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RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics.
Published in:
Nucleic Acids Research, 2012, v. 40, p. W604, doi. 10.1093/nar/gks562
By:
- Novichkov, Pavel S.;
- Brettin, Thomas S.;
- Novichkova, Elena S.;
- Dehal, Paramvir S.;
- Arkin, Adam P.;
- Dubchak, Inna;
- Rodionov, Dmitry A.
Publication type:
Article
RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach.
Published in:
Nucleic Acids Research, 2010, v. 38, n. suppl_2, p. W299, doi. 10.1093/nar/gkq531
By:
- Novichkov, Pavel S.;
- Rodionov, Dmitry A.;
- Stavrovskaya, Elena D.;
- Novichkova, Elena S.;
- Kazakov, Alexey E.;
- Gelfand, Mikhail S.;
- Arkin, Adam P.;
- Mironov, Andrey A.;
- Dubchak, Inna
Publication type:
Article
MicrobesOnline: an integrated portal for comparative and functional genomics.
Published in:
Nucleic Acids Research, 2010, v. 38, p. D396, doi. 10.1093/nar/gkp919
By:
- Dehal, Paramvir S.;
- Joachimiak, Marcin P.;
- Price, Morgan N.;
- Bates, John T.;
- Baumohl, Jason K.;
- Chivian, Dylan;
- Friedland, Greg D.;
- Huang, Katherine H.;
- Keller, Keith;
- Novichkov, Pavel S.;
- Dubchak, Inna L.;
- Alm, Eric J.;
- Arkin, Adam P.
Publication type:
Article
RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes.
Published in:
Nucleic Acids Research, 2010, v. 38, p. D111, doi. 10.1093/nar/gkp894
By:
- Novichkov, Pavel S.;
- Laikova, Olga N.;
- Novichkova, Elena S.;
- Gelfand, Mikhail S.;
- Arkin, Adam P.;
- Dubchak, Inna;
- Rodionov, Dmitry A.
Publication type:
Article
ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes.
Published in:
Nucleic Acids Research, 2009, v. 37, n. suppl_1, p. D448, doi. 10.1093/nar/gkn684
By:
- Novichkov, Pavel S.;
- Ratnere, Igor;
- Wolf, Yuri I.;
- Koonin, Eugene V.;
- Dubchak, Inna
Publication type:
Article
RegTransBase—a database of regulatory sequences and interactions in a wide range of prokaryotic genomes.
Published in:
Nucleic Acids Research, 2007, v. 35, p. d407, doi. 10.1093/nar/gkl865
By:
- Kazakov, Alexei E.;
- Cipriano, Michael J.;
- Novichkov, Pavel S.;
- Minovitsky, Simon;
- Vinogradov, Dmitry V.;
- Arkin, Adam;
- Mironov, Andrey A.;
- Gelfand, Mikhail S.;
- Dubchak, Inna
Publication type:
Article
CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis.
Published in:
GigaScience, 2022, v. 11, p. 1, doi. 10.1093/gigascience/giac089
By:
- Novichkov, Pavel S;
- Chandonia, John-Marc;
- Arkin, Adam P
Publication type:
Article
Comparative Genomics of Transcriptional Regulation of Methionine Metabolism in Proteobacteria.
Published in:
PLoS ONE, 2014, v. 9, n. 11, p. 1, doi. 10.1371/journal.pone.0113714
By:
- Leyn, Semen A.;
- Suvorova, Inna A.;
- Kholina, Tatiana D.;
- Sherstneva, Sofia S.;
- Novichkov, Pavel S.;
- Gelfand, Mikhail S.;
- Rodionov, Dmitry A.
Publication type:
Article
Multiple signaling systems target a core set of transition metal homeostasis genes using similar binding motifs.
Published in:
Molecular Microbiology, 2018, v. 107, n. 6, p. 704, doi. 10.1111/mmi.13909
By:
- Garber, Megan E.;
- Rajeev, Lara;
- Kazakov, Alexey E.;
- Trinh, Jessica;
- Masuno, Duy;
- Thompson, Mitchell G.;
- Kaplan, Nurgul;
- Luk, Joyce;
- Novichkov, Pavel S.;
- Mukhopadhyay, Aindrila
Publication type:
Article
Chlorate reduction in S hewanella algae ACDC is a recently acquired metabolism characterized by gene loss, suboptimal regulation and oxidative stress.
Published in:
Molecular Microbiology, 2014, v. 94, n. 1, p. 107, doi. 10.1111/mmi.12746
By:
- Clark, Iain C.;
- Melnyk, Ryan A.;
- Iavarone, Anthony T.;
- Novichkov, Pavel S.;
- Coates, John D.
