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Two forms of phosphomannomutase in gammaproteobacteria: The overlooked membrane-bound form of AlgC is required for twitching motility of Lysobacter enzymogenes.

Qian G, Fei S, Galperin MY.

Environ Microbiol. 2019 Apr 1. doi: 10.1111/1462-2920.14615. [Epub ahead of print]


Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases in relation to the basic catalytic mechanism.

Shalaeva DN, Cherepanov DA, Galperin MY, Golovin AV, Mulkidjanian AY.

Elife. 2018 Dec 11;7. pii: e37373. doi: 10.7554/eLife.37373.


What bacteria want.

Galperin MY.

Environ Microbiol. 2018 Dec;20(12):4221-4229. doi: 10.1111/1462-2920.14398. Epub 2018 Oct 25. Review.


Structural and Functional Characterization of the BcsG Subunit of the Cellulose Synthase in Salmonella typhimurium.

Sun L, Vella P, Schnell R, Polyakova A, Bourenkov G, Li F, Cimdins A, Schneider TR, Lindqvist Y, Galperin MY, Schneider G, Römling U.

J Mol Biol. 2018 Sep 14;430(18 Pt B):3170-3189. doi: 10.1016/j.jmb.2018.07.008. Epub 2018 Jul 12.


A bacterial coat that is not pure cotton.

Galperin MY, Shalaeva DN.

Science. 2018 Jan 19;359(6373):276-277. doi: 10.1126/science.aar5253. No abstract available.


Phyletic Distribution and Lineage-Specific Domain Architectures of Archaeal Two-Component Signal Transduction Systems.

Galperin MY, Makarova KS, Wolf YI, Koonin EV.

J Bacteriol. 2018 Mar 12;200(7). pii: e00681-17. doi: 10.1128/JB.00681-17. Print 2018 Apr 1.


Proposed Role for KaiC-Like ATPases as Major Signal Transduction Hubs in Archaea.

Makarova KS, Galperin MY, Koonin EV.

MBio. 2017 Dec 5;8(6). pii: e01959-17. doi: 10.1128/mBio.01959-17.


Microbial genome analysis: the COG approach.

Galperin MY, Kristensen DM, Makarova KS, Wolf YI, Koonin EV.

Brief Bioinform. 2017 Sep 14. doi: 10.1093/bib/bbx117. [Epub ahead of print]


Discovery of the Second Messenger Cyclic di-GMP.

Römling U, Galperin MY.

Methods Mol Biol. 2017;1657:1-8. doi: 10.1007/978-1-4939-7240-1_1. Review.


Stand-Alone EAL Domain Proteins Form a Distinct Subclass of EAL Proteins Involved in Regulation of Cell Motility and Biofilm Formation in Enterobacteria.

El Mouali Y, Kim H, Ahmad I, Brauner A, Liu Y, Skurnik M, Galperin MY, Römling U.

J Bacteriol. 2017 Aug 22;199(18). pii: e00179-17. doi: 10.1128/JB.00179-17. Print 2017 Sep 15.


Emergence of cytochrome bc complexes in the context of photosynthesis.

Dibrova DV, Shalaeva DN, Galperin MY, Mulkidjanian AY.

Physiol Plant. 2017 Sep;161(1):150-170. doi: 10.1111/ppl.12586. Epub 2017 Jul 4.


The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes.

Galperin MY, Fernández-Suárez XM, Rigden DJ.

Nucleic Acids Res. 2017 May 19;45(9):5627. doi: 10.1093/nar/gkx021. No abstract available.


Genome Sequence of Uric Acid-Fermenting Eubacterium angustum DSM 1989T (MK-1).

Poehlein A, Galperin MY, Andreesen JR, Daniel R.

Genome Announc. 2017 Jan 12;5(2). pii: e01439-16. doi: 10.1128/genomeA.01439-16.


The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes.

Galperin MY, Fernández-Suárez XM, Rigden DJ.

Nucleic Acids Res. 2017 Jan 4;45(D1):D1-D11. doi: 10.1093/nar/gkw1188. Erratum in: Nucleic Acids Res. 2017 May 19;45(9):5627.


Sustained sensing as an emerging principle in second messenger signaling systems.

Orr MW, Galperin MY, Lee VT.

Curr Opin Microbiol. 2016 Dec;34:119-126. doi: 10.1016/j.mib.2016.08.010. Epub 2016 Oct 1. Review.


Nucleotide binding by the widespread high-affinity cyclic di-GMP receptor MshEN domain.

