Novichkov, Pavel

TitleCompl Biologist Res Sci/Engr
InstitutionLawrence Berkeley National Lab
DepartmentEnviron Genomics & Systems Bio
Address1 Cyclotron Road
Berkeley CA 94720
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Garber ME, Rajeev L, Kazakov AE, Trinh J, Masuno D, Thompson MG, Kaplan N, Luk J, Novichkov P, Mukhopadhyay A. Multiple signaling systems target a core set of transition metal homeostasis genes using similar binding motifs. Mol Microbiol. 2018 Jan 17. PMID: 29341298.
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    2. Wu X, Deutschbauer AM, Kazakov AE, Wetmore KM, Cwick BA, Walker RM, Novichkov P, Arkin AP, Chakraborty R. Draft Genome Sequences of Two Janthinobacteriumlividum Strains, Isolated from Pristine Groundwater Collected from the Oak Ridge Field Research Center. Genome Announc. 2017 Jun 29; 5(26). PMID: 28663297.
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    3. Chakraborty R, Woo H, Dehal P, Walker R, Zemla M, Auer M, Goodwin LA, Kazakov A, Novichkov P, Arkin AP, Hazen TC. Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site. Stand Genomic Sci. 2017; 12:23. PMID: 28194258.
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    4. Vaccaro BJ, Lancaster WA, Thorgersen MP, Zane GM, Younkin AD, Kazakov AE, Wetmore KM, Deutschbauer A, Arkin AP, Novichkov P, Wall JD, Adams MW. Novel Metal Cation Resistance Systems from Mutant Fitness Analysis of Denitrifying Pseudomonas stutzeri. Appl Environ Microbiol. 2016 10 01; 82(19):6046-56. PMID: 27474723.
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    5. Leyn SA, Suvorova IA, Kazakov AE, Ravcheev DA, Stepanova VV, Novichkov P, Rodionov DA. Comparative genomics and evolution of transcriptional regulons in Proteobacteria. Microb Genom. 2016 Jul; 2(7):e000061. PMID: 28348857.
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    6. Kazakov AE, Rajeev L, Chen A, Luning EG, Dubchak I, Mukhopadhyay A, Novichkov P. s54-dependent regulome in Desulfovibrio vulgaris Hildenborough. BMC Genomics. 2015 Nov 10; 16:919. PMID: 26555820; PMCID: PMC4641369.
    7. Rajeev L, Chen A, Kazakov AE, Luning EG, Zane GM, Novichkov P, Wall JD, Mukhopadhyay A. Regulation of Nitrite Stress Response in Desulfovibrio vulgaris Hildenborough, a Model Sulfate-Reducing Bacterium. J Bacteriol. 2015 Nov; 197(21):3400-8. PMID: 26283774; PMCID: PMC4621071.
    8. Leyn SA, Suvorova IA, Kholina TD, Sherstneva SS, Novichkov P, Gelfand MS, Rodionov DA. Comparative genomics of transcriptional regulation of methionine metabolism in Proteobacteria. PLoS One. 2014; 9(11):e113714. PMID: 25411846; PMCID: PMC4239095.
    9. Christensen GA, Zane GM, Kazakov AE, Li X, Rodionov DA, Novichkov P, 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 01; 197(1):29-39. PMID: 25313388; PMCID: PMC4288696.
    10. Clark IC, Melnyk RA, Iavarone AT, Novichkov P, 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. PMID: 25099177.
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    11. Ravcheev DA, Khoroshkin MS, Laikova ON, Tsoy OV, Sernova NV, Petrova SA, Rakhmaninova AB, Novichkov P, Gelfand MS, Rodionov DA. Comparative genomics and evolution of regulons of the LacI-family transcription factors. Front Microbiol. 2014; 5:294. PMID: 24966856; PMCID: PMC4052901.
    12. 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. PMID: 24612352; PMCID: PMC4005408.
    13. 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; 42(Database issue):D184-90. PMID: 24271392; PMCID: PMC3964938.
    14. Novichkov P, 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 Nov 01; 14:745. PMID: 24175918; PMCID: PMC3840689.
    15. Novichkov P, 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. PMID: 24118949.
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    16. Sun EI, Leyn SA, Kazanov MD, Saier MH, Novichkov P, Rodionov DA. Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria. BMC Genomics. 2013 Sep 02; 14:597. PMID: 24060102; PMCID: PMC3766115.
