D. Antonopoulos

发表

The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes

Forest Rohwer, Rick L. Stevens, Robert A. Edwards, 2009, PLoS Comput. Biol..

Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases

K. Nelson, B. Henrissat, D. Antonopoulos, 2009, Proceedings of the National Academy of Sciences.

Spatial scale drives patterns in soil bacterial diversity.

J. Gilbert, D. Antonopoulos, Folker Meyer, 2016, Environmental microbiology.

Decreased diversity of the fecal Microbiome in recurrent Clostridium difficile-associated diarrhea.

D. Antonopoulos, T. Schmidt, V. Young, 2008, The Journal of infectious diseases.

Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

Tom O. Delmont, A. M. Eren, Özcan C. Esen, 2017, Microbiome.

Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project

Rick L. Stevens, James R. Knight, J. Raes, 2010, Standards in genomic sciences.

BMP signaling components in embryonic transcriptomes of the hover fly Episyrphus balteatus (Syrphidae)

Folker Meyer, Steffen Lemke, D. Antonopoulos, 2011, BMC Genomics.

Reproducible Community Dynamics of the Gastrointestinal Microbiota following Antibiotic Perturbation

Hilary G. Morrison, Susan M. Huse, Mitchell L. Sogin, 2009, Infection and Immunity.

A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community

M. Sogin, H. Morrison, D. Antonopoulos, 2013, Microbiome.

Suppressive Subtractive Hybridization Reveals Extensive Horizontal Transfer in the Rumen Metagenome

K. Nelson, D. Antonopoulos, B. White, 2011 .

Application of suppressive subtractive hybridization to uncover the metagenomic diversity of environmental samples.

D. Antonopoulos, B. White, E. Galbraith, 2008, Methods in molecular biology.

Suppressive subtractive hybridization as a tool for identifying genetic diversity in an environmental metagenome: the rumen as a model.

Bryan A White, D. Antonopoulos, B. White, 2004, Environmental microbiology.

Commensal bacteria protect against food allergen sensitization

D. Antonopoulos, S. Mazmanian, K. McCoy, 2014, Proceedings of the National Academy of Sciences.

Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il 10 2 / 2 mice

Yunwei Wang, Dionysios A. Antonopoulos, Vanessa Leone, 2012 .

Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes.

D. Antonopoulos, Folker Meyer, E. Glass, 2010, Cold Spring Harbor protocols.

Metagenomic Alterations in Gut Microbiota Precede and Predict Onset of Colitis in the IL10 Gene-Deficient Murine Model

D. Antonopoulos, J. Miyoshi, V. Leone, 2020, Cellular and molecular gastroenterology and hepatology.

Metagenomic Alterations in Gut Microbiota Precede and Predict Onset of Colitis in the IL10 Gene-Deficient Murine Model

D. Antonopoulos, J. Miyoshi, V. Leone, 2020, bioRxiv.

Bacterial community structure and functional contributions to emergence of health or necrotizing enterocolitis in preterm infants

Kevin P. Keegan, D. Antonopoulos, Folker Meyer, 2013, Microbiome.

Oxalobacter formigenes-Derived Bioactive Factors Stimulate Oxalate Transport by Intestinal Epithelial Cells.

D. Antonopoulos, E. Chang, J. Roy-Chowdhury, 2017, Journal of the American Society of Nephrology : JASN.

Redox Processes Affecting the Speciation of Technetium, Uranium, Neptunium, and Plutonium in Aquatic and Terrestrial Environments

D. Antonopoulos, E. O’Loughlin, M. Boyanov, 2011 .

High-resolution tracking of microbial colonization in Fecal Microbiota Transplantation experiments via metagenome-assembled genomes

Tom O. Delmont, A. M. Eren, H. Morrison, 2016, bioRxiv.

Exercise Prevents Weight Gain and Alters the Gut Microbiota in a Mouse Model of High Fat Diet-Induced Obesity

D. Antonopoulos, Yunwei Wang, V. Leone, 2014, PloS one.

The complete genome sequence for putative H₂- and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome.

K. Williams, J. Gilbert, D. Antonopoulos, 2014, Environmental microbiology.

Mutual reinforcement of pathophysiological host‐microbe interactions in intestinal stasis models

D. Antonopoulos, G. Farrugia, Yunwei Wang, 2017, Physiological reports.

Innate and Adaptive Humoral Responses Coat Distinct Commensal Bacteria with Immunoglobulin A.

