Roger E Bumgarner - Publications

Affiliations: 
University of Washington, Seattle, Seattle, WA 
Area:
Genomics, bacteriology, bioinformatics, spectroscopy

70 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Kittichotirat W, Bumgarner RE, Chen C. Genomic Islands Shape the Genetic Background of Both JP2 and Non-JP2 . Pathogens (Basel, Switzerland). 11. PMID 36145469 DOI: 10.3390/pathogens11091037  0.695
2021 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, ... ... Bumgarner RE, et al. Bacterial cyclic diguanylate signaling networks sense temperature. Nature Communications. 12: 1986. PMID 33790266 DOI: 10.1038/s41467-021-22176-2  0.634
2019 Tjokro NO, Kittichotirat W, Torittu A, Ihalin R, Bumgarner RE, Chen C. Transcriptomic Analysis of Core and Accessory Genes in Different Growth Conditions. Pathogens (Basel, Switzerland). 8. PMID 31816971 DOI: 10.3390/Pathogens8040282  0.704
2019 Bumgarner RE, Harrison D, Hsu JE. Isolates from Deep Tissue Specimens Retrieved During Revision Shoulder Arthroplasty: Similar colony morphology does not indicate clonality. Journal of Clinical Microbiology. PMID 31645372 DOI: 10.1128/Jcm.00121-19  0.338
2016 Tang-Siegel G, Bumgarner R, Ruiz T, Kittichotirat W, Chen W, Chen C. Human Serum-Specific Activation of Alternative Sigma Factors, the Stress Responders in Aggregatibacter actinomycetemcomitans. Plos One. 11: e0160018. PMID 27490177 DOI: 10.1371/Journal.Pone.0160018  0.691
2016 To TT, Liu Q, Watling M, Bumgarner RE, Darveau RP, McLean JS. Draft Genome Sequence of Low-Passage Clinical Isolate Porphyromonas gingivalis MP4-504. Genome Announcements. 4. PMID 27056232 DOI: 10.1128/Genomea.00256-16  0.403
2016 Edlund A, Liu Q, Watling M, To TT, Bumgarner RE, He X, Shi W, McLean JS. 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. Genome Announcements. 4. PMID 26893419 DOI: 10.1128/Genomea.01684-15  0.424
2016 McLean JS, Liu Q, Bor B, Bedree JK, Cen L, Watling M, To TT, Bumgarner RE, He X, Shi W. Draft Genome Sequence of Actinomyces odontolyticus subsp. actinosynbacter Strain XH001, the Basibiont of an Oral TM7 Epibiont. Genome Announcements. 4. PMID 26847892 DOI: 10.1128/Genomea.01685-15  0.446
2016 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. Digital detection of endonuclease mediated gene disruption in the HIV provirus. Scientific Reports. 6: 20064. PMID 26829887 DOI: 10.1038/Srep20064  0.346
2016 Kittichotirat W, Bumgarner RE, Chen C. Evolutionary Divergence of Aggregatibacter actinomycetemcomitans. Journal of Dental Research. 95: 94-101. PMID 26420795 DOI: 10.1177/0022034515608163  0.723
2015 Iyer S, Casey E, Bouzek H, Kim M, Deng W, Larsen BB, Zhao H, Bumgarner RE, Rolland M, Mullins JI. Comparison of Major and Minor Viral SNPs Identified through Single Template Sequencing and Pyrosequencing in Acute HIV-1 Infection. Plos One. 10: e0135903. PMID 26317928 DOI: 10.1371/Journal.Pone.0135903  0.332
2015 Bumgardner EA, Kittichotirat W, Bumgarner RE, Lawrence PK. Comparative genomic analysis of seven Mycoplasma hyosynoviae strains. Microbiologyopen. PMID 25693846 DOI: 10.1002/mbo3.242  0.713
2014 Lawrence PK, Wiener BL, Kolander-Bremer T, Bey RF, Stine DL, Kittichotirat W, Bumgarner RE. Genome-Wide Association Studies of Virulent and Avirulent Haemophilus parasuis Serotype 4 Strains. Genome Announcements. 2. PMID 25189591 DOI: 10.1128/Genomea.00884-14  0.702
2014 Lawrence PK, Bumgardner E, Bey RF, Stine D, Bumgarner RE. Genome sequences of porcine epidemic diarrhea virus: in vivo and in vitro phenotypes. Genome Announcements. 2. PMID 24926047 DOI: 10.1128/Genomea.00503-14  0.416
