D. Rodionov

发表

Structure of the parallel duplex of poly(A) RNA: evaluation of a 50 year-old prediction.

G. Sheldrick, G. Kozlov, K. Gehring, 2013, Angewandte Chemie.

Engineering transcription factors with novel DNA-binding specificity using comparative genomics

Mikhail S. Gelfand, Christopher V. Rao, Eric J. Alm, 2009, Nucleic acids research.

Comparative genomics and functional annotation of bacterial transporters

M. Gelfand, D. Rodionov, 2008 .

Comparative Genomics of Thiamin Biosynthesis in Procaryotes

M. Gelfand, A. Mironov, D. Rodionov, 2002, The Journal of Biological Chemistry.

Effects of microbiota-directed foods in gnotobiotic animals and undernourished children

Michael J. Barratt, C. Sawyer, A. Osterman, 2019, Science.

New Substrates for Tonb-dependent Transport: Do We Only See the 'tip of the Iceberg'?

Dmitry A Rodionov, Kristine Schauer, D. Rodionov, 2022 .

Short-Chain Fatty Acids Modulate Healthy Gut Microbiota Composition and Functional Potential

S. Peterson, D. Rodionov, C. Peterson, 2022, Current Microbiology.

Combined Prebiotic and Microbial Intervention Improves Oral Cholera Vaccination Responses in a Mouse Model of Childhood Undernutrition.

Michael J. Barratt, A. Osterman, J. Gordon, 2020, Cell host & microbe.

Lactose-reduced infant formula with added corn syrup solids is associated with a distinct gut microbiota in Hispanic infants

M. Goran, A. Osterman, J. Millstein, 2020, Gut microbes.

Functional Metabolic Map of Faecalibacterium prausnitzii, a Beneficial Human Gut Microbe

H. Harmsen, I. Thiele, A. Heinken, 2014, Journal of bacteriology.

Towards environmental systems biology of Shewanella

Grigoriy E. Pinchuk, T. Gardner, J. Reed, 2008, Nature Reviews Microbiology.

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

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

The COMBREX Project: Design, Methodology, and Initial Results

Michael Y. Galperin, S. Salzberg, R. Greiner, 2013, PLoS biology.

The Zur regulon of Corynebacterium glutamicum ATCC 13032

A. Tauch, D. Rodionov, J. Schröder, 2010, BMC Genomics.

Identification of a bacterial regulatory system for ribonucleotide reductases by phylogenetic profiling.

M. Gelfand, D. Rodionov, 2005, Trends in genetics : TIG.

The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes

Naryttza N. Diaz, Rick L. Stevens, R. Overbeek, 2005, Nucleic acids research.

Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation.

M. Gelfand, A. Mironov, D. Rodionov, 2002, Nucleic acids research.

Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems.

M. Gelfand, A. Mironov, D. Rodionov, 2004, Nucleic acids research.

Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network in Thermotoga maritima.

N. Grishin, A. Osterman, D. Rodionov, 2012, Environmental microbiology.

Comparative Genomics of the Vitamin B12 Metabolism and Regulation in Prokaryotes*

M. Gelfand, A. Mironov, D. Rodionov, 2003, Journal of Biological Chemistry.

Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch?

M. Gelfand, A. Mironov, D. Rodionov, 2003, Nucleic acids research.

Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria

M. Saier, M. Kazanov, D. Rodionov, 2013, BMC Genomics.

Identification of Genes Encoding the Folate- and Thiamine-Binding Membrane Proteins in Firmicutes

D. Rodionov, A. Hanson, D. Slotboom, 2008, Journal of bacteriology.

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 .

Evolution of Regulatory Motifs of Bacterial Transcription Factors

Mikhail S. Gelfand, Vassily A. Lyubetsky, Konstantin Yu. Gorbunov, 2010, Silico Biol..

Reconstruction Of Regulatory And Metabolic Pathways In Metal-Reducing delta-Proteobacteria

Inna Dubchak, Mikhail S. Gelfand, Adam P. Arkin, 2004 .

Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria

Inna Dubchak, Adam Arkin, Dmitry A Rodionov, 2004, Genome Biology.

