Roger E Bumgarner - Publications

University of Washington, Seattle, Seattle, WA 
Genomics, bacteriology, bioinformatics, spectroscopy

53 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
2020 Hsu JE, Matsen FA, Whitson AJ, Bumgarner RE. Cutibacterium subtype distribution on the skin of primary and revision shoulder arthroplasty patients. Journal of Shoulder and Elbow Surgery. PMID 32417046 DOI: 10.1016/j.jse.2020.02.007  0.32
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  0.96
2016 Doty SL, Sher AW, Fleck ND, Khorasani M, Bumgarner RE, Khan Z, Ko AW, Kim SH, DeLuca TH. Variable Nitrogen Fixation in Wild Populus. Plos One. 11: e0155979. PMID 27196608 DOI: 10.1371/journal.pone.0155979  0.96
2016 Hsu JE, Bumgarner RE, Matsen FA. Propionibacterium in Shoulder Arthroplasty: What We Think We Know Today. The Journal of Bone and Joint Surgery. American Volume. 98: 597-606. PMID 27053589 DOI: 10.2106/JBJS.15.00568  0.32
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  0.96
2015 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. Resistance detected by pyrosequencing following zidovudine monotherapy for prevention of HIV-1 mother-to-child-transmission. Aids (London, England). 29: 1467-71. PMID 26244386 DOI: 10.1097/QAD.0000000000000737  0.96
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  0.96
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  0.96
2014 Lee MJ, Pottinger PS, Butler-Wu S, Bumgarner RE, Russ SM, Matsen FA. Propionibacterium persists in the skin despite standard surgical preparation. The Journal of Bone and Joint Surgery. American Volume. 96: 1447-50. PMID 25187583 DOI: 10.2106/JBJS.M.01474  0.96
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  0.96
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  0.96
2014 Beck IA, Deng W, Payant R, Hall R, Bumgarner RE, Mullins JI, Frenkel LM. Validation of an oligonucleotide ligation assay for quantification of human immunodeficiency virus type 1 drug-resistant mutants by use of massively parallel sequencing. Journal of Clinical Microbiology. 52: 2320-7. PMID 24740080 DOI: 10.1128/JCM.00306-14  0.96
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  0.96
2012 Lo K, Raftery AE, Dombek KM, Zhu J, Schadt EE, Bumgarner RE, Yeung KY. Integrating external biological knowledge in the construction of regulatory networks from time-series expression data. Bmc Systems Biology. 6: 101. PMID 22898396 DOI: 10.1186/1752-0509-6-101  0.96
2012 Zhu J, Sova P, Xu Q, Dombek KM, Xu EY, Vu H, Tu Z, Brem RB, Bumgarner RE, Schadt EE. Stitching together multiple data dimensions reveals interacting metabolomic and transcriptomic networks that modulate cell regulation. Plos Biology. 10: e1001301. PMID 22509135 DOI: 10.1371/journal.pbio.1001301  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.64
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  0.96
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  0.96
2009 Bumgarner RE, Yeung KY. Methods for the inference of biological pathways and networks. Methods in Molecular Biology (Clifton, N.J.). 541: 225-45. PMID 19381545 DOI: 10.1007/978-1-59745-243-4_11  0.96
2009 Annest A, Bumgarner RE, Raftery AE, Yeung KY. Iterative Bayesian Model Averaging: a method for the application of survival analysis to high-dimensional microarray data. Bmc Bioinformatics. 10: 72. PMID 19245714 DOI: 10.1186/1471-2105-10-72  0.96
2008 Chu VT, Gottardo R, Raftery AE, Bumgarner RE, Yeung KY. MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis. Genome Biology. 9: R118. PMID 18652698 DOI: 10.1186/gb-2008-9-7-r118  0.96
2008 Zhu J, Zhang B, Smith EN, Drees B, Brem RB, Kruglyak L, Bumgarner RE, Schadt EE. Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nature Genetics. 40: 854-61. PMID 18552845 DOI: 10.1038/ng.167  0.96
2008 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, et al. Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Nature Biotechnology. 26: 305-12. PMID 18327244 DOI: 10.1038/nbt1391  0.96
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  0.96
2008 Kotla S, Peng T, Bumgarner RE, Gustin KE. Attenuation of the type I interferon response in cells infected with human rhinovirus. Virology. 374: 399-410. PMID 18272195 DOI: 10.1016/j.virol.2008.01.022  0.44
