J. Borneman

发表

Analysis of Bacterial Community Composition by Oligonucleotide Fingerprinting of rRNA Genes

M. Chrobak, D. Crowley, L. Valinsky, 2002, Applied and Environmental Microbiology.

A Metaproteomic Approach to Study Human-Microbial Ecosystems at the Mucosal Luminal Interface

T. Graeber, L. Goodglick, Vanathi Gopalakrishnan, 2011, PloS one.

Building phylogenetic trees from binary oligonucleotide fingerprint vectors

A. Figueroa, T. Jiang, J. Borneman, 2004, The 26th Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

Classification Rules that Include Neutral Zones and Their Application to Microbial Community Profiling

James Borneman, Daniel R. Jeske, Elizabeth Bent, 2007 .

A Modular Organization of the Human Intestinal Mucosal Microbiota and Its Association with Inflammatory Bowel Disease

Rob Knight, James Borneman, Ellen Li, 2013, PloS one.

Identifying Microorganisms Involved in Specific In Situ Functions: Experimental Design Considerations for rRNA Gene-Based Population Studies and Sequence-Selective PCR Assays

J. O. Becker, L. Valinsky, A. Scupham, 2007 .

Identifying microorganisms involved in specific pathogen suppression in soil.

J. O. Becker, J. Borneman, 2007, Annual review of phytopathology.

Reprograming of gut microbiome energy metabolism by the FUT2 Crohn's disease risk polymorphism

James Borneman, Curtis Huttenhower, Justin L Sonnenburg, 2014, The ISME Journal.

Linking metabolic phenotypes to pathogenic traits among “Candidatus Liberibacter asiaticus” and its hosts

J. Borneman, K. Zengler, A. Zepeda, 2020, npj Systems Biology and Applications.

Concurrent gut transcriptome and microbiota profiling following chronic ethanol consumption in nonhuman primates

James Borneman, Suhas Sureshchandra, Wenxiu Ma, 2018, Gut microbes.

PCR Primers That Amplify Fungal rRNA Genes from Environmental Samples

R. J. Hartin, J. Borneman, 2000, Applied and Environmental Microbiology.

Rapid and direct method for extraction of RNA from soil

J. Borneman, E. Triplett, 1997 .

Improving probe set selection for microbial community analysis by leveraging taxonomic information of training sequences

Paul M. Ruegger, G. D. Vedova, Tao Jiang, 2011, BMC Bioinformatics.

Microbial phyllosphere populations are more complex than previously realized

D. Crowley, J. Borneman, Ching-Hong Yang, 2001, Proceedings of the National Academy of Sciences of the United States of America.

Development of a 9600-clone procedure for oligonucleotide fingerprinting of rRNA genes: utilization to identify soil bacterial rRNA genes that correlate in abundance with the development of avocado root rot.

Tao Jiang, A. Figueroa, Bei Yin, 2006, Journal of microbiological methods.

Detection and Investigation of Soil Biological Activity against Meloidogyne incognita.

J. O. Becker, J. Borneman, M. Mckenry, 2008, Journal of nematology.

Suppression of Heterodera schachtii Populations by Dactylella oviparasitica in Four Soils.

J. O. Becker, J. Borneman, R. Olatinwo, 2006, Journal of nematology.

Diet High in Soybean Oil Increases Susceptibility to Colitis in Mice

O. Fiehn, F. Sladek, J. Borneman, 2021, bioRxiv.

Fungi associated with the potato taste defect in coffee beans from Rwanda

Paul M. Ruegger, J. Borneman, P. Rolshausen, 2022, Botanical studies.

Disease-Induced Microbial Shifts in Citrus Indicate Microbiome-Derived Responses to Huanglongbing Across the Disease Severity Spectrum

Paul M. Ruegger, J. Borneman, G. McCollum, 2020, Phytobiomes Journal.

Crohn’s disease in endoscopic remission, obesity, and cases of high genetic risk demonstrates overlapping shifts in the colonic mucosal-luminal interface microbiome

Tytus D. Mak, Paul M. Ruegger, S. Targan, 2022, Genome medicine.