Comparative genomic reconstruction of transcriptional regulatory networks in bacteria.

Dmitry A Rodionov, D. Rodionov, 2007, Chemical reviews.

Genomic Reconstruction of the Transcriptional Regulatory Network in Bacillus subtilis

E. O. Ermakova, M. Kazanov, D. Rodionov, 2013, Journal of bacteriology.

Transcriptional control of central carbon metabolic flux in Bifidobacteria by two functionally similar, yet distinct LacI-type regulators

D. Rodionov, D. van Sinderen, C. Stanton, 2019, Scientific Reports.

Control of Proteobacterial Central Carbon Metabolism by the HexR Transcriptional Regulator

Andrei L Osterman, Dmitry A Rodionov, James K Fredrickson, 2011, The Journal of Biological Chemistry.

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.

Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea.

Dmitry A Rodionov, M. Gelfand, A. Mironov, 2002, Genome research.

Ultrafiltration concentration of whey in a pilot plant

S. I. Lazarev, K. K. Polyansky, D. Rodionov, 2019, Proceedings of the Voronezh State University of Engineering Technologies.

Title Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria Permalink

M. Saier, M. Kazanov, D. Rodionov, 2013 .

Comparative genomics of pyridoxal 5′-phosphate-dependent transcription factor regulons in Bacteria

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

Computational analysis of riboswitch-based regulation.

D. Rodionov, Eric I. Sun, 2014, Biochimica et biophysica acta.

Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum

M. Gelfand, A. Osterman, M. Kazanov, 2012, Nucleic acids research.

Comparative Genomics of DtxR Family Regulons for Metal Homeostasis in Archaea

D. Rodionov, Semen A. Leyn, 2014, Journal of bacteriology.

A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life

V. de Crécy-Lagard, D. Rodionov, S. Merchant, 2009, BMC Genomics.

Zinc-Independent Folate Biosynthesis: Genetic, Biochemical, and Structural Investigations Reveal New Metal Dependence for GTP Cyclohydrolase IB

Scott E. Gabriel, K. Shah, V. de Crécy-Lagard, 2009, Journal of bacteriology.

New Family of Tungstate-Responsive Transcriptional Regulators in Sulfate-Reducing Bacteria

A. Arkin, I. Dubchak, D. Rodionov, 2013, Journal of bacteriology.

Organism Sequencing , Annotation , and Comparative Genomics 1 Genomic Reconstruction and Experimental Validation of Catabolic Pathways in Shewanella Species

A. Osterman, D. Rodionov, M. Romine, 2007 .

Community Metabolic Interactions, Vitamin Production and Prebiotic Potential of Medicinal Herbs Used for Immunomodulation

S. Peterson, D. Rodionov, J. Pérez-Santiago, 2021, Frontiers in Genetics.

Dietary Emulsifier Sodium Stearoyl Lactylate Alters Gut Microbiota in vitro and Inhibits Bacterial Butyrate Producers

S. Peterson, D. Rodionov, D. Scott, 2020, Frontiers in Microbiology.

B-Vitamin Sharing Promotes Stability of Gut Microbial Communities

S. Peterson, A. Osterman, D. Peterson, 2019, Front. Microbiol..

A Novel Transcriptional Regulator Related to Thiamine Phosphate Synthase Controls Thiamine Metabolism Genes in Archaea

D. Rodionov, Semen A. Leyn, I. Rodionova, 2016, Journal of bacteriology.

Complementation of Cobalamin Auxotrophy in Synechococcus sp. Strain PCC 7002 and Validation of a Putative Cobalamin Riboswitch In Vivo

Zhenfeng Liu, D. Rodionov, D. Bryant, 2016, Journal of bacteriology.

Genomic distribution of B-vitamin auxotrophy and uptake transporters in environmental bacteria from the Chloroflexi phylum.

A. Osterman, A. Konopka, D. Rodionov, 2015, Environmental microbiology reports.

Crystal structure of TM1030 from Thermotoga maritima at 2.3 Å resolution reveals molecular details of its transcription repressor function

Slawomir K. Grzechnik, Mitchell D. Miller, A. Godzik, 2007, Proteins: Structure, Function, and Bioinformatics.

