Please enable Javascript

Labmeeting uses lots of Javascript - basically you can't use the site without it. So please enable Javascript in your browser. If your browser does not support Javascript, we recommend Firefox.

Papers authored by Bumgarner RE

Collect these papers and discover other ones on Labmeeting. Learn more.

The derivation of diagnostic markers of chronic myeloid leukemia progression from microarray data.

+ cite this

+ View Abstract

Oehler VG, Yeung KY, Choi YE, Bumgarner RE, Raftery AE, and Radich JP

Blood 114(15):3292-8, 2009 Oct 8 - Who cited this? | PubMed ID: 19654405 | Fulltext

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

+ cite this

+ View Abstract

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

The American journal of pathology 175(3):947-57, 2009 Sep - Who cited this? | PubMed ID: 19700759 | Fulltext

Protinfo PPC: a web server for atomic level prediction of protein complexes.

+ cite this

+ View Abstract

Kittichotirat W, Guerquin M, Bumgarner RE, and Samudrala R

Nucleic acids research 37(Web Server issue):W519-25, 2009 Jul 1 - Who cited this? | PubMed ID: 19420059 | Fulltext

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

+ cite this

+ View Abstract

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

BMC bioinformatics 10:72, 2009 - Who cited this? | PubMed ID: 19245714 | Fulltext

Methods for the inference of biological pathways and networks.

+ cite this

+ View Abstract

Bumgarner RE and Yeung KY

Methods in molecular biology (Clifton, N.J.) 541:1-21, 2009 - Who cited this? | PubMed ID: 19381545 | Fulltext

MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis.

+ cite this

+ View Abstract

Chu VT, Gottardo R, Raftery AE, Bumgarner RE, and Yeung KY

Genome biology 9(7), 2008 Jul 24 - Who cited this? | PubMed ID: 18652698 | Fulltext

Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks.

+ cite this

+ View Abstract

Zhu J, Zhang B, Smith EN, Drees B, Brem RB, Kruglyak L, Bumgarner RE, and Schadt EE

Nature genetics 40(7):854, 2008 Jul - Who cited this? | PubMed ID: 18552845 | Fulltext

Attenuation of the type I interferon response in cells infected with human rhinovirus.

+ cite this

+ View Abstract

Kotla S, Peng T, Bumgarner RE, and Gustin KE

Virology 374(2):399, 2008 May 10 - Who cited this? | PubMed ID: 18272195 | Fulltext

Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE).

+ cite this

+ View Abstract

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,

(show remaining authors)

Nature biotechnology 26(3):305, 2008 Mar - Who cited this? | PubMed ID: 18327244 | Fulltext

Direct multiplexed measurement of gene expression with color-coded probe pairs.

+ cite this

+ View Abstract

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,

(show remaining authors)

Nature biotechnology 26(3):317, 2008 Mar - Who cited this? | PubMed ID: 18278033 | Fulltext

Independent and cooperative antiviral actions of beta interferon and gamma interferon against herpes simplex virus replication in primary human fibroblasts.

+ cite this

+ View Abstract

Peng T, Zhu J, Hwangbo Y, Corey L, and Bumgarner RE

Journal of virology 82(4):1934-45, 2008 Feb - Who cited this? | PubMed ID: 18057251 | Fulltext

Comparative genomics of susceptibility to mammary carcinogenesis among inbred rat strains: role of reduced prolactin signaling in resistance of the Copenhagen strain.

+ cite this

+ View Abstract

Ren X, Zhang X, Kim AS, Mikheev AM, Fang M, Sullivan RC, Bumgarner RE, and Zarbl H

Carcinogenesis 29(1):177-85, 2008 Jan - Who cited this? | PubMed ID: 17916903 | Fulltext

Human rhinovirus attenuates the type I interferon response by disrupting activation of interferon regulatory factor 3.

+ cite this

Peng T, Kotla S, Bumgarner RE, and Gustin KE

Journal of virology 81(11):6161, 2007 Jun - Who cited this? | PubMed ID: 17496231 | Fulltext

Hierarchical gene expression profiles of HUVEC stimulated by different lipid A structures obtained from Porphyromonas gingivalis and Escherichia coli.

