List of works - Roger E Bumgarner

Integrated genomic and proteomic analyses of a systematically perturbed metabolic network

scientific article (publication date: 4 May 2001)

Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

scientific article

The genome of the domesticated apple (Malus × domestica Borkh.)

scientific article

Gene expression in Pseudomonas aeruginosa biofilms

scientific article published in October 2001

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

scientific article

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

scientific article (publication date: 2012)

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

scientific article

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

scientific article

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

scientific article

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

scientific article

Benzene Forms Hydrogen Bonds with Water

scientific article published in Science

A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies

scientific article published in July 2006

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

scientific article

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

scientific article

Differential gene expression profiling of adult murine hematopoietic stem cells

scientific article

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

scientific article published in June 2005

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

scientific article

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

scientific article (publication date: June 2003)

Sample size for detecting differentially expressed genes in microarray experiments

scientific article

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

scientific article

Clustering gene-expression data with repeated measurements

scientific article

Construction of regulatory networks using expression time-series data of a genotyped population

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

Chlamydia trachomatis infection alters host cell transcription in diverse cellular pathways

scientific article published on 24 January 2003

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

scientific article published in March 2006

Proteomic and computational analysis of bronchoalveolar proteins during the course of the acute respiratory distress syndrome

scientific article

Propionibacterium persists in the skin despite standard surgical preparation

scientific article published on September 2014

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

scientific article

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

scientific article published on 17 October 2006

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

scientific article published on 21 April 2005

The Transcriptome and Its Translation during Recovery from Cell Cycle Arrest inSaccharomyces cerevisiae

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

scientific article published on 9 October 2009

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

scientific article

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

scientific article published on 12 February 2008

Functional annotation from predicted protein interaction networks

scientific article

PEDB: the Prostate Expression Database

scientific article

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

scientific article

Genome sequence of a novel species, Propionibacterium humerusii

scientific article

Independent and Cooperative Antiviral Actions of Beta Interferon and Gamma Interferon against Herpes Simplex Virus Replication in Primary Human Fibroblasts

scientific article

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

scientific article

Evolutionary Divergence of Aggregatibacter actinomycetemcomitans

scientific article published on September 29, 2015

On the persistence of supplementary resources in biomedical publications

scientific article published on 19 May 2006

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

scientific article published on 12 December 2006

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

scientific article

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

scientific article

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

scientific article published on May 2006

What Is the Best Reference RNA? And Other Questions Regarding the Design and Analysis of Two-color Microarray Experiments

article

List of works by Roger E Bumgarner

Integrated genomic and proteomic analyses of a systematically perturbed metabolic network

Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

The genome of the domesticated apple (Malus × domestica Borkh.)

Gene expression in Pseudomonas aeruginosa biofilms

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

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

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

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

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

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

Benzene Forms Hydrogen Bonds with Water

A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies

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

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

Differential gene expression profiling of adult murine hematopoietic stem cells

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

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

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

Sample size for detecting differentially expressed genes in microarray experiments

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

Clustering gene-expression data with repeated measurements

Construction of regulatory networks using expression time-series data of a genotyped population

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

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

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

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

Chlamydia trachomatis infection alters host cell transcription in diverse cellular pathways

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

Proteomic and computational analysis of bronchoalveolar proteins during the course of the acute respiratory distress syndrome

Propionibacterium persists in the skin despite standard surgical preparation

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

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

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

The Transcriptome and Its Translation during Recovery from Cell Cycle Arrest inSaccharomyces cerevisiae

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

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

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

Functional annotation from predicted protein interaction networks

PEDB: the Prostate Expression Database

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

Genome sequence of a novel species, Propionibacterium humerusii

Independent and Cooperative Antiviral Actions of Beta Interferon and Gamma Interferon against Herpes Simplex Virus Replication in Primary Human Fibroblasts

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

Evolutionary Divergence of Aggregatibacter actinomycetemcomitans

On the persistence of supplementary resources in biomedical publications

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

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

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

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

What Is the Best Reference RNA? And Other Questions Regarding the Design and Analysis of Two-color Microarray Experiments