Roger Bumgarner

Roger Bumgarner

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Roger Bumgarner

Publications by authors named "Roger Bumgarner"

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Letter to the Editor regarding Qui et al: "Cutibacterium acnes and the shoulder microbiome".

J Shoulder Elbow Surg 2019 Aug;28(8):e275-e276

Department of Microbiology, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.1016/j.jse.2019.04.046DOI Listing
August 2019

Temporal genetic association and temporal genetic causality methods for dissecting complex networks.

Nat Commun 2018 09 28;9(1):3980. Epub 2018 Sep 28.

Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.

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http://dx.doi.org/10.1038/s41467-018-06203-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6162292PMC
September 2018

Genomic Stability of Aggregatibacter actinomycetemcomitans during Persistent Oral Infection in Human.

PLoS One 2013 18;8(6):e66472. Epub 2013 Jun 18.

Division of Periodontology, Diagnostic Sciences and Dental Hygiene, Herman Ostrow School of Dentistry of the University of Southern California, Los Angeles, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0066472PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3688926PMC
October 2017

Variable Nitrogen Fixation in Wild Populus.

PLoS One 2016 19;11(5):e0155979. Epub 2016 May 19.

School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, Washington, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155979PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4873266PMC
July 2017

Draft Genome Sequence of Clinical Isolate 9610.

Genome Announc 2017 Mar 23;5(12). Epub 2017 Mar 23.

Department of Periodontics, University of Washington, Seattle, Washington, USA

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http://genomea.asm.org/lookup/doi/10.1128/genomeA.00024-17
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http://dx.doi.org/10.1128/genomeA.00024-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5364211PMC
March 2017

Comparison of Major and Minor Viral SNPs Identified through Single Template Sequencing and Pyrosequencing in Acute HIV-1 Infection.

PLoS One 2015 28;10(8):e0135903. Epub 2015 Aug 28.

Department of Microbiology, University of Washington, Seattle, WA, 98195, United States of America; Department of Medicine, University of Washington, Seattle, WA, 98195, United States of America; Department of Laboratory Medicine, Seattle, WA, 98195, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0135903PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4552882PMC
June 2016

Propionibacterium in Shoulder Arthroplasty: What We Think We Know Today.

J Bone Joint Surg Am 2016 Apr;98(7):597-606

Departments of Orthopaedics and Sports Medicine (J.E.H and F.A.M.) and Microbiology (R.E.B.), University of Washington, Seattle, Washington

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http://dx.doi.org/10.2106/JBJS.15.00568DOI Listing
April 2016

Draft Genome Sequence of Low-Passage Clinical Isolate Porphyromonas gingivalis MP4-504.

Genome Announc 2016 Apr 7;4(2). Epub 2016 Apr 7.

Department of Periodontics, University of Washington School of Dentistry, Seattle, Washington, USA

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http://dx.doi.org/10.1128/genomeA.00256-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824265PMC
April 2016

Lack of viral control and development of combination antiretroviral therapy escape mutations in macaques after bone marrow transplantation.

AIDS 2015 Aug;29(13):1597-606

aClinical Research Division, Fred Hutchinson Cancer Research Center bWashington National Primate Research Center, Seattle cVaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington dDivision of Pharmacotherapy and Experimental Therapeutics, University of North Carolina, Chapel Hill, North Carolina eDepartment of Microbiology fDepartment of Pediatrics gDepartment of Laboratory Medicine hDepartment of Medicine iDepartment of Pharmaceutics jDepartment of Pathology, University of Washington, Seattle, Washington, USA. *Christopher W. Peterson and Kevin G. Haworth contributed equally to the writing of this article.

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http://pdfs.journals.lww.com/aidsonline/2015/08240/Lack_of_v
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http://content.wkhealth.com/linkback/openurl?sid=WKPTLP:land
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http://dx.doi.org/10.1097/QAD.0000000000000702DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4572605PMC
August 2015

Resistance detected by pyrosequencing following zidovudine monotherapy for prevention of HIV-1 mother-to-child-transmission.