+ cite this

+ View Abstract

Chen C, Coats SR, Bumgarner RE, and Darveau RP

Cellular microbiology 9(4):1028, 2007 Apr - Who cited this? | PubMed ID: 17166236 | Fulltext

cDNA microarray analysis reveals fundamental differences in the expression profiles of primary human monocytes, monocyte-derived macrophages, and alveolar macrophages.

+ cite this

+ View Abstract

Li J, Pritchard DK, Wang X, Park DR, Bumgarner RE, Schwartz SM, and Liles WC

Journal of leukocyte biology 81(1):328, 2007 Jan - Who cited this? | PubMed ID: 17046970 | Fulltext

What is the best reference RNA? And other questions regarding the design and analysis of two-color microarray experiments.

+ cite this

+ View Abstract

Kerr KF, Serikawa KA, Wei C, Peters MA, and Bumgarner RE

Omics : a journal of integrative biology 11(2):152-65, 2007 - Who cited this? | PubMed ID: 17594235 | Fulltext

Context-specific infinite mixtures for clustering gene expression profiles across diverse microarray dataset.

+ cite this

+ View Abstract

Liu X, Sivaganesan S, Yeung KY, Guo J, Bumgarner RE, and Medvedovic M

Bioinformatics (Oxford, England) 22(14):1737-44, 2006 Jul 15 - Who cited this? | PubMed ID: 16709591 | Fulltext

Human rhinovirus attenuates the type I interferon response by disrupting activation of interferon regulatory factor 3.

+ cite this

+ View Abstract

Peng T, Kotla S, Bumgarner RE, and Gustin KE

Journal of virology 80(10):5021-31, 2006 May - Who cited this? | PubMed ID: 16641293 | Fulltext

Bayesian robust inference for differential gene expression in microarrays with multiple samples.

+ cite this

+ View Abstract

Gottardo R, Raftery AE, Yeung KY, and Bumgarner RE

Biometrics 62(1):10, 2006 Mar - Who cited this? | PubMed ID: 16542223 | Fulltext

Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE).

+ cite this

+ View Abstract

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,

(show remaining authors)

Omics : a journal of integrative biology 10(2):205, 2006 Summer - Who cited this? | PubMed ID: 16901227 | Fulltext

On the persistence of supplementary resources in biomedical publications.

+ cite this

+ View Abstract

Anderson NR, Tarczy-Hornoch P, and Bumgarner RE

BMC bioinformatics 7:260, 2006 - Who cited this? | PubMed ID: 16712726 | Fulltext

Chlamydia trachomatis variant with nonfusing inclusions: growth dynamic and host-cell transcriptional response.

+ cite this

+ View Abstract

Xia M, Suchland RJ, Bumgarner RE, Peng T, Rockey DD, and Stamm WE

The Journal of infectious diseases 192(7):1229-36, 2005 Oct 1 - Who cited this? | PubMed ID: 16136466 | Fulltext

Identification of high and low responders to lipopolysaccharide in normal subjects: an unbiased approach to identify modulators of innate immunity.

+ cite this

+ View Abstract

Wurfel MM, Park WY, Radella F, Ruzinski J, Sandstrom A, Strout J, Bumgarner RE, and Martin TR

Journal of immunology (Baltimore, Md. : 1950) 175(4):2570-8, 2005 Aug 15 - Who cited this? | PubMed ID: 16081831 | Fulltext

Donuts, scratches and blanks: robust model-based segmentation of microarray images.

+ cite this

+ View Abstract

Li Q, Fraley C, Bumgarner RE, Yeung KY, and Raftery AE

Bioinformatics (Oxford, England) 21(12):2875-82, 2005 Jun 15 - Who cited this? | PubMed ID: 15845656 | Fulltext

Multifunctionality of PAI-1 in fibrogenesis: evidence from obstructive nephropathy in PAI-1-overexpressing mice.

+ cite this

+ View Abstract

Matsuo S, López-Guisa JM, Cai X, Okamura DM, Alpers CE, Bumgarner RE, Peters MA, Zhang G, and Eddy AA

Kidney international 67(6):2221-38, 2005 Jun - Who cited this? | PubMed ID: 15882265 | Fulltext

Bayesian model averaging: development of an improved multi-class, gene selection and classification tool for microarray data.