Crystal structures of the first condensation domain of CDA synthetase suggest conformational changes during the synthetic cycle of nonribosomal peptide synthetases.

D. Rodionov, T. Schmeing, K. Bloudoff, 2013, Journal of molecular biology.

Nicotinamide mononucleotide synthetase is the key enzyme for an alternative route of NAD biosynthesis in Francisella tularensis

E. V. Nikolaev, A. Osterman, D. Rodionov, 2009, Proceedings of the National Academy of Sciences.

Comparative Genomics Reveals the Regulatory Complexity of Bifidobacterial Arabinose and Arabino-Oligosaccharide Utilization

D. Rodionov, D. van Sinderen, Aleksandr A. Arzamasov, 2018, Front. Microbiol..

The Use of Subsystems to Encode Biosynthesis of Vitamins and Cofactors

R. Overbeek, A. Osterman, D. Rodionov, 2010 .

Comparative genomics and functional analysis of the NiaP family uncover nicotinate transporters from bacteria, plants, and mammals

A. Osterman, J. Gregory, D. Rodionov, 2011, Functional & Integrative Genomics.

Rex (Encoded by DVU_0916) in Desulfovibrio vulgaris Hildenborough Is a Repressor of Sulfate Adenylyl Transferase and Is Regulated by NADH

I-Min A. Dubchak, A. Arkin, I. Dubchak, 2014, Journal of bacteriology.

Running title: Characterization of Rex in D. vulgaris Hildenborough

A. Arkin, I. Dubchak, D. Rodionov, 2014 .

Priority effects shape the structure of infant-type Bifidobacterium communities on human milk oligosaccharides

A. Osterman, Aina Gotoh, Lin Jiang, 2022, The ISME Journal.

Microbial liberation of N-methylserotonin from orange fiber in gnotobiotic mice and humans

Michael J. Barratt, A. Osterman, B. Henrissat, 2022, Cell.

Elucidation of roles for vitamin B12 in regulation of folate, ubiquinone, and methionine metabolism

T. Clauss, T. Metz, Young-Mo Kim, 2017, Proceedings of the National Academy of Sciences.

Diversity and Versatility of the Thermotoga maritima Sugar Kinome

A. Osterman, A. Best, D. Rodionov, 2012, Journal of bacteriology.

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

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

B Vitamins and Their Role in Immune Regulation and Cancer

S. Peterson, A. Osterman, D. Rodionov, 2020, Nutrients.

Transcription Factor Family-Based Reconstruction of Singleton Regulons and Study of the Crp/Fnr, ArsR, and GntR Families in Desulfovibrionales Genomes

A. Arkin, I. Dubchak, M. Price, 2012, Journal of bacteriology.

Comparative Genomic Reconstruction of Transcriptional Regulatory Networks in Bacteria

D. Rodionov, 2007 .

Microbial liberation of N-methylserotonin from orange fiber in gnotobiotic mice and humans

Michael J. Barratt, A. Osterman, B. Henrissat, 2022, Cell.

Products of gut microbial Toll/interleukin-1 receptor domain NADase activities in gnotobiotic mice and Bangladeshi children with malnutrition

Alex L. Yenkin, Mark A. Zaydman, Michael J. Barratt, 2022, Cell reports.

A Riboflavin Transporter in Bdellovibrio exovorous JSS

Zhongge Zhang, D. Rodionov, I. Rodionova, 2019, Journal of Molecular Microbiology and Biotechnology.

Genomic reconstruction of short-chain fatty acid production by the human gut microbiota

D. Rodionov, I. Suvorova, S. Iablokov, 2022, Frontiers in Molecular Biosciences.

Comparative Genomics of Transcriptional Regulation of Methionine Metabolism in Proteobacteria

M. Gelfand, D. Rodionov, I. Suvorova, 2014, PloS one.

Expression and purification of recombinant M-Pol I from Saccharomyces cerevisiae with alpha-1,6 mannosylpolymerase activity.