2008 Peng T, Zhu J, Hwangbo Y, Corey L, Bumgarner RE. Independent and cooperative antiviral actions of beta interferon and gamma interferon against herpes simplex virus replication in primary human fibroblasts Journal of Virology. 82: 1934-1945. PMID 18057251 DOI: 10.1128/JVI.01649-07  0.96
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  0.96
2007 Kerr KF, Serikawa KA, Wei C, Peters MA, Bumgarner RE. What is the best reference RNA? And other questions regarding the design and analysis of two-color microarray experiments. Omics : a Journal of Integrative Biology. 11: 152-65. PMID 17594235 DOI: 10.1089/omi.2007.0012  0.64
2007 Peng T, Kotla S, Bumgarner RE, Gustin KE. Human rhinovirus attenuates the type I interferon response by disrupting activation of interferon regulatory factor 3. Journal of Virology. 81: 6161. PMID 17496231 DOI: 10.1128/JVI.00433-07  0.44
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  0.96
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  0.64
2006 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, et al. Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE). Omics : a Journal of Integrative Biology. 10: 205-8. PMID 16901227 DOI: 10.1089/omi.2006.10.205  0.96
2006 Peng T, Kotla S, Bumgarner RE, Gustin KE. Human rhinovirus attenuates the type I interferon response by disrupting activation of interferon regulatory factor 3. Journal of Virology. 80: 5021-31. PMID 16641293 DOI: 10.1128/JVI.80.10.5021-5031.2006  0.44
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  0.96
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  0.96
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  0.96
2005 Li Q, Fraley C, Bumgarner RE, Yeung KY, Raftery AE. Donuts, scratches and blanks: robust model-based segmentation of microarray images. Bioinformatics (Oxford, England). 21: 2875-82. PMID 15845656 DOI: 10.1093/bioinformatics/bti447  0.96
2005 Yeung KY, Bumgarner RE, Raftery AE. Bayesian model averaging: development of an improved multi-class, gene selection and classification tool for microarray data. Bioinformatics (Oxford, England). 21: 2394-402. PMID 15713736 DOI: 10.1093/bioinformatics/bti319  0.96
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  0.64
2004 Yeung KY, Medvedovic M, Bumgarner RE. From co-expression to co-regulation: how many microarray experiments do we need? Genome Biology. 5: R48. PMID 15239833 DOI: 10.1186/gb-2004-5-7-r48  0.96
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  0.64
2003 Yeung KY, Bumgarner RE. Multiclass classification of microarray data with repeated measurements: application to cancer. Genome Biology. 4: R83. PMID 14659020 DOI: 10.1186/gb-2003-4-12-r83  0.96
2003 Geiss GK, Carter VS, He Y, Kwieciszewski BK, Holzman T, Korth MJ, Lazaro CA, Fausto N, Bumgarner RE, Katze MG. Gene expression profiling of the cellular transcriptional network regulated by alpha/beta interferon and its partial attenuation by the hepatitis C virus nonstructural 5A protein Journal of Virology. 77: 6367-6375. PMID 12743294 DOI: 10.1128/JVI.77.11.6367-6375.2003  0.96
2003 Yeung KY, Medvedovic M, Bumgarner RE. Clustering gene-expression data with repeated measurements. Genome Biology. 4: R34. PMID 12734014  0.96
2003 Smith MW, Yue ZN, Geiss GK, Sadovnikova NY, Carter VS, Boix L, Lazaro CA, Rosenberg GB, Bumgarner RE, Fausto N, Bruix J, Katze MG. Identification of novel tumor markers in hepatitis C virus-associated hepatocellular carcinoma. Cancer Research. 63: 859-64. PMID 12591738  0.96
2003 Van 't Wout AB, Lehrman GK, Mikheeva SA, O'Keeffe GC, Katze MG, Bumgarner RE, Geiss GK, Mullins JI. Cellular gene expression upon human immunodeficiency virus type 1 infection of CD4+-T-cell lines Journal of Virology. 77: 1392-1402. PMID 12502855 DOI: 10.1128/JVI.77.2.1392-1402.2003  0.96
2002 Geiss GK, Salvatore M, Tumpey TM, Carter VS, Wang X, Basler CF, Taubenberger JK, Bumgarner RE, Palese P, Katze MG, García-Sastre A. 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 potential contribution to pandemic influenza. Proceedings of the National Academy of Sciences of the United States of America. 99: 10736-41. PMID 12149435 DOI: 10.1073/pnas.112338099  0.96
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