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Items: 43

1.

Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome.

Rodionov DA, Arzamasov AA, Khoroshkin MS, Iablokov SN, Leyn SA, Peterson SN, Novichkov PS, Osterman AL.

Front Microbiol. 2019 Jun 12;10:1316. doi: 10.3389/fmicb.2019.01316. eCollection 2019.

2.

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

Rajeev L, Luning EG, Zane GM, Juba TR, Kazakov AE, Novichkov PS, Wall JD, Mukhopadhyay A.

PLoS One. 2019 Apr 9;14(4):e0214960. doi: 10.1371/journal.pone.0214960. eCollection 2019.

3.

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

Mutalik VK, Novichkov PS, Price MN, Owens TK, Callaghan M, Carim S, Deutschbauer AM, Arkin AP.

Nat Commun. 2019 Jan 18;10(1):308. doi: 10.1038/s41467-018-08177-8.

4.

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

Rajeev L, Garber ME, Zane GM, Price MN, Dubchak I, Wall JD, Novichkov PS, Mukhopadhyay A, Kazakov AE.

Environ Microbiol. 2019 Feb;21(2):784-799. doi: 10.1111/1462-2920.14500. Epub 2019 Jan 16.

PMID:
30536693
5.

KBase: The United States Department of Energy Systems Biology Knowledgebase.

Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, Kamimura RT, Kumari S, Drake MM, Brettin TS, Glass EM, Chivian D, Gunter D, Weston DJ, Allen BH, Baumohl J, Best AA, Bowen B, Brenner SE, Bun CC, Chandonia JM, Chia JM, Colasanti R, Conrad N, Davis JJ, Davison BH, DeJongh M, Devoid S, Dietrich E, Dubchak I, Edirisinghe JN, Fang G, Faria JP, Frybarger PM, Gerlach W, Gerstein M, Greiner A, Gurtowski J, Haun HL, He F, Jain R, Joachimiak MP, Keegan KP, Kondo S, Kumar V, Land ML, Meyer F, Mills M, Novichkov PS, Oh T, Olsen GJ, Olson R, Parrello B, Pasternak S, Pearson E, Poon SS, Price GA, Ramakrishnan S, Ranjan P, Ronald PC, Schatz MC, Seaver SMD, Shukla M, Sutormin RA, Syed MH, Thomason J, Tintle NL, Wang D, Xia F, Yoo H, Yoo S, Yu D.

Nat Biotechnol. 2018 Jul 6;36(7):566-569. doi: 10.1038/nbt.4163. No abstract available.

6.

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

Garber ME, Rajeev L, Kazakov AE, Trinh J, Masuno D, Thompson MG, Kaplan N, Luk J, Novichkov PS, Mukhopadhyay A.

Mol Microbiol. 2018 Mar;107(6):704-717. doi: 10.1111/mmi.13909. Epub 2018 Jan 23.

7.

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

Wu X, Deutschbauer AM, Kazakov AE, Wetmore KM, Cwick BA, Walker RM, Novichkov PS, Arkin AP, Chakraborty R.

Genome Announc. 2017 Jun 29;5(26). pii: e00582-17. doi: 10.1128/genomeA.00582-17.

8.

Comparative genomics and evolution of transcriptional regulons in Proteobacteria.

Leyn SA, Suvorova IA, Kazakov AE, Ravcheev DA, Stepanova VV, Novichkov PS, Rodionov DA.

Microb Genom. 2016 Jul 11;2(7):e000061. doi: 10.1099/mgen.0.000061. eCollection 2016 Jul.

9.

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

Vaccaro BJ, Lancaster WA, Thorgersen MP, Zane GM, Younkin AD, Kazakov AE, Wetmore KM, Deutschbauer A, Arkin AP, Novichkov PS, Wall JD, Adams MW.

Appl Environ Microbiol. 2016 Sep 16;82(19):6046-56. doi: 10.1128/AEM.01845-16. Print 2016 Oct 1.

10.

σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough.

Kazakov AE, Rajeev L, Chen A, Luning EG, Dubchak I, Mukhopadhyay A, Novichkov PS.

BMC Genomics. 2015 Nov 10;16:919. doi: 10.1186/s12864-015-2176-y.

11.

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

Rajeev L, Chen A, Kazakov AE, Luning EG, Zane GM, Novichkov PS, Wall JD, Mukhopadhyay A.

J Bacteriol. 2015 Nov;197(21):3400-8. doi: 10.1128/JB.00319-15. Epub 2015 Aug 17.

