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Michael Galperin

TitleAssociate Researcher
InstitutionUniversity of California San Diego
DepartmentChemistry and Biochemistry
Address9500 Gilman Drive #0340
La Jolla CA 92093
Phone858-246-0511
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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. Sun L, Vella P, Schnell R, Polyakova A, Bourenkov G, Li F, Cimdins A, Schneider TR, Lindqvist Y, Galperin M, Schneider G, Römling U. Structural and Functional Characterization of the BcsG Subunit of the Cellulose Synthase in Salmonella typhimurium. J Mol Biol. 2018 Jul 12. PMID: 30017920.
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    2. Cabra G, Jensen A, Galperin M. On simulation of local fluxes in molecular junctions. J Chem Phys. 2018 May 28; 148(20):204103. PMID: 29865820.
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    3. Galperin M, Makarova KS, Wolf YI, Koonin EV. Phyletic Distribution and Lineage-Specific Domain Architectures of Archaeal Two-Component Signal Transduction Systems. J Bacteriol. 2018 Apr 01; 200(7). PMID: 29263101.
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    4. Galperin M, Shalaeva DN. A bacterial coat that is not pure cotton. Science. 2018 01 19; 359(6373):276-277. PMID: 29348224.
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    5. Makarova KS, Galperin M, Koonin EV. Proposed Role for KaiC-Like ATPases as Major Signal Transduction Hubs in Archaea. MBio. 2017 Dec 05; 8(6). PMID: 29208747.
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    6. Poehlein A, Yutin N, Daniel R, Galperin M. Erratum: Proposal for the reclassification of obligately purine-fermenting bacteria Clostridium acidurici (Barker 1938) and Clostridium purinilyticum (Dürre et al. 1981) as Gottschalkia acidurici gen. nov. comb. nov. and Gottschalkia purinilytica comb. nov. and of Eubacterium angustum (Beuscher and Andreesen 1985) as Andreesenia angusta gen. nov. comb. nov. in the family Gottschalkiaceae fam. nov. Int J Syst Evol Microbiol. 2017 10; 67(10):4287-4288. PMID: 29022546.
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    7. Galperin M, Kristensen DM, Makarova KS, Wolf YI, Koonin EV. Microbial genome analysis: the COG approach. Brief Bioinform. 2017 Sep 14. PMID: 28968633.
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    8. Miwa K, Chen F, Galperin M. Towards Noise Simulation in Interacting Nonequilibrium Systems Strongly Coupled to Baths. Sci Rep. 2017 Aug 29; 7(1):9735. PMID: 28851909.
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    9. El Mouali Y, Kim H, Ahmad I, Brauner A, Liu Y, Skurnik M, Galperin M, Römling U. Stand-Alone EAL Domain Proteins Form a Distinct Subclass of EAL Proteins Involved in Regulation of Cell Motility and Biofilm Formation in Enterobacteria. J Bacteriol. 2017 09 15; 199(18). PMID: 28652301.
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    10. Poehlein A, Yutin N, Daniel R, Galperin M. Proposal for the reclassification of obligately purine-fermenting bacteria Clostridium acidurici (Barker 1938) and Clostridium purinilyticum (Dürre et al. 1981) as Gottschalkia acidurici gen. nov. comb. nov. and Gottschalkiapurinilytica comb. nov. and of Eubacterium angustum (Beuscher and Andreesen 1985) as Andreesenia angusta gen. nov. comb. nov. in the family Gottschalkiaceae fam. nov. Int J Syst Evol Microbiol. 2017 Aug; 67(8):2711-2719. PMID: 28853681.
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    11. Dibrova DV, Shalaeva DN, Galperin M, Mulkidjanian AY. Emergence of cytochrome bc complexes in the context of photosynthesis. Physiol Plant. 2017 Sep; 161(1):150-170. PMID: 28493482.
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    12. Galperin M. Photonics and spectroscopy in nanojunctions: a theoretical insight. Chem Soc Rev. 2017 Jul 03; 46(13):4000-4019. PMID: 28398449.
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    13. Galperin M, Fernández-Suárez XM, Rigden DJ. The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. Nucleic Acids Res. 2017 05 19; 45(9):5627. PMID: 28100696.
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    14. Poehlein A, Galperin M, Andreesen JR, Daniel R. Genome Sequence of Uric Acid-Fermenting Eubacterium angustum DSM 1989T (MK-1). Genome Announc. 2017 Jan 12; 5(2). PMID: 28082491.
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    15. Galperin M, Fernández-Suárez XM, Rigden DJ. The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. Nucleic Acids Res. 2017 Jan 04; 45(D1):D1-D11. PMID: 28053160.
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    16. Römling U, Galperin M. Discovery of the Second Messenger Cyclic di-GMP. Methods Mol Biol. 2017; 1657:1-8. PMID: 28889281.
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    17. Galperin M, Brover V, Tolstoy I, Yutin N. Phylogenomic analysis of the family Peptostreptococcaceae (Clostridium cluster XI) and proposal for reclassification of Clostridium litorale (Fendrich et al. 1991) and Eubacterium acidaminophilum (Zindel et al. 1989) as Peptoclostridium litorale gen. nov. comb. nov. and Peptoclostridium acidaminophilum comb. nov. Int J Syst Evol Microbiol. 2016 Dec; 66(12):5506-5513. PMID: 27902180.
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    18. Orr MW, Galperin M, Lee VT. Sustained sensing as an emerging principle in second messenger signaling systems. Curr Opin Microbiol. 2016 Dec; 34:119-126. PMID: 27700990.
