faculty
Roger Bumgarner
rogerb@uw.edu
Associate Professor
University of Washington
,Microbiology
Gene Expression, Cell Cycle & Chromosome Biology
Microbiology, Infection & Immunity
Faculty Contact Information
Building: Rosen Building, South Lake Union
Room: Room 262B
Box: 358070
Phone: 206-732-6137
https://microbiology.washington.edu/users/roger-e-bumgarner
Research Summary
A fundamental issue facing modern biology is the development of methods and tools to convert genomics and function genomics data into mechanistic understanding. Genome sequences and computational methods have provided us with tools to identify and annotate genes and other functional sequences with varying degrees of accuracy. Annotated sequence information in turn enables tools such as RNA-Seq, microarrays, 2-D gels, protein mass spectrometry and yeast 2-hybrids to measure RNA and protein levels and physical interactions on genome-wide or near genome-wide scales.
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Publications
The following publications were retrieved from PubMed:
Hsu JE, Harrison D, Anderson K, Huang C, Whitson AJ, Matsen FA 3rd, Bumgarner RE.
J Shoulder Elbow Surg. 2021 Aug 16;
Bacterial cyclic diguanylate signaling networks sense temperature.
Almblad H, Randall TE, Liu F, Leblanc K, Groves RA, Kittichotirat W, Winsor GL, Fournier N, Au E, Groizeleau J, Rich JD, Lou Y, Granton E, Jennings LK, Singletary LA, Winstone TML, Good NM, Bumgarner RE, Hynes MF, Singh M, Stietz MS, Brinkman FSL, Kumar A, Brassinga AKC, Parsek MR, Tseng BS, Lewis IA, Yipp BG, MacCallum JL, Harrison JJ.
Nat Commun. 2021 Mar 31; 1(12)1986
Hsu JE, Matsen FA 3rd, Whitson AJ, Bumgarner RE.
J Shoulder Elbow Surg. 2020 Oct; 10(29)2051-2055
Tjokro NO, Kittichotirat W, Torittu A, Ihalin R, Bumgarner RE, Chen C.
Pathogens. 2019 Dec 3; 4(8)
Bumgarner RE, Harrison D, Hsu JE.
J Clin Microbiol. 2020 Jan 28; 2(58)
Letter to the Editor regarding Qui et al: "Cutibacterium acnes and the shoulder microbiome".
Long DR, Hsu JE, Salipante SJ, Bumgarner RE.
J Shoulder Elbow Surg. 2019 Aug; 8(28)e275-e276
Temporal genetic association and temporal genetic causality methods for dissecting complex networks.
Lin L, Chen Q, Hirsch JP, Yoo S, Yeung K, Bumgarner RE, Tu Z, Schadt EE, Zhu J.
Nat Commun. 2018 Sep 28; 1(9)3980
Draft Genome Sequence of Tannerella forsythia Clinical Isolate 9610.
Hanson-Drury S, To TT, Liu Q, Vo AT, Kim M, Watling M, Bumgarner RS, McLean JS.
Genome Announc. 2017 Mar 23; 12(5)
Tang-Siegel G, Bumgarner R, Ruiz T, Kittichotirat W, Chen W, Chen C.
PLoS One. 2016; 8(11)e0160018
Variable Nitrogen Fixation in Wild Populus.
Doty SL, Sher AW, Fleck ND, Khorasani M, Bumgarner RE, Khan Z, Ko AW, Kim SH, DeLuca TH.
PLoS One. 2016; 5(11)e0155979
Draft Genome Sequence of Low-Passage Clinical Isolate Porphyromonas gingivalis MP4-504.
To TT, Liu Q, Watling M, Bumgarner RE, Darveau RP, McLean JS.
Genome Announc. 2016 Apr 7; 2(4)
Propionibacterium in Shoulder Arthroplasty: What We Think We Know Today.
Hsu JE, Bumgarner RE, Matsen FA 3rd.