D. Antonopoulos, P. Wilson, A. Dent, 2015, Immunity.

Characterization of the gene encoding glutamate dehydrogenase (gdhA) from the ruminal bacterium Ruminococcus flavefaciens FD-1

D. Antonopoulos, B. White, R. Mackie, 2003, Archives of Microbiology.

Insights into the pathogenesis of ulcerative colitis from a murine model of stasis-induced dysbiosis, colonic metaplasia, and genetic susceptibility.

J. Alverdy, B. Shogan, M. Ward, 2016, American journal of physiology. Gastrointestinal and liver physiology.

Early Transcriptomic Changes in the Ileal Pouch Provide Insight into the Molecular Pathogenesis of Pouchitis and Ulcerative Colitis.

A. M. Eren, D. Antonopoulos, D. Rubin, 2017, Inflammatory bowel diseases.

Dietary fat-induced taurocholic acid production promotes pathobiont and colitis in IL-10−/− mice

Yunwei Wang, Dionysios A. Antonopoulos, Vanessa Leone, 2012, Nature.

Inhibition of Microbial Methane Oxidation by 2-Chloro-6-Methylpyridine

D. Antonopoulos, S. Owens, K. Arend, 2022, bioRxiv.

A communal catalogue reveals Earth’s multiscale microbial diversity

Rick L. Stevens, William A. Walters, Nicole M. Gaudelli, 2017, Nature.

Diversity of bacteria at healthy human conjunctiva.

D. Antonopoulos, Jennifer M. Brulc, Xiang Gao, 2011, Investigative ophthalmology & visual science.

Metagenomic Profiling of a Microbial Assemblage Associated with the California Mussel: A Node in Networks of Carbon and Nitrogen Cycling

D. Antonopoulos, Folker Meyer, C. Pfister, 2010, PloS one.

Diversity and Strain Specificity of Plant Cell Wall Degrading Enzymes Revealed by the Draft Genome of Ruminococcus flavefaciens FD-1

Alvaro G. Hernandez, B. Henrissat, D. Antonopoulos, 2009, PloS one.

Phylogenetic reconstruction of Gram-positive organisms based on comparative sequence analysis of molecular chaperones from the ruminal microorganism Ruminococcus flavefaciens FD-1.

D. Antonopoulos, B. White, W. M. Russell, 2003, FEMS microbiology letters.

16S rRNA gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis

D. Antonopoulos, Jun Sun, Yunwei Wang, 2009, The ISME Journal.

Fecal microbiota transplant rescues mice from human pathogen mediated sepsis by restoring systemic immunity

B. Shakhsheer, Jennifer R. Defazio, S. Christley, 2020, Nature Communications.

Natural polyreactive IgA antibodies coat the intestinal microbiota

D. Antonopoulos, P. Wilson, Carole J Henry, 2017, Science.

Gender bias in autoimmunity is influenced by microbiota.

Aly A. Khan, Laura Graham, D. Antonopoulos, 2013, Immunity.

PATRIC as a unique resource for studying antimicrobial resistance

Rida Assaf, Fangfang Xia, Rick Stevens, 2017, Briefings Bioinform..

Healthy infants harbor intestinal bacteria that protect against food allergy

D. Antonopoulos, P. Belda-Ferre, R. Berni Canani, 2018, Nature Medicine.

Polymorphic Immune Mechanisms Regulate Commensal Repertoire.

Aly A. Khan, D. Antonopoulos, A. Chervonsky, 2019, Cell reports.

Microbiota-dependent proteolysis of gluten subverts diet-mediated protection against type 1 diabetes.

Aly A. Khan, D. Antonopoulos, A. Chervonsky, 2022, Cell host & microbe.