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    19. Wang YC, Chin KH, Tu ZL, He J, Jones CJ, Sanchez DZ, Yildiz FH, Galperin M, Chou SH. Nucleotide binding by the widespread high-affinity cyclic di-GMP receptor MshEN domain. Nat Commun. 2016 Aug 31; 7:12481. PMID: 27578558.
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    20. Gao Y, Galperin M. Simulation of optical response functions in molecular junctions. J Chem Phys. 2016 Jun 28; 144(24):244106. PMID: 27369496.
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    21. Gao Y, Galperin M, Nitzan A. On the widths of Stokes lines in Raman scattering from molecules adsorbed at metal surfaces and in molecular conduction junctions. J Chem Phys. 2016 Jun 28; 144(24):244114. PMID: 27369504.
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    22. Gao Y, Galperin M. Optical spectroscopy of molecular junctions: Nonequilibrium Green's functions perspective. J Chem Phys. 2016 May 07; 144(17):174113. PMID: 27155631.
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    23. Rigden DJ, Fernández-Suárez XM, Galperin M. The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection. Nucleic Acids Res. 2016 Jan 04; 44(D1):D1-6. PMID: 26740669; PMCID: PMC4702933.
    24. Chou SH, Galperin M. Diversity of Cyclic Di-GMP-Binding Proteins and Mechanisms. J Bacteriol. 2016 01 01; 198(1):32-46. PMID: 26055114.
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    25. Galperin M, Nitzan A. Nuclear Dynamics at Molecule-Metal Interfaces: A Pseudoparticle Perspective. J Phys Chem Lett. 2015 Dec 17; 6(24):4898-903. PMID: 26589690.
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    26. Roelofs KG, Jones CJ, Helman SR, Shang X, Orr MW, Goodson JR, Galperin M, Yildiz FH, Lee VT. 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. PLoS Pathog. 2015 Oct; 11(10):e1005232. PMID: 26506097; PMCID: PMC4624772.
    27. Shalaeva DN, Galperin M, Mulkidjanian AY. Eukaryotic G protein-coupled receptors as descendants of prokaryotic sodium-translocating rhodopsins. Biol Direct. 2015 Oct 15; 10:63. PMID: 26472483; PMCID: PMC4608122.
    28. Hengge R, Galperin M, Ghigo JM, Gomelsky M, Green J, Hughes KT, Jenal U, Landini P. Systematic Nomenclature for GGDEF and EAL Domain-Containing Cyclic Di-GMP Turnover Proteins of Escherichia coli. J Bacteriol. 2016 01 01; 198(1):7-11. PMID: 26148715.
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    29. Römling U, Galperin M. Bacterial cellulose biosynthesis: diversity of operons, subunits, products, and functions. Trends Microbiol. 2015 Sep; 23(9):545-57. PMID: 26077867.
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    30. Shalaeva DN, Dibrova DV, Galperin M, Mulkidjanian AY. Modeling of interaction between cytochrome c and the WD domains of Apaf-1: bifurcated salt bridges underlying apoptosome assembly. Biol Direct. 2015 May 27; 10:29. PMID: 26014357; PMCID: PMC4445527.
    31. Galperin M, Ratner MA, Nitzan A. Comment on "Frequency-domain stimulated and spontaneous light emission signals at molecular junctions" [J. Chem. Phys. 141, 074107 (2014)]. J Chem Phys. 2015 Apr 07; 142(13):137101. PMID: 25854261.
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    32. Esposito M, Ochoa MA, Galperin M. Quantum thermodynamics: a nonequilibrium Green's function approach. Phys Rev Lett. 2015 Feb 27; 114(8):080602. PMID: 25768745.
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    33. Ochoa MA, Selzer Y, Peskin U, Galperin M. Pump-Probe Noise Spectroscopy of Molecular Junctions. J Phys Chem Lett. 2015 Feb 05; 6(3):470-6. PMID: 26261965.
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    34. Makarova KS, Galperin M, Koonin EV. Comparative genomic analysis of evolutionarily conserved but functionally uncharacterized membrane proteins in archaea: Prediction of novel components of secretion, membrane remodeling and glycosylation systems. Biochimie. 2015 Nov; 118:302-12. PMID: 25583072.
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    35. Galperin M, Rigden DJ, Fernández-Suárez XM. The 2015 Nucleic Acids Research Database Issue and molecular biology database collection. Nucleic Acids Res. 2015 Jan; 43(Database issue):D1-5. PMID: 25593347; PMCID: PMC4383995.
    36. Galperin M, Makarova KS, Wolf YI, Koonin EV. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 2015 Jan; 43(Database issue):D261-9. PMID: 25428365; PMCID: PMC4383993.
    37. Ochoa MA, Galperin M, Ratner MA. A non-equilibrium equation-of-motion approach to quantum transport utilizing projection operators. J Phys Condens Matter. 2014 Nov 12; 26(45):455301. PMID: 25318540.
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    38. Baratz A, White AJ, Galperin M, Baer R. Effects of Electromagnetic Coupling on Conductance Switching of a Gated Tunnel Junction. J Phys Chem Lett. 2014 Oct 16; 5(20):3545-50. PMID: 26278607.
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    39. Fang X, Ahmad I, Blanka A, Schottkowski M, Cimdins A, Galperin M, Römling U, Gomelsky M. GIL, a new c-di-GMP-binding protein domain involved in regulation of cellulose synthesis in enterobacteria. Mol Microbiol. 2014 Aug; 93(3):439-52. PMID: 24942809.