J Bone Joint Surg Am. 2016 Apr 6; 7(98)597-606
Edlund A, Liu Q, Watling M, To TT, Bumgarner RE, He X, Shi W, McLean JS.
Genome Announc. 2016 Feb 18; 1(4)
McLean JS, Liu Q, Bor B, Bedree JK, Cen L, Watling M, To TT, Bumgarner RE, He X, Shi W.
Genome Announc. 2016 Feb 4; 1(4)
Digital detection of endonuclease mediated gene disruption in the HIV provirus.
Sedlak RH, Liang S, Niyonzima N, De Silva Feelixge HS, Roychoudhury P, Greninger AL, Weber ND, Boissel S, Scharenberg AM, Cheng A, Magaret A, Bumgarner R, Stone D, Jerome KR.
Sci Rep. 2016 Feb 2; (6)20064
Evolutionary Divergence of Aggregatibacter actinomycetemcomitans.
Kittichotirat W, Bumgarner RE, Chen C.
J Dent Res. 2016 Jan; 1(95)94-101
Peterson CW, Haworth KG, Polacino P, Huang ML, Sykes C, Obenza WM, Repetto AC, Kashuba A, Bumgarner R, DeRosa SC, Woolfrey AE, Jerome KR, Mullins JI, Hu SL, Kiem HP.
AIDS. 2015 Aug 24; 13(29)1597-606
Iyer S, Casey E, Bouzek H, Kim M, Deng W, Larsen BB, Zhao H, Bumgarner RE, Rolland M, Mullins JI.
PLoS One. 2015; 8(10)e0135903
Olson SC, Ngo-Giang-Huong N, Beck I, Deng W, Britto P, Shapiro DE, Bumgarner RE, Mullins JI, Van Dyke RB, Jourdain G, Frenkel LM.
AIDS. 2015 Jul 31; 12(29)1467-71
Comparative genomic analysis of seven Mycoplasma hyosynoviae strains.
Bumgardner EA, Kittichotirat W, Bumgarner RE, Lawrence PK.
Microbiologyopen. 2015 Apr; 2(4)343-359
Genome-Wide Association Studies of Virulent and Avirulent Haemophilus parasuis Serotype 4 Strains.
Lawrence PK, Wiener BL, Kolander-Bremer T, Bey RF, Stine DL, Kittichotirat W, Bumgarner RE.
Genome Announc. 2014 Sep 4; 5(2)
Propionibacterium persists in the skin despite standard surgical preparation.
Lee MJ, Pottinger PS, Butler-Wu S, Bumgarner RE, Russ SM, Matsen FA 3rd.
J Bone Joint Surg Am. 2014 Sep 3; 17(96)1447-50
Genome sequences of porcine epidemic diarrhea virus: in vivo and in vitro phenotypes.
Lawrence PK, Bumgardner E, Bey RF, Stine D, Bumgarner RE.
Genome Announc. 2014 Jun 12; 3(2)
Bumgardner E, Bey RF, Kittichotirat W, Bumgarner RE, Lawrence PK.
Genome Announc. 2014 Jun 5; 3(2)
Beck IA, Deng W, Payant R, Hall R, Bumgarner RE, Mullins JI, Frenkel LM.
J Clin Microbiol. 2014 Jul; 7(52)2320-7
Lawrence PK, Bey RF, Wiener B, Kittichotirat W, Bumgarner RE.
Genome Announc. 2014 Mar 27; 2(2)
Matsen FA 3rd, Butler-Wu S, Carofino BC, Jette JL, Bertelsen A, Bumgarner R.
J Bone Joint Surg Am. 2013 Dec 4; 23(95)e1811-7
Sun R, Kittichotirat W, Wang J, Jan M, Chen W, Asikainen S, Bumgarner R, Chen C.
PLoS One. 2013; 6(8)e66472
Laksmana T, Kittichotirat W, Huang Y, Chen W, Jorgensen M, Bumgarner R, Chen C.
Open Dent J. 2012; (6)255-61
Overview of DNA microarrays: types, applications, and their future.
