Dr. Roger E. Bumgarner

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University of Washington
School of Medicine
Microbiology
Associate ProfessorAppointed: 2004
Associate Editor
Editorial board
Genomics
Appointed: 2006
BMC Genomics
Editorial Board
MemberAppointed: 2005
BMC Bioinformatics
Editorial Board
MemberAppointed: 2005
University of Washington
School of Medicine
Microbiology
Director, Center for Expression ArraysAppointed: 2001
Professional Headshot of Roger E. Bumgarner

Mailing Address

Box 358070
960 Republican St.
Seattle, Washington 98109
United States

Contact Information

Phone: (206) 732-6137
Fax: (206) 732-6055
rogerb@u.washington.edu
http://expression.washington.edu/bumgarnerlab

Qualifications

Ph.D., University of Arizona, Physical Chemistry, 1988.
M.S., Eastern Illinois University, Chemistry, 1983.
B.S., Eastern Illinois University, Chemistry, 1982.
A.S., Elgin Community College, 1980.

Expertise and Research Interests

Dr. Bumgarner received his Bachelor and Master of Science degrees from Eastern Illinois University and his Ph.D. from the University of Arizona. His initial field of study and research was physical chemistry with a focus on high-resolution molecular spectroscopy. In 1988, he moved to the California Institute of Technology to accept a Bantrell Fellow in the Department of Geology and Planetary Science. This was followed by a two year Research Fellowship with Dr. Leroy Hood in the Department of Biology, where he worked on DNA sequencing technology. Dr. Bumgarner transferred to the University of Washington in 1992 as part of the newly formed Department of Molecular Biotechnology. For the next six years, he worked on DNA sequencing and array technology before moving to the Department of Microbiology in 1998.

During the past 20 years, Dr. Bumgarner has authored and co-authored numerous scientific papers in research areas ranging from chemical physics to cancer to HIV research. He has helped found three companies in the Pacific Northwest and currently serves on the scientific advisory board of Integra Ventures, a local venture capital fund. He is a co-inventor of a commercial genotyping software package, SAGATM (sold by LiCor BioSciences), and has developed software for DNA array analysis. Dr. Bumgarner is presently an Associate Professor in the Department of Microbiology at the University of Washington (UW) and the Director of the UW Center for Expression Arrays.

Other Expertise

POST-GRADUATE TRAINING:
8/88-8/90: Bantrell Fellow, Div of Geology and Planetary Sciences, California Institute of Technology.
Mentor: Dr. Geoffery Blake
8/90-9/91: Research Fellow, Div of Geology and Planetary Sciences, California Institute of Technology.
9/91-6/92: Senior Research Fellow, Div of Biology, California Institute of Technology.
Mentor: Dr. Leroy Hood
7/95-4/98: Research Scientist, Dept of Molecular Biotechnology, Univ of Washington, Seattle.
Mentor: Dr. Leroy Hood

Future Research

RESEARCH INTERESTS:
Bioinformatics - The development of software and databases to analyze and store microarray data and to integrate genomics and functional genomics data to predict networks.

Host-virus interaction - We use functional genomics technologies to investigate how viruses interact with and perturb the host with a particular focus on the host innate immune response.

Keywords

COS Keywords:

Bioinformatics, Genomics, Microbiology, Molecular Spectroscopy, Physical Chemistry.

Additional Terms:

Bioinformatics, Comparative Genomics, Expression Analysis, Host-virus Interactions.

Memberships

Microarray Gene Expression Data Society

Honors and Awards

2005, Outstanding Graduate Alumnus Award, Eastern Illinois University, Department of Chemistry
1995, Distinguished Alumnus Award, Elgin Community College
1988-1990, Bantrell Fellow, California Institute of Technology, Division of Geology and Planetary Sciences
1987-1988, Carl S. Marvel Fellow, University of Arizona, Department of Chemistry

Previous Positions

2002-2004, Assistant Professor, University of Washington, School of Medicine, Microbiology
1998-2002, Research Assistant Professor, University of Washington, School of Medicine, Microbiology
1995-1998, Sr. Research Scientist, University of Washington, School of Medicine, Molecular Biotechnology
1992-1995, Acting Assistant Professor, University of Washington, School of Medicine, Molecular Biotechnology