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    40. Dibrova DV, Galperin M, Mulkidjanian AY. Phylogenomic reconstruction of archaeal fatty acid metabolism. Environ Microbiol. 2014 Apr; 16(4):907-18. PMID: 24818264.
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    41. White AJ, Tretiak S, Galperin M. Raman scattering in molecular junctions: a pseudoparticle formulation. Nano Lett. 2014 Feb 12; 14(2):699-703. PMID: 24447295.
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    42. Fernández-Suárez XM, Rigden DJ, Galperin M. The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection. Nucleic Acids Res. 2014 Jan; 42(Database issue):D1-6. PMID: 24316579; PMCID: PMC3965027.
    43. Galperin M. Genome Diversity of Spore-Forming Firmicutes. Microbiol Spectr. 2013 Dec; 1(2). PMID: 26184964.
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    44. 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 M, 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. The COMBREX project: design, methodology, and initial results. PLoS Biol. 2013; 11(8):e1001638. PMID: 24013487; PMCID: PMC3754883.
    45. Gomelsky M, Galperin M. Bacterial second messengers, cGMP and c-di-GMP, in a quest for regulatory dominance. EMBO J. 2013 Sep 11; 32(18):2421-3. PMID: 23963313; PMCID: PMC3770956.
    46. Dibrova DV, Cherepanov DA, Galperin M, Skulachev VP, Mulkidjanian AY. Evolution of cytochrome bc complexes: from membrane-anchored dehydrogenases of ancient bacteria to triggers of apoptosis in vertebrates. Biochim Biophys Acta. 2013 Nov-Dec; 1827(11-12):1407-27. PMID: 23871937.
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    47. Yutin N, Galperin M. A genomic update on clostridial phylogeny: Gram-negative spore formers and other misplaced clostridia. Environ Microbiol. 2013 Oct; 15(10):2631-41. PMID: 23834245.
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    48. White AJ, Migliore A, Galperin M, Nitzan A. Quantum transport with two interacting conduction channels. J Chem Phys. 2013 May 07; 138(17):174111. PMID: 23656118.
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    49. Ivankov DN, Payne SH, Galperin M, Bonissone S, Pevzner PA, Frishman D. How many signal peptides are there in bacteria? Environ Microbiol. 2013 Apr; 15(4):983-90. PMID: 23556536.
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    50. Römling U, Galperin M, Gomelsky M. Cyclic di-GMP: the first 25 years of a universal bacterial second messenger. Microbiol Mol Biol Rev. 2013 Mar; 77(1):1-52. PMID: 23471616; PMCID: PMC3591986.
    51. Jahn BO, Ottosson H, Galperin M, Fransson J. Organic single molecular structures for light induced spin-pump devices. ACS Nano. 2013 Feb 26; 7(2):1064-71. PMID: 23350843.
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    52. Fernández-Suárez XM, Galperin M. The 2013 Nucleic Acids Research Database Issue and the online molecular biology database collection. Nucleic Acids Res. 2013 Jan; 41(Database issue):D1-7. PMID: 23203983; PMCID: PMC3531151.
    53. Galperin M, Nitzan A. Cooperative effects in inelastic tunneling. J Phys Chem B. 2013 Apr 25; 117(16):4449-53. PMID: 23113610.
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    54. Mulkidjanian AY, Bychkov AY, Dibrova DV, Galperin M, Koonin EV. Open questions on the origin of life at anoxic geothermal fields. Orig Life Evol Biosph. 2012 Oct; 42(5):507-16. PMID: 23132762.
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    55. Dibrova DV, Chudetsky MY, Galperin M, Koonin EV, Mulkidjanian AY. The role of energy in the emergence of biology from chemistry. Orig Life Evol Biosph. 2012 Oct; 42(5):459-68. PMID: 23100130.
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    56. Galperin M, Mekhedov SL, Puigbo P, Smirnov S, Wolf YI, Rigden DJ. Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes. Environ Microbiol. 2012 Nov; 14(11):2870-90. PMID: 22882546.
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    57. White AJ, Galperin M. Inelastic transport: a pseudoparticle approach. Phys Chem Chem Phys. 2012 Oct 28; 14(40):13809-19. PMID: 22797677.
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    58. Galperin M, Nitzan A. Molecular optoelectronics: the interaction of molecular conduction junctions with light. Phys Chem Chem Phys. 2012 Jul 14; 14(26):9421-38. PMID: 22648067.
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    59. Mulkidjanian AY, Bychkov AY, Dibrova DV, Galperin M, Koonin EV. Origin of first cells at terrestrial, anoxic geothermal fields. Proc Natl Acad Sci U S A. 2012 Apr 03; 109(14):E821-30. PMID: 22331915.
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    60. Peskin U, Galperin M. Coherently controlled molecular junctions. J Chem Phys. 2012 Jan 28; 136(4):044107. PMID: 22299861.
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    61. Galperin M, Fernández-Suárez XM. The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. Nucleic Acids Res. 2012 Jan; 40(Database issue):D1-8. PMID: 22144685.
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    62. Galperin M, Koonin EV. Divergence and convergence in enzyme evolution. J Biol Chem. 2012 Jan 02; 287(1):21-8. PMID: 22069324.
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    63. McInerney JO, Martin WF, Koonin EV, Allen JF, Galperin M, Lane N, Archibald JM, Embley TM. Planctomycetes and eukaryotes: a case of analogy not homology. Bioessays. 2011 Nov; 33(11):810-7. PMID: 21858844.