Bumgarner R
Curr Protoc Mol Biol. 2013 Jan; (Chapter 22)Unit 22.1.
Huang Y, Kittichotirat W, Mayer MP, Hall R, Bumgarner R, Chen C.
Mol Oral Microbiol. 2013 Feb; 1(28)1-17
Brinkman CL, Bumgarner R, Kittichotirat W, Dunman PM, Kuechenmeister LJ, Weaver KE.
J Bacteriol. 2013 Jan; 1(195)156-66
Lo K, Raftery AE, Dombek KM, Zhu J, Schadt EE, Bumgarner RE, Yeung KY.
BMC Syst Biol. 2012 Aug 16; (6)101
Srinivasan S, Hoffman NG, Morgan MT, Matsen FA, Fiedler TL, Hall RW, Ross FJ, McCoy CO, Bumgarner R, Marrazzo JM, Fredricks DN.
PLoS One. 2012; 6(7)e37818
Zhu J, Sova P, Xu Q, Dombek KM, Xu EY, Vu H, Tu Z, Brem RB, Bumgarner RE, Schadt EE.
PLoS Biol. 2012; 4(10)e1001301
Laser capture microdissection enables cellular and molecular studies of tooth root development.
Sun JX, Horst OV, Bumgarner R, Lakely B, Somerman MJ, Zhang H.
Int J Oral Sci. 2012 Mar; 1(4)7-13
Chen C, Kittichotirat W, Chen W, Downey JS, Bumgarner R.
J Bacteriol. 2012 Apr; 7(194)1837
Construction of regulatory networks using expression time-series data of a genotyped population.
Yeung KY, Dombek KM, Lo K, Mittler JE, Zhu J, Schadt EE, Bumgarner RE, Raftery AE.
Proc Natl Acad Sci U S A. 2011 Nov 29; 48(108)19436-41
Taniya T, Tanaka S, Yamaguchi-Kabata Y, Hanaoka H, Yamasaki C, Maekawa H, Barrero RA, Lenhard B, Datta MW, Shimoyama M, Bumgarner R, Chakraborty R, Hopkinson I, Jia L, Hide W, Auffray C, Minoshima S, Imanishi T, Gojobori T.
Genomics. 2012 Jan; 1(99)1-9
Kittichotirat W, Bumgarner RE, Asikainen S, Chen C.
PLoS One. 2011; 7(6)e22420
Kittichotirat W, Good NM, Hall R, Bringel F, Lajus A, Médigue C, Smalley NE, Beck D, Bumgarner R, Vuilleumier S, Kalyuzhnaya MG.
J Bacteriol. 2011 Sep; 17(193)4541-2
Genome sequence of a novel species, Propionibacterium humerusii.
Butler-Wu SM, Sengupta DJ, Kittichotirat W, Matsen FA 3rd, Bumgarner RE.
J Bacteriol. 2011 Jul; 14(193)3678
Suzuki M, Pritchard DK, Becker L, Hoofnagle AN, Tanimura N, Bammler TK, Beyer RP, Bumgarner R, Vaisar T, de Beer MC, de Beer FC, Miyake K, Oram JF, Heinecke JW.
Circulation. 2010 Nov 9; 19(122)1919-27
A three-way comparative genomic analysis of Mannheimia haemolytica isolates.
Lawrence PK, Kittichotirat W, McDermott JE, Bumgarner RE.
BMC Genomics. 2010 Oct 4; (11)535
Kittichotirat W, Bumgarner R, Chen C.
BMC Genomics. 2010 Sep 8; (11)489
The genome of the domesticated apple (Malus × domestica Borkh.).
Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E, Eldredge G, Fitzgerald LM, Gutin N, Lanchbury J, Macalma T, Mitchell JT, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu VT, King ST, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater MM, Masiero S, Lasserre P, Lespinasse Y, Allan AC, Bus V, Chagné D, Crowhurst RN, Gleave AP, Lavezzo E, Fawcett JA, Proost S, Rouzé P, Sterck L, Toppo S, Lazzari B, Hellens RP, Durel CE, Gutin A, Bumgarner RE, Gardiner SE, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R.