Identification of Polymorphisms of the CSN2 Gene Encoding β-Casein in Greek Local Breeds of Cattle

D. Antonopoulos, A. Chatzilazarou, T. Tsironi, 2021, Veterinary sciences.

Identification of Polymorphisms of Gene CSN2 of B Casein in Greek Cow Breeds (Holstein) by Restriction Fragment Length Polymorphism

D. Antonopoulos, D. Houhoula, Despina Vougiouklaki, 2020 .

Standard Colonic Lavage Alters the Natural State of Mucosal-Associated Microbiota in the Human Colon

D. Antonopoulos, S. Hanauer, Yunwei Wang, 2012, PloS one.

A microbial community growth model for dynamic phenotype predictions

D. Antonopoulos, G. Babnigg, A. Freiburger, 2022, bioRxiv.

Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis

Folker Meyer, Patrick D Schloss, Dongjuan Dai, 2013, Microbiome.

Reproducible Community Dynamics of the Gastrointestinal Microbiota 2

M. Sogin, H. Morrison, D. Antonopoulos, 2009 .

Genetic and Metabolic Signals during Acute Enteric Bacterial Infection Alter the Microbiota and Drive Progression to Chronic Inflammatory Disease.

D. Antonopoulos, Jennifer M. Brulc, B. Kirschner, 2016, Cell host & microbe.

Regional Mucosa-Associated Microbiota Determine Physiological Expression of TLR2 and TLR4 in Murine Colon

D. Antonopoulos, A. Chervonsky, S. Devkota, 2010, PloS one.

Fecal microbiota transplant rescues mice from human pathogen mediated sepsis by restoring systemic immunity

B. Shakhsheer, Jennifer R. Defazio, S. Christley, 2020, Nature Communications.

Chapter 3 ANALYZING METAGENOMIC DATA : INFERRING MICROBIAL COMMUNITY FUNCTION WITH MG-RAST

D. Antonopoulos, Folker Meyer, E. Glass, 2010 .

Molecular Methods To Study Complex Microbial Communities

D. Antonopoulos, Jennifer M. Brulc, B. White, 2009 .

Maternal activation of gap genes in the hover fly Episyrphus

Folker Meyer, Steffen Lemke, D. Antonopoulos, 2010, Development.

Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions

D. Antonopoulos, Jennifer M. Brulc, E. Johnston, 2016, PloS one.

Reduction of Sb(V) by coupled biotic-abiotic processes under sulfidogenic conditions

D. Antonopoulos, E. O’Loughlin, T. Flynn, 2021, Heliyon.

Patient-Specific Bacteroides Genome Variants in Pouchitis

Tom O. Delmont, M. Sogin, A. M. Eren, 2016, mBio.

Parallelized, Aerobic, Single Carbon-Source Enrichments from Different Natural Environments Contain Divergent Microbial Communities

Kenneth M. Kemner, Dionysios A. Antonopoulos, Sarah M. Owens, 2017, Front. Microbiol..

From genomics to metagenomics.

Elizabeth M Glass, Folker Meyer, Narayan Desai, 2012, Current opinion in biotechnology.

Geochemical and microbiological processes contributing to the transformation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in contaminated aquifer material.

D. Antonopoulos, M. Kwon, E. O’Loughlin, 2011, Chemosphere.

Effects of dissimilatory sulfate reduction on FeIII (hydr)oxide reduction and microbial community development

D. Antonopoulos, Jennifer M. Brulc, E. Johnston, 2014 .

Interleukin-15 promotes intestinal dysbiosis with butyrate deficiency associated with increased susceptibility to colitis

D. Antonopoulos, S. Mazmanian, C. Weber, 2016, The ISME Journal.

A gene-targeted approach to investigate the intestinal butyrate-producing bacterialcommunity

H. Morrison, D. Antonopoulos, J. Tiedje, 2013, Microbiome.

Early-life microbial intervention reduces colitis risk promoted by antibiotic-induced gut dysbiosis

Tom O. Delmont, M. Sogin, A. M. Eren, 2020, bioRxiv.

Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon

J. Alverdy, D. Antonopoulos, Folker Meyer, 2010, Applied Microbiology and Biotechnology.

Perturbation of the Small Intestine Microbial Ecology by Streptomycin Alters Pathology in a Salmonella enterica Serovar Typhimurium Murine Model of Infection

D. Antonopoulos, V. Young, G. Duhamel, 2009, Infection and Immunity.

Early-life microbial restitution reduces colitis risk promoted by antibiotic-induced gut dysbiosis in IL-10-/- mice.

Tom O. Delmont, A. M. Eren, D. Antonopoulos, 2021, Gastroenterology.