Improving oligonucleotide fingerprinting of rRNA genes by implementation of polony microarray technology.

Daniel R. Jeske, Paul M. Ruegger, Tao Jiang, 2012, Journal of microbiological methods.

Commensal microbiota alter the abundance and TCR responsiveness of splenic naïve CD4+ T lymphocytes.

J. Borneman, J. Braun, Tiffany T. Huang, 2005, Clinical immunology.

Resident enteric microbiota and CD8+ T cells shape the abundance of marginal zone B cells

J. Borneman, D. Rawlings, J. Braun, 2008, European journal of immunology.

An in vitro pipeline to screen and select citrus-associated microbiota with potential anti- 1 Candidatus Liberibacter asiaticus properties 2

J. Borneman, G. McCollum, P. Rolshausen, 2020 .

Analysis of microbial community composition using oligonucleotide fingerprinting of 1 ribosomal RNA genes 2 3 Running Title : Oligonucleotide fingerprinting of ribosomal RNA genes 4 5

G. D. Vedova, M. Chrobak, D. Crowley, 2002 .

Microbiota T Cells and Commensal + Cells by CD8 Systemic Control of Plasmacytoid Dendritic

J. Borneman, J. Braun, Laura L. Presley, 2008 .

Diet High in Soybean Oil Increases Susceptibility to Colitis in Mice

Paul M. Ruegger, F. Sladek, J. Borneman, 2021, bioRxiv.

Biocontrol Efficacy Among Strains of Pochonia chlamydosporia Obtained from a Root-Knot Nematode Suppressive Soil.

J. O. Becker, J. Borneman, Jiue-in Yang, 2012, Journal of nematology.

Clustering Scatter Plots Using Data Depth Measures

Xiaoxiao Li, James Borneman, Daniel R. Jeske, 2011, DMIN.

65 Detecting Disease-Related Biological Neighborhoods by Human Mucosal Interface Metaproteome Analysis

L. Goodglick, J. Borneman, J. Braun, 2010 .

Detecting Disease-related Biological Neighborhoods by Human Mucosal Interface Metaproteome Analysis

L. Goodglick, J. Borneman, J. Braun, 2010 .

Biclustering scatter plots using data depth measures

James Borneman, Daniel R. Jeske, Xinping Cui, 2013, Stat. Anal. Data Min..

A diazotrophic bacterial endophyte isolated from stems of Zea mays L. and Zea luxurians Iltis and Doebley

J. Borneman, E. Triplett, P. Ludden, 1996, Plant and Soil.

Intestinal bacteria modify lymphoma incidence and latency by affecting systemic inflammatory state, oxidative stress, and leukocyte genotoxicity.

Paul M. Ruegger, J. Borneman, R. Schiestl, 2013, Cancer research.

Intestinal bacterial indicator phylotypes associate with impaired DNA double-stranded break sensors but augmented skeletal bone micro-structure.

Paul M. Ruegger, T. Helbich, J. Borneman, 2019, Carcinogenesis.

Announcement of the International Citrus Microbiome (Phytobiome) Consortium.

J. Setubal, J. Borneman, J. Graham, 2015 .

Bacterial Microbiome Dynamics in Post Pull-Through Hirschsprung-Associated Enterocolitis (HAEC): An Experimental Study Employing the Endothelin Receptor B-Null Mouse Model

Paul M. Ruegger, J. Borneman, P. Frykman, 2018, Front. Surg..

Bayes Neutral Zone Classifiers With Applications to Nonparametric Unsupervised Settings

J. Borneman, D. Jeske, Paul Reugger, 2012, Journal of Agricultural, Biological, and Environmental Statistics.

Correlations between Root-Associated Microorganisms and Peach Replant Disease Symptoms in a California Soil

J. O. Becker, Paul M. Ruegger, J. Borneman, 2012, PloS one.

Abundant and Diverse Fungal Microbiota in the Murine Intestine

N. Rao, A. Scupham, J. Borneman, 2006, Applied and Environmental Microbiology.

Two Food Waste By-Products Selectively Stimulate Beneficial Resident Citrus Host-Associated Microbes in a Zero-Runoff Indoor Plant Production System

Paul M. Ruegger, J. Borneman, R. Popa, 2020, Frontiers in Sustainable Food Systems.

