D. Ravcheev

发表

Systems biology of bacteria-host interactions

I. Thiele, A. Heinken, D. Ravcheev, 2016 .

RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria

William J. Riehl, A. Arkin, I. Dubchak, 2013, BMC Genomics.

Nitrogen Fixation and Molecular Oxygen: Comparative Genomic Reconstruction of Transcription Regulation in Alphaproteobacteria

M. Gelfand, D. Ravcheev, O. Tsoy, 2016, Frontiers in Microbiology.

Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes

V. de Crécy-Lagard, I. Thiele, Stefanía Magnúsdóttir, 2015, Front. Genet..

Inference of the Transcriptional Regulatory Network in Staphylococcus aureus by Integration of Experimental and Genomics-Based Evidence

Matthew DeJongh, Aaron A. Best, Pavel S. Novichkov, 2011, Journal of bacteriology.

Comparative Genomics and Evolution of Bacterial Regulatory Systems

M. Gelfand, A. Mironov, E. Kotelnikova, 2006 .

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

Ronan M. T. Fleming, Eugen Bauer, Ines Thiele, 2016, Nature Biotechnology.

Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks

Adam Godzik, Andrei L Osterman, Dmitry A Rodionov, 2013, BMC Genomics.

Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis

I. Thiele, D. Ravcheev, 2016, Front. Microbiol..

Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease

Ronan M. T. Fleming, R. Fleming, I. Thiele, 2019, Microbiome.

The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease

R. Fleming, I. Thiele, Reinhard Schneider, 2018, bioRxiv.

Comparative genomic analysis of the human gut microbiome reveals a broad distribution of metabolic pathways for the degradation of host-synthetized mucin glycans

I. Thiele, D. Ravcheev, 2017, 1703.10524.

AGORA2: Large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities

Ronan M. T. Fleming, Janaka N. Edirisinghe, R. Fleming, 2020, bioRxiv.

Regulation of bacterial respiration: Comparison of microarray and comparative genomics data

D. Ravcheev, M. S. Gelfand, M. O. Tsiganova, 2007, Molecular Biology.

Comparative Genomic Analysis Reveals Novel Microcompartment-Associated Metabolic Pathways in the Human Gut Microbiome

I. Thiele, D. Ravcheev, S. Smajic, 2019, Front. Genet..

Comparative Genomic Analysis of the Hexuronate Metabolism Genes and Their Regulation in Gammaproteobacteria

M. Gelfand, D. Rodionov, I. Suvorova, 2011, Journal of bacteriology.

Regulation and Evolution of the Malonate and Propionate 1 Catabolism in the Proteobacteria 2 3

M. Gelfand, I. Suvorova, D. Ravcheev, 2012 .

Genomic analysis of the respiration the microbiota of human intestine

I. Thiele, D. Ravcheev, 2015 .

Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota

Ines Thiele, Dmitry A. Ravcheev, I. Thiele, 2014, Front. Microbiol..

Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima

Karsten Zengler, Dmitry A. Rodionov, Dmitry A. Ravcheev, 2013, Front. Microbiol..

Comparative Genomic Analysis of the Human Gut Microbiome Reveals a Broad Distribution of Metabolic Pathways for the Degradation of Host-Synthetized Mucin Glycans and Utilization of Mucin-Derived Monosaccharides

Ines Thiele, Dmitry A. Ravcheev, I. Thiele, 2017, Front. Genet..

The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease

Piotr Gawron, Inna Kuperstein, Ronan M. T. Fleming, 2018, bioRxiv.

Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine

Ronan M. T. Fleming, Janaka N. Edirisinghe, R. Fleming, 2023, Nature Biotechnology.

Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease

Ronan M. T. Fleming, R. Fleming, I. Thiele, 2019, Microbiome.

Temporal regulation of gene expression of the Escherichia coli bacteriophage phiEco32.

M. Gelfand, K. Severinov, M. Djordjevic, 2012, Journal of molecular biology.

Comparative genomics and evolution of regulons of the LacI-family transcription factors

Mikhail S. Gelfand, Pavel S. Novichkov, Dmitry A. Rodionov, 2014, Front. Microbiol..

Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae)

Andrey A Mironov, M. Gelfand, A. Mironov, 2007, BMC Genomics.

[Comparative genomics analysis of nitrate and nitrite respiration in gamma proteobacteria].

A. Mironov, A. B. Rakhmaninova, D. Ravcheev, 2005, Molekuliarnaia biologiia.

Regulation of Nitrate and Nitrite Respiration in γ-Proteobacteria: A Comparative Genomics Study

M. Gelfand, A. Mironov, A. B. Rakhmaninova, 2005, Molecular Biology.

Transcriptional Regulation of Central Carbon and Energy Metabolism in Bacteria by Redox-Responsive Repressor Rex

Karsten Zengler, Pavel S. Novichkov, Dmitry A. Rodionov, 2011, Journal of bacteriology.

Purine Regulon of Gamma-Proteobacteria: A Detailed Description

M. Gelfand, A. Mironov, A. B. Rakhmaninova, 2002, Russian Journal of Genetics.

Personalized modeling of the human gut microbiome reveals distinct bile acid deconjugation and biotransformation potential in healthy and IBD individuals

Ronan M. T. Fleming, Federico Baldini, Ines Thiele, 2017, bioRxiv.

Redox-Responsive Repressor Rex Modulates Alcohol Production and Oxidative Stress Tolerance in Clostridium acetobutylicum

D. Rodionov, Yang Gu, Weihong Jiang, 2014, Journal of bacteriology.

oxidative stress tolerance in Clostridium acetobutylicum

D. Rodionov, Yang Gu, Weihong Jiang, 2014 .

Two novel regulators of N‐acetyl‐galactosamine utilization pathway and distinct roles in bacterial infections

D. Rodionov, D. Ravcheev, Youjun Feng, 2015, MicrobiologyOpen.

Paracoccus denitrificans possesses two BioR homologs having a role in regulation of biotin metabolism

D. Ravcheev, Youjun Feng, Huimin Zhang, 2015, MicrobiologyOpen.

Comparative Genomics of Ethanolamine Utilization

A. Mushegian, D. Ravcheev, O. Tsoy, 2009, Journal of bacteriology.

Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks

A. Godzik, A. Osterman, D. Rodionov, 2013, BMC Genomics.

Regulation and Evolution of Malonate and Propionate Catabolism in Proteobacteria

M. Gelfand, I. Suvorova, D. Ravcheev, 2012, Journal of bacteriology.

Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus

Inna Dubchak, Ross Overbeek, Andrei L Osterman, 2011, BMC Genomics.

Comparative genomics and evolution of transcriptional regulons in Proteobacteria

D. Rodionov, I. Suvorova, D. Ravcheev, 2016, Microbial genomics.

A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length

Mikhail S. Gelfand, Andrey A. Mironov, Vsevolod J. Makeev, 2005, Bioinform..

Comparative genomics and evolution of transcriptional regulons in Proteobacteria

D. Rodionov, I. Suvorova, D. Ravcheev, 2016, Microbial genomics.

Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria

Dmitry A Rodionov, Aaron A Best, A. Best, 2013, BMC Genomics.