P. Novichkov

发表

Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea

E. Koonin, Y. Wolf, K. Makarova, 2007, Biology Direct.

PHOG: a database of supergenomes built from proteome complements

A. Mironov, I. V. Merkeev, P. Novichkov, 2006, BMC Evolutionary Biology.

KBase: The United States Department of Energy Systems Biology Knowledgebase

Rick L. Stevens, James J. Davis, Kevin P. Keegan, 2018, Nature Biotechnology.

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

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

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

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

Distinct Patterns of Expression and Evolution of Intronless and Intron-Containing Mammalian Genes

A. N. Spiridonov, E. Koonin, A. Ogurtsov, 2010, Molecular biology and evolution.

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.

Genomic Reconstruction of the Transcriptional Regulatory Network in Bacillus subtilis

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

Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation

A. Arkin, A. Deutschbauer, J. Chandonia, 2020, Frontiers in Microbiology.

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.

Genome-Wide Molecular Clock and Horizontal Gene Transfer in Bacterial Evolution

Mikhail S. Gelfand, Eugene V. Koonin, Yuri I. Wolf, 2004, Journal of bacteriology.

High-throughput mapping of the phage resistance landscape in E. coli

Vivek K. Mutalik, A. Arkin, A. Deutschbauer, 2020, PLoS biology.

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

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

σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough

I. Dubchak, A. Mukhopadhyay, Amy Chen, 2015, BMC Genomics.

Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site

Paramvir S. Dehal, Lynne A. Goodwin, Hannah L. Woo, 2017, Standards in genomic sciences.

TOGs vs COGs : a Database of Supergenomes Built from Proteome Complements

A. Mironov, I. V. Merkeev, P. Novichkov, 2006 .

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

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

Lawrence Berkeley National Laboratory Recent Work Title Multiple signaling systems target a core set of transition metal homeostasis genes using similar binding motifs Permalink

A. Mukhopadhyay, Jessica Trinh, P. Novichkov, 2018 .

A dual functioning small RNA/Riboswitch controls the expression of the methionine biosynthesis regulator SahR in Desulfovibrio vulgaris Hildenborough

P. Novichkov, K. Bender, A. S. Burns, 2019 .

Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria

Vivek K. Mutalik, A. Arkin, A. Deutschbauer, 2019, Nature Communications.

Dub-seq: dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits

Vivek K. Mutalik, A. Arkin, A. Deutschbauer, 2018, bioRxiv.

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 .

Draft Genome Sequence of Bacillus sp. Strain EB106-08-02-XG196, Isolated from High-Nitrate-Contaminated Sediment

A. Arkin, A. Deutschbauer, J. Chandonia, 2020, Microbiology Resource Announcements.

A new family of transcriptional regulators of tungstoenzymes and molybdate/tungstate transport

I. Dubchak, M. Price, A. Mukhopadhyay, 2018, Environmental microbiology.

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 Genomics of Transcriptional Regulation of Methionine Metabolism in Proteobacteria

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

Tungsten and molybdenum play an essential role as catalytic components of molybdoenzymes and tungstoenzymes

I. Dubchak, M. Price, A. Mukhopadhyay, 2019 .

Chlorate reduction in Shewanella algae ACDC is a recently acquired metabolism characterized by gene loss, suboptimal regulation and oxidative stress

R. A. Melnyk, J. Coates, P. Novichkov, 2014, Molecular microbiology.

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

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

CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis

J. Chandonia, P. Novichkov, Adam P Arkin, 2022, GigaScience.

Novel Metal Cation Resistance Systems from Mutant Fitness Analysis of Denitrifying Pseudomonas stutzeri

Adam P. Arkin, Pavel S. Novichkov, W. Andrew Lancaster, 2016, Applied and Environmental Microbiology.

The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages

Eugene V Koonin, Yuri I Wolf, David J Lipman, 2009, Proceedings of the National Academy of Sciences.

Prediction of the exon-intron structure by comparison of genomic sequences

M. Gelfand, A. Mironov, P. Novichkov, 2000, Molecular Biology.

Gene recognition in eukaryotic DNA by comparison of genomic sequences

Mikhail S. Gelfand, Andrey A. Mironov, Pavel S. Novichkov, 2001, Bioinform..

Trends in Prokaryotic Evolution Revealed by Comparison of Closely Related Bacterial and Archaeal Genomes

Inna Dubchak, Eugene V. Koonin, Yuri I. Wolf, 2008, Journal of bacteriology.

Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome

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

High-throughput mapping of the phage resistance landscape in E. coli

Vivek K. Mutalik, A. Arkin, A. Deutschbauer, 2020, bioRxiv.