An In Vitro Pipeline for Screening and Selection of Citrus-Associated Microbiota with Potential Anti-“Candidatus Liberibacter asiaticus” Properties

J. Borneman, G. McCollum, P. Rolshausen, 2020, Applied and Environmental Microbiology.

Malassezia Is Associated with Crohn's Disease and Exacerbates Colitis in Mouse Models.

S. Targan, D. Underhill, D. McGovern, 2019, Cell host & microbe.

High Levels of Oxidative Stress Create a Microenvironment That Significantly Decreases the Diversity of the Microbiota in Diabetic Chronic Wounds and Promotes Biofilm Formation

J. Borneman, D. Jeske, M. Martins-Green, 2020, Frontiers in Cellular and Infection Microbiology.

Microbial Landscape of the Grapevine Endosphere in the Context of Pierce’s Disease

Paul M. Ruegger, J. Borneman, P. Rolshausen, 2017 .

Preserving accuracy in GenBank

Nils Hallenberg, Ning Zhang, Scott E. Baker, 2008 .

Improved resolution of bacteria by high throughput sequence analysis of the rRNA internal transcribed spacer.

Paul M. Ruegger, J. Borneman, J. Braun, 2014, Journal of microbiological methods.

A screen of Crohn’s disease-associated microbial metabolites identifies ascorbate as a novel metabolic inhibitor of activated human T cells

F. Bushman, C. Huttenhower, H. Vlamakis, 2018, Mucosal Immunology.

Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation

J. Borneman, E. Triplett, J Borneman, 1997, Applied and environmental microbiology.

Molecular microbial diversity of an agricultural soil in Wisconsin

J. Borneman, E. Triplett, J Borneman, 1996, Applied and environmental microbiology.

The pH sensing receptor AopalH plays important roles in the nematophagous fungus Arthrobotrys oligospora.

J. Borneman, Jinkui Yang, Ke-Qin Zhang, 2019, Fungal biology.

Molecular Mechanisms of the Interactions Between Nematodes and Nematophagous Microorganisms

J. Borneman, Ke-Qin Zhang, Juan Li, 2020 .

Microbial, metabolomic, and immunologic dynamics in a relapsing genetic mouse model of colitis induced by T-synthase deficiency

Paul M. Ruegger, A. Fornace, D. McGovern, 2017, Gut microbes.

Systemic Control of Plasmacytoid Dendritic Cells by CD8+ T Cells and Commensal Microbiota1

J. Borneman, J. Braun, Laura L. Presley, 2008, The Journal of Immunology.

A screen of Crohn’s disease-associated microbial metabolites identifies ascorbate as a novel metabolic inhibitor of activated human T cells

F. Bushman, C. Huttenhower, H. Vlamakis, 2018, Mucosal Immunology.

Commensal Microbiota and CD8+ T Cells Shape the Formation of Invariant NKT Cells

J. Borneman, J. Braun, M. Kronenberg, 2009, The Journal of Immunology.

Early-life effects of juvenile Western diet and exercise on adult gut microbiome composition in mice

Paul M. Ruegger, T. Garland, J. Borneman, 2021, Journal of Experimental Biology.

HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota

Paul M. Ruegger, J. Borneman, J. Braun, 2013, Microbiome.

Host–microbe relationships in inflammatory bowel disease detected by bacterial and metaproteomic analysis of the mucosal–luminal interface

Paul M. Ruegger, L. Goodglick, D. McGovern, 2012, Inflammatory bowel diseases.

The Role of Coral-Associated Bacterial Communities in Australian Subtropical White Syndrome of Turbinaria mesenterina

J. Borneman, L. Pereg, E. Bent, 2012, PloS one.

Bacterial rRNA Genes Associated with Soil Suppressiveness against the Plant-Parasitic Nematode Heterodera schachtii

J. O. Becker, L. Valinsky, Bei Yin, 2003, Applied and Environmental Microbiology.

Polony Identification Using the EM Algorithm Based on a Gaussian Mixture Model

Tao Jiang, Wei Li, James Borneman, 2010, 2010 IEEE International Conference on BioInformatics and BioEngineering.