2014 Bumgardner E, Bey RF, Kittichotirat W, Bumgarner RE, Lawrence PK. Genome Sequences of Seven Mycoplasma hyosynoviae Strains Isolated from the Joint Tissue of Infected Swine (Sus scrofa). Genome Announcements. 2. PMID 24903877 DOI: 10.1128/Genomea.00552-14  0.723
2014 Lawrence PK, Bey RF, Wiener B, Kittichotirat W, Bumgarner RE. Genome Sequence of a Presumptive Mannheimia haemolytica Strain with an A1/A6-Cross-Reactive Serotype from a White-Tailed Deer (Odocoileus virginianus). Genome Announcements. 2. PMID 24675846 DOI: 10.1128/Genomea.00114-14  0.718
2013 Sun R, Kittichotirat W, Wang J, Jan M, Chen W, Asikainen S, Bumgarner R, Chen C. Genomic Stability of Aggregatibacter actinomycetemcomitans during Persistent Oral Infection in Human. Plos One. 8: e66472. PMID 23824402 DOI: 10.1371/Journal.Pone.0066472  0.74
2013 Brinkman CL, Bumgarner R, Kittichotirat W, Dunman PM, Kuechenmeister LJ, Weaver KE. Characterization of the effects of an rpoC mutation that confers resistance to the Fst peptide toxin-antitoxin system toxin. Journal of Bacteriology. 195: 156-66. PMID 23104812 DOI: 10.1128/Jb.01597-12  0.663
2012 Laksmana T, Kittichotirat W, Huang Y, Chen W, Jorgensen M, Bumgarner R, Chen C. Metagenomic analysis of subgingival microbiota following non-surgical periodontal therapy: a pilot study. The Open Dentistry Journal. 6: 255-61. PMID 23341849 DOI: 10.2174/1874210601206010255  0.665
2012 Huang Y, Kittichotirat W, Mayer MP, Hall R, Bumgarner R, Chen C. Comparative genomic hybridization and transcriptome analysis with a pan-genome microarray reveal distinctions between JP2 and non-JP2 genotypes of Aggregatibacter actinomycetemcomitans. Molecular Oral Microbiology. 28: 1-17. PMID 23194436 DOI: 10.1111/Omi.12005  0.736
2012 Sun JX, Horst OV, Bumgarner R, Lakely B, Somerman MJ, Zhang H. Laser capture microdissection enables cellular and molecular studies of tooth root development. International Journal of Oral Science. 4: 7-13. PMID 22422086 DOI: 10.1038/Ijos.2012.15  0.324
2012 Chen C, Kittichotirat W, Chen W, Downey JS, Bumgarner R. Genome sequence of a serotype b non-JP2 aggregatibacter actinomycetemcomitans strain, ANH9381, from a periodontally healthy individual. Journal of Bacteriology. 194: 1837. PMID 22408240 DOI: 10.1128/Jb.06770-11  0.728
2012 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, et al. A prioritization analysis of disease association by data-mining of functional annotation of human genes. Genomics. 99: 1-9. PMID 22019378 DOI: 10.1016/J.Ygeno.2011.10.002  0.31
2011 Yeung KY, Dombek KM, Lo K, Mittler JE, Zhu J, Schadt EE, Bumgarner RE, Raftery AE. Construction of regulatory networks using expression time-series data of a genotyped population. Proceedings of the National Academy of Sciences of the United States of America. 108: 19436-41. PMID 22084118 DOI: 10.1073/Pnas.1116442108  0.306
2011 Kittichotirat W, Bumgarner RE, Asikainen S, Chen C. Identification of the pangenome and its components in 14 distinct Aggregatibacter actinomycetemcomitans strains by comparative genomic analysis. Plos One. 6: e22420. PMID 21811606 DOI: 10.1371/Journal.Pone.0022420  0.715
2011 Kittichotirat W, Good NM, Hall R, Bringel F, Lajus A, Médigue C, Smalley NE, Beck D, Bumgarner R, Vuilleumier S, Kalyuzhnaya MG. Genome sequence of Methyloversatilis universalis FAM5T, a methylotrophic representative of the order Rhodocyclales. Journal of Bacteriology. 193: 4541-2. PMID 21725020 DOI: 10.1128/Jb.05331-11  0.714