Nat Genet. 2010 Oct; 10(42)833-9
Chen C, Kittichotirat W, Chen W, Downey JS, Si Y, Bumgarner R.
J Bacteriol. 2010 May; 10(192)2643-4
Genome sequences of Mannheimia haemolytica serotype A2: ovine and bovine isolates.
Lawrence PK, Kittichotirat W, Bumgarner RE, McDermott JE, Herndon DR, Knowles DP, Srikumaran S.
J Bacteriol. 2010 Feb; 4(192)1167-8
Genome sequence of Aggregatibacter actinomycetemcomitans serotype c strain D11S-1.
Chen C, Kittichotirat W, Si Y, Bumgarner R.
J Bacteriol. 2009 Dec; 23(191)7378-9
Li J, Campbell JS, Mitchell C, McMahan RS, Yu X, Riehle KJ, Bumgarner RE, Fausto N.
Am J Pathol. 2009 Sep; 3(175)947-57
The derivation of diagnostic markers of chronic myeloid leukemia progression from microarray data.
Oehler VG, Yeung KY, Choi YE, Bumgarner RE, Raftery AE, Radich JP.
Blood. 2009 Oct 8; 15(114)3292-8
Trusov A, Bumgarner R, Valijev R, Chestnova R, Talevski S, Vragoterova C, Neeley ES.
Int J Tuberc Lung Dis. 2009 Jul; 7(13)836-41
Protinfo PPC: a web server for atomic level prediction of protein complexes.
Kittichotirat W, Guerquin M, Bumgarner RE, Samudrala R.
Nucleic Acids Res. 2009 Jul; Web Server issue(37)W519-25
Methods for the inference of biological pathways and networks.
Bumgarner RE, Yeung KY.
Methods Mol Biol. 2009; (541)225-45
Annest A, Bumgarner RE, Raftery AE, Yeung KY.
BMC Bioinformatics. 2009 Feb 26; (10)72
Chang DW, Hayashi S, Gharib SA, Vaisar T, King ST, Tsuchiya M, Ruzinski JT, Park DR, Matute-Bello G, Wurfel MM, Bumgarner R, Heinecke JW, Martin TR.
Am J Respir Crit Care Med. 2008 Oct 1; 7(178)701-9
MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis.
Chu VT, Gottardo R, Raftery AE, Bumgarner RE, Yeung KY.
Genome Biol. 2008; 7(9)R118
Zhu J, Zhang B, Smith EN, Drees B, Brem RB, Kruglyak L, Bumgarner RE, Schadt EE.
Nat Genet. 2008 Jul; 7(40)854-61
Deutsch EW, Ball CA, Berman JJ, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen JH, Daian F, Dauga D, Davidson DR, Gimenez G, Goo YA, Grimmond S, Henrich T, Herrmann BG, Johnson MH, Korb M, Mills JC, Oudes AJ, Parkinson HE, Pascal LE, Pollet N, Quackenbush J, Ramialison M, Ringwald M, Salgado D, Sansone SA, Sherlock G, Stoeckert CJ Jr, Swedlow J, Taylor RC, Walashek L, Warford A, Wilkinson DG, Zhou Y, Zon LI, Liu AY, True LD.
Nat Biotechnol. 2008 Mar; 3(26)305-12
Direct multiplexed measurement of gene expression with color-coded probe pairs.
Geiss GK, Bumgarner RE, Birditt B, Dahl T, Dowidar N, Dunaway DL, Fell HP, Ferree S, George RD, Grogan T, James JJ, Maysuria M, Mitton JD, Oliveri P, Osborn JL, Peng T, Ratcliffe AL, Webster PJ, Davidson EH, Hood L, Dimitrov K.