A. Berghuis, D. Rodionov, A. Herscovics, 2009, Protein expression and purification.

Evolution of transcriptional regulation of histidine metabolism in Gram-positive bacteria

M. Gelfand, D. Rodionov, A. Vitreschak, 2022, BMC Genomics.

Biotin uptake in prokaryotes by solute transporters with an optional ATP-binding cassette-containing module

D. Rodionov, T. Eitinger, P. Hebbeln, 2007, Proceedings of the National Academy of Sciences.

Cpe1786/IscR of Clostridium perfringens represses expression of genes involved in Fe-S cluster biogenesis.

D. Rodionov, I. Martin-Verstraete, M. Monot, 2017, Research in microbiology.

Transport of Magnesium by a Bacterial Nramp-Related Gene

Benjamin G. Freedman, Catherine A. Wakeman, W. Winkler, 2014, PLoS genetics.

Linking the duodenal microbiota to stunting in a cohort of undernourished Bangladeshi children with enteropathy

Michael J. Barratt, R. Haque, A. Osterman, 2020, The New England journal of medicine.

Genetic Divergence of Vibrio vulnificus Clinical Isolates with Mild to Severe Outcomes

A. Godzik, D. Rodionov, Semen A. Leyn, 2022, mBio.

A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli

Jonathan M. Monk, M. Saier, Zhongge Zhang, 2021, Scientific Reports.

Novel Metabolic Pathways and Regulons for Hexuronate Utilization in Proteobacteria

J. Gerlt, S. Almo, D. Rodionov, 2018, Journal of bacteriology.

Ribulokinase and Transcriptional Regulation of Arabinose Metabolism in Clostridium acetobutylicum

D. Rodionov, Yang Gu, Weihong Jiang, 2011, Journal of bacteriology.

Computational identi¢cationofBioR,a transcriptional regulatorof

M. Gelfand, D. Rodionov, 2006 .

BACTERIAL NADQ (COG4111) IS A NUDIX-LIKE, ATP-RESPONSIVE REGULATOR OF NAD BIOSYNTHESIS.

D. Rodionov, L. Sorci, N. Raffaelli, 2022, Journal of structural biology.

Comparative Genomics of Arginine Biosynthesis Pathways and Regulons in Human Microbiome

Olga M. Sigalova, D. Rodionov, 2015 .

Phenylacetic Acid Catabolism and Its Transcriptional Regulation in Corynebacterium glutamicum

J. Kalinowski, C. Rückert, D. Rodionov, 2012, Applied and Environmental Microbiology.

Control of methionine metabolism by the SahR transcriptional regulator in Proteobacteria.

A. Arkin, A. Deutschbauer, M. Price, 2014, Environmental microbiology.

Microbial liberation of N-methylserotonin from orange fiber in gnotobiotic mice and humans

Michael J. Barratt, A. Osterman, B. Henrissat, 2022, Cell.

A novel transcription factor PunR and Nac are involved in purine and purine nucleoside transporter punC regulation in E. coli

Anand V. Sastry, B. Palsson, M. Saier, 2021 .

Genetic Divergence of Vibrio vulnificus Clinical Isolates with Mild to Severe Outcomes

A. Godzik, D. Rodionov, Semen A. Leyn, 2022, mBio.

Transcriptional regulation of NAD metabolism in bacteria: NrtR family of Nudix-related regulators

Dmitry A. Rodionov, Nadia Raffaelli, Hong Zhang, 2008, Nucleic acids research.

Reconstruction of xylose utilization pathway and regulons in Firmicutes

Weiwen Zhang, D. Rodionov, Yang Gu, 2010, BMC Genomics.

Definition of a Consensus DNA-binding Site for PecS, a Global Regulator of Virulence Gene Expression in Erwinia chrysanthemi and Identification of New Members of the PecS Regulon*

D. Rodionov, C. Rouanet, W. Nasser, 2004, Journal of Biological Chemistry.

Living without Fur: the subtlety and complexity of iron-responsive gene regulation in the symbiotic bacterium Rhizobium and other α-proteobacteria

Mikhail S. Gelfand, Sun Lei, Dmitry A. Rodionov, 2007, BioMetals.

The effects of micronutrient deficiencies on bacterial species from the human gut microbiota

Michael J. Barratt, A. Osterman, J. Gordon, 2017, Science Translational Medicine.

