio.1001624DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3742443PMC
March 2014

Revisiting and revising the purinosome.

Mol Biosyst 2014 Mar 10;10(3):369-74. Epub 2014 Jan 10.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.

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http://dx.doi.org/10.1039/c3mb70397eDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4151177PMC
March 2014

Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness.

Nat Chem Biol 2014 Mar 2;10(3):178-80. Epub 2014 Feb 2.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA.

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http://dx.doi.org/10.1038/nchembio.1450DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932624PMC
March 2014

Statistical approach to protein quantification.

Mol Cell Proteomics 2014 Feb 19;13(2):666-77. Epub 2013 Nov 19.

Seminar for Statistics, Eidgenössische Technische Hochschule (ETH) Zurich, Rämistrasse 101, 8092 Zurich, Switzerland;

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http://www.mcponline.org/lookup/doi/10.1074/mcp.M112.025445
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http://dx.doi.org/10.1074/mcp.M112.025445DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3916661PMC
February 2014

Identification and characterization of the constituent human serum antibodies elicited by vaccination.

Proc Natl Acad Sci U S A 2014 Feb 27;111(6):2259-64. Epub 2014 Jan 27.

Department of Chemical Engineering, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, Center for Systems and Synthetic Biology, Department of Biomedical Engineering, Department of Chemistry and Biochemistry, and Applied Research Laboratories, University of Texas at Austin, Austin, TX 78712-1062.

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http://dx.doi.org/10.1073/pnas.1317793111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3926051PMC
February 2014

Prediction and validation of gene-disease associations using methods inspired by social network analyses.

PLoS One 2013 1;8(5):e58977. Epub 2013 May 1.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058977PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3641094PMC
November 2013

Transiently transfected purine biosynthetic enzymes form stress bodies.

PLoS One 2013 6;8(2):e56203. Epub 2013 Feb 6.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0056203PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566086PMC
August 2013

Prediction of gene-phenotype associations in humans, mice, and plants using phenologs.

BMC Bioinformatics 2013 Jun 21;14:203. Epub 2013 Jun 21.

Center for Systems & Synthetic Biology, Institute for Cellular & Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA.

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http://dx.doi.org/10.1186/1471-2105-14-203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3704650PMC
June 2013

The proteomic response to mutants of the Escherichia coli RNA degradosome.

Mol Biosyst 2013 Apr;9(4):750-7

University of Texas at Austin, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Austin, TX, USA.

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http://dx.doi.org/10.1039/c3mb25513aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3709862PMC
April 2013

Dynamic reorganization of metabolic enzymes into intracellular bodies.

Annu Rev Cell Dev Biol 2012 ;28:89-111

Center for Systems and Synthetic Biology, University of Texas, Austin, Texas 78712, USA.

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http://www.annualreviews.org/doi/10.1146/annurev-cellbio-101
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http://dx.doi.org/10.1146/annurev-cellbio-101011-155841DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4089986PMC
March 2013

Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response.

Proc Natl Acad Sci U S A 2013 Feb 4;110(8):2993-8. Epub 2013 Feb 4.

Department of Chemical Engineering, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712-1062, USA.

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http://dx.doi.org/10.1073/pnas.1213737110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3581903PMC
February 2013

Role of Pseudomonas aeruginosa peptidoglycan-associated outer membrane proteins in vesicle formation.

J Bacteriol 2013 Jan 2;195(2):213-9. Epub 2012 Nov 2.

Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA.

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http://www.marcottelab.org/paper-pdfs/JBacteriol_Wessel_2012
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http://jb.asm.org/cgi/doi/10.1128/JB.01253-12
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3553829PMC
January 2013

Evolutionarily repurposed networks reveal the well-known antifungal drug thiabendazole to be a novel vascular disrupting agent.

PLoS Biol 2012 21;10(8):e1001379. Epub 2012 Aug 21.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA.

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http://dx.doi.org/10.1371/journal.pbio.1001379DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3423972PMC
December 2012

Id2a functions to limit Notch pathway activity and thereby influence the transition from proliferation to differentiation of retinoblasts during zebrafish retinogenesis.

Dev Biol 2012 Nov 8;371(2):280-92. Epub 2012 Sep 8.

Section of Molecular Cell and Developmental Biology, The University of Texas at Austin, Austin, TX 78712, USA.

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http://dx.doi.org/10.1016/j.ydbio.2012.08.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3477674PMC
November 2012

Label-free protein quantitation using weighted spectral counting.

Methods Mol Biol 2012 ;893:321-41

Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA.

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http://dx.doi.org/10.1007/978-1-61779-885-6_20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654649PMC
September 2012

RFX2 is broadly required for ciliogenesis during vertebrate development.

Dev Biol 2012 Mar 29;363(1):155-65. Epub 2011 Dec 29.