Nat Biotechnol. 2008 Mar; 3(26)317-25
Attenuation of the type I interferon response in cells infected with human rhinovirus.
Kotla S, Peng T, Bumgarner RE, Gustin KE.
Virology. 2008 May 10; 2(374)399-410
Peng T, Zhu J, Hwangbo Y, Corey L, Bumgarner RE.
J Virol. 2008 Feb; 4(82)1934-45
Ren X, Zhang X, Kim AS, Mikheev AM, Fang M, Sullivan RC, Bumgarner RE, Zarbl H.
Carcinogenesis. 2008 Jan; 1(29)177-85
Kerr KF, Serikawa KA, Wei C, Peters MA, Bumgarner RE.
OMICS. 2007 Summer; 2(11)152-65
Peng T, Kotla S, Bumgarner RE, Gustin KE.
J Virol. 2007 Jun; 11(81)6161
Evolutionary and biomedical insights from the rhesus macaque genome.
Rhesus Macaque Genome Sequencing and Analysis Consortium., Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC, Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T, Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding Y, Dinh HH, Dugan-Rocha S, Fulton LA, Gabisi RA, Garner TT, Godfrey J, Hawes AC, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Kirkness EF, Cree A, Fowler RG, Lee S, Lewis LR, Li Z, Liu YS, Moore SM, Muzny D, Nazareth LV, Ngo DN, Okwuonu GO, Pai G, Parker D, Paul HA, Pfannkoch C, Pohl CS, Rogers YH, Ruiz SJ, Sabo A, Santibanez J, Schneider BW, Smith SM, Sodergren E, Svatek AF, Utterback TR, Vattathil S, Warren W, White CS, Chinwalla AT, Feng Y, Halpern AL, Hillier LW, Huang X, Minx P, Nelson JO, Pepin KH, Qin X, Sutton GG, Venter E, Walenz BP, Wallis JW, Worley KC, Yang SP, Jones SM, Marra MA, Rocchi M, Schein JE, Baertsch R, Clarke L, Csürös M, Glasscock J, Harris RA, Havlak P, Jackson AR, Jiang H, Liu Y, Messina DN, Shen Y, Song HX, Wylie T, Zhang L, Birney E, Han K, Konkel MK, Lee J, Smit AF, Ullmer B, Wang H, Xing J, Burhans R, Cheng Z, Karro JE, Ma J, Raney B, She X, Cox MJ, Demuth JP, Dumas LJ, Han SG, Hopkins J, Karimpour-Fard A, Kim YH, Pollack JR, Vinar T, Addo-Quaye C, Degenhardt J, Denby A, Hubisz MJ, Indap A, Kosiol C, Lahn BT, Lawson HA, Marklein A, Nielsen R, Vallender EJ, Clark AG, Ferguson B, Hernandez RD, Hirani K, Kehrer-Sawatzki H, Kolb J, Patil S, Pu LL, Ren Y, Smith DG, Wheeler DA, Schenck I, Ball EV, Chen R, Cooper DN, Giardine B, Hsu F, Kent WJ, Lesk A, Nelson DL, O'brien WE, Prüfer K, Stenson PD, Wallace JC, Ke H, Liu XM, Wang P, Xiang AP, Yang F, Barber GP, Haussler D, Karolchik D, Kern AD, Kuhn RM, Smith KE, Zwieg AS.
Science. 2007 Apr 13; 5822(316)222-34
Chen C, Coats SR, Bumgarner RE, Darveau RP.
Cell Microbiol. 2007 Apr; 4(9)1028-38
Li J, Pritchard DK, Wang X, Park DR, Bumgarner RE, Schwartz SM, Liles WC.
J Leukoc Biol. 2007 Jan; 1(81)328-35
Deutsch EW, Ball CA, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen J, Davidson D, Eichner LJ, Goo YA, Grimmond S, Henrich T, Johnson MH, Korb M, Mills JC, Oudes A, Parkinson HE, Pascal LE, Quackenbush J, Ramialison M, Ringwald M, Sansone SA, Sherlock G, Stoeckert CJ Jr, Swedlow J, Taylor RC, Walashek L, Zhou Y, Liu AY, True LD.