12.

Comparative genomics of transcriptional regulation of methionine metabolism in Proteobacteria.

Leyn SA, Suvorova IA, Kholina TD, Sherstneva SS, Novichkov PS, Gelfand MS, Rodionov DA.

PLoS One. 2014 Nov 20;9(11):e113714. doi: 10.1371/journal.pone.0113714. eCollection 2014.

13.

Rex (encoded by DVU_0916) in Desulfovibrio vulgaris Hildenborough is a repressor of sulfate adenylyl transferase and is regulated by NADH.

Christensen GA, Zane GM, Kazakov AE, Li X, Rodionov DA, Novichkov PS, Dubchak I, Arkin AP, Wall JD.

J Bacteriol. 2015 Jan 1;197(1):29-39. doi: 10.1128/JB.02083-14. Epub 2014 Oct 13.

14.

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

Clark IC, Melnyk RA, Iavarone AT, Novichkov PS, Coates JD.

Mol Microbiol. 2014 Oct;94(1):107-25. doi: 10.1111/mmi.12746. Epub 2014 Sep 5.

15.

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

Ravcheev DA, Khoroshkin MS, Laikova ON, Tsoy OV, Sernova NV, Petrova SA, Rakhmaninova AB, Novichkov PS, Gelfand MS, Rodionov DA.

Front Microbiol. 2014 Jun 11;5:294. doi: 10.3389/fmicb.2014.00294. eCollection 2014.

16.

RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria.

Novichkov PS, Kazakov AE, Ravcheev DA, Leyn SA, Kovaleva GY, Sutormin RA, Kazanov MD, Riehl W, Arkin AP, Dubchak I, Rodionov DA.

BMC Genomics. 2013 Nov 1;14:745. doi: 10.1186/1471-2164-14-745.

17.

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

Novichkov PS, Li X, Kuehl JV, Deutschbauer AM, Arkin AP, Price MN, Rodionov DA.

Environ Microbiol. 2014 Jan;16(1):1-8. doi: 10.1111/1462-2920.12273. Epub 2013 Oct 9.

PMID:
24118949
18.

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

Sun EI, Leyn SA, Kazanov MD, Saier MH Jr, Novichkov PS, Rodionov DA.

BMC Genomics. 2013 Sep 2;14:597. doi: 10.1186/1471-2164-14-597.

19.

New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria.

Kazakov AE, Rajeev L, Luning EG, Zane GM, Siddartha K, Rodionov DA, Dubchak I, Arkin AP, Wall JD, Mukhopadhyay A, Novichkov PS.

J Bacteriol. 2013 Oct;195(19):4466-75. doi: 10.1128/JB.00679-13. Epub 2013 Aug 2.

20.

Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis.

Leyn SA, Kazanov MD, Sernova NV, Ermakova EO, Novichkov PS, Rodionov DA.

J Bacteriol. 2013 Jun;195(11):2463-73. doi: 10.1128/JB.00140-13. Epub 2013 Mar 15.

21.

Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria.

Ravcheev DA, Best AA, Sernova NV, Kazanov MD, Novichkov PS, Rodionov DA.

BMC Genomics. 2013 Feb 12;14:94. doi: 10.1186/1471-2164-14-94.

22.

Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes.

Kazakov AE, Rodionov DA, Price MN, Arkin AP, Dubchak I, Novichkov PS.

J Bacteriol. 2013 Jan;195(1):29-38. doi: 10.1128/JB.01977-12. Epub 2012 Oct 19.

23.

RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics.

Novichkov PS, Brettin TS, Novichkova ES, Dehal PS, Arkin AP, Dubchak I, Rodionov DA.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W604-8. doi: 10.1093/nar/gks562. Epub 2012 Jun 14.

24.

Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor Rex.

Ravcheev DA, Li X, Latif H, Zengler K, Leyn SA, Korostelev YD, Kazakov AE, Novichkov PS, Osterman AL, Rodionov DA.

J Bacteriol. 2012 Mar;194(5):1145-57. doi: 10.1128/JB.06412-11. Epub 2011 Dec 30.

25.

Control of proteobacterial central carbon metabolism by the HexR transcriptional regulator: a case study in Shewanella oneidensis.

Leyn SA, Li X, Zheng Q, Novichkov PS, Reed S, Romine MF, Fredrickson JK, Yang C, Osterman AL, Rodionov DA.