Wang YC, Chin KH, Tu ZL, He J, Jones CJ, Sanchez DZ, Yildiz FH, Galperin MY, Chou SH.

Nat Commun. 2016 Aug 31;7:12481. doi: 10.1038/ncomms12481.


The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection.

Rigden DJ, Fernández-Suárez XM, Galperin MY.

Nucleic Acids Res. 2016 Jan 4;44(D1):D1-6. doi: 10.1093/nar/gkv1356.


Systematic Identification of Cyclic-di-GMP Binding Proteins in Vibrio cholerae Reveals a Novel Class of Cyclic-di-GMP-Binding ATPases Associated with Type II Secretion Systems.

Roelofs KG, Jones CJ, Helman SR, Shang X, Orr MW, Goodson JR, Galperin MY, Yildiz FH, Lee VT.

PLoS Pathog. 2015 Oct 27;11(10):e1005232. doi: 10.1371/journal.ppat.1005232. eCollection 2015 Oct.


Eukaryotic G protein-coupled receptors as descendants of prokaryotic sodium-translocating rhodopsins.

Shalaeva DN, Galperin MY, Mulkidjanian AY.

Biol Direct. 2015 Oct 15;10:63. doi: 10.1186/s13062-015-0091-4.


Systematic Nomenclature for GGDEF and EAL Domain-Containing Cyclic Di-GMP Turnover Proteins of Escherichia coli.

Hengge R, Galperin MY, Ghigo JM, Gomelsky M, Green J, Hughes KT, Jenal U, Landini P.

J Bacteriol. 2015 Jul 6;198(1):7-11. doi: 10.1128/JB.00424-15. Print 2016 Jan 1.


Bacterial cellulose biosynthesis: diversity of operons, subunits, products, and functions.

Römling U, Galperin MY.

Trends Microbiol. 2015 Sep;23(9):545-57. doi: 10.1016/j.tim.2015.05.005. Epub 2015 Jun 12. Review.


Ancient Systems of Sodium/Potassium Homeostasis as Predecessors of Membrane Bioenergetics.

Dibrova DV, Galperin MY, Koonin EV, Mulkidjanian AY.

Biochemistry (Mosc). 2015 May;80(5):495-516. doi: 10.1134/S0006297915050016.


Diversity of Cyclic Di-GMP-Binding Proteins and Mechanisms.

Chou SH, Galperin MY.

J Bacteriol. 2016 Jan 1;198(1):32-46. Review.


Modeling of interaction between cytochrome c and the WD domains of Apaf-1: bifurcated salt bridges underlying apoptosome assembly.

Shalaeva DN, Dibrova DV, Galperin MY, Mulkidjanian AY.

Biol Direct. 2015 May 27;10:29. doi: 10.1186/s13062-015-0059-4.


The 2015 Nucleic Acids Research Database Issue and molecular biology database collection.

Galperin MY, Rigden DJ, Fernández-Suárez XM.

Nucleic Acids Res. 2015 Jan;43(Database issue):D1-5. doi: 10.1093/nar/gku1241.


Expanded microbial genome coverage and improved protein family annotation in the COG database.

Galperin MY, Makarova KS, Wolf YI, Koonin EV.

Nucleic Acids Res. 2015 Jan;43(Database issue):D261-9. doi: 10.1093/nar/gku1223. Epub 2014 Nov 26.


GIL, a new c-di-GMP-binding protein domain involved in regulation of cellulose synthesis in enterobacteria.

Fang X, Ahmad I, Blanka A, Schottkowski M, Cimdins A, Galperin MY, Römling U, Gomelsky M.

Mol Microbiol. 2014 Aug;93(3):439-52. doi: 10.1111/mmi.12672. Epub 2014 Jul 1.


Phylogenomic reconstruction of archaeal fatty acid metabolism.

Dibrova DV, Galperin MY, Mulkidjanian AY.

Environ Microbiol. 2014 Apr;16(4):907-18. doi: 10.1111/1462-2920.12359.


The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection.

Fernández-Suárez XM, Rigden DJ, Galperin MY.

Nucleic Acids Res. 2014 Jan;42(Database issue):D1-6. doi: 10.1093/nar/gkt1282. Epub 2013 Dec 6.


Genome Diversity of Spore-Forming Firmicutes.

Galperin MY.

Microbiol Spectr. 2013 Dec;1(2). doi: 10.1128/microbiolspectrum.TBS-0015-2012.


The COMBREX project: design, methodology, and initial results.

Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S.