Publications

  • Rhesus Macaque Genome Sequencing Consortium (2007) Evolutionary and biomedical insights from the rhesus macaque genome Science, Science, 316 (5822), 222
  • Serikawa KA, Kerr KF, Wei C, Bumgarner RE (2007) What Is the Best Reference RNA? And Other Questions Regarding the Design and Analysis of Two-colorMicroarray Experiments, 'Omics, 11 (2), 215
  • Gottardo R., Raftery AE, Yeung KY, Bumgarner RE (2006) Bayesian robust inference for differential gene expression in microarrays with multiple samples, Biometrics, 62 (1), 10-8
  • Matsuo S, Lopez-Guisa JM, Cai X, Okamura DM, Alpers CE, Bumgarner RE, Peters MA, Zhang G, Eddy AA (Jun 2005) Multifunctionality of PAI-1 in fibrogenesis: evidence from obstructive nephropathy in PAI-1-overexpressing mice, Kidney International, 67 (6), 2221-38
  • Li Q, Fraley C, Bumgarner RE, Yeung KY, Raftery AE (Jun 2005) Donuts, scratches and blanks: robust model-based segmentation of microarray images, Bioinformatics (oxford, England), 21 (12), 2875-82
  • Yeung KY, Bumgarner RE, Raftery AE (May 2005) Bayesian model averaging: development of an improved multi-class, gene, Bioinformatics (oxford, England), 21 (10), 2394-402
  • Wei C, Li J, Bumgarner RE, Sample Size for Detecting Differentially Expressed Genes in Microarray Experiments, Bmc Genomics [electronic Resource], 5(1), 87, Nov 2004
  • Medvedovic M, Yeung KY, Bumgarner RE (May 2004) Bayesian Mixture Model Based Clustering of Replicated Microarray Data, Bioinformatics (oxford, England), 20 (8), 1222-32
  • Yeung KY, Medvedovic M, Bumgarner RE (2004) From Co-expression to Co-regulation: How Many Microarray Experiments Do We Need?, Genome Biology, 5 (7), R48
  • Smith MW, Yue ZN, Geiss GK, Sadovnikova NY, Carter VS, Boix L, Lazaro CA, Rosenberg GB, Bumgarner RE, Fausto N, Bruix J, Katze MG (February 2003) Identification of novel tumor markers in hepatitis C virus-associated hepatocellular carcinoma, Cancer Research, 63 (4), 859-64
  • Xia M, Bumgarner RE, Lampe MF, Stamm WE (February 2003) Chlamydia trachomatis infection alters host cell transcription in diverse cellular pathways, Journal of Infectious Diseases, 187 (3), 424-34
  • van 't Wout AB, Lehrman GK, Mikheeva SA, O'Keeffe GC, Katze MG, Bumgarner RE, Geiss GK, Mullins JI (January 2003) Cellular gene expression upon human immunodeficiency virus type 1 infection of CD4(+)-T-cell lines, Journal of Virology, 77 (2), 1392-402
  • Yeung KY, Bumgarner RE (2003) Multiclass classification of microarray data with repeated measurements:, Genome Biology, 4 (12), R83
  • Yeung KY, Medvedovic M, Bumgarner RE (2003) Clustering Gene-expression Data With Repeated Measurements, Genome Biology, 4 (5), R34
  • Yeung KY, Bumgarner RE (2003) Multiclass Classification of Microarray Data With Repeated Measurements: Application to Cancer, Genome Biology, 4 (12), R83
  • Geiss GK, Salvatore M, Tumpey TM, Carter VS, Wang X, Basler CF, Taubenberger JK, Bumgarner RE, Palese P, Katze MG, Garcia-Sastre A (Aug 2002) Cellular transcriptional profiling in influenza A virus-infected lung epithelial cells: the role of the nonstructural NS1 protein in the evasion of the host innate defense and its potentia, Proceedings of the National Academy of Sciences (USA), 99 (16), 10736-41
  • Park IK, He Y, Lin F, Laerum OD, Tian Q, Bumgarner R, Klug CA, Li K, Kuhr C, Doyle MJ, Xie T, Schummer M, Sun Y, Goldsmith A, Clarke MF, Weissman IL, Hood L, Li L (January 2002) Differential gene expression profiling of adult murine hematopoietic stem cells, Blood, 99 (2), 488-98
  • Park IK, He Y, Lin F, Laerum OD, Tian Q, Bumgarner R, Klug CA, Li K, Kuhr C, Doyle MJ, Xie T, Schummer M, Sun Y, Goldsmith A, Clarke MF, Weissman IL, Hood L, Li L (Jan 2002) Differential gene expression profiling of adult murine hematopoietic stem cells., Blood, 99 (2), 488-98 Abstract