J Biol Chem. 2011 Oct 14;286(41):35782-94. doi: 10.1074/jbc.M111.267963. Epub 2011 Aug 17.

26.

Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus.

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.

BMC Genomics. 2011 Jun 15;12 Suppl 1:S3. doi: 10.1186/1471-2164-12-S1-S3.

27.

Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidence.

Ravcheev DA, Best AA, Tintle N, Dejongh M, Osterman AL, Novichkov PS, Rodionov DA.

J Bacteriol. 2011 Jul;193(13):3228-40. doi: 10.1128/JB.00350-11. Epub 2011 Apr 29.

28.

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach.

Novichkov PS, Rodionov DA, Stavrovskaya ED, Novichkova ES, Kazakov AE, Gelfand MS, Arkin AP, Mironov AA, Dubchak I.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W299-307. doi: 10.1093/nar/gkq531. Epub 2010 Jun 11.

29.

Distinct patterns of expression and evolution of intronless and intron-containing mammalian genes.

Shabalina SA, Ogurtsov AY, Spiridonov AN, Novichkov PS, Spiridonov NA, Koonin EV.

Mol Biol Evol. 2010 Aug;27(8):1745-9. doi: 10.1093/molbev/msq086. Epub 2010 Apr 1.

30.

MicrobesOnline: an integrated portal for comparative and functional genomics.

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.

Nucleic Acids Res. 2010 Jan;38(Database issue):D396-400. doi: 10.1093/nar/gkp919. Epub 2009 Nov 11.

31.

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes.

Novichkov PS, Laikova ON, Novichkova ES, Gelfand MS, Arkin AP, Dubchak I, Rodionov DA.

Nucleic Acids Res. 2010 Jan;38(Database issue):D111-8. doi: 10.1093/nar/gkp894. Epub 2009 Nov 1.

32.

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

Wolf YI, Novichkov PS, Karev GP, Koonin EV, Lipman DJ.

Proc Natl Acad Sci U S A. 2009 May 5;106(18):7273-80. doi: 10.1073/pnas.0901808106. Epub 2009 Apr 7.

33.

Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes.

Novichkov PS, Wolf YI, Dubchak I, Koonin EV.

J Bacteriol. 2009 Jan;191(1):65-73. doi: 10.1128/JB.01237-08. Epub 2008 Oct 31.

34.

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

Novichkov PS, Ratnere I, Wolf YI, Koonin EV, Dubchak I.

Nucleic Acids Res. 2009 Jan;37(Database issue):D448-54. doi: 10.1093/nar/gkn684. Epub 2008 Oct 9.

35.

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

Makarova KS, Sorokin AV, Novichkov PS, Wolf YI, Koonin EV.

Biol Direct. 2007 Nov 27;2:33.

36.

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

Kazakov AE, Cipriano MJ, Novichkov PS, Minovitsky S, Vinogradov DV, Arkin A, Mironov AA, Gelfand MS, Dubchak I.

Nucleic Acids Res. 2007 Jan;35(Database issue):D407-12. Epub 2006 Nov 16.

37.

PHOG: a database of supergenomes built from proteome complements.

Merkeev IV, Novichkov PS, Mironov AA.

BMC Evol Biol. 2006 Jun 22;6:52.

38.

Genome-wide molecular clock and horizontal gene transfer in bacterial evolution.

Novichkov PS, Omelchenko MV, Gelfand MS, Mironov AA, Wolf YI, Koonin EV.

J Bacteriol. 2004 Oct;186(19):6575-85.

39.

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

Kalinina OV, Novichkov PS, Mironov AA, Gelfand MS, Rakhmaninova AB.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W424-8.

40.

Gene recognition in eukaryotic DNA by comparison of genomic sequences.

Novichkov PS, Gelfand MS, Mironov AA.

Bioinformatics. 2001 Nov;17(11):1011-8.

PMID:
11724729
41.

Comparative analysis of regulatory patterns in bacterial genomes.

Gelfand MS, Novichkov PS, Novichkova ES, Mironov AA.

Brief Bioinform. 2000 Nov;1(4):357-71. Review.

PMID:
11465053
42.

Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors.

Mironov AA, Novichkov PS, Gelfand MS.

Bioinformatics. 2001 Jan;17(1):13-5.

PMID:
11222258
43.

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

Novichkov PS, Gel'fand MS, Mironov AA.

Mol Biol (Mosk). 2000 Mar-Apr;34(2):230-6. Russian. No abstract available.

PMID:
10779949

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