AIDS 2015 Jul;29(12):1467-71

aUniversity of Washington bSeattle Children's Research Institute, Seattle, Washington, USA cInstitut de Recherche pour le Développement (IRD) UMI 174-PHPT, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand dHarvard School of Public Health, Boston, Massachusetts eTulane University School of Medicine, New Orleans, Louisiana, USA.

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http://content.wkhealth.com/linkback/openurl?sid=WKPTLP:land
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http://dx.doi.org/10.1097/QAD.0000000000000737DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4618483PMC
July 2015

Comparative genomic analysis of seven Mycoplasma hyosynoviae strains.

Microbiologyopen 2015 Apr 18;4(2):343-359. Epub 2015 Feb 18.

Newport Laboratories Inc., Worthington, Minnesota.

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http://dx.doi.org/10.1002/mbo3.242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4398514PMC
April 2015

Propionibacterium persists in the skin despite standard surgical preparation.

J Bone Joint Surg Am 2014 Sep;96(17):1447-50

Departments of Sports Medicine and Orthopaedic Surgery (M.J.L., S.M.R., and F.A.M.) and Microbiology (R.E.B.), Divisions of Allergy and Infectious Diseases (P.S.P.) and Laboratory Medicine and Clinical Microbiology (S.B-W.), University of Washington Medical Center, University of Washington, Box 356500, 1959 N.E. Pacific Street, Seattle, WA 98195. E-mail address for M.J. Lee:

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http://jbjs.org/content/jbjsam/96/17/1447.full.pdf
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http://jbjs.org/cgi/doi/10.2106/JBJS.M.01474
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http://dx.doi.org/10.2106/JBJS.M.01474DOI Listing
September 2014

Validation of an oligonucleotide ligation assay for quantification of human immunodeficiency virus type 1 drug-resistant mutants by use of massively parallel sequencing.

J Clin Microbiol 2014 Jul 16;52(7):2320-7. Epub 2014 Apr 16.

Seattle Children's Research Institute, Seattle, Washington, USA Department of Pediatrics, University of Washington, Seattle, Washington, USA Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA Department of Global Health, University of Washington, Seattle, Washington, USA

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http://dx.doi.org/10.1128/JCM.00306-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4097683PMC
July 2014

Genome sequences of porcine epidemic diarrhea virus: in vivo and in vitro phenotypes.

Genome Announc 2014 Jun 12;2(3). Epub 2014 Jun 12.

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

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http://dx.doi.org/10.1128/genomeA.00503-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4056290PMC
June 2014

Origin of propionibacterium in surgical wounds and evidence-based approach for culturing propionibacterium from surgical sites.

J Bone Joint Surg Am 2013 Dec;95(23):e1811-7

Department of Orthopedics and Sports Medicine, University of Washington Medical Center, Box 356500, 1959 N.E. Pacific Street, Seattle, WA 98195. E-mail address for F.A. Matsen III:

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http://dx.doi.org/10.2106/JBJS.L.01733DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4098017PMC
December 2013

Characterization of the effects of an rpoC mutation that confers resistance to the Fst peptide toxin-antitoxin system toxin.

J Bacteriol 2013 Jan 26;195(1):156-66. Epub 2012 Oct 26.

Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA.

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http://dx.doi.org/10.1128/JB.01597-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3536179PMC
January 2013

Overview of DNA microarrays: types, applications, and their future.

Authors:
Roger Bumgarner

Curr Protoc Mol Biol 2013 Jan;Chapter 22:Unit 22.1.

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

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http://dx.doi.org/10.1002/0471142727.mb2201s101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4011503PMC
January 2013

Integrating external biological knowledge in the construction of regulatory networks from time-series expression data.

BMC Syst Biol 2012 Aug 16;6:101. Epub 2012 Aug 16.

Department of Microbiology, University of Washington, Box 358070, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1186/1752-0509-6-101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465231PMC
August 2012

Construction of regulatory networks using expression time-series data of a genotyped population.