+ cite this

+ View Abstract

Yeung KY, Bumgarner RE, and Raftery AE

Bioinformatics (Oxford, England) 21(10):2394, 2005 May 15 - Who cited this? | PubMed ID: 15713736 | Fulltext

Standardizing global gene expression analysis between laboratories and across platforms.

+ cite this

+ View Abstract

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,

(show remaining authors)

Nature methods 2(5):351-6, 2005 May - Who cited this? | PubMed ID: 15846362 | Fulltext

Sample size for detecting differentially expressed genes in microarray experiments.

+ cite this

+ View Abstract

Wei C, Li J, and Bumgarner RE

BMC genomics 5(1):87, 2004 Nov 8 - Who cited this? | PubMed ID: 15533245 | Fulltext

Bayesian mixture model based clustering of replicated microarray data.

+ cite this

+ View Abstract

Medvedovic M, Yeung KY, and Bumgarner RE

Bioinformatics (Oxford, England) 20(8):1222, 2004 May 22 - Who cited this? | PubMed ID: 14871871 | Fulltext

From co-expression to co-regulation: how many microarray experiments do we need?.

+ cite this

+ View Abstract

Yeung KY, Medvedovic M, and Bumgarner RE

Genome biology 5(7):R48, 2004 - Who cited this? | PubMed ID: 15239833 | Fulltext

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.

+ cite this

+ View Abstract

Geiss GK, Carter VS, He Y, Kwieciszewski BK, Holzman T, Korth MJ, Lazaro CA, Fausto N, Bumgarner RE, and Katze MG

Journal of virology 77(11):6367-75, 2003 Jun - Who cited this? | PubMed ID: 12743294 | Fulltext

Identification of novel tumor markers in hepatitis C virus-associated hepatocellular carcinoma.

+ cite this

+ View Abstract

Smith MW, Yue ZN, Geiss GK, Sadovnikova NY, Carter VS, Boix L, Lazaro CA, Rosenberg GB, Bumgarner RE, Fausto N, Bruix J, and Katze MG

Cancer research 63(4):859-64, 2003 Feb 15 - Who cited this? | PubMed ID: 12591738 | Fulltext

Chlamydia trachomatis infection alters host cell transcription in diverse cellular pathways.

+ cite this

+ View Abstract

Xia M, Bumgarner RE, Lampe MF, and Stamm WE

The Journal of infectious diseases 187(3):424-34, 2003 Feb 1 - Who cited this? | PubMed ID: 12552426 | Fulltext

Multiclass classification of microarray data with repeated measurements: application to cancer.

+ cite this

+ View Abstract

Yeung KY and Bumgarner RE

Genome biology 4(12):R83, 2003 - Who cited this? | PubMed ID: 14659020 | Fulltext

RNA amplification, fidelity and reproducibility of expression profiling.

+ cite this

+ View Abstract

Li J, Adams L, Schwartz SM, and Bumgarner RE

Comptes rendus biologies 326(10-11):1021-30, 2003 - Who cited this? | PubMed ID: 14744109 | Fulltext

Cellular gene expression upon human immunodeficiency virus type 1 infection of CD4(+)-T-cell lines.

+ cite this

+ View Abstract

van 't Wout AB, Lehrman GK, Mikheeva SA, O'Keeffe GC, Katze MG, Bumgarner RE, Geiss GK, and Mullins JI

Journal of virology 77(2):1392-402, 2003 Jan - Who cited this? | PubMed ID: 12502855 | Fulltext

Clustering gene-expression data with repeated measurements.

+ cite this

+ View Abstract

Yeung KY, Medvedovic M, and Bumgarner RE

Genome biology 4(5):R34, 2003 - Who cited this? | PubMed ID: 12734014 | Fulltext

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.

+ cite this

+ View Abstract

Geiss GK, Salvatore M, Tumpey TM, Carter VS, Wang X, Basler CF, Taubenberger JK, Bumgarner RE, Palese P, Katze MG, and García-Sastre A

Proceedings of the National Academy of Sciences of the United States of America 99(16):10736-41, 2002 Aug 6 - Who cited this? | PubMed ID: 12149435 | Fulltext

Gene expression in Pseudomonas aeruginosa biofilms.

