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Author Details

Pavel S Novichkov
Lawrence Berkeley National Laboratory
2000
55
25
PMIDPaper TitleJournal TitlePublished Year
36251274CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis.Gigascience2022
34113324Binary Metabolic Phenotypes and Phenotype Diversity Metrics for the Functional Characterization of Microbial Communities.Front Microbiol2021
33537340Metabolic Phenotypes as Potential Biomarkers for Linking Gut Microbiome With Inflammatory Bowel Diseases.Front Mol Biosci2021
33122416Draft Genome Sequence of <i>Bacillus</i> sp. Strain EB106-08-02-XG196, Isolated from High-Nitrate-Contaminated Sediment.Microbiol Resour Announc2020
33193240Characterization of a Metal-Resistant <i>Bacillus</i> Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation.Front Microbiol2020
30659179Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria.Nat Commun2019
31275260Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome.Front Microbiol2019
30964892LurR is a regulator of the central lactate oxidation pathway in sulfate-reducing Desulfovibrio species.PLoS One2019
30536693A new family of transcriptional regulators of tungstoenzymes and molybdate/tungstate transport.Environ Microbiol2019
29341298Multiple signaling systems target a core set of transition metal homeostasis genes using similar binding motifs.Mol Microbiol2018
30190458Jungle Express is a versatile repressor system for tight transcriptional control.Nat Commun2018
29979655KBase: The United States Department of Energy Systems Biology Knowledgebase.Nat Biotechnol2018
30375402Author Correction: Jungle Express is a versatile repressor system for tight transcriptional control.Nat Commun2018
28663297Draft Genome Sequences of Two <i>Janthinobacterium</i><i>lividum</i> Strains, Isolated from Pristine Groundwater Collected from the Oak Ridge Field Research Center.Genome Announc2017
28194258Complete genome sequence of <i>Pseudomonas stutzeri</i> strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site.Stand Genomic Sci2017
27474723Novel Metal Cation Resistance Systems from Mutant Fitness Analysis of Denitrifying Pseudomonas stutzeri.Appl Environ Microbiol2016
28348857Comparative genomics and evolution of transcriptional regulons in <i>Proteobacteria</i>.Microb Genom2016
25313388Rex (encoded by DVU_0916) in Desulfovibrio vulgaris Hildenborough is a repressor of sulfate adenylyl transferase and is regulated by NADH.J Bacteriol2015
26555820Ï¿54-dependent regulome in Desulfovibrio vulgaris Hildenborough.BMC Genomics2015
26283774Regulation of Nitrite Stress Response in Desulfovibrio vulgaris Hildenborough, a Model Sulfate-Reducing Bacterium.J Bacteriol2015
24118949Control of methionine metabolism by the SahR transcriptional regulator in Proteobacteria.Environ Microbiol2014
25411846Comparative genomics of transcriptional regulation of methionine metabolism in Proteobacteria.PLoS One2014
24966856Comparative genomics and evolution of regulons of the LacI-family transcription factors.Front Microbiol2014
25099177Chlorate reduction in Shewanella algaeâ¿¿ACDC is a recently acquired metabolism characterized by gene loss, suboptimal regulation and oxidative stress.Mol Microbiol2014
24612352Activation of phenotypic subpopulations in response to ciprofloxacin treatment in Acinetobacter baumannii.Mol Microbiol2014
24271392Network portal: a database for storage, analysis and visualization of biological networks.Nucleic Acids Res2014
23086211Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes.J Bacteriol2013
24060102Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria.BMC Genomics2013
24175918RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria.BMC Genomics2013
23913324New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria.J Bacteriol2013
23398941Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria.BMC Genomics2013
23504016Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis.J Bacteriol2013
23547897RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes.BMC Genomics2013
22210771Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor Rex.J Bacteriol2012
22700702RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics.Nucleic Acids Res2012
21531804Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidence.J Bacteriol2011
21810205Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus.BMC Genomics2011
21849503Control of proteobacterial central carbon metabolism by the HexR transcriptional regulator: a case study in Shewanella oneidensis.J Biol Chem2011
21791533VISTA Region Viewer (RViewer)--a computational system for prioritizing genomic intervals for biomedical studies.Bioinformatics2011
19906701MicrobesOnline: an integrated portal for comparative and functional genomics.Nucleic Acids Res2010
20542910RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach.Nucleic Acids Res2010
20360214Distinct patterns of expression and evolution of intronless and intron-containing mammalian genes.Mol Biol Evol2010
19884135RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes.Nucleic Acids Res2010
18978059Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes.J Bacteriol2009
19351897The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages.Proc Natl Acad Sci U S A2009
18845571ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes.Nucleic Acids Res2009
17142223RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes.Nucleic Acids Res2007
18042280Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea.Biol Direct2007
16792803PHOG: a database of supergenomes built from proteome complements.BMC Evol Biol2006
15375139Genome-wide molecular clock and horizontal gene transfer in bacterial evolution.J Bacteriol2004
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Collaborators

Dmitry A Rodionov
Sanford Burnham Prebys Medical Discovery Institute
Co-authored papers 22
Adam P Arkin
Lawrence Berkeley National Laboratory
Co-authored papers 20
Inna Dubchak
Lawrence Berkeley National Laboratory
Co-authored papers 17
Andrey A Mironov
Lomonosov Moscow State University
Co-authored papers 9
Grant M Zane
University of Missouri
Co-authored papers 6
Andrei L Osterman
Sanford Burnham Prebys Medical Discovery Institute
Co-authored papers 6
Lara Rajeev
Lawrence Berkeley National Laboratory
Co-authored papers 6
Aindrila Mukhopadhyay
Joint BioEnergy Institute
Co-authored papers 6
Adam M Deutschbauer
Lawrence Berkeley National Laboratory
Co-authored papers 6
Judy D Wall
University of Missouri
Co-authored papers 6
Morgan N Price
Lawrence Berkeley National Laboratory
Co-authored papers 5
Paramvir S Dehal
Lawrence Berkeley National Laboratory
Co-authored papers 4
Paul D Adams
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Co-authored papers 4
John-Marc Chandonia
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Co-authored papers 4
Terry C Hazen
University of Tennessee
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Hope College
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Michael P Thorgersen
University of Georgia
Co-authored papers 3
Michael W W Adams
University of Georgia
Co-authored papers 3
Romy Chakraborty
Lawrence Berkeley National Laboratory
Co-authored papers 3
Nathan Tintle
The Fatty Acid Research Institute
Co-authored papers 2
Roman A Sutormin
Lawrence Berkeley National Laboratory
Co-authored papers 2
Marcin P Joachimiak
E O Lawrence Berkeley National Laboratory, UCSF Medical Center, University of California, Berkeley, University of Chicago
Co-authored papers 2
William J Riehl
Lawrence Berkeley National Laboratory
Co-authored papers 2
Farris L Poole
University of Georgia
Co-authored papers 2
Jason K Baumohl
E.O. Lawrence Berkeley National Laboratory
Co-authored papers 2
Steven W Singer
Co-authored papers 2
Nathan J Hillson
Lawrence Berkeley National Laboratory
Co-authored papers 2
Matthew DeJongh
Hope College
Co-authored papers 2
Thomas Brettin
University of Chicago
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Blake A Simmons
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Release 1.2