Bacteria and bacterial rRNA genes associated with the development of colitis in IL‐10−/− Mice

J. Borneman, J. Braun, D. Straus, 2008, Inflammatory bowel diseases.

Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships

Paul M. Ruegger, S. Horvath, C. Huttenhower, 2013, Microbiome.

Identifying microorganisms which fill a niche similar to that of the pathogen: a new investigative approach for discovering biological control organisms

A. Scupham, Bei Yin, J. Borneman, 2004, Plant and Soil.

Association of Systemic Sclerosis With a Unique Colonic Microbial Consortium

D. McGovern, D. Furst, J. Borneman, 2016, Arthritis & rheumatology.

Herpes simplex virus infection, Acyclovir and IVIG treatment all independently cause gut dysbiosis

Paul M. Ruegger, J. Borneman, E. Cantin, 2019, bioRxiv.

A Probabilistic Approach to Accurate Abundance-Based Binning of Metagenomic Reads

Tao Jiang, Olga Tanaseichuk, James Borneman, 2012, WABI.

Dominant Role of the Gut Microbiota in Chemotherapy Induced Neuropathic Pain

Paul M. Ruegger, D. McKemy, J. Borneman, 2019, Scientific Reports.

Chemopreventive Metabolites Are Correlated with a Change in Intestinal Microbiota Measured in A-T Mice and Decreased Carcinogenesis

Paul M. Ruegger, A. Fornace, J. Borneman, 2016, PloS one.

Classification of oligonucleotide fingerprints: application for microbial community and gene expression analyses

Katechan Jampachaisri, James Borneman, S. James Press, 2005, Bioinform..

High Levels of Oxidative Stress and Skin Microbiome are Critical for Initiation and Development of Chronic Wounds in Diabetic Mice

Paul M. Ruegger, J. Borneman, M. Martins-Green, 2019, Scientific Reports.

A Pleiotropic Missense Variant in SLC39A8 Is Associated With Crohn's Disease and Human Gut Microbiome Composition.

Judy H. Cho, M. Daly, L. Klei, 2016, Gastroenterology.

A pleiotropic missense variant in SLC 39 A 8 is associated with Crohn ’ s disease and human gut microbiome composition Short Title : SLC 39 A 8 associated with CD and gut microbiome

Judy H. Cho, M. Daly, L. Klei, 2016 .

Phylogeny-based classification of microbial communities

Tao Jiang, Olga Tanaseichuk, James Borneman, 2014, Bioinform..

An experimental approach for identifying microorganisms involved in specified functions: utilisation for understanding a nematode suppressive soil

Bei Yin, J. Borneman, R. Olatinwo, 2004, Australasian Plant Pathology.

CULTURE-INDEPENDENT ANALYSIS OF ENDOPHYTIC MICROBIAL COMMUNITIES IN GRAPEVINE IN RELATION TO PIERCE’S DISEASE Project Leaders:

J. Borneman, D. Cooksey, 2007 .

Induction of Beet-Cyst Nematode Suppressiveness by the Fungi Dactylella oviparasitica and Fusarium oxysporum in Field Microplots.

J. O. Becker, J. Borneman, R. Olatinwo, 2006, Phytopathology.

Identification of Fungal rDNA Associated with Soil Suppressiveness Against Heterodera schachtii Using Oligonucleotide Fingerprinting.

J. O. Becker, L. Valinsky, Bei Yin, 2003, Phytopathology.

Probe selection algorithms with applications in the analysis of microbial communities

Marek Chrobak, Tao Jiang, Gianluca Della Vedova, 2001, ISMB.

Culture-Independent Identification of Microorganisms That Respond to Specified Stimuli

James Borneman, J. Borneman, 1999, Applied and Environmental Microbiology.

