Enikeeva F.N, Severinov K.V, Gelfand M.S. Restriction-modification systems and bacteriophage invasion: Who wins? J Theor Biol. PubMed PDF
Mazin P.V, Gelfand M.S, Mironov A.A, Rakhmaninova A.B, Rubinov A.R, Russell R.B, Kalinina O.V. An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies. Algorithms Mol Biol. 5: 29. PubMed PDF
Gelfand M.S. Introduction: 4th International Moscow Conference on Computational Molecular Biology MCCMB'09. J Bioinform Comput Biol. 8: v-ii. PubMed PDF
Novichkov P.S, Rodionov D.A, Stavrovskaya E.D, Novichkova E.S, Kazakov A.E, Gelfand M.S, Arkin A.P, Mironov A.A, Dubchak I. RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Res. PubMed PDF
Sorokin V.A, Gelfand M.S, Artamonova I.I. Evolutionary dynamics of clustered irregularly interspaced short palindromic repeat systems in the ocean metagenome. Appl Environ Microbiol. 76: 2136-44. PubMed PDF
Shustrova E.N, Artamonova I.I. [Evolutionary history of the SSX family of human C/T-antigens]. Mol Biol (Mosk). 2009, 43: 1025-31. PubMed PDF
T. Eitinger, D.A. Rodionov, M. Grote, E. Schneider. Canonical and ECF-type ATP-binding cassette importers in prokaryotes: diversity in modular organization and cellular functions. FEMS Microbiol Rev. PubMed PDF
Y. Gu, Y. Ding, C. Ren, Z. Sun, D.A. Rodionov, W. Zhang, S. Yang, C. Yang, W. Jiang. Reconstruction of xylose utilization pathway and regulons in Firmicutes. BMC Genomics. 11: 255. PubMed PDF
J. Schroder, N. Jochmann, D.A. Rodionov, A. Tauch. The Zur regulon of Corynebacterium glutamicum ATCC 13032. BMC Genomics. 11: 12. PubMed PDF
Rogoza T, Goginashvili A, Rodionova S, Ivanov M, Viktorovskaya O, Rubel A, Volkov K, Mironova L. Non-Mendelian determinant [ISP +] in yeast is a nuclear-residing prion form of the global transcriptional regulator Sfp1. Proc Natl Acad Sci U S A. PubMed PDF
Gelfand M.S, Ramensky V.E. Positive Selection and Alternative Splicing in Humans. Encyclopedia Of Life Sciences, 2009, DOI: 10.1002/9780470015902.a0021735 Abstract PDF
Medvedeva Y.A, Fridman M.V, Oparina N.J, Malko D.B, Ermakova E.O, Kulakovskiy I.V, Heinzel A, Makeev V.J. Intergenic, gene terminal, and intragenic CpG islands in the human genome. BMC Genomics. 11: 48. PubMed PDF
Novichkov P.S, Laikova O.N, Novichkova E.S, Gelfand M.S, Arkin A.P, Dubchak I, Rodionov D.A. RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res. 38: D111-8. PubMed PDF
Rakitin D.I, Gelfand M.S. Cometabolic Activity of Aphid Acyrthosiphon pisum and Symbiotic Bacterium Buchnera aphidicola APS. Molekulyarnaya Biologiya. 2009, 43(6): 1093-95 PDF
Yus E, Maier T, Michalodimitrakis K, van Noort V, Yamada T, Chen W, Wodke J, Guell M, Martinez S, Bourgeois R, Kuhner S, Raineri E, Letunic I, Kalinina O, Rode M, Herrmann R, Gutierrez-Gallego R, Russell R, Gavin A, Bork P, Serrano L. Impact of Genome Reduction on Bacterial Metabolism and Its Regulation. Science, 2009, 27: 1263-1268 PDF
Huang N, De Ingeniis J, Galeazzi L, Mancini C, Korostelev Y.D, Rakhmaninova A.B, Gelfand M.S, Rodionov D.A, Raffaelli N, Zhang H. Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism. Structure. 2009, 17: 939-51. PubMed PDF
Haas C.E, Rodionov D.A, Kropat J, Malasarn D, Merchant S.S, de Crecy-Lagard V. A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life. BMC Genomics. 2009, 10: 470. PubMed PDF
Sankaran B, Bonnett S.A, Shah K, Gabriel S, Reddy R, Schimmel P, Rodionov D.A, de Crecy-Lagard V, Helmann J.D, Iwata-Reuyl D, Swairjo M.A. Zinc-independent folate biosynthesis: genetic, biochemical, and structural investigations reveal new metal dependence for GTP cyclohydrolase IB. J Bacteriol. 2009, 191: 6936-49. PubMed PDF
Tsoy O, Ravcheev D, Mushegian A. Comparative genomics of ethanolamine utilization. J Bacteriol. 2009, 191(23):7157-64 PubMed PDF
Kalinina O.V, Gelfand M.S, Russell R.B. Combining specificity determining and conserved residues improves functional site prediction. BMC Bioinformatics. 2009, 10: 174. PubMed PDF