    17. Kazakov AE, Rajeev L, Luning EG, Zane GM, Siddartha K, Rodionov DA, Dubchak I, Arkin AP, Wall JD, Mukhopadhyay A, Novichkov P. New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria. J Bacteriol. 2013 Oct; 195(19):4466-75. PMID: 23913324; PMCID: PMC3807478.
    18. Leyn SA, Kazanov MD, Sernova NV, Ermakova EO, Novichkov P, Rodionov DA. Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis. J Bacteriol. 2013 Jun; 195(11):2463-73. PMID: 23504016; PMCID: PMC3676070.
    19. Ravcheev DA, Best AA, Sernova NV, Kazanov MD, Novichkov P, Rodionov DA. Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria. BMC Genomics. 2013 Feb 12; 14:94. PMID: 23398941; PMCID: PMC3616900.
    20. Kazakov AE, Rodionov DA, Price MN, Arkin AP, Dubchak I, Novichkov P. 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. PMID: 23086211; PMCID: PMC3536172.
    21. Novichkov P, 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. PMID: 22700702; PMCID: PMC3394319.
    22. Ravcheev DA, Li X, Latif H, Zengler K, Leyn SA, Korostelev YD, Kazakov AE, Novichkov P, 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. PMID: 22210771; PMCID: PMC3294762.
    23. Leyn SA, Li X, Zheng Q, Novichkov P, 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. PMID: 21849503; PMCID: PMC3195618.
    24. 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. PMID: 21791533; PMCID: PMC3167054.
    25. Rodionov DA, Novichkov P, 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 Jun 15; 12 Suppl 1:S3. PMID: 21810205; PMCID: PMC3223726.
    26. Ravcheev DA, Best AA, Tintle N, Dejongh M, Osterman AL, Novichkov P, 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. PMID: 21531804; PMCID: PMC3133287.
    27. Novichkov P, 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. PMID: 20542910; PMCID: PMC2896116.
    28. Shabalina SA, Ogurtsov AY, Spiridonov AN, Novichkov P, 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. PMID: 20360214; PMCID: PMC2908711.
    29. Dehal PS, Joachimiak MP, Price MN, Bates JT, Baumohl JK, Chivian D, Friedland GD, Huang KH, Keller K, Novichkov P, 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. PMID: 19906701; PMCID: PMC2808868.
    30. Novichkov P, 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. PMID: 19884135; PMCID: PMC2808921.
    31. Wolf YI, Novichkov P, 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 05; 106(18):7273-80. PMID: 19351897.
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    32. Novichkov P, 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. PMID: 18978059; PMCID: PMC2612427.
    33. Novichkov P, 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. PMID: 18845571; PMCID: PMC2686458.
    34. Makarova KS, Sorokin AV, Novichkov P, Wolf YI, Koonin EV. Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. Biol Direct. 2007 Nov 27; 2:33. PMID: 18042280; PMCID: PMC2222616.
    35. Kazakov AE, Cipriano MJ, Novichkov P, 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. PMID: 17142223; PMCID: PMC1669780.
    36. Merkeev IV, Novichkov P, Mironov AA. PHOG: a database of supergenomes built from proteome complements. BMC Evol Biol. 2006 Jun 22; 6:52. PMID: 16792803; PMCID: PMC1523204.
    37. Novichkov P, 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. PMID: 15375139; PMCID: PMC516599.
    38. Kalinina OV, Novichkov P, 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 01; 32(Web Server issue):W424-8. PMID: 15215423; PMCID: PMC441529.
    39. Novichkov P, Gelfand MS, Mironov AA. Gene recognition in eukaryotic DNA by comparison of genomic sequences. Bioinformatics. 2001 Nov; 17(11):1011-8. PMID: 11724729.
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    40. Mironov AA, Novichkov P, Gelfand MS. Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors. Bioinformatics. 2001 Jan; 17(1):13-5. PMID: 11222258.
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    41. Gelfand MS, Novichkov P, Novichkova ES, Mironov AA. Comparative analysis of regulatory patterns in bacterial genomes. Brief Bioinform. 2000 Nov; 1(4):357-71. PMID: 11465053.
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    42. Novichkov P, 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. PMID: 10779949.
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