The DOE Systems Biology Knowledgebase (KBase)

Fangfang Xia, Rick Stevens, Mark Gerstein, 2016, bioRxiv.

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..

RegTransBase—a database of regulatory sequences and interactions in a wide range of prokaryotic genomes

Inna Dubchak, Mikhail S. Gelfand, Adam P. Arkin, 2006, Nucleic Acids Res..

MicrobesOnline: an integrated portal for comparative and functional genomics

Inna Dubchak, Adam P. Arkin, Katherine H. Huang, 2009, Nucleic Acids Res..

Comparative Analysis of Regulatory Patterns in Bacterial Genomes

Mikhail S. Gelfand, Andrey A. Mironov, Pavel S. Novichkov, 2000, Briefings Bioinform..

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

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

LurR is a regulator of the central lactate oxidation pathway in sulfate-reducing Desulfovibrio species

A. Mukhopadhyay, J. Wall, P. Novichkov, 2019, PloS one.

Multiple signaling systems target a core set of transition metal homeostasis genes using similar binding motifs

A. Mukhopadhyay, Jessica Trinh, P. Novichkov, 2018, Molecular microbiology.

Regulation of Nitrite Stress Response in Desulfovibrio vulgaris Hildenborough, a Model Sulfate-Reducing Bacterium

A. Mukhopadhyay, Amy Chen, J. Wall, 2015, Journal of bacteriology.

Jungle Express is a versatile repressor system for tight transcriptional control

Vivek K. Mutalik, J. H. Pereira, B. Simmons, 2018, Nature Communications.

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.

Activation of phenotypic subpopulations in response to ciprofloxacin treatment in Acinetobacter baumannii

P. Novichkov, A. Kazakov, V. Godoy, 2014, Molecular microbiology.

Author Correction: Jungle Express is a versatile repressor system for tight transcriptional control

Nathan J Hillson, Paul D Adams, Vivek K. Mutalik, 2018, Nature Communications.

SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins

Mikhail S. Gelfand, Andrey A. Mironov, Pavel S. Novichkov, 2004, Nucleic Acids Res..

ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes

Inna Dubchak, Eugene V. Koonin, Yuri I. Wolf, 2008, Nucleic Acids Res..

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

Alexander V. Tyakht, D. Rodionov, A. Tyakht, 2021, Frontiers in Molecular Biosciences.

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..

Draft Genome Sequences of Two Janthinobacterium lividum Strains, Isolated from Pristine Groundwater Collected from the Oak Ridge Field Research Center

Kelly M. Wetmore, A. Arkin, A. Deutschbauer, 2017, Genome Announcements.

Draft Genome Sequences of Two Janthinobacteriumlividum Strains, Isolated from Pristine Groundwater Collected from the Field Research Center.

Kelly M. Wetmore, P. Novichkov, A. Kazakov, 2017 .

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.

Network portal: a database for storage, analysis and visualization of biological networks

Ning Jiang, David J. Reiss, Nitin S. Baliga, 2013, Nucleic Acids Res..

Large Scale Comparative Visualisation of Regulatory Networks with TRNDiff

Lawrence Buckingham, James M. Hogan, Pavel S. Novichkov, 2015, ICCS.

Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria

Vivek K. Mutalik, A. Arkin, A. Deutschbauer, 2019, Nature Communications.

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.

RegTransBase—a database of regulatory sequences and interactions in a wide range of prokaryotic genomes

A. Arkin, M. Gelfand, I. Dubchak, 2006, Nucleic Acids Res..

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..

Jungle Express is a versatile repressor system for tight transcriptional control

Vivek K. Mutalik, J. H. Pereira, B. Simmons, 2018, Nature Communications.

[Prediction of the exon-intron structure by comparing nucleotide sequences from various genomes].

A A Mironov, A. Mironov, P. Novichkov, 2000, Молекулярная биология.

VISTA Region Viewer (RViewer) - a computational system for prioritizing genomic intervals for biomedical studies

I. Dubchak, Simon Minovitsky, D. Boffelli, 2011, Bioinform..

The DOE Systems Biology Knowledgebase (KBase)

Robert W. Cottingham, Rick L. Stevens, James J. Davis, 2016, bioRxiv.

Mikhail S. Gelfand, Andrey A. Mironov, Pavel S. Novichkov, 2001, Bioinform..

Inaugural Article: The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages

D. Lipman, E. Koonin, Y. Wolf, 2009 .

Control of Proteobacterial Central Carbon Metabolism by the HexR Transcriptional Regulator

Samantha B. Reed, A. Osterman, D. Rodionov, 2011, The Journal of Biological Chemistry.