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    64. Rigden DJ, Woodhead DD, Wong PW, Galperin M. New structural and functional contexts of the Dx[DN]xDG linear motif: insights into evolution of calcium-binding proteins. PLoS One. 2011; 6(6):e21507. PMID: 21720552.
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    65. Fransson J, Galperin M. Spin Seebeck coefficient of a molecular spin pump. Phys Chem Chem Phys. 2011 Aug 28; 13(32):14350-7. PMID: 21655558.
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    66. 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 M, 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. Towards BioDBcore: a community-defined information specification for biological databases. Database (Oxford). 2011; 2011:baq027. PMID: 21205783.
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    67. Galperin M, Cochrane GR. The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. Nucleic Acids Res. 2011 Jan; 39(Database issue):D1-6. PMID: 21177655.
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    68. 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 M, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Mizrachi IK, 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. Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res. 2011 Jan; 39(Database issue):D7-10. PMID: 21097465.
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    69. Mulkidjanian AY, Galperin M. On the abundance of zinc in the evolutionarily old protein domains. Proc Natl Acad Sci U S A. 2010 Sep 07; 107(36):E137; author reply E138. PMID: 20693418.
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    70. Tchigvintsev A, Xu X, Singer A, Chang C, Brown G, Proudfoot M, Cui H, Flick R, Anderson WF, Joachimiak A, Galperin M, Savchenko A, Yakunin AF. Structural insight into the mechanism of c-di-GMP hydrolysis by EAL domain phosphodiesterases. J Mol Biol. 2010 Sep 24; 402(3):524-38. PMID: 20691189.
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    71. Galperin M, Koonin EV. From complete genome sequence to 'complete' understanding? Trends Biotechnol. 2010 Aug; 28(8):398-406. PMID: 20647113.
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    72. Dibrova DV, Galperin M, Mulkidjanian AY. Characterization of the N-ATPase, a distinct, laterally transferred Na+-translocating form of the bacterial F-type membrane ATPase. Bioinformatics. 2010 Jun 15; 26(12):1473-6. PMID: 20472544.
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    73. Omelchenko MV, Galperin M, Wolf YI, Koonin EV. Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution. Biol Direct. 2010 Apr 30; 5:31. PMID: 20433725.
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    74. Galperin M. Diversity of structure and function of response regulator output domains. Curr Opin Microbiol. 2010 Apr; 13(2):150-9. PMID: 20226724.
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    75. Galperin M, Higdon R, Kolker E. Interplay of heritage and habitat in the distribution of bacterial signal transduction systems. Mol Biosyst. 2010 Apr; 6(4):721-8. PMID: 20237650.
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    76. Cochrane GR, Galperin M. The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources. Nucleic Acids Res. 2010 Jan; 38(Database issue):D1-4. PMID: 19965766.
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    77. Mulkidjanian AY, Galperin M. On the origin of life in the zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth. Biol Direct. 2009 Aug 24; 4:27. PMID: 19703275; PMCID: PMC2749021.
    78. Yeganeh S, Ratner MA, Galperin M, Nitzan A. Transport in state space: voltage-dependent conductance calculations of benzene-1,4-dithiol. Nano Lett. 2009 May; 9(5):1770-4. PMID: 19323475.
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    79. Allen MA, Lauro FM, Williams TJ, Burg D, Siddiqui KS, De Francisci D, Chong KW, Pilak O, Chew HH, De Maere MZ, Ting L, Katrib M, Ng C, Sowers KR, Galperin M, Anderson IJ, Ivanova N, Dalin E, Martinez M, Lapidus A, Hauser L, Land M, Thomas T, Cavicchioli R. The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation. ISME J. 2009 Sep; 3(9):1012-35. PMID: 19404327.
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    80. Galperin M, Ratner MA, Nitzan A. Raman scattering in current-carrying molecular junctions. J Chem Phys. 2009 Apr 14; 130(14):144109. PMID: 19368431.
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    81. Mulkidjanian AY, Galperin M, Koonin EV. Co-evolution of primordial membranes and membrane proteins. Trends Biochem Sci. 2009 Apr; 34(4):206-15. PMID: 19303305.
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    82. Wan X, Tuckerman JR, Saito JA, Freitas TA, Newhouse JS, Denery JR, Galperin M, Gonzalez G, Gilles-Gonzalez MA, Alam M. Globins synthesize the second messenger bis-(3'-5')-cyclic diguanosine monophosphate in bacteria. J Mol Biol. 2009 May 01; 388(2):262-70. PMID: 19285985.
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    83. Galperin M. Microbial genomics as pursuit of happiness. Microb Biotechnol. 2009 Mar; 2(2):135-6. PMID: 21261894; PMCID: PMC3815821.
    84. Jenal U, Galperin M. Single domain response regulators: molecular switches with emerging roles in cell organization and dynamics. Curr Opin Microbiol. 2009 Apr; 12(2):152-60. PMID: 19246239.
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    85. Galperin M, Ratner MA, Nitzan A. Raman scattering from nonequilibrium molecular conduction junctions. Nano Lett. 2009 Feb; 9(2):758-62. PMID: 19159246.
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    86. Galperin M. Sorting out the mix in microbial genomics. Environ Microbiol. 2008 Dec; 10(12):3187-92. PMID: 19025554.
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    87. de Lorenzo V, Galperin M. Microbial systems biology: bottom up and top down. FEMS Microbiol Rev. 2009 Jan; 33(1):1-2. PMID: 19054117.
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    88. Galperin M, Cochrane GR. Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009. Nucleic Acids Res. 2009 Jan; 37(Database issue):D1-4. PMID: 19033364.