Nurtdinov R.N, Mironov A.A, Gelfand M.S. Rodent-specific alternative exons are more frequent in rapidly evolving genes and in paralogs. BMC Evol Biol. 2009, 9: 142. PubMed PDF
Gelfand MS, Kazakov AE, Korostelev YD, Laikova ON, Mironov AA, Rakhmaninova AB, Ravcheev DA, Rodionov DA, Vitreschak AG. Evolution of Regulatory Systems in Bacteria. Lecture Notes in Bioinformatics. 2009; 5542 (ISBRA 2009): 1-4
Sorci L, Martynowski D, Rodionov D.A, Eyobo Y, Zogaj X, Klose K.E, Nikolaev E.V, Magni G, Zhang H, Osterman A.L. Nicotinamide mononucleotide synthetase is the key enzyme for an alternative route of NAD biosynthesis in Francisella tularensis. Proc Natl Acad Sci U S A. 2009, 106: 3083-8. PubMed PDF
Desai T.A, Rodionov D.A, Gelfand M.S, Alm E.J, Rao C.V. Engineering transcription factors with novel DNA-binding specificity using comparative genomics. Nucleic Acids Res. 2009, 37: 2493-503. PubMed PDF
Raker V.A, Mironov A.A, Gelfand M.S, Pervouchine D.D. Modulation of alternative splicing by long-range RNA structures in Drosophila. Nucleic Acids Res. 2009, 37(14):4533-44 PubMed PDF
Kurmangaliyev Y.Z., Gelfand M.S. Computational analysis of splicing errors and mutations in human transcripts. BMC Genomics. 2008, 9(1): 13. PubMed PDF
Zhang Y, Rodionov D.A, Gelfand M.S, Gladyshev V.N. Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization. BMC Genomics. 2009, 10: 78. PubMed PDF
Sadovskaya N.S, Gelfand M.S. Benchmarking of programs that predict the position of transmembrane segments in beta-barrel proteins. Biophysics, 2008, Vol. 53, No. 2, pp. 134–139. PDF
A. Eudes, G.B. Erkens, D.J. Slotboom, D.A. Rodionov, V. Naponelli, A.D. Hanson. Identification of genes encoding the folate- and thiamine-binding membrane proteins in Firmicutes. J Bacteriol. 2008, 190: 7591-4. PubMed PDF
A.E. Kazakov, D.A. Rodionov, E. Alm, A.P. Arkin, I. Dubchak, M.S. Gelfand. Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria. J Bacteriol. 2009, 191: 52-64. PubMed PDF
D.A. Rodionov, P. Hebbeln, A. Eudes, J. ter Beek, I.A. Rodionova, G.B. Erkens, D.J. Slotboom, M.S. Gelfand, A.L. Osterman, A.D. Hanson, T. Eitinger. A novel class of modular transporters for vitamins in prokaryotes. J Bacteriol. 2009, 191: 42-51. PubMed PDF
G.E. Pinchuk, D.A. Rodionov, C. Yang, X. Li, A.L. Osterman, E. Dervyn, O.V. Geydebrekht, S.B. Reed, M.F. Romine, F.R. Collart, J.H. Scott, J.K. Fredrickson, A.S. Beliaev. Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization. Proc Natl Acad Sci U S A. 2009, PubMed PDF
D.A. Rodionov, J. De Ingeniis, C. Mancini, F. Cimadamore, H. Zhang, A.L. Osterman, N. Raffaelli. Transcriptional regulation of NAD metabolism in bacteria: NrtR family of Nudix-related regulators. Nucleic Acids Res. 2008, 36: 2047-59. PubMed PDF
D.A. Rodionov, X. Li, I.A. Rodionova, C. Yang, L. Sorci, E. Dervyn, D. Martynowski, H. Zhang, M.S. Gelfand, A.L. Osterman. Transcriptional regulation of NAD metabolism in bacteria: genomic reconstruction of NiaR (YrxA) regulon. Nucleic Acids Res. 2008, 36: 2032-46. PubMed PDF
V. Sorokin, K. Severinov, M.S. Gelfand. Systematic prediction of control proteins and their DNA binding sites. Nucleic Acids Res. 2009, 37: 441-51. PubMed PDF
Ramensky V.E, Nurtdinov R.N, Neverov A.D, Mironov A.A, Gelfand M.S. Positive selection in alternatively spliced exons of human genes. Am J Hum Genet. 2008, 83: 94-8. PubMed PDF
Kurmangaliev EZh, Gel'fand MS. [Alternative splicing tends to involve phosphorylation sites] Russian. Mol Biol (Mosk). 2009, 43(3):572-4. PubMed PDF
Sernova N.V, Gelfand M.S. Identification of replication origins in prokaryotic genomes. Brief Bioinform. 2008, 9: 376-91. PubMed PDF
J.K. Fredrickson, M.F. Romine, A.S. Beliaev, J.M. Auchtung, M.E. Driscoll, T.S. Gardner, K.H. Nealson, A.L. Osterman, G. Pinchuk, J.L. Reed, D.A. Rodionov, J.L. Rodrigues, D.A. Saffarini, M.H. Serres, A.M. Spormann, I.B. Zhulin, J.M. Tiedje. Towards environmental systems biology of Shewanella. Nat Rev Microbiol. 2008, 6: 592-603. PubMed PDF