Autoimmune susceptibility gene PTPN2 is required for clearance of adherent-invasive Escherichia coli by integrating bacterial uptake and lysosomal defence

J. Borneman, M. Tremblay, M. Spalinger, 2021, Gut.

Suppression of the Plant-Parasitic Nematode Heterodera schachtii by the Fungus Dactylella oviparasitica.

J. O. Becker, Bei Yin, J. Borneman, 2006, Phytopathology.

Dactylella oviparasitica parasitism of the sugar beet cyst nematode observed in trixenic culture plates

J. O. Becker, J. Borneman, J. S. Becker, 2013 .

Population Dynamics of Dactylella oviparasitica and Heterodera schachtii: Toward a Decision Model for Sugar Beet Planting.

J. Borneman, D. Jeske, P. Timper, 2012, Journal of nematology.

Assessment of Parasitic Activity of Fusarium Strains Obtained from a Heterodera schachtii-Suppressive Soil.

J. O. Becker, Bei Yin, J. Borneman, 2008, Journal of nematology.

Soil Reclamation Gradient Bacterial Functional Redundancy along a

D. Crowley, J. Borneman, G. Sparovek, 2014 .

Section 8 update: BrdU Substrate Utilization Assay

Bei Yin, J. Borneman, E. Bent, 2004 .

Bacterial Functional Redundancy along a Soil Reclamation Gradient

James Borneman, Gerd Sparovek, David Crowley, 2000, Applied and Environmental Microbiology.

A Fast Algorithm for Approximate String Matching on Gene Sequences

Tao Jiang, Zheng Liu, Xin Chen, 2005, CPM.

Particle Radiation Side-Effects: Intestinal Microbiota Composition Shapes Interferon-γ-Induced Osteo-Immunogenicity

Paul M. Ruegger, T. Helbich, J. Borneman, 2021, Radiation Research.

Environment and Diet Influence the Bacterial Microbiome of Ambigolimax valentianus, an Invasive Slug in California

J. Borneman, M. Maltz, E. Aronson, 2021, Insects.

A newly discovered gene, tfuA, involved in the production of the ribosomally synthesized peptide antibiotic trifolitoxin

J. Borneman, E. Triplett, B. Breil, 1996, Journal of bacteriology.

Bacteria Associated with Immunoregulatory Cells in Mice

J. Borneman, J. Braun, Laura L. Presley, 2009, Applied and Environmental Microbiology.

A functional myo-inositol catabolism pathway is essential for rhizopine utilization by Sinorhizobium meliloti.

Szi Fei Feng, J. Borneman, F. D. de Bruijn, 1998, Microbiology.

Effect of Heterodera schachtii female age on susceptibility to three fungal hyperparasites in the genus Hyalorbilia

J. O. Becker, J. Borneman, J. S. Becker, 2020, Journal of nematology.

Neutral Zone Classifiers Using a Decision-Theoretic Approach With Application to DNA Array Analyses

James Borneman, Hua Yu, Daniel R. Jeske, 2010, Journal of agricultural, biological, and environmental statistics.

A Disease-Associated Microbial and Metabolomics State in Relatives of Pediatric Inflammatory Bowel Disease Patients

Paul M. Ruegger, M. Dubinsky, A. Fornace, 2016, Cellular and molecular gastroenterology and hepatology.

Bayes Neutral Zone Classifiers With Applications to Nonparametric Unsupervised Settings

James Borneman, Daniel R. Jeske, Scott Benecke, 2012, Journal of Agricultural, Biological, and Environmental Statistics.

Shifts in fungal communities during decomposition of boreal forest litter

K. Treseder, K. McGuire, J. Borneman, 2014 .

Functional diversity in resource use by fungi.

S. Allison, K. McGuire, J. Borneman, 2010, Ecology.

Section 3 update: Oligonucleotide Fingerprinting of Ribosomal RNA Genes (OFRG)

L. Valinsky, A. Scupham, A. Figueroa, 2004 .

Oligonucleotide Fingerprinting of rRNA Genes for Analysis of Fungal Community Composition

James Borneman, Gianluca Della Vedova, L. Valinsky, 2002, Applied and Environmental Microbiology.

