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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.


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;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.

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