+ cite this

+ View Abstract

Whiteley M, Bangera MG, Bumgarner RE, Parsek MR, Teitzel GM, Lory S, and Greenberg EP

Nature 413(6858):860-4, 2001 Oct 25 - Who cited this? | PubMed ID: 11677611 | Fulltext

Global impact of influenza virus on cellular pathways is mediated by both replication-dependent and -independent events.

+ cite this

+ View Abstract

Geiss GK, An MC, Bumgarner RE, Hammersmark E, Cunningham D, and Katze MG

Journal of virology 75(9):4321-31, 2001 May - Who cited this? | PubMed ID: 11287581 | Fulltext

Interaction of pseudomonas aeruginosa with epithelial cells: identification of differentially regulated genes by expression microarray analysis of human cDNAs.

+ cite this

+ View Abstract

Ichikawa JK, Norris A, Bangera MG, Geiss GK, van 't Wout AB, Bumgarner RE, and Lory S

Proceedings of the National Academy of Sciences of the United States of America 97(17):9659-64, 2000 Aug 15 - Who cited this? | PubMed ID: 10931941 | Fulltext

Large-scale monitoring of host cell gene expression during HIV-1 infection using cDNA microarrays.

+ cite this

+ View Abstract

Geiss GK, Bumgarner RE, An MC, Agy MB, van 't Wout AB, Hammersmark E, Carter VS, Upchurch D, Mullins JI, and Katze MG

Virology 266(1):8-16, 2000 Jan 5 - Who cited this? | PubMed ID: 10612655 | Fulltext

Comparative hybridization of an array of 21,500 ovarian cDNAs for the discovery of genes overexpressed in ovarian carcinomas.

+ cite this

+ View Abstract

Schummer M, Ng WV, Bumgarner RE, Nelson PS, Schummer B, Bednarski DW, Hassell L, Baldwin RL, Karlan BY, and Hood L

Gene 238(2):375-85, 1999 Oct 1 - Who cited this? | PubMed ID: 10570965 | Fulltext

Snapshot of a large dynamic replicon in a halophilic archaeon: megaplasmid or minichromosome?.

+ cite this

+ View Abstract

Ng WV, Ciufo SA, Smith TM, Bumgarner RE, Baskin D, Faust J, Hall B, Loretz C, Seto J, Slagel J, Hood L, and DasSarma S

Genome research 8(11):1131-41, 1998 Nov - Who cited this? | PubMed ID: 9847077 | Fulltext

An expressed-sequence-tag database of the human prostate: sequence analysis of 1168 cDNA clones.

+ cite this

+ View Abstract

Nelson PS, Ng WL, Schummer M, True LD, Liu AY, Bumgarner RE, Ferguson C, Dimak A, and Hood L

Genomics 47(1):12-25, 1998 Jan 1 - Who cited this? | PubMed ID: 9465292 | Fulltext

Inexpensive handheld device for the construction of high-density nucleic acid arrays.

+ cite this

+ View Abstract

Schummer M, Ng W, Nelson PS, Bumgarner RE, and Hood L

BioTechniques 23(6):1087-92, 1997 Dec - Who cited this? | PubMed ID: 9421641 | Fulltext

An analysis of the dynamic range and linearity of an infrared DNA sequencer.

+ cite this

+ View Abstract

McIndoe RA, Hood L, and Bumgarner RE

Electrophoresis 17(4):652-8, 1996 Apr - Who cited this? | PubMed ID: 8738322 | Fulltext

Search Google Scholar for Bumgarner RE

Join Labmeeting

Organize and search your PDF collection
Collect papers
Search millions of papers
Keep up to date with paper alerts
Read your papers from anywhere
Recommend papers to colleagues
Manage your lab

Labmeeting is a web service for researchers. Sign up with your academic email address.

Individuals or corporations not affiliated with an academic institution can request a trial subscription.

Got a question?
The Labmeeting Network
has the answer.
Ask scientists at top universities like Harvard, Stanford, and MIT for their expert opinion!