Publication type:
Article
Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-018-08177-8
By:
- Mutalik, Vivek K.;
- Novichkov, Pavel S.;
- Price, Morgan N.;
- Owens, Trenton K.;
- Callaghan, Mark;
- Carim, Sean;
- Deutschbauer, Adam M.;
- Arkin, Adam P.
Publication type:
Article
SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins.
Published in:
Nucleic Acids Research, 2004, v. 32, n. suppl 2, p. w424, doi. 10.1093/nar/gkh391
By:
- Kalinina, Olga V.;
- Novichkov, Pavel S.;
- Mironov, Andrey A.;
- Gelfand, Mikhail S.;
- Rakhmaninova, Aleksandra B.
Publication type:
Article
High-throughput mapping of the phage resistance landscape in E. coli.
Published in:
PLoS Biology, 2020, v. 18, n. 10, p. 1, doi. 10.1371/journal.pbio.3000877
By:
- Mutalik, Vivek K.;
- Adler, Benjamin A.;
- Rishi, Harneet S.;
- Piya, Denish;
- Zhong, Crystal;
- Koskella, Britt;
- Kutter, Elizabeth M.;
- Calendar, Richard;
- Novichkov, Pavel S.;
- Price, Morgan N.;
- Deutschbauer, Adam M.;
- Arkin, Adam P.
Publication type:
Article
Control of methionine metabolism by the SahR transcriptional regulator in Proteobacteria.
Published in:
Environmental Microbiology, 2014, v. 16, n. 1, p. 1, doi. 10.1111/1462-2920.12273
By:
- Novichkov, Pavel S.;
- Li, Xiaoqing;
- Kuehl, Jennifer V.;
- Deutschbauer, Adam M.;
- Arkin, Adam P.;
- Price, Morgan N.;
- Rodionov, Dmitry A.
Publication type:
Article
Distinct Patterns of Expression and Evolution of Intronless and Intron-Containing Mammalian Genes.
Published in:
Molecular Biology & Evolution, 2010, v. 27, n. 8, p. 1745, doi. 10.1093/molbev/msq086
By:
- Shabalina, Svetlana A.;
- Ogurtsov, Aleksey Y.;
- Spiridonov, Alexey N.;
- Novichkov, Pavel S.;
- Spiridonov, Nikolay A.;
- Koonin, Eugene V.
Publication type:
Article
Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors.
Published in:
Bioinformatics, 2001, v. 17, n. 1, p. 13, doi. 10.1093/bioinformatics/17.1.13
By:
- Mironov, Andrey A.;
- Novichkov, Pavel S.;
- Gelfand, Mikhail S.
Publication type:
Article
Binary Metabolic Phenotypes and Phenotype Diversity Metrics for the Functional Characterization of Microbial Communities.
Published in:
Frontiers in Microbiology, 2021, v. 12, p. 1, doi. 10.3389/fmicb.2021.653314
By:
- Iablokov, Stanislav N.;
- Novichkov, Pavel S.;
- Osterman, Andrei L.;
- Rodionov, Dmitry A.
Publication type:
Article
Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation.
Published in:
Frontiers in Microbiology, 2020, v. 11, p. N.PAG, doi. 10.3389/fmicb.2020.587127
By:
- Ge, Xiaoxuan;
- Thorgersen, Michael P.;
- Poole II, Farris L.;
- Deutschbauer, Adam M.;
- Chandonia, John-Marc;
- Novichkov, Pavel S.;
- Gushgari-Doyle, Sara;
- Lui, Lauren M.;
- Nielsen, Torben;
- Chakraborty, Romy;
- Adams, Paul D.;
- Arkin, Adam P.;
- Hazen, Terry C.;
- Adams, Michael W. W.
Publication type:
Article
Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea.
Published in:
Biology Direct, 2007, v. 2, p. 33, doi. 10.1186/1745-6150-2-33
By:
- Makarova, Kira S.;
- Sorokin, Alexander V.;
- Novichkov, Pavel S.;
- Wolf, Yuri I.;
- Koonin, Eugene V.
Publication type:
Article
Comparative genomics and evolution of regulons of the LacI-family transcription factors.
Published in:
Frontiers in Microbiology, 2014, v. 5, p. 1, doi. 10.3389/fmicb.2014.00294
By:
- Ravcheev, Dmitry A.;
- Khoroshkin, Matvei S.;
- Laikova, Olga N.;
- Tsoy, Olga V.;
- Sernova, Natalia V.;
- Petrova, Svetlana A.;
- Rakhmaninova, Aleksandra B.;
- Novichkov, Pavel S.;
- Gelfand, Mikhail S.;
- Rodionov, Dmitry A.
Publication type:
Article
Comparative genomics and evolution of regulons of the LacI-family transcription factors.