Schauer K, Rodionov D.A, H. de Reuse. New substrates for TonB-dependent transport: do we only see the 'tip of the iceberg'? Trends Biochem Sci. 2008, 33: 330-8. PubMed PDF
I.V. Merkeev, A.A. Mironov. [Orphan genes: function, evolution, composition]. Mol Biol (Mosk). Russian. 2008, 42: 143-9 PubMed PDF
Vitreschak AG, Mironov AA, Lyubetsky VA, Gelfand MS. Comparative genomic analysis of T-box regulatory systems in bacteria. RNA. 2008 Apr;14(4):717-35. PubMed PDF
Yang C, Rodionov DA, Rodionova IA, Li X, Osterman AL. Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathways. J Bacteriol. 2008, 190(5):1773-82 PubMed PDF
Rodionov DA, Gelfand MS. Comparative genomics and functional annotation of bacterial transporters. Physics of Life Reviews, 2008, 5: 22-49. PDF
Kovaleva GY, Gelfand MS. Transcriptional regulation of the methionine and cysteine transport and metabolism in streptococci. FEMS Microbiol Lett. 2007, 276(2):207-15. PubMed
Kazanov MD, Vitreschak AG, Gelfand MS. Abundance and functional diversity of riboswitches in microbial communities.BMC Genomics. 2007, 8:347. PubMed PDF
Makarova KS, Omelchenko MV, Gaidamakova EK, Matrosova VY, Vasilenko A, Zhai M, Lapidus A, Copeland A, Kim E, Land M, Mavrommatis K, Pitluck S, Richardson PM, Detter C, Brettin T, Saunders E, Lai B, Ravel B, Kemner KM, Wolf YI, Sorokin A, Gerasimova AV, Gelfand MS, Fredrickson JK, Koonin EV, Daly MJ. Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks. PLoS ONE. 2007 Sep, 2(9):e955. PubMed PDF
Nurtdinov RN, Neverov AD, Favorov AV, Mironov AA, Gelfand MS. Conserved and species-specific alternative splicing in mammalian genomes. BMC Evol Biol. 2007, 7(1):249. PubMed PDF
Nikolaev SI, Montoya-Burgos JI, Popadin K, Parand L, Margulies EH. Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements. Proc Natl Acad Sci U S A. 2007, 104(51):20443-8. PubMed PDF
Sycheva LV, Permina EA, Gelfand MS. [Taxon-Specific Regulation of the SOS Response in gamma-Proteobacteria]. Mol. Biol. (Mosk). 2007, 41(5):827-35. Russian. PubMed PDF
Tsyganova MO, Gelfand MS, Ravcheev DA. [Regulation of respiration in enterobacteria: comparison of microarray and comparative genomic data]. Mol. Biol. (Mosk). 2007, 41(3): 556-71. Russian. PubMed PDF
Popadin KY, Mamirova LA, Kondrashov FA. A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures. BMC Bioinformatics. 2007, 8(1):441 PubMed PDF
Novikova M, Metlitskaya A, Datsenko K, Kazakov T, Kazakov A, Wanner B, Severinov K. The Escherichia coli Yej transporter is required for the uptake of translation inhibitor microcin C. J Bacteriol. 2007, 189(22):8361-5. PubMed PDF
Ermakova EO, Nurtdinov RN, Gelfand MS. Overlapping alternative donor splice sites in the human genome. JBCB. 2007, 5(5):991-1004. PubMed PDF
Severinov K, Semenova E, Kazakov A, Kazakov T, Gelfand MS. Low-molecular-weight post-translationally modified microcins. Mol Microbiol. 2007, 65(6):1380-94. PubMed PDF
Kolesov G, Wunderlich Z, Laikova ON, Gelfand MS, Mirny LA. How gene order is influenced by the biophysics of transcription regulation. Proc Natl Acad Sci U S A. 2007, 104(35):13948-53. PubMed PDF
Bazykin GA, Kondrashov FA, Brudno M, Poliakov A, Dubchak I, Kondrashov AS. Extensive parallelism in protein evolution. Biol Direct. 2007, 2:20. PubMed PDF
Artamonova II, Gelfand MS. Comparative genomics and evolution of alternative splicing: the pessimists' science. Chem Rev. 2007, 107(8):3407-30. PubMed PDF
V. Ramensky, A. Sobol, N. Zaitseva, A. Rubinov, V. Zosimov. A novel approach to local similarity of protein binding sites substantially improves computational drug design results. Proteins. 2007, 69: 349-57. PubMed PDF
Popadin K, Polishchuk LV, Mamirova L, Knorre D, Gunbin K. Accumulation of slightly deleterious mutations in mitochondrial protein-coding genes of large versus small mammals. Proc Natl Acad Sci USA. 2007, 104(33):13390-5. PubMed PDF
Enikeeva FN, Kotelnikova EA, Gelfand MS, