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    22833 Publications
    3073 Total Profiles
    24 Edited Profiles

    Novichkov, Pavel

    TitleCompl Biologist Res Sci/Engr
    SchoolLawrence Berkeley National Lab
    DepartmentPhysical Biosciences
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/495-2913

       Bibliographic 
       Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can sign in to make corrections and additions, or contact us for help.
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      1. Kazakov AE, Rajeev L, Chen A, Luning EG, Dubchak I, Mukhopadhyay A, Novichkov PS. s(54)-dependent regulome in Desulfovibrio vulgaris Hildenborough. BMC Genomics. 2015; 16(1):919.
        View in: PubMed
      2. Rajeev L, Chen A, Kazakov AE, Luning EG, Zane GM, Novichkov PS, Wall JD, Mukhopadhyay A. Regulation of Nitrite Stress Response in Desulfovibrio vulgaris Hildenborough, a Model Sulfate-Reducing Bacterium. J Bacteriol. 2015 Nov 1; 197(21):3400-8.
        View in: PubMed
      3. Leyn SA, Suvorova IA, Kholina TD, Sherstneva SS, Novichkov PS, Gelfand MS, Rodionov DA. Comparative genomics of transcriptional regulation of methionine metabolism in proteobacteria. PLoS One. 2014; 9(11):e113714.
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      4. Christensen GA, Zane GM, Kazakov AE, Li X, Rodionov DA, Novichkov PS, Dubchak I, Arkin AP, Wall JD. Rex (Encoded by DVU_0916) in Desulfovibrio vulgaris Hildenborough Is a Repressor of Sulfate Adenylyl Transferase and Is Regulated by NADH. J Bacteriol. 2015 Jan 1; 197(1):29-39.
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      5. Clark IC, Melnyk RA, Iavarone AT, Novichkov PS, Coates JD. Chlorate reduction in Shewanella algae ACDC is a recently acquired metabolism characterized by gene loss, suboptimal regulation and oxidative stress. Mol Microbiol. 2014 Oct; 94(1):107-25.
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      6. Ravcheev DA, Khoroshkin MS, Laikova ON, Tsoy OV, Sernova NV, Petrova SA, Rakhmaninova AB, Novichkov PS, Gelfand MS, Rodionov DA. Comparative genomics and evolution of regulons of the LacI-family transcription factors. Front Microbiol. 2014; 5:294.
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      7. Macguire AE, Ching MC, Diamond BH, Kazakov A, Novichkov P, Godoy VG. Activation of phenotypic subpopulations in response to ciprofloxacin treatment in Acinetobacter baumannii. Mol Microbiol. 2014 Apr; 92(1):138-52.
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      8. Turkarslan S, Wurtmann EJ, Wu WJ, Jiang N, Bare JC, Foley K, Reiss DJ, Novichkov P, Baliga NS. Network portal: a database for storage, analysis and visualization of biological networks. Nucleic Acids Res. 2014 Jan 1; 42(1):D184-90.
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      9. Novichkov PS, Kazakov AE, Ravcheev DA, Leyn SA, Kovaleva GY, Sutormin RA, Kazanov MD, Riehl W, Arkin AP, Dubchak I, Rodionov DA. RegPrecise 3.0 - A resource for genome-scale exploration of transcriptional regulation in bacteria. BMC Genomics. 2013; 14:745.
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      10. Novichkov PS, Li X, Kuehl JV, Deutschbauer AM, Arkin AP, Price MN, Rodionov DA. Control of methionine metabolism by the SahR transcriptional regulator in Proteobacteria. Environ Microbiol. 2014 Jan; 16(1):1-8.
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      11. Sun EI, Leyn SA, Kazanov MD, Saier MH, Novichkov PS, Rodionov DA. Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria. BMC Genomics. 2013; 14:597.
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      12. Kazakov AE, Rajeev L, Luning EG, Zane GM, Siddartha K, Rodionov DA, Dubchak I, Arkin AP, Wall JD, Mukhopadhyay A, Novichkov PS. New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria. J Bacteriol. 2013 Oct; 195(19):4466-75.
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      13. Leyn SA, Kazanov MD, Sernova NV, Ermakova EO, Novichkov PS, Rodionov DA. Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis. J Bacteriol. 2013 Jun; 195(11):2463-73.
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      14. Ravcheev DA, Best AA, Sernova NV, Kazanov MD, Novichkov PS, Rodionov DA. Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria. BMC Genomics. 2013; 14:94.
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      15. Kazakov AE, Rodionov DA, Price MN, Arkin AP, Dubchak I, Novichkov PS. Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes. J Bacteriol. 2013 Jan; 195(1):29-38.
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      16. Novichkov PS, Brettin TS, Novichkova ES, Dehal PS, Arkin AP, Dubchak I, Rodionov DA. RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics. Nucleic Acids Res. 2012 Jul; 40(Web Server issue):W604-8.
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      17. Ravcheev DA, Li X, Latif H, Zengler K, Leyn SA, Korostelev YD, Kazakov AE, Novichkov PS, Osterman AL, Rodionov DA. Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor Rex. J Bacteriol. 2012 Mar; 194(5):1145-57.