OMICS. 2006 Summer; 2(10)205-8
Kuo WP, Liu F, Trimarchi J, Punzo C, Lombardi M, Sarang J, Whipple ME, Maysuria M, Serikawa K, Lee SY, McCrann D, Kang J, Shearstone JR, Burke J, Park DJ, Wang X, Rector TL, Ricciardi-Castagnoli P, Perrin S, Choi S, Bumgarner R, Kim JH, Short GF 3rd, Freeman MW, Seed B, Jensen R, Church GM, Hovig E, Cepko CL, Park P, Ohno-Machado L, Jenssen TK.
Nat Biotechnol. 2006 Jul; 7(24)832-40
On the persistence of supplementary resources in biomedical publications.
Anderson NR, Tarczy-Hornoch P, Bumgarner RE.
BMC Bioinformatics. 2006 May 19; (7)260
Liu X, Sivaganesan S, Yeung KY, Guo J, Bumgarner RE, Medvedovic M.
Bioinformatics. 2006 Jul 15; 14(22)1737-44
Peng T, Kotla S, Bumgarner RE, Gustin KE.
J Virol. 2006 May; 10(80)5021-31
Bayesian robust inference for differential gene expression in microarrays with multiple samples.
Gottardo R, Raftery AE, Yeung KY, Bumgarner RE.
Biometrics. 2006 Mar; 1(62)10-8
Xia M, Suchland RJ, Bumgarner RE, Peng T, Rockey DD, Stamm WE.
J Infect Dis. 2005 Oct 1; 7(192)1229-36
Wurfel MM, Park WY, Radella F, Ruzinski J, Sandstrom A, Strout J, Bumgarner RE, Martin TR.
J Immunol. 2005 Aug 15; 4(175)2570-8
Functional annotation from predicted protein interaction networks.
McDermott J, Bumgarner R, Samudrala R.
Bioinformatics. 2005 Aug 1; 15(21)3217-26
Matsuo S, López-Guisa JM, Cai X, Okamura DM, Alpers CE, Bumgarner RE, Peters MA, Zhang G, Eddy AA.
Kidney Int. 2005 Jun; 6(67)2221-38
Standardizing global gene expression analysis between laboratories and across platforms.
Bammler T, Beyer RP, Bhattacharya S, Boorman GA, Boyles A, Bradford BU, Bumgarner RE, Bushel PR, Chaturvedi K, Choi D, Cunningham ML, Deng S, Dressman HK, Fannin RD, Farin FM, Freedman JH, Fry RC, Harper A, Humble MC, Hurban P, Kavanagh TJ, Kaufmann WK, Kerr KF, Jing L, Lapidus JA, Lasarev MR, Li J, Li YJ, Lobenhofer EK, Lu X, Malek RL, Milton S, Nagalla SR, O'malley JP, Palmer VS, Pattee P, Paules RS, Perou CM, Phillips K, Qin LX, Qiu Y, Quigley SD, Rodland M, Rusyn I, Samson LD, Schwartz DA, Shi Y, Shin JL, Sieber SO, Slifer S, Speer MC, Spencer PS, Sproles DI, Swenberg JA, Suk WA, Sullivan RC, Tian R, Tennant RW, Todd SA, Tucker CJ, Van Houten B, Weis BK, Xuan S, Zarbl H, Members of the Toxicogenomics Research Consortium..
Nat Methods. 2005 May; 5(2)351-6
Donuts, scratches and blanks: robust model-based segmentation of microarray images.
Li Q, Fraley C, Bumgarner RE, Yeung KY, Raftery AE.
Bioinformatics. 2005 Jun 15; 12(21)2875-82
Yeung KY, Bumgarner RE, Raftery AE.
Bioinformatics. 2005 May 15; 10(21)2394-402
Sample size for detecting differentially expressed genes in microarray experiments.