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    89. Saw JH, Mountain BW, Feng L, Omelchenko MV, Hou S, Saito JA, Stott MB, Li D, Zhao G, Wu J, Galperin M, Koonin EV, Makarova KS, Wolf YI, Rigden DJ, Dunfield PF, Wang L, Alam M. Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1. Genome Biol. 2008; 9(11):R161. PMID: 19014707.
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    90. Galperin M. The quest for biofuels fuels genome sequencing. Environ Microbiol. 2008 Oct; 10(10):2471-5. PMID: 18821974.
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    91. Galperin M, Nitzan A, Ratner MA. The non-linear response of molecular junctions: the polaron model revisited. J Phys Condens Matter. 2008 Sep 17; 20(37):374107. PMID: 21694414.
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    92. Galperin M. New feel for new phyla. Environ Microbiol. 2008 Aug; 10(8):1927-33. PMID: 18665943.
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    93. Hou S, Makarova KS, Saw JH, Senin P, Ly BV, Zhou Z, Ren Y, Wang J, Galperin M, Omelchenko MV, Wolf YI, Yutin N, Koonin EV, Stott MB, Mountain BW, Crowe MA, Smirnova AV, Dunfield PF, Feng L, Wang L, Alam M. Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biol Direct. 2008 Jul 01; 3:26. PMID: 18593465.
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    94. Rigden DJ, Galperin M. Sequence analysis of GerM and SpoVS, uncharacterized bacterial 'sporulation' proteins with widespread phylogenetic distribution. Bioinformatics. 2008 Aug 15; 24(16):1793-7. PMID: 18562273.
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    95. Galperin M. Genomes of model organisms: know thy tools. Environ Microbiol. 2008 Jun; 10(6):1383-91. PMID: 18474084.
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    96. Galperin M. Telling bacteria: do not LytTR. Structure. 2008 May; 16(5):657-9. PMID: 18462668.
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    97. Mulkidjanian AY, Dibrov P, Galperin M. The past and present of sodium energetics: may the sodium-motive force be with you. Biochim Biophys Acta. 2008 Jul-Aug; 1777(7-8):985-92. PMID: 18485887.
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    98. Galperin M. The dawn of synthetic genomics. Environ Microbiol. 2008 Apr; 10(4):821-5. PMID: 18353151.
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    99. Mulkidjanian AY, Galperin M, Makarova KS, Wolf YI, Koonin EV. Evolutionary primacy of sodium bioenergetics. Biol Direct. 2008 Apr 01; 3:13. PMID: 18380897.
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    100. Galperin M, Tretiak S. Linear optical response of current-carrying molecular junction: a nonequilibrium Green's function-time-dependent density functional theory approach. J Chem Phys. 2008 Mar 28; 128(12):124705. PMID: 18376958.
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    101. Galperin M, Ratner MA, Nitzan A, Troisi A. Nuclear coupling and polarization in molecular transport junctions: beyond tunneling to function. Science. 2008 Feb 22; 319(5866):1056-60. PMID: 18292333.
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    102. Galperin M. Social bacteria and asocial eukaryotes. Environ Microbiol. 2008 Feb; 10(2):281-8. PMID: 18199122.
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    103. Galperin M. Some bacteria degrade explosives, others prefer boiling methanol. Environ Microbiol. 2007 Dec; 9(12):2905-10. PMID: 17991022.
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    104. Galperin M. The Molecular Biology Database Collection: 2008 update. Nucleic Acids Res. 2008 Jan; 36(Database issue):D2-4. PMID: 18025043.
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    105. Mulkidjanian AY, Makarova KS, Galperin M, Koonin EV. Inventing the dynamo machine: the evolution of the F-type and V-type ATPases. Nat Rev Microbiol. 2007 11; 5(11):892-9. PMID: 17938630.
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    106. Yeganeh S, Galperin M, Ratner MA. Switching in molecular transport junctions: polarization response. J Am Chem Soc. 2007 Oct 31; 129(43):13313-20. PMID: 17915864.
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    107. Galperin M. Dark matter in a deep-sea vent and in human mouth. Environ Microbiol. 2007 Oct; 9(10):2385-91. PMID: 17803764.
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    108. Mulkidjanian AY, Galperin M. Physico-chemical and evolutionary constraints for the formation and selection of first biopolymers: towards the consensus paradigm of the abiogenic origin of life. Chem Biodivers. 2007 Sep; 4(9):2003-15. PMID: 17886857.
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    109. Galperin M. Genomics against flatulence. Environ Microbiol. 2007 Aug; 9(8):1869-77. PMID: 17635535.
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    110. Galperin M. Linear chromosomes in bacteria: no straight edge advantage? Environ Microbiol. 2007 Jun; 9(6):1357-62. PMID: 17504473.
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    111. Galperin M. Mycobacterial genomes for all tastes: from BCG to biodegradation of naphtalene and pyrene. Environ Microbiol. 2007 Apr; 9(4):839-45. PMID: 17359256.
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    112. Bumbaca D, Littlejohn JE, Nayakanti H, Lucas AH, Rigden DJ, Galperin M, Jedrzejas MJ. Genome-based identification and characterization of a putative mucin-binding protein from the surface of Streptococcus pneumoniae. Proteins. 2007 Feb 15; 66(3):547-58. PMID: 17115425.
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    113. Galperin M. Using archaeal genomics to fight global warming and clostridia to fight cancer. Environ Microbiol. 2007 Feb; 9(2):279-86. PMID: 17222127.