Proc Natl Acad Sci U S A 2011 Nov 14;108(48):19436-41. Epub 2011 Nov 14.

Department of Microbiology, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1073/pnas.1116442108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228453PMC
November 2011

Genome sequence of a novel species, Propionibacterium humerusii.

J Bacteriol 2011 Jul 13;193(14):3678. Epub 2011 May 13.

Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.1128/JB.05036-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3133328PMC
July 2011

The genome of the domesticated apple (Malus × domestica Borkh.).

Nat Genet 2010 Oct 29;42(10):833-9. Epub 2010 Aug 29.

Istituto Agrario San Michele all'Adige Research and Innovation Centre, Foundation Edmund Mach, Trento, Italy.

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http://dx.doi.org/10.1038/ng.654DOI Listing
October 2010

A three-way comparative genomic analysis of Mannheimia haemolytica isolates.

BMC Genomics 2010 Oct 4;11:535. Epub 2010 Oct 4.

Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164-7040, USA.

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http://dx.doi.org/10.1186/1471-2164-11-535DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091684PMC
October 2010

Markedly different genome arrangements between serotype a strains and serotypes b or c strains of Aggregatibacter actinomycetemcomitans.

BMC Genomics 2010 Sep 8;11:489. Epub 2010 Sep 8.

Division of Periodontology, Diagnostic Sciences and Dental Hygiene, Herman Ostrow School of Dentistry of the University of Southern California, Los Angeles, CA, USA.

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http://dx.doi.org/10.1186/1471-2164-11-489DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2996985PMC
September 2010

Genome sequence of naturally competent Aggregatibacter actinomycetemcomitans serotype a strain D7S-1.

J Bacteriol 2010 May 26;192(10):2643-4. Epub 2010 Mar 26.

Division of Periodontology, Diagnostic Sciences and Dental Hygiene, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90089, USA.

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http://dx.doi.org/10.1128/JB.00157-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2863555PMC
May 2010

Genome sequences of Mannheimia haemolytica serotype A2: ovine and bovine isolates.

J Bacteriol 2010 Feb 4;192(4):1167-8. Epub 2009 Dec 4.

Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164-7040, USA.

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http://dx.doi.org/10.1128/JB.01527-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812981PMC
February 2010

Genome sequence of Aggregatibacter actinomycetemcomitans serotype c strain D11S-1.

J Bacteriol 2009 Dec 9;191(23):7378-9. Epub 2009 Oct 9.

Division of Primary Oral Health Care, University of Southern California School of Dentistry, Los Angeles, CA 90089, USA.

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http://dx.doi.org/10.1128/JB.01203-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2786557PMC
December 2009

The derivation of diagnostic markers of chronic myeloid leukemia progression from microarray data.

Blood 2009 Oct 4;114(15):3292-8. Epub 2009 Aug 4.

Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1182/blood-2009-03-212969DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2759651PMC
October 2009

Relationships between deficits in tissue mass and transcriptional programs after partial hepatectomy in mice.

Am J Pathol 2009 Sep 21;175(3):947-57. Epub 2009 Aug 21.

Department of Pathology, School of Medicine, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.2353/ajpath.2009.090043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2731115PMC
September 2009

Protinfo PPC: a web server for atomic level prediction of protein complexes.

Nucleic Acids Res 2009 Jul 6;37(Web Server issue):W519-25. Epub 2009 May 6.

Department of Microbiology, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.1093/nar/gkp306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703994PMC
July 2009

Methods for the inference of biological pathways and networks.

Methods Mol Biol 2009 ;541:225-45

Department of Microbiology, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.1007/978-1-59745-243-4_11DOI Listing
June 2009

Iterative Bayesian Model Averaging: a method for the application of survival analysis to high-dimensional microarray data.

BMC Bioinformatics 2009 Feb 26;10:72. Epub 2009 Feb 26.