Wei C, Li J, Bumgarner RE.
BMC Genomics. 2004 Nov 8; (5)87
From co-expression to co-regulation: how many microarray experiments do we need?
Yeung KY, Medvedovic M, Bumgarner RE.
Genome Biol. 2004; 7(5)R48
Bayesian mixture model based clustering of replicated microarray data.
Medvedovic M, Yeung KY, Bumgarner RE.
Bioinformatics. 2004 May 22; 8(20)1222-32
RNA amplification, fidelity and reproducibility of expression profiling.
Li J, Adams L, Schwartz SM, Bumgarner RE.
C R Biol. 2003 Oct-Nov; 10-11(326)1021-30
Multiclass classification of microarray data with repeated measurements: application to cancer.
Yeung KY, Bumgarner RE.
Genome Biol. 2003; 12(4)R83
Geiss GK, Carter VS, He Y, Kwieciszewski BK, Holzman T, Korth MJ, Lazaro CA, Fausto N, Bumgarner RE, Katze MG.
J Virol. 2003 Jun; 11(77)6367-75
Clustering gene-expression data with repeated measurements.
Yeung KY, Medvedovic M, Bumgarner RE.
Genome Biol. 2003; 5(4)R34
Serikawa KA, Xu XL, MacKay VL, Law GL, Zong Q, Zhao LP, Bumgarner R, Morris DR.
Mol Cell Proteomics. 2003 Mar; 3(2)191-204
Identification of novel tumor markers in hepatitis C virus-associated hepatocellular carcinoma.
Smith MW, Yue ZN, Geiss GK, Sadovnikova NY, Carter VS, Boix L, Lazaro CA, Rosenberg GB, Bumgarner RE, Fausto N, Bruix J, Katze MG.
Cancer Res. 2003 Feb 15; 4(63)859-64
Chlamydia trachomatis infection alters host cell transcription in diverse cellular pathways.
Xia M, Bumgarner RE, Lampe MF, Stamm WE.
J Infect Dis. 2003 Feb 1; 3(187)424-34
Cellular gene expression upon human immunodeficiency virus type 1 infection of CD4(+)-T-cell lines.
van 't Wout AB, Lehrman GK, Mikheeva SA, O'Keeffe GC, Katze MG, Bumgarner RE, Geiss GK, Mullins JI.
J Virol. 2003 Jan; 2(77)1392-402
Geiss GK, Salvatore M, Tumpey TM, Carter VS, Wang X, Basler CF, Taubenberger JK, Bumgarner RE, Palese P, Katze MG, García-Sastre A.
Proc Natl Acad Sci U S A. 2002 Aug 6; 16(99)10736-41
Differential gene expression profiling of adult murine hematopoietic stem cells.
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.
Blood. 2002 Jan 15; 2(99)488-98
Gene expression in Pseudomonas aeruginosa biofilms.
Whiteley M, Bangera MG, Bumgarner RE, Parsek MR, Teitzel GM, Lory S, Greenberg EP.
Nature. 2001 Oct 25; 6858(413)860-4
Geiss G, Jin G, Guo J, Bumgarner R, Katze MG, Sen GC.
J Biol Chem. 2001 Aug 10; 32(276)30178-82
Integrated genomic and proteomic analyses of a systematically perturbed metabolic network.
Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L.
Science. 2001 May 4; 5518(292)929-34
Geiss GK, An MC, Bumgarner RE, Hammersmark E, Cunningham D, Katze MG.
J Virol. 2001 May; 9(75)4321-31
Lin B, White JT, Ferguson C, Wang S, Vessella R, Bumgarner R, True LD, Hood L, Nelson PS.
Cancer Res. 2001 Feb 15; 4(61)1611-8
Ichikawa JK, Norris A, Bangera MG, Geiss GK, van 't Wout AB, Bumgarner RE, Lory S.
Proc Natl Acad Sci U S A. 2000 Aug 15; 17(97)9659-64
PART-1: a novel human prostate-specific, androgen-regulated gene that maps to chromosome 5q12.