The effects of warming and soil chemistry on bacterial community structure in Arctic tundra soils

D. Antonopoulos, J. Jastrow, C. Liang, 2020, Soil Biology and Biochemistry.

Healthy infants harbor intestinal bacteria that protect against food allergy

D. Antonopoulos, P. Belda-Ferre, R. Berni Canani, 2019, Nature Medicine.

Niche and neutral processes both shape community structure in parallelized, aerobic, single carbon-source enrichments

Stephanie M. Greenwald, D. Antonopoulos, S. Owens, 2017, bioRxiv.

Niche and neutral processes both shape community structure in parallelized, aerobic, single carbon-source enrichments

Stephanie M. Greenwald, D. Antonopoulos, S. Owens, 2017, bioRxiv.

Strain-specific genomic regions of Ruminococcus flavefaciens FD-1 as revealed by combinatorial random-phase genome sequencing and suppressive subtractive hybridization.

Karen E Nelson, Bryan A White, K. Nelson, 2004, Environmental microbiology.

Biogeochemical dynamics and microbial community development under sulfate- and iron-reducing conditions based on electron shuttle amendment

D. Antonopoulos, Jennifer M. Brulc, E. Johnston, 2021, PloS one.

Meeting Report: The 2nd Annual Argonne Soils Workshop, Argonne National Laboratory, Chicago Illinois, USA, October 6-8, 2010

J. Gilbert, D. Antonopoulos, Folker Meyer, 2011, Standards in genomic sciences.

Design and evaluation of a Lactobacillus group-specific ribosomal RNA-targeted hybridization probe and its application to the study of intestinal microecology in pigs.

D. Antonopoulos, R. Mackie, A. Sghir, 1998, Systematic and applied microbiology.

Bacterial community structure and functional contributions to emergence of health or necrotizing enterocolitis in preterm infants

Kevin P. Keegan, D. Antonopoulos, Folker Meyer, 2013, Microbiome.

Abundance and Diversity of Dockerin-Containing Proteins in the Fiber-Degrading Rumen Bacterium, Ruminococcus flavefaciens FD-1

A. Travis, B. Henrissat, D. Antonopoulos, 2010, PloS one.

Conservation and Divergence in Cellulosome Architecture between Two Strains of Ruminococcus flavefaciens

Raphael Lamed, Edward A. Bayer, Bryan A. White, 2006, Journal of bacteriology.

Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects

J. Vineis, H. Morrison, D. Antonopoulos, 2014, Microbiome.

Regional differences in colonic mucosa-associated microbiota determine the physiological expression of host heat shock proteins.

D. Antonopoulos, Yunwei Wang, Y. Tao, 2010, American journal of physiology. Gastrointestinal and liver physiology.

Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

Tom O. Delmont, A. M. Eren, Özcan C. Esen, 2017, Microbiome.

Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects

M. Sogin, J. Vineis, H. Morrison, 2014, Microbiome.

Molecular Glue Discovery: Current and Future Approaches.

D. Antonopoulos, G. Babnigg, Vivian Lu, 2023, Journal of medicinal chemistry.

Effectual Gold Nanoprobe Sensor for Screening Cow Milk Adulteration in Goat Milk—Comparison With Conventional PCR

D. Antonopoulos, J. Impe, Aliki Tsakni, 2021 .

Genetic Deletion of the Bacterial Sensor NOD2 Improves Murine Crohn’s Disease-like Ileitis Independent of Functional Dysbiosis

D. Antonopoulos, E. Chang, F. Cominelli, 2016, Mucosal Immunology.

Conservation and Divergence in Cellulosome Architecture between Two Strains of Ruminococcus ﬂavefaciens (cid:1)

D. Antonopoulos, B. White, E. Bayer, 2006 .

Engineering of increased L-Threonine production in bacteria by combinatorial cloning and machine learning

D. Antonopoulos, T. Brettin, B. Parrello, 2023, Metabolic engineering communications.

Gender bias in autoimmunity is influenced by microbiota.

Aly A. Khan, Laura Graham, D. Antonopoulos, 2013, Immunity.

Innate and Adaptive Humoral Responses Coat Distinct Commensal Bacteria with Immunoglobulin A.

D. Antonopoulos, P. Wilson, A. Dent, 2015, Immunity.