  • Whiteley M, Bangera MG, Bumgarner RE, Parsek MR, Teitzel GM, Lory S, Greenberg EP (October 2001) Gene expression in Pseudomonas aeruginosa biofilms, Nature, 413 (6858), 860-4
  • Geiss G, Jin G, Guo J, Bumgarner R, Katze MG, Sen GC (August 2001) A comprehensive view of regulation of gene expression by double-stranded RNA-mediated cell signaling, Journal of Biological Chemistry, 276 (32), 30178-82
  • Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L (May 2001) Integrated genomic and proteomic analyses of a systematically perturbed metabolic network, Science, 292 (5518), 929-34
  • Geiss GK, An MC, Bumgarner RE, Hammersmark E, Cunningham D, Katze MG (May 2001) Global impact of influenza virus on cellular pathways is mediated by both replication-dependent and -independent events, Journal of Virology, 75 (9), 4321-31
  • Ichikawa JK, Norris A, Bangera MG, Geiss GK, van 't Wout AB, Bumgarner RE, Lory S, Interaction of pseudomonas aeruginosa with epithelial cells: identification of differentially regulated genes by expression microarray analysis of human cDNAs, Proceedings of the National Academy of Sciences (USA), 97(17), 9659-64, August 2000
  • Lin B, White JT, Ferguson C, Bumgarner R, Friedman C, Trask B, Ellis W, Lange P, Hood L, Nelson PS (February 2000) PART-1: a novel human prostate-specific, androgen-regulated gene that maps to chromosome 5q12, Cancer Research, 60 (4), 858-63
  • Lin B, White JT, Ferguson C, Bumgarner R, Friedman C, Trask B, Ellis W, Lange P, Hood L, Nelson PS (Feb 2000) PART-1: a novel human prostate-specific, androgen-regulated gene that maps to chromosome 5q12., Cancer Research, 60 (4), 858-63 Abstract
  • Nelson PS, Clegg N, Eroglu B, Hawkins V, Bumgarner R, Smith T, Hood L (Jan 2000) The prostate expression database (PEDB): status and enhancements in 2000, Nucleic Acids Research, 28 (1), 212-3
  • Geiss GK, Bumgarner RE, An MC, Agy MB, van 't Wout AB, Hammersmark E, Carter VS, Upchurch D, Mullins JI, Katze MG (Jan 2000) Large-scale monitoring of host cell gene expression during HIV-1 infection using cDNA microarrays, Virology, 266 (1), 8-16
  • Nelson PS, Hawkins V, Schummer M, Bumgarner R, Ng WL, Ideker T, Ferguson C, Hood L (15 Dec 1999) Negative selection: a method for obtaining low-abundance cDNAs using high-density cDNA clone arrays, Genetic Analysis, 15 (6), 209-15
  • Hawkins V, Doll D, Bumgarner R, Smith T, Abajian C, Hood L, Nelson PS (Jan 1999) PEDB: the Prostate Expression Database., Nucleic Acids Research, 27 (1), 204-8 Abstract
  • Ng WV, Ciufo SA, Smith TM, Bumgarner RE, Baskin D, Faust J, Hall B, Loretz C, Seto J, Slagel J, Hood L, DasSarma S (November 1998) Snapshot of a large dynamic replicon in a halophilic archaeon: megaplasmid or minichromosome?, Genome Research, 8 (11), 1131-41
  • Nelson PS, Ng WL, Schummer M, True LD, Liu AY, Bumgarner RE, Ferguson C, Dimak A, Hood L (1 1998) An expressed-sequence-tag database of the human prostate: sequence analysis of 1168 cDNA clones, Genomics, 47 (1), 12-25
  • Schummer M, Ng W, Nelson PS, Bumgarner RE, Hood L (December 1997) Inexpensive handheld device for the construction of high-density nucleic acid arrays, Biotechniques, 23 (6), 1087-92
  • Stoughton R, Bumgarner R, Frederick WJ 3rd, McIndoe RA (Jan 1997) Data-adaptive algorithms for calling alleles in repeat polymorphisms., Electrophoresis, 18 (1), 1-5 Abstract
  • Stoughton R, Bumgarner R, Frederick WJ 3rd, McIndoe RA (Jan 1997) Data-adaptive algorithms for calling alleles in repeat polymorphisms., Electrophoresis, 18 (1), 1-5 Abstract
  • McIndoe RA, Hood L, Bumgarner RE (Apr 1996) An analysis of the dynamic range and linearity of an infrared DNA sequencer., Electrophoresis, 17 (4), 652-8 Abstract

Profile Details

Last Updated: 8/1/2007

COS Expertise ID #803040
Reference this profile directly: http://myprofile.cos.com/bumgarner