Institute of Technology/Computing and Software Systems, University of Washington, Tacoma, WA 98402, USA.

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http://dx.doi.org/10.1186/1471-2105-10-72DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2657791PMC
February 2009

MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis.

Genome Biol 2008 24;9(7):R118. Epub 2008 Jul 24.

Department of Microbiology, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1186/gb-2008-9-7-r118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2530872PMC
October 2008

Attenuation of the type I interferon response in cells infected with human rhinovirus.

Virology 2008 May 12;374(2):399-410. Epub 2008 Feb 12.

Department of Microbiology, Molecular Biology and Biochemistry, University of Idaho, Moscow, Idaho 83844-3052, USA.

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http://dx.doi.org/10.1016/j.virol.2008.01.022DOI Listing
May 2008

Independent and cooperative antiviral actions of beta interferon and gamma interferon against herpes simplex virus replication in primary human fibroblasts.

J Virol 2008 Feb 5;82(4):1934-45. Epub 2007 Dec 5.

Department of Microbiology, School of Medicine, University of Washington, Seattle, WA 98195-8070, USA.

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http://dx.doi.org/10.1128/JVI.01649-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2258722PMC
February 2008

Comparative genomics of susceptibility to mammary carcinogenesis among inbred rat strains: role of reduced prolactin signaling in resistance of the Copenhagen strain.

Carcinogenesis 2008 Jan 4;29(1):177-85. Epub 2007 Oct 4.

Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1093/carcin/bgm224DOI Listing
January 2008

What is the best reference RNA? And other questions regarding the design and analysis of two-color microarray experiments.

OMICS 2007 ;11(2):152-65

Department of Biostatistics, University of Washington, Seattle, Washington 98195, USA.

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http://dx.doi.org/10.1089/omi.2007.0012DOI Listing
September 2007

Human rhinovirus attenuates the type I interferon response by disrupting activation of interferon regulatory factor 3.

J Virol 2007 Jun;81(11):6161

Department of Microbiology, School of Medicine, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.1128/JVI.00433-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1900254PMC
June 2007

Hierarchical gene expression profiles of HUVEC stimulated by different lipid A structures obtained from Porphyromonas gingivalis and Escherichia coli.

Cell Microbiol 2007 Apr 12;9(4):1028-38. Epub 2006 Dec 12.

Department of Periodontics and Oral Biology, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1111/j.1462-5822.2006.00849.xDOI Listing
April 2007

Evolutionary and biomedical insights from the rhesus macaque genome.