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    114. Galperin M, Nikolskaya AN. Identification of sensory and signal-transducing domains in two-component signaling systems. Methods Enzymol. 2007; 422:47-74. PMID: 17628134.
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    115. Galperin M. The Molecular Biology Database Collection: 2007 update. Nucleic Acids Res. 2007 Jan; 35(Database issue):D3-4. PMID: 17148484.
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    116. Galperin M. The fuzzy border between a cell and an organelle. Environ Microbiol. 2006 Dec; 8(12):2062-7. PMID: 17107547.
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    117. D'Souza M, Glass EM, Syed MH, Zhang Y, Rodriguez A, Maltsev N, Galperin M. Sentra: a database of signal transduction proteins for comparative genome analysis. Nucleic Acids Res. 2007 Jan; 35(Database issue):D271-3. PMID: 17135204.
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    118. Galperin M. A square archaeon, the smallest eukaryote and the largest bacteria. Environ Microbiol. 2006 Oct; 8(10):1683-7. PMID: 16958749.
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    119. Galperin M, Kolker E. New metrics for comparative genomics. Curr Opin Biotechnol. 2006 Oct; 17(5):440-7. PMID: 16978854.
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    120. Mulkidjanian AY, Koonin EV, Makarova KS, Mekhedov SL, Sorokin A, Wolf YI, Dufresne A, Partensky F, Burd H, Kaznadzey D, Haselkorn R, Galperin M. The cyanobacterial genome core and the origin of photosynthesis. Proc Natl Acad Sci U S A. 2006 Aug 29; 103(35):13126-31. PMID: 16924101.
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    121. Galperin M. Sampling of microbial diversity by complete genomes. Environ Microbiol. 2006 Aug; 8(8):1313-7. PMID: 16872395.
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    122. Galperin M, Nitzan A. Optical properties of current carrying molecular wires. J Chem Phys. 2006 Jun 21; 124(23):234709. PMID: 16821943.
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    123. Galperin M. Structural classification of bacterial response regulators: diversity of output domains and domain combinations. J Bacteriol. 2006 Jun; 188(12):4169-82. PMID: 16740923.
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    124. Galperin M. Genomes to aid in bioremediation of dry cleaning solvents, mothballs and more. Environ Microbiol. 2006 Jun; 8(6):949-55. PMID: 16689716.
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    125. Galperin M, Nitzan A, Ratner MA. Molecular transport junctions: current from electronic excitations in the leads. Phys Rev Lett. 2006 Apr 28; 96(16):166803. PMID: 16712256.
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    126. Galperin M. The minimal genome keeps growing. Environ Microbiol. 2006 Apr; 8(4):569-73. PMID: 16584469.
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    127. Makarova KS, Koonin EV, Haselkorn R, Galperin M. Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion. Bioinformatics. 2006 Jun 01; 22(11):1297-301. PMID: 16543275.
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    128. Galperin M. Protecting sausages with bacteria instead of salt. Environ Microbiol. 2006 Feb; 8(2):185-92. PMID: 16423007.
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    129. Galperin M. The Molecular Biology Database Collection: 2006 update. Nucleic Acids Res. 2006 Jan 01; 34(Database issue):D3-5. PMID: 16381871.
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    130. Galperin M, Moroz OV, Wilson KS, Murzin AG. House cleaning, a part of good housekeeping. Mol Microbiol. 2006 Jan; 59(1):5-19. PMID: 16359314.
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    131. Galperin M. More cool news from marine bacteria. Environ Microbiol. 2005 Dec; 7(12):1864-7. PMID: 16309385.
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    132. Galperin M, Nitzan A. Current-induced light emission and light-induced current in molecular-tunneling junctions. Phys Rev Lett. 2005 Nov 11; 95(20):206802. PMID: 16384081.
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    133. Amikam D, Galperin M. PilZ domain is part of the bacterial c-di-GMP binding protein. Bioinformatics. 2006 Jan 01; 22(1):3-6. PMID: 16249258.
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    134. Galperin M. The secret of being cool. Environ Microbiol. 2005 Oct; 7(10):1499-504. PMID: 16156723.
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    135. Habibian R, Dzioba J, Barrett J, Galperin M, Loewen PC, Dibrov P. Functional analysis of conserved polar residues in Vc-NhaD, Na+/H+ antiporter of Vibrio cholerae. J Biol Chem. 2005 Nov 25; 280(47):39637-43. PMID: 16186100.
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    136. Galperin M. To finish or not to finish? Environ Microbiol. 2005 Aug; 7(8):1061-4. PMID: 16011744.
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    137. Römling U, Gomelsky M, Galperin M. C-di-GMP: the dawning of a novel bacterial signalling system. Mol Microbiol. 2005 Aug; 57(3):629-39. PMID: 16045609.
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    138. Teplyakov A, Obmolova G, Toedt J, Galperin M, Gilliland GL. Crystal structure of the bacterial YhcH protein indicates a role in sialic acid catabolism. J Bacteriol. 2005 Aug; 187(16):5520-7. PMID: 16077096.
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    139. Galperin M. A census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial IQ, extroverts and introverts. BMC Microbiol. 2005 Jun 14; 5:35. PMID: 15955239.
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    140. Galperin M. The vibrio that sheds light. Environ Microbiol. 2005 Jun; 7(6):757-60. PMID: 15892694.
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    141. Galperin M, Nitzan A, Ratner MA, Stewart DR. Molecular transport junctions: asymmetry in inelastic tunneling processes. J Phys Chem B. 2005 May 05; 109(17):8519-22. PMID: 16852002.