A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate.

Zasha Weinberg, Dmitry A Rodionov, R. Breaker, 2010, Chemistry & biology.

Comparative genomics of the KdgR regulon in Erwinia chrysanthemi 3937 and other gamma-proteobacteria.

Dmitry A Rodionov, M. Gelfand, D. Rodionov, 2004, Microbiology.

Identification of Nicotinamide Mononucleotide Deamidase of the Bacterial Pyridine Nucleotide Cycle Reveals a Novel Broadly Conserved Amidohydrolase Family*

A. Osterman, D. Rodionov, M. Romine, 2011, The Journal of Biological Chemistry.

Carbohydrates great and small, from dietary fiber to sialic acids: How glycans influence the gut microbiome and affect human health

K. Zengler, D. Rodionov, Joanna Coker, 2021, Gut microbes.

Evaluating microbiome-directed fibre snacks in gnotobiotic mice and humans

Michael J. Barratt, A. Osterman, A. Raman, 2021, Nature.

Genomics and Enzymology of NAD Biosynthesis

A. Osterman, D. Rodionov, O. Kurnasov, 2010 .

Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children

Michael J. Barratt, A. Osterman, B. Henrissat, 2016, Science.

Structural Analysis of the Tobramycin and Gentamicin Clinical Resistome Reveals Limitations for Next-generation Aminoglycoside Design.

A. Berghuis, D. Rodionov, A. Bassenden, 2016, ACS chemical biology.

Role of a Zn‐independent DksA in Zn homeostasis and stringent response

V. de Crécy-Lagard, Crysten E. Blaby-Haas, D. Rodionov, 2011, Molecular microbiology.

A Novel Class of Modular Transporters for Vitamins in Prokaryotes

M. Gelfand, A. Osterman, D. Rodionov, 2008, Journal of bacteriology.

Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate

A. Osterman, B. Stec, D. Rodionov, 2007, Proceedings of the National Academy of Sciences.

The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation

Fangfang Xia, Daniela Bartels, Tobias Paczian, 2006, Nucleic Acids Res..

Computational Reconstruction of Iron- and Manganese-Responsive Transcriptional Networks in α-Proteobacteria

Mikhail S. Gelfand, Dmitry A. Rodionov, Jonathan D. Todd, 2006, PLoS Comput. Biol..

Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element.

Andrey A Mironov, Dmitry A Rodionov, M. Gelfand, 2003, RNA.

Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima

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

Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides

Bernard Henrissat, Nicolas Terrapon, Dmitry A. Rodionov, 2015, Science.

Bifidobacterium infantis treatment promotes weight gain in Bangladeshi infants with severe acute malnutrition

Michael J. Barratt, A. Osterman, J. Gordon, 2022, Science Translational Medicine.

Human Milk Oligosaccharide Utilization in Intestinal Bifidobacteria Is Governed by Global Transcriptional Regulator NagR

A. Osterman, D. Rodionov, Aleksandr A. Arzamasov, 2022, bioRxiv.

Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli

Anand V. Sastry, D. Rodionov, Y. Hefner, 2021, Communications Biology.

Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli

Anand V. Sastry, B. Palsson, M. Saier, 2021, Communications Biology.

Synthesis of the novel transporter YdhC, is regulated by the YdhB transcription factor controlling adenosine and adenine uptake

Anand V. Sastry, B. Palsson, M. Saier, 2020, bioRxiv.

Bioremediation of a Common Product of Food Processing by a Human Gut Bacterium.

Andrei L Osterman, Dmitry A Rodionov, A. Osterman, 2019, Cell host & microbe.

A sparse covarying unit that describes healthy and impaired human gut microbiota development

Michael J. Barratt, G. Kang, R. Haque, 2019, Science.

Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome

S. Peterson, A. Osterman, D. Rodionov, 2019, Front. Microbiol..

Experimental Strategies for Functional Annotation and Metabolism Discovery: Targeted Screening of Solute Binding Proteins and Unbiased Panning of Metabolomes

Ronald J. Quinn, Steven C. Almo, Matthew P. Jacobson, 2014, Biochemistry.

Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization

Yan Zhang, Dmitry A Rodionov, M. Gelfand, 2009, BMC Genomics.

Comparative Genomics of Regulation of Fatty Acid and Branched-Chain Amino Acid Utilization in Proteobacteria

Inna Dubchak, Mikhail S. Gelfand, Dmitry A. Rodionov, 2008, Journal of bacteriology.

Flat-Chamber Electrobaromembrane Apparatus with Improved Characteristics and its Calculation Method

S. V. Kovalev, D. A. Rodionov, S. I. Lazarev, 2019, Chemical and Petroleum Engineering.

Study and Method of Calculating the Efficiency of Roll-Type Devices, Taking Into Account the Hydrodynamics of Flow

S. I. Lazarev, D. Rodionov, A. Levin, 2018, Chemical and Petroleum Engineering.

Comparative and Functional Genomic Analysis of Prokaryotic Nickel and Cobalt Uptake Transporters: Evidence for a Novel Group of ATP-Binding Cassette Transporters

M. Gelfand, D. Rodionov, T. Eitinger, 2006, Journal of bacteriology.

IscR‐dependent gene expression links iron‐sulphur cluster assembly to the control of O2‐regulated genes in Escherichia coli

F. Blattner, D. Rodionov, P. Kiley, 2006, Molecular microbiology.

Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks

Inna Dubchak, Mikhail S. Gelfand, Adam P. Arkin, 2005, PLoS Comput. Biol..

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes

Inna Dubchak, Mikhail S. Gelfand, Adam P. Arkin, 2009, Nucleic Acids Res..

Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization

A. Osterman, E. Dervyn, F. Collart, 2009, Proceedings of the National Academy of Sciences.

Glycerate 2-Kinase of Thermotoga maritima and Genomic Reconstruction of Related Metabolic Pathways

A. Osterman, D. Rodionov, C. Yang, 2007, Journal of bacteriology.

Novel inositol catabolic pathway in Thermotoga maritima.

A. Osterman, D. Rodionov, K. Noll, 2013, Environmental microbiology.

Underlying mechanisms for syntrophic metabolism of essential enzyme cofactors in microbial communities

A. Osterman, W. Nelson, D. Rodionov, 2017, The ISME Journal.

Computational identification of BioR, a transcriptional regulator of biotin metabolism in Alphaproteobacteria, and of its binding signal.

M. Gelfand, D. Rodionov, 2006, FEMS microbiology letters.

Prediction of enzymatic pathways by integrative pathway mapping

Henry Lin, Andrej Sali, Matthew P Jacobson, 2018, eLife.

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

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

Novel Transcriptional Regulons for Autotrophic Cycle Genes in Crenarchaeota

D. Rodionov, Semen A. Leyn, I. Rodionova, 2015, Journal of bacteriology.

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.

Biochemical and Regulatory Analyses of Xylanolytic Regulons in Caldicellulosiruptor bescii Reveal Genus-Wide Features of Hemicellulose Utilization

D. Rodionov, M. Adams, Tunyaboon Laemthong, 2022, Applied and environmental microbiology.

Transcriptional Regulation of Plant Biomass Degradation and Carbohydrate Utilization Genes in the Extreme Thermophile Caldicellulosiruptor bescii

I. Nookaew, D. Rodionov, M. Adams, 2021, mSystems.

Genomic Reconstruction of Carbohydrate Utilization Capacities in Microbial-Mat Derived Consortia

D. Rodionov, Semen A. Leyn, M. Romine, 2017, Front. Microbiol..

N-Acetylgalactosamine Utilization Pathway and Regulon in Proteobacteria

D. Rodionov, Semen A. Leyn, Chen Yang, 2012, The Journal of Biological Chemistry.

Transcriptional regulation of NAD metabolism in bacteria: genomic reconstruction of NiaR (YrxA) regulon

Mikhail S. Gelfand, Chen Yang, Dmitry A. Rodionov, 2008, Nucleic acids research.