Authors:
Richard A Gibbs Jeffrey Rogers Michael G Katze Roger Bumgarner George M Weinstock Elaine R Mardis Karin A Remington Robert L Strausberg J Craig Venter Richard K Wilson Mark A Batzer Carlos D Bustamante Evan E Eichler Matthew W Hahn Ross C Hardison Kateryna D Makova Webb Miller Aleksandar Milosavljevic Robert E Palermo Adam Siepel James M Sikela Tony Attaway Stephanie Bell Kelly E Bernard Christian J Buhay Mimi N Chandrabose Marvin Dao Clay Davis Kimberly D Delehaunty Yan Ding Huyen H Dinh Shannon Dugan-Rocha Lucinda A Fulton Ramatu Ayiesha Gabisi Toni T Garner Jennifer Godfrey Alicia C Hawes Judith Hernandez Sandra Hines Michael Holder Jennifer Hume Shalini N Jhangiani Vandita Joshi Ziad Mohid Khan Ewen F Kirkness Andrew Cree R Gerald Fowler Sandra Lee Lora R Lewis Zhangwan Li Yih-Shin Liu Stephanie M Moore Donna Muzny Lynne V Nazareth Dinh Ngoc Ngo Geoffrey O Okwuonu Grace Pai David Parker Heidie A Paul Cynthia Pfannkoch Craig S Pohl Yu-Hui Rogers San Juana Ruiz Aniko Sabo Jireh Santibanez Brian W Schneider Scott M Smith Erica Sodergren Amanda F Svatek Teresa R Utterback Selina Vattathil Wesley Warren Courtney Sherell White Asif T Chinwalla Yucheng Feng Aaron L Halpern Ladeana W Hillier Xiaoqiu Huang Pat Minx Joanne O Nelson Kymberlie H Pepin Xiang Qin Granger G Sutton Eli Venter Brian P Walenz John W Wallis Kim C Worley Shiaw-Pyng Yang Steven M Jones Marco A Marra Mariano Rocchi Jacqueline E Schein Robert Baertsch Laura Clarke Miklós Csürös Jarret Glasscock R Alan Harris Paul Havlak Andrew R Jackson Huaiyang Jiang Yue Liu David N Messina Yufeng Shen Henry Xing-Zhi Song Todd Wylie Lan Zhang Ewan Birney Kyudong Han Miriam K Konkel Jungnam Lee Arian F A Smit Brygg Ullmer Hui Wang Jinchuan Xing Richard Burhans Ze Cheng John E Karro Jian Ma Brian Raney Xinwei She Michael J Cox Jeffery P Demuth Laura J Dumas Sang-Gook Han Janet Hopkins Anis Karimpour-Fard Young H Kim Jonathan R Pollack Tomas Vinar Charles Addo-Quaye Jeremiah Degenhardt Alexandra Denby Melissa J Hubisz Amit Indap Carolin Kosiol Bruce T Lahn Heather A Lawson Alison Marklein Rasmus Nielsen Eric J Vallender Andrew G Clark Betsy Ferguson Ryan D Hernandez Kashif Hirani Hildegard Kehrer-Sawatzki Jessica Kolb Shobha Patil Ling-Ling Pu Yanru Ren David Glenn Smith David A Wheeler Ian Schenck Edward V Ball Rui Chen David N Cooper Belinda Giardine Fan Hsu W James Kent Arthur Lesk David L Nelson William E O'brien Kay Prüfer Peter D Stenson James C Wallace Hui Ke Xiao-Ming Liu Peng Wang Andy Peng Xiang Fan Yang Galt P Barber David Haussler Donna Karolchik Andy D Kern Robert M Kuhn Kayla E Smith Ann S Zwieg

Science 2007 Apr;316(5822):222-34

Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1126/science.1139247DOI Listing
April 2007

cDNA microarray analysis reveals fundamental differences in the expression profiles of primary human monocytes, monocyte-derived macrophages, and alveolar macrophages.

J Leukoc Biol 2007 Jan 17;81(1):328-35. Epub 2006 Oct 17.

Department of Pathology, University of Washington, 815 Mercer Street, Seattle, WA 98109-4714, USA.

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http://dx.doi.org/10.1189/jlb.0206124DOI Listing
January 2007

Human rhinovirus attenuates the type I interferon response by disrupting activation of interferon regulatory factor 3.

J Virol 2006 May;80(10):5021-31

Department of Microbiology, School Of Medicine, University of Washington, Moscow, Idaho 83844-3052, USA.

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http://dx.doi.org/10.1128/JVI.80.10.5021-5031.2006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1472094PMC
May 2006

On the persistence of supplementary resources in biomedical publications.

BMC Bioinformatics 2006 May 19;7:260. Epub 2006 May 19.

Division of Biomedical Health Informatics, University of Washington, USA.

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http://dx.doi.org/10.1186/1471-2105-7-260DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1481620PMC
May 2006

Bayesian robust inference for differential gene expression in microarrays with multiple samples.

Biometrics 2006 Mar;62(1):10-8

Department of Statistics, University of Washington, Box 354322, Seattle, Washington 98195, USA.

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http://dx.doi.org/10.1111/j.1541-0420.2005.00397.xDOI Listing
March 2006

Chlamydia trachomatis variant with nonfusing inclusions: growth dynamic and host-cell transcriptional response.

J Infect Dis 2005 Oct 25;192(7):1229-36. Epub 2005 Aug 25.