2011 Butler-Wu SM, Sengupta DJ, Kittichotirat W, Matsen FA, Bumgarner RE. Genome sequence of a novel species, Propionibacterium humerusii. Journal of Bacteriology. 193: 3678. PMID 21571999 DOI: 10.1128/Jb.05036-11  0.696
2010 Lawrence PK, Kittichotirat W, McDermott JE, Bumgarner RE. A three-way comparative genomic analysis of Mannheimia haemolytica isolates. Bmc Genomics. 11: 535. PMID 20920355 DOI: 10.1186/1471-2164-11-535  0.679
2010 Kittichotirat W, Bumgarner R, Chen C. Markedly different genome arrangements between serotype a strains and serotypes b or c strains of Aggregatibacter actinomycetemcomitans. Bmc Genomics. 11: 489. PMID 20825670 DOI: 10.1186/1471-2164-11-489  0.741
2010 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, ... ... Bumgarner RE, et al. The genome of the domesticated apple (Malus × domestica Borkh.). Nature Genetics. 42: 833-9. PMID 20802477 DOI: 10.1038/Ng.654  0.381
2010 Chen C, Kittichotirat W, Chen W, Downey JS, Si Y, Bumgarner R. Genome sequence of naturally competent Aggregatibacter actinomycetemcomitans serotype a strain D7S-1. Journal of Bacteriology. 192: 2643-4. PMID 20348265 DOI: 10.1128/Jb.00157-10  0.726
2010 Lawrence PK, Kittichotirat W, Bumgarner RE, McDermott JE, Herndon DR, Knowles DP, Srikumaran S. Genome sequences of Mannheimia haemolytica serotype A2: ovine and bovine isolates. Journal of Bacteriology. 192: 1167-8. PMID 19966002 DOI: 10.1128/Jb.01527-09  0.694
2010 Lawrence PK, Kittichotirat W, Bumgarner RE, McDermott JE, Herndon DR, Knowles DP, Srikumaran S. Genome sequences of Mannheimia haemolytica serotype A2: Ovine and bovine isolates (Journal of Bacteriology (2010) 192, 4 (1167-1168)) Journal of Bacteriology. 192: 5272. DOI: 10.1128/Jb.00901-10  0.678
2009 Chen C, Kittichotirat W, Si Y, Bumgarner R. Genome sequence of Aggregatibacter actinomycetemcomitans serotype c strain D11S-1. Journal of Bacteriology. 191: 7378-9. PMID 19820097 DOI: 10.1128/Jb.01203-09  0.717
2009 Li J, Campbell JS, Mitchell C, McMahan RS, Yu X, Riehle KJ, Bumgarner RE, Fausto N. Relationships between deficits in tissue mass and transcriptional programs after partial hepatectomy in mice. The American Journal of Pathology. 175: 947-57. PMID 19700759 DOI: 10.2353/Ajpath.2009.090043  0.7
2009 Oehler VG, Yeung KY, Choi YE, Bumgarner RE, Raftery AE, Radich JP. The derivation of diagnostic markers of chronic myeloid leukemia progression from microarray data. Blood. 114: 3292-8. PMID 19654405 DOI: 10.1182/Blood-2009-03-212969  0.301
2009 Kittichotirat W, Guerquin M, Bumgarner RE, Samudrala R. Protinfo PPC: A web server for atomic level prediction of protein complexes Nucleic Acids Research. 37: W519-W525. PMID 19420059 DOI: 10.1093/Nar/Gkp306  0.64
2008 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, et al. Direct multiplexed measurement of gene expression with color-coded probe pairs. Nature Biotechnology. 26: 317-25. PMID 18278033 DOI: 10.1038/Nbt1385  0.328
2008 Ren X, Zhang X, Kim AS, Mikheev AM, Fang M, Sullivan RC, Bumgarner RE, Zarbl H. Comparative genomics of susceptibility to mammary carcinogenesis among inbred rat strains: role of reduced prolactin signaling in resistance of the Copenhagen strain. Carcinogenesis. 29: 177-85. PMID 17916903 DOI: 10.1093/Carcin/Bgm224  0.362
2008 Yeung KY, Oehler V, Choi E, Bumgarner RE, Raftery AE, Radich J. Derivation of Diagnostic Gene Predictors for the Progression of Chronic Myeloid Leukemia from Microarray Data and Independent PCR Validation Blood. 112: 3211-3211. DOI: 10.1182/Blood.V112.11.3211.3211  0.314