PLoS Biol. 2013;11(8):e1001638. doi: 10.1371/journal.pbio.1001638. Epub 2013 Aug 27. No abstract available.


Bacterial second messengers, cGMP and c-di-GMP, in a quest for regulatory dominance.

Gomelsky M, Galperin MY.

EMBO J. 2013 Sep 11;32(18):2421-3. doi: 10.1038/emboj.2013.193. Epub 2013 Aug 20. No abstract available.


Evolution of cytochrome bc complexes: from membrane-anchored dehydrogenases of ancient bacteria to triggers of apoptosis in vertebrates.

Dibrova DV, Cherepanov DA, Galperin MY, Skulachev VP, Mulkidjanian AY.

Biochim Biophys Acta. 2013 Nov-Dec;1827(11-12):1407-27. doi: 10.1016/j.bbabio.2013.07.006. Epub 2013 Jul 19. Review.


A genomic update on clostridial phylogeny: Gram-negative spore formers and other misplaced clostridia.

Yutin N, Galperin MY.

Environ Microbiol. 2013 Oct;15(10):2631-41. doi: 10.1111/1462-2920.12173. Epub 2013 Jul 9.


How many signal peptides are there in bacteria?

Ivankov DN, Payne SH, Galperin MY, Bonissone S, Pevzner PA, Frishman D.

Environ Microbiol. 2013 Apr;15(4):983-90. doi: 10.1111/1462-2920.12105.


Cyclic di-GMP: the first 25 years of a universal bacterial second messenger.

Römling U, Galperin MY, Gomelsky M.

Microbiol Mol Biol Rev. 2013 Mar;77(1):1-52. doi: 10.1128/MMBR.00043-12. Review.


The 2013 Nucleic Acids Research Database Issue and the online molecular biology database collection.

Fernández-Suárez XM, Galperin MY.

Nucleic Acids Res. 2013 Jan;41(Database issue):D1-7. doi: 10.1093/nar/gks1297. Epub 2012 Nov 30.


Open questions on the origin of life at anoxic geothermal fields.

Mulkidjanian AY, Bychkov AY, Dibrova DV, Galperin MY, Koonin EV.

Orig Life Evol Biosph. 2012 Oct;42(5):507-16. doi: 10.1007/s11084-012-9315-0. Epub 2012 Nov 7.


The role of energy in the emergence of biology from chemistry.

Dibrova DV, Chudetsky MY, Galperin MY, Koonin EV, Mulkidjanian AY.

Orig Life Evol Biosph. 2012 Oct;42(5):459-68. doi: 10.1007/s11084-012-9308-z.


Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes.

Galperin MY, Mekhedov SL, Puigbo P, Smirnov S, Wolf YI, Rigden DJ.

Environ Microbiol. 2012 Nov;14(11):2870-90. doi: 10.1111/j.1462-2920.2012.02841.x. Epub 2012 Aug 13.


Origin of first cells at terrestrial, anoxic geothermal fields.

Mulkidjanian AY, Bychkov AY, Dibrova DV, Galperin MY, Koonin EV.

Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):E821-30. doi: 10.1073/pnas.1117774109. Epub 2012 Feb 13.


The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection.

Galperin MY, Fernández-Suárez XM.

Nucleic Acids Res. 2012 Jan;40(Database issue):D1-8. doi: 10.1093/nar/gkr1196. Epub 2011 Dec 5.


Divergence and convergence in enzyme evolution.

Galperin MY, Koonin EV.

J Biol Chem. 2012 Jan 2;287(1):21-8. doi: 10.1074/jbc.R111.241976. Epub 2011 Nov 8. Review.


Planctomycetes and eukaryotes: a case of analogy not homology.

McInerney JO, Martin WF, Koonin EV, Allen JF, Galperin MY, Lane N, Archibald JM, Embley TM.

Bioessays. 2011 Nov;33(11):810-7. doi: 10.1002/bies.201100045. Epub 2011 Aug 22.


New structural and functional contexts of the Dx[DN]xDG linear motif: insights into evolution of calcium-binding proteins.

Rigden DJ, Woodhead DD, Wong PW, Galperin MY.

PLoS One. 2011;6(6):e21507. doi: 10.1371/journal.pone.0021507. Epub 2011 Jun 24.


Towards BioDBcore: a community-defined information specification for biological databases.

Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Karsch Mizrachi I, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C; BioDBCore Working Group.

Database (Oxford). 2011 Jan 4;2011:baq027. doi: 10.1093/database/baq027. Print 2011.

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