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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;28(8):e275-e276. doi: 10.1016/j.jse.2019.04.046. No abstract available.


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;9(1):3980. doi: 10.1038/s41467-018-06203-3.


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;5(12). pii: e00024-17. doi: 10.1128/genomeA.00024-17.


Human Serum-Specific Activation of Alternative Sigma Factors, the Stress Responders in Aggregatibacter actinomycetemcomitans.

Tang-Siegel G, Bumgarner R, Ruiz T, Kittichotirat W, Chen W, Chen C.

PLoS One. 2016 Aug 4;11(8):e0160018. doi: 10.1371/journal.pone.0160018. eCollection 2016.


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 May 19;11(5):e0155979. doi: 10.1371/journal.pone.0155979. eCollection 2016.


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;4(2). pii: e00256-16. doi: 10.1128/genomeA.00256-16.


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;98(7):597-606. doi: 10.2106/JBJS.15.00568. Review.


High-Quality Draft Genome Sequence of Low-pH-Active Veillonella parvula Strain SHI-1, Isolated from Human Saliva within an In Vitro Oral Biofilm Model.

Edlund A, Liu Q, Watling M, To TT, Bumgarner RE, He X, Shi W, McLean JS.

Genome Announc. 2016 Feb 18;4(1). pii: e01684-15. doi: 10.1128/genomeA.01684-15.


Draft Genome Sequence of Actinomyces odontolyticus subsp. actinosynbacter Strain XH001, the Basibiont of an Oral TM7 Epibiont.

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;4(1). pii: e01685-15. doi: 10.1128/genomeA.01685-15.


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. doi: 10.1038/srep20064.


Evolutionary Divergence of Aggregatibacter actinomycetemcomitans.

Kittichotirat W, Bumgarner RE, Chen C.

J Dent Res. 2016 Jan;95(1):94-101. doi: 10.1177/0022034515608163. Epub 2015 Sep 29.


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

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;29(13):1597-606. doi: 10.1097/QAD.0000000000000702.


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

Iyer S, Casey E, Bouzek H, Kim M, Deng W, Larsen BB, Zhao H, Bumgarner RE, Rolland M, Mullins JI.

PLoS One. 2015 Aug 28;10(8):e0135903. doi: 10.1371/journal.pone.0135903. eCollection 2015.


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

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;29(12):1467-71. doi: 10.1097/QAD.0000000000000737.


Comparative genomic analysis of seven Mycoplasma hyosynoviae strains.

Bumgardner EA, Kittichotirat W, Bumgarner RE, Lawrence PK.

Microbiologyopen. 2015 Apr;4(2):343-359. doi: 10.1002/mbo3.242. Epub 2015 Feb 18.


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;2(5). pii: e00884-14. doi: 10.1128/genomeA.00884-14.


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;96(17):1447-50. doi: 10.2106/JBJS.M.01474.


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;2(3). pii: e00503-14. doi: 10.1128/genomeA.00503-14.


Genome Sequences of Seven Mycoplasma hyosynoviae Strains Isolated from the Joint Tissue of Infected Swine (Sus scrofa).

Bumgardner E, Bey RF, Kittichotirat W, Bumgarner RE, Lawrence PK.

Genome Announc. 2014 Jun 5;2(3). pii: e00552-14. doi: 10.1128/genomeA.00552-14.


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

Beck IA, Deng W, Payant R, Hall R, Bumgarner RE, Mullins JI, Frenkel LM.

J Clin Microbiol. 2014 Jul;52(7):2320-7. doi: 10.1128/JCM.00306-14. Epub 2014 Apr 16.


Genome Sequence of a Presumptive Mannheimia haemolytica Strain with an A1/A6-Cross-Reactive Serotype from a White-Tailed Deer (Odocoileus virginianus).

Lawrence PK, Bey RF, Wiener B, Kittichotirat W, Bumgarner RE.

Genome Announc. 2014 Mar 27;2(2). pii: e00114-14. doi: 10.1128/genomeA.00114-14.


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

Matsen FA 3rd, Butler-Wu S, Carofino BC, Jette JL, Bertelsen A, Bumgarner R.

J Bone Joint Surg Am. 2013 Dec 4;95(23):e1811-7. doi: 10.2106/JBJS.L.01733.


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

Sun R, Kittichotirat W, Wang J, Jan M, Chen W, Asikainen S, Bumgarner R, Chen C.

PLoS One. 2013 Jun 18;8(6):e66472. doi: 10.1371/journal.pone.0066472. Print 2013.


Metagenomic analysis of subgingival microbiota following non-surgical periodontal therapy: a pilot study.

Laksmana T, Kittichotirat W, Huang Y, Chen W, Jorgensen M, Bumgarner R, Chen C.

Open Dent J. 2012;6:255-61. doi: 10.2174/1874210601206010255. Epub 2012 Dec 28.


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

Bumgarner R.

Curr Protoc Mol Biol. 2013 Jan;Chapter 22:Unit 22.1.. doi: 10.1002/0471142727.mb2201s101.


Comparative genomic hybridization and transcriptome analysis with a pan-genome microarray reveal distinctions between JP2 and non-JP2 genotypes of Aggregatibacter actinomycetemcomitans.

Huang Y, Kittichotirat W, Mayer MP, Hall R, Bumgarner R, Chen C.