2007 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, et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science (New York, N.Y.). 316: 222-34. PMID 17431167 DOI: 10.1126/Science.1139247  0.396
2007 Chen C, Coats SR, Bumgarner RE, Darveau RP. Hierarchical gene expression profiles of HUVEC stimulated by different lipid A structures obtained from Porphyromonas gingivalis and Escherichia coli. Cellular Microbiology. 9: 1028-38. PMID 17166236 DOI: 10.1111/J.1462-5822.2006.00849.X  0.306
2007 Li J, Pritchard DK, Wang X, Park DR, Bumgarner RE, Schwartz SM, Liles WC. cDNA microarray analysis reveals fundamental differences in the expression profiles of primary human monocytes, monocyte-derived macrophages, and alveolar macrophages. Journal of Leukocyte Biology. 81: 328-35. PMID 17046970 DOI: 10.1189/Jlb.0206124  0.721
2006 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, ... ... Bumgarner R, et al. A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nature Biotechnology. 24: 832-40. PMID 16823376 DOI: 10.1038/Nbt1217  0.359
2006 Liu X, Sivaganesan S, Yeung KY, Guo J, Bumgarner RE, Medvedovic M. Context-specific infinite mixtures for clustering gene expression profiles across diverse microarray dataset. Bioinformatics (Oxford, England). 22: 1737-44. PMID 16709591 DOI: 10.1093/Bioinformatics/Btl184  0.302
2006 Gottardo R, Raftery AE, Yeung KY, Bumgarner RE. Bayesian robust inference for differential gene expression in microarrays with multiple samples. Biometrics. 62: 10-8. PMID 16542223 DOI: 10.1111/J.1541-0420.2005.00397.X  0.319
2005 Xia M, Suchland RJ, Bumgarner RE, Peng T, Rockey DD, Stamm WE. Chlamydia trachomatis variant with nonfusing inclusions: growth dynamic and host-cell transcriptional response. The Journal of Infectious Diseases. 192: 1229-36. PMID 16136466 DOI: 10.1086/444394  0.359
2005 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, et al. Standardizing global gene expression analysis between laboratories and across platforms. Nature Methods. 2: 351-6. PMID 15846362 DOI: 10.1038/Nmeth754  0.308
2005 Yeung K, Bumgarner R. Genome Biology. 6: 405. DOI: 10.1186/Gb-2005-6-13-405  0.301
2004 Wei C, Li J, Bumgarner RE. Sample size for detecting differentially expressed genes in microarray experiments. Bmc Genomics. 5: 87. PMID 15533245 DOI: 10.1186/1471-2164-5-87  0.707
2003 Li J, Adams L, Schwartz SM, Bumgarner RE. RNA amplification, fidelity and reproducibility of expression profiling. Comptes Rendus Biologies. 326: 1021-30. PMID 14744109 DOI: 10.1016/J.Crvi.2003.09.015  0.709
2003 Serikawa KA, Xu XL, MacKay VL, Law GL, Zong Q, Zhao LP, Bumgarner R, Morris DR. The transcriptome and its translation during recovery from cell cycle arrest in Saccharomyces cerevisiae. Molecular & Cellular Proteomics : McP. 2: 191-204. PMID 12684541 DOI: 10.1074/Mcp.D200002-Mcp200  0.387
2003 Xia M, Bumgarner RE, Lampe MF, Stamm WE. Chlamydia trachomatis infection alters host cell transcription in diverse cellular pathways. The Journal of Infectious Diseases. 187: 424-34. PMID 12552426 DOI: 10.1086/367962  0.324
2001 Whiteley M, Bangera MG, Bumgarner RE, Parsek MR, Teitzel GM, Lory S, Greenberg EP. Gene expression in Pseudomonas aeruginosa biofilms. Nature. 413: 860-4. PMID 11677611 DOI: 10.1038/35101627  0.312