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      18. Leyn SA, Li X, Zheng Q, Novichkov PS, Reed S, Romine MF, Fredrickson JK, Yang C, Osterman AL, Rodionov DA. Control of proteobacterial central carbon metabolism by the HexR transcriptional regulator: a case study in Shewanella oneidensis. J Biol Chem. 2011 Oct 14; 286(41):35782-94.
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      19. Lukashin I, Novichkov P, Boffelli D, Paciorkowski AR, Minovitsky S, Yang S, Dubchak I. VISTA Region Viewer (RViewer)--a computational system for prioritizing genomic intervals for biomedical studies. Bioinformatics. 2011 Sep 15; 27(18):2595-7.
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      20. Rodionov DA, Novichkov PS, Stavrovskaya ED, Rodionova IA, Li X, Kazanov MD, Ravcheev DA, Gerasimova AV, Kazakov AE, Kovaleva GY, Permina EA, Laikova ON, Overbeek R, Romine MF, Fredrickson JK, Arkin AP, Dubchak I, Osterman AL, Gelfand MS. Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. BMC Genomics. 2011; 12 Suppl 1:S3.
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      21. Ravcheev DA, Best AA, Tintle N, Dejongh M, Osterman AL, Novichkov PS, Rodionov DA. Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidence. J Bacteriol. 2011 Jul; 193(13):3228-40.
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      22. Novichkov PS, Rodionov DA, Stavrovskaya ED, Novichkova ES, Kazakov AE, Gelfand MS, Arkin AP, Mironov AA, Dubchak I. RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Res. 2010 Jul; 38(Web Server issue):W299-307.
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      23. Shabalina SA, Ogurtsov AY, Spiridonov AN, Novichkov PS, Spiridonov NA, Koonin EV. Distinct patterns of expression and evolution of intronless and intron-containing mammalian genes. Mol Biol Evol. 2010 Aug; 27(8):1745-9.
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      24. Dehal PS, Joachimiak MP, Price MN, Bates JT, Baumohl JK, Chivian D, Friedland GD, Huang KH, Keller K, Novichkov PS, Dubchak IL, Alm EJ, Arkin AP. MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Res. 2010 Jan; 38(Database issue):D396-400.
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      25. Novichkov PS, Laikova ON, Novichkova ES, Gelfand MS, Arkin AP, Dubchak I, Rodionov DA. RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res. 2010 Jan; 38(Database issue):D111-8.
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      26. Wolf YI, Novichkov PS, Karev GP, Koonin EV, Lipman DJ. The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages. Proc Natl Acad Sci U S A. 2009 May 5; 106(18):7273-80.
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      27. Novichkov PS, Wolf YI, Dubchak I, Koonin EV. Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes. J Bacteriol. 2009 Jan; 191(1):65-73.
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      28. Novichkov PS, Ratnere I, Wolf YI, Koonin EV, Dubchak I. ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes. Nucleic Acids Res. 2009 Jan; 37(Database issue):D448-54.
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      29. Makarova KS, Sorokin AV, Novichkov PS, Wolf YI, Koonin EV. Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. Biol Direct. 2007; 2:33.
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      30. Kazakov AE, Cipriano MJ, Novichkov PS, Minovitsky S, Vinogradov DV, Arkin A, Mironov AA, Gelfand MS, Dubchak I. RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Nucleic Acids Res. 2007 Jan; 35(Database issue):D407-12.
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      31. Merkeev IV, Novichkov PS, Mironov AA. PHOG: a database of supergenomes built from proteome complements. BMC Evol Biol. 2006; 6:52.
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      32. Novichkov PS, Omelchenko MV, Gelfand MS, Mironov AA, Wolf YI, Koonin EV. Genome-wide molecular clock and horizontal gene transfer in bacterial evolution. J Bacteriol. 2004 Oct; 186(19):6575-85.
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      33. Kalinina OV, Novichkov PS, Mironov AA, Gelfand MS, Rakhmaninova AB. SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins. Nucleic Acids Res. 2004 Jul 1; 32(Web Server issue):W424-8.
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      34. Novichkov PS, Gelfand MS, Mironov AA. Gene recognition in eukaryotic DNA by comparison of genomic sequences. Bioinformatics. 2001 Nov; 17(11):1011-8.
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      35. Mironov AA, Novichkov PS, Gelfand MS. Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors. Bioinformatics. 2001 Jan; 17(1):13-5.
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      36. Gelfand MS, Novichkov PS, Novichkova ES, Mironov AA. Comparative analysis of regulatory patterns in bacterial genomes. Brief Bioinform. 2000 Nov; 1(4):357-71.
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      37. Novichkov PS, Gel'fand MS, Mironov AA. [Prediction of the exon-intron structure by comparing nucleotide sequences from various genomes]. Mol Biol (Mosk). 2000 Mar-Apr; 34(2):230-6.
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