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    142. Galperin M. On the bottom of the deep blue sea. Environ Microbiol. 2005 Apr; 7(4):453-8. PMID: 15816911.
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    143. Galperin M. Life is not defined just in base pairs. Environ Microbiol. 2005 Feb; 7(2):149-52. PMID: 15658982.
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    144. Kolker E, Picone AF, Galperin M, Romine MF, Higdon R, Makarova KS, Kolker N, Anderson GA, Qiu X, Auberry KJ, Babnigg G, Beliaev AS, Edlefsen P, Elias DA, Gorby YA, Holzman T, Klappenbach JA, Konstantinidis KT, Land ML, Lipton MS, McCue LA, Monroe M, Pasa-Tolic L, Pinchuk G, Purvine S, Serres MH, Tsapin S, Zakrajsek BA, Zhu W, Zhou J, Larimer FW, Lawrence CE, Riley M, Collart FR, Yates JR, Smith RD, Giometti CS, Nealson KH, Fredrickson JK, Tiedje JM. Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. Proc Natl Acad Sci U S A. 2005 Feb 08; 102(6):2099-104. PMID: 15684069.
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    145. Moroz OV, Murzin AG, Makarova KS, Koonin EV, Wilson KS, Galperin M. Dimeric dUTPases, HisE, and MazG belong to a new superfamily of all-alpha NTP pyrophosphohydrolases with potential "house-cleaning" functions. J Mol Biol. 2005 Mar 25; 347(2):243-55. PMID: 15740738.
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    146. Galperin M. The Molecular Biology Database Collection: 2005 update. Nucleic Acids Res. 2005 Jan 01; 33(Database issue):D5-24. PMID: 15608247.
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    147. Galperin M, Ratner MA, Nitzan A. Hysteresis, switching, and negative differential resistance in molecular junctions: a polaron model. Nano Lett. 2005 Jan; 5(1):125-30. PMID: 15792425.
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    148. Galperin M, Ratner MA, Nitzan A. Inelastic electron tunneling spectroscopy in molecular junctions: peaks and dips. J Chem Phys. 2004 Dec 15; 121(23):11965-79. PMID: 15634159.
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    149. Hou S, Saw JH, Lee KS, Freitas TA, Belisle C, Kawarabayasi Y, Donachie SP, Pikina A, Galperin M, Koonin EV, Makarova KS, Omelchenko MV, Sorokin A, Wolf YI, Li QX, Keum YS, Campbell S, Denery J, Aizawa S, Shibata S, Malahoff A, Alam M. Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy. Proc Natl Acad Sci U S A. 2004 Dec 28; 101(52):18036-41. PMID: 15596722.
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    150. Galperin M. Genomes back-to-back: when sequencing race is a good thing. Environ Microbiol. 2004 Dec; 6(12):1205-9. PMID: 15560818.
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    151. Rigden DJ, Galperin M. The DxDxDG motif for calcium binding: multiple structural contexts and implications for evolution. J Mol Biol. 2004 Oct 29; 343(4):971-84. PMID: 15476814.
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    152. Galperin M, Koonin EV. 'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res. 2004; 32(18):5452-63. PMID: 15479782.
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    153. Moroz OV, Harkiolaki M, Galperin M, Vagin AA, González-Pacanowska D, Wilson KS. The crystal structure of a complex of Campylobacter jejuni dUTPase with substrate analogue sheds light on the mechanism and suggests the "basic module" for dimeric d(C/U)TPases. J Mol Biol. 2004 Oct 01; 342(5):1583-97. PMID: 15364583.
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    154. Galperin M. The bugs that came in from the cold. Environ Microbiol. 2004 Oct; 6(10):1001-4. PMID: 15344925.
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    155. Galperin M. Looking at big brothers for clues. Environ Microbiol. 2004 Aug; 6(8):767-8. PMID: 15250878.
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    156. Rigden DJ, Mello LV, Galperin M. The PA14 domain, a conserved all-beta domain in bacterial toxins, enzymes, adhesins and signaling molecules. Trends Biochem Sci. 2004 Jul; 29(7):335-9. PMID: 15236739.
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    157. Galperin M. Bacterial signal transduction network in a genomic perspective. Environ Microbiol. 2004 Jun; 6(6):552-67. PMID: 15142243; PMCID: PMC1414778.
    158. Galperin M. Metagenomics: from acid mine to shining sea. Environ Microbiol. 2004 Jun; 6(6):543-5. PMID: 15142241.
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    159. Galperin M, Baker AJ. From biofouling to bioremediation: the good, the bad and the vague. Curr Opin Biotechnol. 2004 Jun; 15(3):167-9. PMID: 15193321.
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    160. Galperin M. All bugs, big and small. Environ Microbiol. 2004 May; 6(5):435-7. PMID: 15049916.
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    161. Kolker E, Makarova KS, Shabalina S, Picone AF, Purvine S, Holzman T, Cherny T, Armbruster D, Munson RS, Kolesov G, Frishman D, Galperin M. Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae. Nucleic Acids Res. 2004; 32(8):2353-61. PMID: 15121896.
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    162. Bumbaca D, Littlejohn JE, Nayakanti H, Rigden DJ, Galperin M, Jedrzejas MJ. Sequence analysis and characterization of a novel fibronectin-binding repeat domain from the surface of Streptococcus pneumoniae. OMICS. 2004; 8(4):341-56. PMID: 15703481.