2001 Geiss G, Jin G, Guo J, Bumgarner R, Katze MG, Sen GC. A comprehensive view of regulation of gene expression by double-stranded RNA-mediated cell signaling. The Journal of Biological Chemistry. 276: 30178-82. PMID 11487589 DOI: 10.1074/Jbc.C100137200  0.319
2000 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 of the United States of America. 97: 9659-9664. PMID 10931941 DOI: 10.1073/Pnas.160140297  0.357
2000 Nelson PS, Clegg N, Eroglu B, Hawkins V, Bumgarner R, Smith T, Hood L. The prostate expression database (PEDB): status and enhancements in 2000. Nucleic Acids Research. 28: 212-3. PMID 10592228 DOI: 10.1093/Nar/28.1.212  0.31
1999 Nelson PS, Hawkins V, Schummer M, Bumgarner R, Ng WL, Ideker T, Ferguson C, Hood L. Negative selection: a method for obtaining low-abundance cDNAs using high-density cDNA clone arrays. Genetic Analysis : Biomolecular Engineering. 15: 209-15. PMID 10609756 DOI: 10.1016/S1050-3862(99)00006-6  0.337
1999 Schummer M, Ng WV, Bumgarner RE, Nelson PS, Schummer B, Bednarski DW, Hassell L, Baldwin RL, Karlan BY, Hood L. Comparative hybridization of an array of 21 500 ovarian cDNAs for the discovery of genes overexpressed in ovarian carcinomas Gene. 238: 375-385. PMID 10570965 DOI: 10.1016/S0378-1119(99)00342-X  0.307
1999 Hawkins V, Doll D, Bumgarner R, Smith T, Abajian C, Hood L, Nelson PS. PEDB: the Prostate Expression Database. Nucleic Acids Research. 27: 204-8. PMID 9847181 DOI: 10.1093/Nar/27.1.204  0.32
1999 Zong Q, Bumgarner R, Abid R, Anthony CB, De Bengdetti A, Morris DR. Genome-wide analysis of translation state: the effects of eukaryotic translation initiation factor 4E level Nature Genetics. 23: 85-85. DOI: 10.1038/14436  0.321
1998 Ng WV, Ciufo SA, Smith TM, Bumgarner RE, Baskin D, Faust J, Hall B, Loretz C, Seto J, Slagel J, Hood L, DasSarma S. Snapshot of a large dynamic replicon in a halophilic archaeon: megaplasmid or minichromosome? Genome Research. 8: 1131-41. PMID 9847077 DOI: 10.1101/Gr.8.11.1131  0.365
1998 Nelson PS, Ng WL, Schummer M, True LD, Liu AY, Bumgarner RE, Ferguson C, Dimak A, Hood L. An expressed-sequence-tag database of the human prostate: sequence analysis of 1168 cDNA clones. Genomics. 47: 12-25. PMID 9465292 DOI: 10.1006/Geno.1997.5035  0.3
1988 Kukolich SG, Rund JV, Pauley DJ, Bumgarner RE. Nitrogen quadrupole coupling in cyclopentadienylnickel nitrosyl Journal of the American Chemical Society. 110: 7356-7357. DOI: 10.1021/Ja00230A015  0.389
1988 Bumgarner RE, Pauley DJ, Kukolich SG. Microwave measurements on ArH2S, ArHDS and ArD2S complexes Journal of Molecular Structure. 190: 163-171. DOI: 10.1016/0022-2860(88)80281-3  0.432
1988 Bumgarner RE, Choe JI, Kukolich SG, Butcher RJ. High-resolution spectroscopy of the ν6 and ν8 bands of formic acid Journal of Molecular Spectroscopy. 132: 261-276. DOI: 10.1016/0022-2852(88)90073-2  0.414
1987 Bumgarner RE, Pauley DJ, Kukolich SG. Microwave spectra and structure for SO2⋅⋅⋅H2S, SO2⋅⋅⋅HDS, and SO2⋅⋅⋅D2S complexes Journal of Chemical Physics. 87: 3749-3752. DOI: 10.1063/1.452929  0.429
1987 Kukolich SG, Bumgarner RE, Pauley DJ. The microwave spectrum of the ONN-HF complex Chemical Physics Letters. 141: 12-15. DOI: 10.1016/0009-2614(87)80083-0  0.42
1986 Pauley DJ, Bumgarner RE, Kukolich SG. Microwave spectrum of the SO2-H2S complex Chemical Physics Letters. 132: 67-68. DOI: 10.1016/0009-2614(86)80696-0  0.427
1985 Bumgarner RE, Cogley CD, Kukolich SG. Microwave spectrum of the HI-HF complex Chemical Physics Letters. 122: 535-537. DOI: 10.1016/0009-2614(85)87263-8  0.418
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