What Is the Evidence for the Loss of Microbial Diversity

J. Borneman, 2014 .

from a Culture-Independent Perspective on Rhizosphere Microbial Communities Effects of Bacterial Antibiotic Production

J. Borneman, E. Triplett, E. Robleto, 2013 .

Effects of Bacterial Antibiotic Production on Rhizosphere Microbial Communities from a Culture-Independent Perspective

J. Borneman, E. Triplett, E. Robleto, 1998, Applied and Environmental Microbiology.

Oligonucleotide fingerprinting of ribosomal RNA genes (OFRG)

Katechan Jampachaisri, James Borneman, G Della Vedova, 2004 .

The Autoimmune Susceptibility Gene, PTPN2, Restricts Expansion of a Novel Mouse Adherent-Invasive E. coli

Paul M. Ruegger, J. Borneman, M. Tremblay, 2019, bioRxiv.

Title: The Autoimmune Susceptibility Gene, PTPN2, Restricts Expansion of a Novel Mouse

Paul M. Ruegger, J. Borneman, M. Tremblay, 2019 .

Clustering Binary Fingerprint Vectors with Missing Values for DNA Array Data Analysis

Tao Jiang, James Borneman, Andres Figueroa, 2004, J. Comput. Biol..

Clustering binary fingerprint vectors with missing values for DNA array data analysis

Tao Jiang, James Borneman, Andres Figueroa, 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

Diet High in Soybean Oil Increases Susceptibility to Colitis in Mice

Paul M. Ruegger, F. Sladek, J. Borneman, 2021, bioRxiv.

Separating metagenomic short reads into genomes via clustering

Tao Jiang, Olga Tanaseichuk, James Borneman, 2011, Algorithms for Molecular Biology.

Diet high in linoleic acid dysregulates the intestinal endocannabinoid system and increases susceptibility to colitis in Mice

Paul M. Ruegger, F. Sladek, J. Borneman, 2023, Gut microbes.

Bacterial and Fungal Next Generation Sequencing Datasets and Metadata from Citrus Infected with ‘Candidatus Liberibacter asiaticus’

Paul M. Ruegger, J. Borneman, G. McCollum, 2018 .

Investigations into peach seedling stunting caused by a replant soil.

J. O. Becker, J. Borneman, M. Mckenry, 2009, FEMS microbiology ecology.

PRISE (PRImer SElector): software for designing sequence-selective PCR primers.

Paul M. Ruegger, M. Chrobak, J. Borneman, 2008, Journal of microbiological methods.

The autoimmune susceptibility gene, PTPN2, restricts expansion of a novel mouse adherent-invasive E. coli

Paul M. Ruegger, J. Borneman, M. Tremblay, 2020, Gut microbes.

Resident enteric microbiota and CD8+ T cells shape the abundance of marginal zone B cells

J. Borneman, D. Rawlings, J. Braun, 2008, European journal of immunology.

Host–microbe relationships in inflammatory bowel disease detected by bacterial and metaproteomic analysis of the mucosal–luminal interface

Paul M. Ruegger, L. Goodglick, D. McGovern, 2012, Inflammatory Bowel Diseases.

PRISE2: Software for designing sequence-selective PCR primers and probes

M. Chrobak, J. Borneman, Yu-Ting Huang, 2014, BMC Bioinformatics.

Phenotypic and molecular analysis of a pasteuria strain parasitic to the sting nematode.

J. O. Becker, R. Giblin-Davis, J. Borneman, 2001, Journal of nematology.

Haloalkene oxidation by the soluble methane monooxygenase from Methylosinus trichosporium OB3b: mechanistic and environmental implications.

B. Fox, L. Wackett, J. Borneman, 1990, Biochemistry.

Effect of Repetitive Applications of the Biocontrol Bacterium Pseudomonas putida 06909-rif/nal on Citrus Soil Microbial Communities.

D. Crowley, J. Borneman, K. Steddom, 2002, Phytopathology.

Hyalorbilia oviparasitica Clade Detected in Field Soils Cropped to Sugar Beets and Enriched in the Presence of Heterodera schachtii and a Host Crop

J. O. Becker, Paul M. Ruegger, J. Borneman, 2020 .