Lin B, White JT, Ferguson C, Bumgarner R, Friedman C, Trask B, Ellis W, Lange P, Hood L, Nelson PS.
Cancer Res. 2000 Feb 15; 4(60)858-63
Large-scale monitoring of host cell gene expression during HIV-1 infection using cDNA microarrays.
Geiss GK, Bumgarner RE, An MC, Agy MB, van 't Wout AB, Hammersmark E, Carter VS, Upchurch D, Mullins JI, Katze MG.
Virology. 2000 Jan 5; 1(266)8-16
Negative selection: a method for obtaining low-abundance cDNAs using high-density cDNA clone arrays.
Nelson PS, Hawkins V, Schummer M, Bumgarner R, Ng WL, Ideker T, Ferguson C, Hood L.
Genet Anal. 1999 Dec 15; 6(15)209-15
The prostate expression database (PEDB): status and enhancements in 2000.
Nelson PS, Clegg N, Eroglu B, Hawkins V, Bumgarner R, Smith T, Hood L.
Nucleic Acids Res. 2000 Jan 1; 1(28)212-3
Schummer M, Ng WV, Bumgarner RE, Nelson PS, Schummer B, Bednarski DW, Hassell L, Baldwin RL, Karlan BY, Hood L.
Gene. 1999 Oct 1; 2(238)375-85
Ethics in orthodontic practice, Part 5.
Gottlieb EL, Bumgarner R, Cole WA, Hairfield M, Hicks TT Jr, Mowbray PD Jr.
J Clin Orthod. 1999 Jul; 7(33)383-6
PEDB: the Prostate Expression Database.
Hawkins V, Doll D, Bumgarner R, Smith T, Abajian C, Hood L, Nelson PS.
Nucleic Acids Res. 1999 Jan 1; 1(27)204-8
Snapshot of a large dynamic replicon in a halophilic archaeon: megaplasmid or minichromosome?
Ng WV, Ciufo SA, Smith TM, Bumgarner RE, Baskin D, Faust J, Hall B, Loretz C, Seto J, Slagel J, Hood L, DasSarma S.
Genome Res. 1998 Nov; 11(8)1131-41
An expressed-sequence-tag database of the human prostate: sequence analysis of 1168 cDNA clones.
Nelson PS, Ng WL, Schummer M, True LD, Liu AY, Bumgarner RE, Ferguson C, Dimak A, Hood L.
Genomics. 1998 Jan 1; 1(47)12-25
Inexpensive handheld device for the construction of high-density nucleic acid arrays.
Schummer M, Ng W, Nelson PS, Bumgarner RE, Hood L.
Biotechniques. 1997 Dec; 6(23)1087-92
Data-adaptive algorithms for calling alleles in repeat polymorphisms.
Stoughton R, Bumgarner R, Frederick WJ 3rd, McIndoe RA.
Electrophoresis. 1997 Jan; 1(18)1-5
Tuberculosis control in South Africa--time for a new paradigm?
Graf P, Kumaresan J, Bumgarner R, Kochi A.
S Afr Med J. 1996 May; 5(86)562-3; author reply 564-5
An analysis of the dynamic range and linearity of an infrared DNA sequencer.
McIndoe RA, Hood L, Bumgarner RE.
Electrophoresis. 1996 Apr; 4(17)652-8
Benzene forms hydrogen bonds with water.
Suzuki S, Green PG, Bumgarner RE, Dasgupta S, Goddard WA 3rd, Blake GA.
Science. 1992 Aug 14; 5072(257)942-5
Diseases from fish and shellfish ingestion.
Dembert ML, Strosahl KF, Bumgarner RL.
Am Fam Physician. 1981 Aug; 2(24)103-8
Intravenous avertin; a preliminary report.
BUMGARNER RW, POKORNY RL, MORCH ET, LORHAN PH.
J Kans Med Soc. 1952 Mar; 3(53)124-7
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