Genomic encyclopedia of sugar utilization pathways in the Shewanella genus

R. Overbeek, A. Osterman, K. Nealson, 2010, BMC Genomics.

Genomics-Based Reconstruction and Predictive Profiling of Amino Acid Biosynthesis in the Human Gut Microbiome

D. Rodionov, S. Iablokov, German A. Ashniev, 2022, Microorganisms.

Identifying determinants of bacterial fitness in a model of human gut microbial succession

Yangqing Peng, A. Osterman, A. Raman, 2020, Proceedings of the National Academy of Sciences.

Linking the duodenal microbiota to stunting in a cohort of undernourished Bangladeshi children with enteropathy.

Michael J. Barratt, A. Osterman, J. Gordon, 2020, The New England journal of medicine.

Comparative Genomics and Experimental Characterization of N-Acetylglucosamine Utilization Pathway of Shewanella oneidensis*

Andrei L Osterman, Dmitry A Rodionov, Kenneth H Nealson, 2006, Journal of Biological Chemistry.

RegTransBase – a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes

A. Arkin, M. Gelfand, I. Dubchak, 2013, BMC Genomics.

Canonical and ECF-type ATP-binding cassette importers in prokaryotes: diversity in modular organization and cellular functions.

M. Grote, D. Rodionov, E. Schneider, 2011, FEMS microbiology reviews.

Binary Metabolic Phenotypes and Phenotype Diversity Metrics for the Functional Characterization of Microbial Communities

A. Osterman, D. Rodionov, S. Iablokov, 2021, Frontiers in Microbiology.

Metabolic Phenotypes as Potential Biomarkers for Linking Gut Microbiome With Inflammatory Bowel Diseases

D. Rodionov, A. Tyakht, S. Iablokov, 2021, Frontiers in Molecular Biosciences.

Transcriptional regulation of pentose utilisation systems in the Bacillus/Clostridium group of bacteria.

M S Gelfand, M. Gelfand, A. Mironov, 2001, FEMS microbiology letters.

A novel transcriptional regulator of L-arabinose utilization in human gut bacteria

A. Joachimiak, D. Rodionov, Youngchang Kim, 2015, Nucleic acids research.

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

Inna Dubchak, Mikhail S. Gelfand, Adam P. Arkin, 2010, Nucleic Acids Res..

A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea

Steven C. Almo, Dmitry A. Rodionov, Matthew W. Vetting, 2017, Nucleic acids research.

Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria

A A Mironov, A B Rakhmaninova, M. Gelfand, 2000, Molecular microbiology.

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.

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.

16S rRNA gene profiling and genome reconstruction reveal community metabolic interactions and prebiotic potential of medicinal herbs used in neurodegenerative disease and as nootropics

S. Peterson, D. Rodionov, P. Mills, 2019, PloS one.

Crystallographic and thermodynamic characterization of phenylaminopyridine bisphosphonates binding to human farnesyl pyrophosphate synthase

A. Berghuis, D. Rodionov, Y. Tsantrizos, 2017, PloS one.

Prebiotic Potential of Culinary Spices Used to Support Digestion and Bioabsorption

S. Peterson, D. Rodionov, P. Mills, 2019, Evidence-based complementary and alternative medicine : eCAM.

CyuR is a Dual Regulator for L-Cysteine Dependent Antimicrobial Resistance in Escherichia coli

Jonathan M. Monk, D. Rodionov, Christopher Dalldorf, 2023, bioRxiv.

Critical heat flux in a locally heated liquid film driven by gas flow in a minichannel

D. Rodionov, O. Kabov, D. Zaitsev, 2009 .

Study of thermocapillary film rupture using a fiber optical thickness probe

Oleg Kabov, D. A. Rodionov, Dmitry Zaitsev, 2007 .

The Rhizobium leguminosarum regulator IrrA affects the transcription of a wide range of genes in response to Fe availability

Dmitry A. Rodionov, Jonathan D. Todd, Andrew W. B. Johnston, 2006, Molecular Genetics and Genomics.