Published in:
Frontiers in Microbiology, 2014, v. 5, p. 1, doi. 10.3389/fmicb.2014.00294
By:
- Ravcheev, Dmitry A.;
- Khoroshkin, Matvei S.;
- Laikova, Olga N.;
- Tsoy, Olga V.;
- Sernova, Natalia V.;
- Petrova, Svetlana A.;
- Rakhmaninova, Aleksandra B.;
- Novichkov, Pavel S.;
- Gelfand, Mikhail S.;
- Rodionov, Dmitry A.
Publication type:
Article
LurR is a regulator of the central lactate oxidation pathway in sulfate-reducing Desulfovibrio species.
Published in:
PLoS ONE, 2019, v. 14, n. 4, p. 1, doi. 10.1371/journal.pone.0214960
By:
- Rajeev, Lara;
- Luning, Eric G.;
- Zane, Grant M.;
- Juba, Thomas R.;
- Kazakov, Alexey E.;
- Novichkov, Pavel S.;
- Wall, Judy D.;
- Mukhopadhyay, Aindrila
Publication type:
Article
σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough.
Published in:
BMC Genomics, 2015, v. 16, p. 1, doi. 10.1186/s12864-015-2176-y
By:
- Kazakov, Alexey E.;
- Rajeev, Lara;
- Amy Chen;
- Luning, Eric G.;
- Dubchak, Inna;
- Mukhopadhyay, Aindrila;
- Novichkov, Pavel S.
Publication type:
Article
σ<sup>54</sup>-dependent regulome in Desulfovibrio vulgaris Hildenborough.
Published in:
BMC Genomics, 2015, v. 16, p. 1, doi. 10.1186/s12864-015-2176-y
By:
- Kazakov, Alexey E.;
- Rajeev, Lara;
- Chen, Amy;
- Luning, Eric G.;
- Dubchak, Inna;
- Mukhopadhyay, Aindrila;
- Novichkov, Pavel S.
Publication type:
Article
RegPrecise 3.0 -- A resource for genome-scale exploration of transcriptional regulation in bacteria.
Published in:
BMC Genomics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2164-14-745
By:
- Novichkov, Pavel S.;
- Kazakov, Alexey E.;
- Ravcheev, Dmitry A.;
- Leyn, Semen A.;
- Kovaleva, Galina Y.;
- Sutormin, Roman A.;
- Kazanov, Marat D.;
- Riehl, William;
- Arkin, Adam P.;
- Dubchak, Inna;
- Rodionov, Dmitry A.
Publication type:
Article
Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria.
Published in:
BMC Genomics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2164-14-597
By:
- Sun, Eric I.;
- Leyn, Semen A.;
- Kazanov, Marat D.;
- Saier Jr., Milton H.;
- Novichkov, Pavel S.;
- Rodionov, Dmitry A.
Publication type:
Article
Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria.
Published in:
BMC Genomics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2164-14-94
By:
- Ravcheev, Dmitry A.;
- Best, Aaron A.;
- Sernova, Natalia V.;
- Kazanov, Marat D.;
- Novichkov, Pavel S.;
- Rodionov, Dmitry A.
Publication type:
Article
Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus.
Published in:
BMC Genomics, 2011, v. 12, p. 1, doi. 10.1186/1471-2164-12-S1-S3
By:
- Rodionov, Dmitry A.;
- Novichkov, Pavel S.;
- Stavrovskaya, Elena D.;
- Rodionova, Irina A.;
- Xiaoqing Li;
- Kazanov, Marat D.;
- Ravcheev, Dmitry A.;
- Gerasimova, Anna V.;
- Kazakov, Alexey E.;
- Yu Kovaleva, Galina;
- Permina, Elizabeth A.;
- Laikova, Olga N.;
- Overbeek, Ross;
- Romine, Margaret F.;
- Fredrickson, James K.;
- Arkin, Adam P.;
- Dubchak, Inna;
- Osterman, Andrei L.;
- Gelfand, Mikhail S.
Publication type:
Article
PHOG: a database of supergenomes built from proteome complements.
Published in:
BMC Evolutionary Biology, 2006, v. 6, p. 52, doi. 10.1186/1471-2148-6-52
By:
- Merkeev, Igor V.;
- Novichkov, Pavel S.;
- Mironov, Andrey A.
Publication type:
Article
Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome.
Published in:
Frontiers in Microbiology, 2019, p. N.PAG, doi. 10.3389/fmicb.2019.01316
By:
- Rodionov, Dmitry A.;
- Arzamasov, Aleksandr A.;
- Khoroshkin, Matvei S.;
- Iablokov, Stanislav N.;
- Leyn, Semen A.;
- Peterson, Scott N.;
- Novichkov, Pavel S.;
- Osterman, Andrei L.
Publication type:
Article

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