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    163. Raghunathan A, Price ND, Galperin M, Makarova KS, Purvine S, Picone AF, Cherny T, Xie T, Reilly TJ, Munson R, Tyler RE, Akerley BJ, Smith AL, Palsson BO, Kolker E. In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium. OMICS. 2004; 8(1):25-41. PMID: 15107235.
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    164. Galperin M. The Molecular Biology Database Collection: 2004 update. Nucleic Acids Res. 2004 Jan 01; 32(Database issue):D3-22. PMID: 14681349.
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    165. Dibrov P, Dibrov E, Pierce GN, Galperin M. Salt in the wound: a possible role of Na+ gradient in chlamydial infection. J Mol Microbiol Biotechnol. 2004; 8(1):1-6. PMID: 15741735.
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    166. Galperin M, Nitzan A. NEGF-HF method in molecular junction property calculations. Ann N Y Acad Sci. 2003 Dec; 1006:48-67. PMID: 14976009.
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    167. Dufresne A, Salanoubat M, Partensky F, Artiguenave F, Axmann IM, Barbe V, Duprat S, Galperin M, Koonin EV, Le Gall F, Makarova KS, Ostrowski M, Oztas S, Robert C, Rogozin IB, Scanlan DJ, Tandeau de Marsac N, Weissenbach J, Wincker P, Wolf YI, Hess WR. Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc Natl Acad Sci U S A. 2003 Aug 19; 100(17):10020-5. PMID: 12917486.
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    168. Kolker E, Purvine S, Galperin M, Stolyar S, Goodlett DR, Nesvizhskii AI, Keller A, Xie T, Eng JK, Yi E, Hood L, Picone AF, Cherny T, Tjaden BC, Siegel AF, Reilly TJ, Makarova KS, Palsson BO, Smith AL. Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20. J Bacteriol. 2003 Aug; 185(15):4593-602. PMID: 12867470.
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    169. Rigden DJ, Jedrzejas MJ, Moroz OV, Galperin M. Structural diversity of calcium-binding proteins in bacteria: single-handed EF-hands? Trends Microbiol. 2003 Jul; 11(7):295-7. PMID: 12875810.
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    170. Mulkidjanian AY, Cherepanov DA, Galperin M. Survival of the fittest before the beginning of life: selection of the first oligonucleotide-like polymers by UV light. BMC Evol Biol. 2003 May 28; 3:12. PMID: 12773209.
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    171. Rigden DJ, Jedrzejas MJ, Galperin M. Amidase domains from bacterial and phage autolysins define a family of gamma-D,L-glutamate-specific amidohydrolases. Trends Biochem Sci. 2003 May; 28(5):230-4. PMID: 12765833.
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    172. Rigden DJ, Jedrzejas MJ, Galperin M. An extracellular calcium-binding domain in bacteria with a distant relationship to EF-hands. FEMS Microbiol Lett. 2003 Apr 11; 221(1):103-10. PMID: 12694917.
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    173. Cohen GN, Barbe V, Flament D, Galperin M, Heilig R, Lecompte O, Poch O, Prieur D, Quérellou J, Ripp R, Thierry JC, Van der Oost J, Weissenbach J, Zivanovic Y, Forterre P. An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi. Mol Microbiol. 2003 Mar; 47(6):1495-512. PMID: 12622808.
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    174. Mirkin BG, Fenner TI, Galperin M, Koonin EV. Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol Biol. 2003 Jan 06; 3:2. PMID: 12515582; PMCID: PMC149225.
    175. Zhulin IB, Nikolskaya AN, Galperin M. Common extracellular sensory domains in transmembrane receptors for diverse signal transduction pathways in bacteria and archaea. J Bacteriol. 2003 Jan; 185(1):285-94. PMID: 12486065; PMCID: PMC141854.
    176. Rigden DJ, Galperin M, Jedrzejas MJ. Analysis of structure and function of putative surface-exposed proteins encoded in the Streptococcus pneumoniae genome: a bioinformatics-based approach to vaccine and drug design. Crit Rev Biochem Mol Biol. 2003; 38(2):143-68. PMID: 12749697.
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    177. Jordan IK, Henze K, Fedorova ND, Koonin EV, Galperin M. Phylogenomic analysis of the Giardia intestinalis transcarboxylase reveals multiple instances of domain fusion and fission in the evolution of biotin-dependent enzymes. J Mol Microbiol Biotechnol. 2003; 5(3):172-89. PMID: 12766347.
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    178. Dzioba J, Häse CC, Gosink K, Galperin M, Dibrov P. Experimental verification of a sequence-based prediction: F(1)F(0)-type ATPase of Vibrio cholerae transports protons, not Na(+) ions. J Bacteriol. 2003 Jan; 185(2):674-8. PMID: 12511516; PMCID: PMC145325.
    179. Nikolskaya AN, Mulkidjanian AY, Beech IB, Galperin M. MASE1 and MASE2: two novel integral membrane sensory domains. J Mol Microbiol Biotechnol. 2003; 5(1):11-6. PMID: 12673057.
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    180. Rigden DJ, Mosolov VV, Galperin M. Sequence conservation in the chagasin family suggests a common trend in cysteine proteinase binding by unrelated protein inhibitors. Protein Sci. 2002 Aug; 11(8):1971-7. PMID: 12142451; PMCID: PMC2373688.
    181. Nikolskaya AN, Galperin M. A novel type of conserved DNA-binding domain in the transcriptional regulators of the AlgR/AgrA/LytR family. Nucleic Acids Res. 2002 Jun 01; 30(11):2453-9. PMID: 12034833; PMCID: PMC117183.
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