Section of Molecular Cell and Developmental Biology, University of Texas at Austin, Austin, TX 78712, USA.

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http://dx.doi.org/10.1016/j.ydbio.2011.12.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3640985PMC
March 2012

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses.

Nat Rev Genet 2012 Mar 13;13(4):227-32. Epub 2012 Mar 13.

Center for Genomics and Systems Biology, New York University, New York 10003, USA.

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http://dx.doi.org/10.1038/nrg3185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654667PMC
March 2012

Protein expression regulation under oxidative stress.

Mol Cell Proteomics 2011 Dec 20;10(12):M111.009217. Epub 2011 Sep 20.

Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA.

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http://dx.doi.org/10.1074/mcp.M111.009217DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3237073PMC
December 2011

Revisiting the negative example sampling problem for predicting protein-protein interactions.

Bioinformatics 2011 Nov 9;27(21):3024-8. Epub 2011 Sep 9.

Center for Systems and Synthetic Biology, Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr514DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3198576PMC
November 2011

Genetic dissection of the biotic stress response using a genome-scale gene network for rice.

Proc Natl Acad Sci U S A 2011 Nov 31;108(45):18548-53. Epub 2011 Oct 31.

Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 262 Seongsanno, Seodaemun-gu, Seoul 120-749, Korea.

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http://www.pnas.org/content/108/45/18548.full.pdf
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https://journals.plos.org/plosone/article/file?id=10.1371/jo
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http://www.pnas.org/cgi/doi/10.1073/pnas.1110384108
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3215029PMC
November 2011

Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network.

Nat Protoc 2011 Aug 25;6(9):1429-42. Epub 2011 Aug 25.

Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea.

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http://dx.doi.org/10.1038/nprot.2011.372DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654671PMC
August 2011

MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines.

J Proteome Res 2011 Jul 29;10(7):2949-58. Epub 2011 Apr 29.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA.

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http://dx.doi.org/10.1021/pr2002116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3128686PMC
July 2011

Prioritizing candidate disease genes by network-based boosting of genome-wide association data.

Genome Res 2011 Jul 2;21(7):1109-21. Epub 2011 May 2.

Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 262 Seongsanno, Seodaemun-gu, Seoul, Korea.

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http://dx.doi.org/10.1101/gr.118992.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129253PMC
July 2011

High-throughput immunofluorescence microscopy using yeast spheroplast cell-based microarrays.

Methods Mol Biol 2011 ;706:83-95

Department of Genetics, Yale University, New Haven, CT, USA.

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http://dx.doi.org/10.1007/978-1-61737-970-3_7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654672PMC
March 2011

A role for central spindle proteins in cilia structure and function.

Cytoskeleton (Hoboken) 2011 Feb 12;68(2):112-24. Epub 2011 Jan 12.

Section of Molecular Cell and Developmental Biology, University of Texas at Austin, Austin, Texas, USA.

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http://dx.doi.org/10.1002/cm.20498DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4089984PMC
February 2011

Protein abundances are more conserved than mRNA abundances across diverse taxa.

Proteomics 2010 Dec;10(23):4209-12

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, TX, USA.

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http://dx.doi.org/10.1002/pmic.201000327DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3113407PMC
December 2010

It's the machine that matters: Predicting gene function and phenotype from protein networks.

J Proteomics 2010 Oct 15;73(11):2277-89. Epub 2010 Jul 15.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712-1064, USA.

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http://dx.doi.org/10.1016/j.jprot.2010.07.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2953423PMC
October 2010

Characterising and predicting haploinsufficiency in the human genome.

PLoS Genet 2010 Oct 14;6(10):e1001154. Epub 2010 Oct 14.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.

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https://dx.plos.org/10.1371/journal.pgen.1001154
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2954820PMC
October 2010

Parallel evolution in Pseudomonas aeruginosa over 39,000 generations in vivo.

mBio 2010 Sep 21;1(4). Epub 2010 Sep 21.

Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas, USA.

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http://dx.doi.org/10.1128/mBio.00199-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2939680PMC
September 2010

Predicting genetic modifier loci using functional gene networks.

Genome Res 2010 Aug 9;20(8):1143-53. Epub 2010 Jun 9.

Department of Biotechnology, College of Life science and Biotechnology, Yonsei University, Seodaemun-ku, Seoul 120-749, South Korea.

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http://dx.doi.org/10.1101/gr.102749.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2909577PMC
August 2010

Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line.

Mol Syst Biol 2010 Aug;6:400

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78229-3900, USA.

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http://dx.doi.org/10.1038/msb.2010.59DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2947365PMC
August 2010

Defining the pathway of cytoplasmic maturation of the 60S ribosomal subunit.

Mol Cell 2010 Jul;39(2):196-208

Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, TX 78712, USA.

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http://dx.doi.org/10.1016/j.molcel.2010.06.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2925414PMC
July 2010