Mol Oral Microbiol. 2013 Feb;28(1):1-17. doi: 10.1111/omi.12005. Epub 2012 Oct 12.


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

Brinkman CL, Bumgarner R, Kittichotirat W, Dunman PM, Kuechenmeister LJ, Weaver KE.

J Bacteriol. 2013 Jan;195(1):156-66. doi: 10.1128/JB.01597-12. Epub 2012 Oct 26.


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

Lo K, Raftery AE, Dombek KM, Zhu J, Schadt EE, Bumgarner RE, Yeung KY.

BMC Syst Biol. 2012 Aug 16;6:101. doi: 10.1186/1752-0509-6-101.


Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria.

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;7(6):e37818. doi: 10.1371/journal.pone.0037818. Epub 2012 Jun 18.


Stitching together multiple data dimensions reveals interacting metabolomic and transcriptomic networks that modulate cell regulation.

Zhu J, Sova P, Xu Q, Dombek KM, Xu EY, Vu H, Tu Z, Brem RB, Bumgarner RE, Schadt EE.

PLoS Biol. 2012;10(4):e1001301. doi: 10.1371/journal.pbio.1001301. Epub 2012 Apr 3.


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;4(1):7-13. doi: 10.1038/ijos.2012.15. Epub 2012 Mar 16.


Genome sequence of a serotype b non-JP2 aggregatibacter actinomycetemcomitans strain, ANH9381, from a periodontally healthy individual.

Chen C, Kittichotirat W, Chen W, Downey JS, Bumgarner R.

J Bacteriol. 2012 Apr;194(7):1837. doi: 10.1128/JB.06770-11.


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;108(48):19436-41. doi: 10.1073/pnas.1116442108. Epub 2011 Nov 14.


A prioritization analysis of disease association by data-mining of functional annotation of human genes.

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;99(1):1-9. doi: 10.1016/j.ygeno.2011.10.002. Epub 2011 Oct 14.


Identification of the pangenome and its components in 14 distinct Aggregatibacter actinomycetemcomitans strains by comparative genomic analysis.

Kittichotirat W, Bumgarner RE, Asikainen S, Chen C.

PLoS One. 2011;6(7):e22420. doi: 10.1371/journal.pone.0022420. Epub 2011 Jul 19.


Genome sequence of Methyloversatilis universalis FAM5T, a methylotrophic representative of the order Rhodocyclales.

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;193(17):4541-2. doi: 10.1128/JB.05331-11. Epub 2011 Jul 1.


Genome sequence of a novel species, Propionibacterium humerusii.

Butler-Wu SM, Sengupta DJ, Kittichotirat W, Matsen FA 3rd, Bumgarner RE.

J Bacteriol. 2011 Jul;193(14):3678. doi: 10.1128/JB.05036-11. Epub 2011 May 13.


High-density lipoprotein suppresses the type I interferon response, a family of potent antiviral immunoregulators, in macrophages challenged with lipopolysaccharide.

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;122(19):1919-27. doi: 10.1161/CIRCULATIONAHA.110.961193. Epub 2010 Oct 25.


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. doi: 10.1186/1471-2164-11-535.


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

Kittichotirat W, Bumgarner R, Chen C.

BMC Genomics. 2010 Sep 8;11:489. doi: 10.1186/1471-2164-11-489.


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;42(10):833-9. doi: 10.1038/ng.654. Epub 2010 Aug 29.


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

Chen C, Kittichotirat W, Chen W, Downey JS, Si Y, Bumgarner R.

J Bacteriol. 2010 May;192(10):2643-4. doi: 10.1128/JB.00157-10. Epub 2010 Mar 26.


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;192(4):1167-8. doi: 10.1128/JB.01527-09. Epub 2009 Dec 4. Erratum in: J Bacteriol. 2010 Oct;192(19):5272.


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

Chen C, Kittichotirat W, Si Y, Bumgarner R.

J Bacteriol. 2009 Dec;191(23):7378-9. doi: 10.1128/JB.01203-09. Epub 2009 Oct 9.


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

Li J, Campbell JS, Mitchell C, McMahan RS, Yu X, Riehle KJ, Bumgarner RE, Fausto N.

Am J Pathol. 2009 Sep;175(3):947-57. doi: 10.2353/ajpath.2009.090043. Epub 2009 Aug 21.


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;114(15):3292-8. doi: 10.1182/blood-2009-03-212969. Epub 2009 Aug 4.


Comparison of Lumin LED fluorescent attachment, fluorescent microscopy and Ziehl-Neelsen for AFB diagnosis.

Trusov A, Bumgarner R, Valijev R, Chestnova R, Talevski S, Vragoterova C, Neeley ES.

Int J Tuberc Lung Dis. 2009 Jul;13(7):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;37(Web Server issue):W519-25. doi: 10.1093/nar/gkp306. Epub 2009 May 6.


Methods for the inference of biological pathways and networks.

Bumgarner RE, Yeung KY.

Methods Mol Biol. 2009;541:225-45. doi: 10.1007/978-1-59745-243-4_11. Review.


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

Annest A, Bumgarner RE, Raftery AE, Yeung KY.

BMC Bioinformatics. 2009 Feb 26;10:72. doi: 10.1186/1471-2105-10-72.

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