Division of Infectious Diseases, Department of Medicine, University of Washington, Seattle, USA.

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http://dx.doi.org/10.1086/444394DOI Listing
October 2005

Functional annotation from predicted protein interaction networks.

Bioinformatics 2005 Aug 26;21(15):3217-26. Epub 2005 May 26.

Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/bti514DOI Listing
August 2005

Identification of high and low responders to lipopolysaccharide in normal subjects: an unbiased approach to identify modulators of innate immunity.

J Immunol 2005 Aug;175(4):2570-8

Medical Research Service, Veterans Affairs Puget Sound Medical Center and Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Washington School of Medicine, Seattle 98105, USA.

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http://www.jimmunol.org/content/175/4/2570.full.pdf
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http://dx.doi.org/10.4049/jimmunol.175.4.2570DOI Listing
August 2005

Donuts, scratches and blanks: robust model-based segmentation of microarray images.

Bioinformatics 2005 Jun 21;21(12):2875-82. Epub 2005 Apr 21.

Department of Statistics, Box 354322 University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1093/bioinformatics/bti447DOI Listing
June 2005

Multifunctionality of PAI-1 in fibrogenesis: evidence from obstructive nephropathy in PAI-1-overexpressing mice.

Kidney Int 2005 Jun;67(6):2221-38

Children's Hospital and Regional Medical Center and Department of Pediatrics, University of Washington, Seattle, Washington 98105, USA.

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http://dx.doi.org/10.1111/j.1523-1755.2005.00327.xDOI Listing
June 2005

Bayesian model averaging: development of an improved multi-class, gene selection and classification tool for microarray data.

Bioinformatics 2005 May 15;21(10):2394-402. Epub 2005 Feb 15.

Department of Microbiology, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1093/bioinformatics/bti319DOI Listing
May 2005

Sample size for detecting differentially expressed genes in microarray experiments.

BMC Genomics 2004 Nov 8;5:87. Epub 2004 Nov 8.

Department of Microbiology, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1186/1471-2164-5-87DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC533874PMC
November 2004

From co-expression to co-regulation: how many microarray experiments do we need?

Genome Biol 2004 28;5(7):R48. Epub 2004 Jun 28.

Department of Microbiology, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1186/gb-2004-5-7-r48DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC463312PMC
October 2004

RNA amplification, fidelity and reproducibility of expression profiling.

C R Biol 2003 Oct-Nov;326(10-11):1021-30

Department of Pathology, University of Washington, Seattle, WA, USA.

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May 2004

Multiclass classification of microarray data with repeated measurements: application to cancer.

Genome Biol 2003 24;4(12):R83. Epub 2003 Nov 24.

Department of Microbiology, Box 358070, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1186/gb-2003-4-12-r83DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC329422PMC
March 2004

Clustering gene-expression data with repeated measurements.

Genome Biol 2003 25;4(5):R34. Epub 2003 Apr 25.

Department of Microbiology, University of Washington, Seattle, WA 98195, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC156590PMC
http://dx.doi.org/10.1186/gb-2003-4-5-r34DOI Listing
July 2003

The transcriptome and its translation during recovery from cell cycle arrest in Saccharomyces cerevisiae.

Mol Cell Proteomics 2003 Mar 7;2(3):191-204. Epub 2003 Apr 7.

Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.

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http://dx.doi.org/10.1074/mcp.D200002-MCP200DOI Listing
March 2003

Chlamydia trachomatis infection alters host cell transcription in diverse cellular pathways.

J Infect Dis 2003 Feb 24;187(3):424-34. Epub 2003 Jan 24.

Division of Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA.

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http://dx.doi.org/10.1086/367962DOI Listing
February 2003

Identification of novel tumor markers in hepatitis C virus-associated hepatocellular carcinoma.

Cancer Res 2003 Feb;63(4):859-64

Department of Microbiology, School of Medicine, and Washington National Primate Research Center, University of Washington, Seattle, Washington 98195, USA.

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February 2003