Genome-Scale Metabolic Model of Caldicellulosiruptor bescii Reveals Optimal Metabolic Engineering Strategies for Bio-based Chemical Production

D. Rodionov, M. Adams, R. Kelly, 2021, mSystems.

Alteration of Community Metabolism by Prebiotics and Medicinal Herbs

S. Peterson, D. Rodionov, J. Pérez-Santiago, 2023, Microorganisms.

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

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

Transcriptional Regulation of Carbohydrate Utilization Pathways in the Bifidobacterium Genus

D. Rodionov, D. van Sinderen, Semen A. Leyn, 2016, Front. Microbiol..

Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism.

Dmitry A Rodionov, Nadia Raffaelli, Hong Zhang, 2009, Structure.

Comparative genomics and evolution of transcriptional regulons in Proteobacteria

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

Identification and Regulation of Genes for Cobalamin Transport in the Cyanobacterium Synechococcus sp. Strain PCC 7002

Dmitry A. Rodionov, Donald A. Bryant, D. Rodionov, 2016, Journal of bacteriology.

Comparative genomics and functional analysis of the NiaP family uncover nicotinate transporters from bacteria, plants, and mammals

A. Osterman, J. Gregory, D. Rodionov, 2012, Functional & Integrative Genomics.

Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile

D. Rodionov, I. Martin-Verstraete, M. Monot, 2012, Nucleic acids research.

Optimizing Strategies for Bio-Based Ethanol Production Using Genome-Scale Metabolic Modeling of the Hyperthermophilic Archaeon, Pyrococcus furiosus

D. Rodionov, M. Adams, G. Lipscomb, 2023, Applied and environmental microbiology.

RegTransBase – a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes

Inna Dubchak, Adam P Arkin, Dmitry A Rodionov, 2013, BMC Genomics.

Personalized Response of Parkinson’s Disease Gut Microbiota to Nootropic Medicinal Herbs In Vitro: A Proof of Concept

S. Peterson, D. Rodionov, C. Peterson, 2023, Microorganisms.

Bioactive glycans in a microbiome-directed food for malnourished children

Ye, Michael J. Barratt, A. Osterman, 2023, medRxiv.

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.

Prediction of enzymatic pathways by integrative pathway mapping

Matthew J. O’Meara, Daniel Russel, A. Sali, 2018, eLife.

Comparative genomics and functional analysis of rhamnose catabolic pathways and regulons in bacteria

Aaron A. Best, Dmitry A. Rodionov, James K. Fredrickson, 2013, Front. Microbiol..

Prevotella copri-linked effects of a therapeutic food for malnutrition

Daniel M. Webber, Michael J. Barratt, A. Osterman, 2023, bioRxiv.

RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics

Inna Dubchak, Thomas S. Brettin, Adam P. Arkin, 2012, Nucleic Acids Res..

The Zur regulon of Corynebacterium glutamicum ATCC 13032

A. Tauch, D. Rodionov, Jasmin Schröder, 2009, BMC Genomics.

Canonical and ECF-type ATP-binding cassette importers in prokaryotes: diversity in modular organization and cellular functions.

M. Grote, D. Rodionov, E. Schneider, 2011, FEMS microbiology reviews.

New substrates for TonB-dependent transport: do we only see the 'tip of the iceberg'?

D. Rodionov, H. de Reuse, Kristine Schauer, 2008, Trends in biochemical sciences.

Novel Transcriptional Regulons for Autotrophic Cycle Genes in Crenarchaeota

D. Rodionov, Semen A. Leyn, I. Rodionova, 2015, Journal of bacteriology.

Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism.

M. Gelfand, D. Rodionov, Hong Zhang, 2009, Structure.

Nicotinamide mononucleotide synthetase is the key enzyme for an alternative route of NAD biosynthesis in Francisella tularensis

E. V. Nikolaev, A. Osterman, D. Rodionov, 2009, Proceedings of the National Academy of Sciences.

Ribulokinase and Transcriptional Regulation of Arabinose Metabolism in Clostridium acetobutylicum

D. Rodionov, Yang Gu, Weihong Jiang, 2011, Journal of bacteriology.

Negative transcriptional control of biotin metabolism genes by the TetR-type regulator BioQ in biotin-auxotrophic Corynebacterium glutamicum ATCC 13032.

J. Schneider, A. Tauch, D. Rodionov, 2012, Journal of biotechnology.