Publications by authors named "Gennifer Merrihew"

31Publications

Highly Parallel Quantification and Compartment Localization of Transcription Factors and Nuclear Proteins.

Cell Rep 2020 02;30(8):2463-2471.e5

Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA; University of Washington, Department of Genome Sciences, Seattle, WA 98195, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2020.01.096DOI Listing
February 2020

Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows.

J Am Soc Mass Spectrom 2019 Apr 22;30(4):669-684. Epub 2019 Jan 22.

Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, WA, USA.

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http://dx.doi.org/10.1007/s13361-018-2122-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6445824PMC
April 2019

Glucocerebrosidase deficiency promotes protein aggregation through dysregulation of extracellular vesicles.

PLoS Genet 2018 09 26;14(9):e1007694. Epub 2018 Sep 26.

Department of Genome Sciences, University of Washington, Seattle, WA, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1007694DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6175534PMC
September 2018

Proteomics Analysis Identifies Orthologs of Human Chitinase-Like Proteins as Inducers of Tube Morphogenesis Defects in .

Genetics 2017 06 12;206(2):973-984. Epub 2017 Apr 12.

Department of Genome Sciences, University of Washington, Seattle, Washington 98195-5065

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http://dx.doi.org/10.1534/genetics.116.199323DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499198PMC
June 2017

Staphylococcus aureus Protein A Mediates Interspecies Interactions at the Cell Surface of Pseudomonas aeruginosa.

mBio 2016 05 24;7(3). Epub 2016 May 24.

Department of Microbiology, University of Washington, Seattle, Washington, USA Department of Pediatrics, University of Washington, Seattle, Washington, USA

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http://dx.doi.org/10.1128/mBio.00538-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4895107PMC
May 2016

The EARP Complex and Its Interactor EIPR-1 Are Required for Cargo Sorting to Dense-Core Vesicles.

PLoS Genet 2016 05 18;12(5):e1006074. Epub 2016 May 18.

Department of Biochemistry, University of Washington, Seattle, Washington, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1006074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4871572PMC
May 2016

Comparison of data acquisition strategies on quadrupole ion trap instrumentation for shotgun proteomics.

J Am Soc Mass Spectrom 2014 Dec 27;25(12):2048-59. Epub 2014 Sep 27.

Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.

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http://dx.doi.org/10.1007/s13361-014-0981-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417682PMC
December 2014

Comparative analysis of the transcriptome across distant species.

Nature 2014 Aug;512(7515):445-8

1] Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA [2].

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http://dx.doi.org/10.1038/nature13424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155737PMC
August 2014

Proteogenomic database construction driven from large scale RNA-seq data.

J Proteome Res 2014 Jan 17;13(1):21-8. Epub 2013 Jul 17.

Department of Electrical and Computing Engineering, ¶Department of Bioinformatics and Systems Biology, and §Department of Computer Science, University of California, San Diego , La Jolla, California 92093, United States.

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http://dx.doi.org/10.1021/pr400294cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034692PMC
January 2014

Multiplexed MS/MS for improved data-independent acquisition.

Nat Methods 2013 Aug 23;10(8):744-6. Epub 2013 Jun 23.

Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.

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http://dx.doi.org/10.1038/nmeth.2528DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3881977PMC
August 2013

The PINK1-Parkin pathway promotes both mitophagy and selective respiratory chain turnover in vivo.

Proc Natl Acad Sci U S A 2013 Apr 18;110(16):6400-5. Epub 2013 Mar 18.

Neurobiology and Behavior Program and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1073/pnas.1221132110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631677PMC
April 2013

De novo correction of mass measurement error in low resolution tandem MS spectra for shotgun proteomics.

J Am Soc Mass Spectrom 2012 Dec 25;23(12):2075-82. Epub 2012 Sep 25.

Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1007/s13361-012-0482-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3515694PMC
December 2012

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Authors:
Mark B Gerstein Zhi John Lu Eric L Van Nostrand Chao Cheng Bradley I Arshinoff Tao Liu Kevin Y Yip Rebecca Robilotto Andreas Rechtsteiner Kohta Ikegami Pedro Alves Aurelien Chateigner Marc Perry Mitzi Morris Raymond K Auerbach Xin Feng Jing Leng Anne Vielle Wei Niu Kahn Rhrissorrakrai Ashish Agarwal Roger P Alexander Galt Barber Cathleen M Brdlik Jennifer Brennan Jeremy Jean Brouillet Adrian Carr Ming-Sin Cheung Hiram Clawson Sergio Contrino Luke O Dannenberg Abby F Dernburg Arshad Desai Lindsay Dick Andréa C Dosé Jiang Du Thea Egelhofer Sevinc Ercan Ghia Euskirchen Brent Ewing Elise A Feingold Reto Gassmann Peter J Good Phil Green Francois Gullier Michelle Gutwein Mark S Guyer Lukas Habegger Ting Han Jorja G Henikoff Stefan R Henz Angie Hinrichs Heather Holster Tony Hyman A Leo Iniguez Judith Janette Morten Jensen Masaomi Kato W James Kent Ellen Kephart Vishal Khivansara Ekta Khurana John K Kim Paulina Kolasinska-Zwierz Eric C Lai Isabel Latorre Amber Leahey Suzanna Lewis Paul Lloyd Lucas Lochovsky Rebecca F Lowdon Yaniv Lubling Rachel Lyne Michael MacCoss Sebastian D Mackowiak Marco Mangone Sheldon McKay Desirea Mecenas Gennifer Merrihew David M Miller Andrew Muroyama John I Murray Siew-Loon Ooi Hoang Pham Taryn Phippen Elicia A Preston Nikolaus Rajewsky Gunnar Rätsch Heidi Rosenbaum Joel Rozowsky Kim Rutherford Peter Ruzanov Mihail Sarov Rajkumar Sasidharan Andrea Sboner Paul Scheid Eran Segal Hyunjin Shin Chong Shou Frank J Slack Cindie Slightam Richard Smith William C Spencer E O Stinson Scott Taing Teruaki Takasaki Dionne Vafeados Ksenia Voronina Guilin Wang Nicole L Washington Christina M Whittle Beijing Wu Koon-Kiu Yan Georg Zeller Zheng Zha Mei Zhong Xingliang Zhou Julie Ahringer Susan Strome Kristin C Gunsalus Gos Micklem X Shirley Liu Valerie Reinke Stuart K Kim LaDeana W Hillier Steven Henikoff Fabio Piano Michael Snyder Lincoln Stein Jason D Lieb Robert H Waterston

Science 2010 Dec 22;330(6012):1775-87. Epub 2010 Dec 22.

Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1126/science.1196914DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142569PMC
December 2010

Post analysis data acquisition for the iterative MS/MS sampling of proteomics mixtures.

J Proteome Res 2009 Apr;8(4):1870-5

University of Washington, Department of Genome Sciences, Seattle, Washington 98195, USA.

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http://dx.doi.org/10.1021/pr800828pDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2671646PMC
April 2009

Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries.

Anal Chem 2006 Aug;78(16):5678-84

Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.

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http://dx.doi.org/10.1021/ac060279nDOI Listing
August 2006

High genetic diversity in the chemoreceptor superfamily of Caenorhabditis elegans.

Genetics 2005 Apr 1;169(4):1985-96. Epub 2004 Nov 1.

Department of Genome Sciences, University of Washington, Seattle, 98195, USA.

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http://dx.doi.org/10.1534/genetics.104.035329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449585PMC
April 2005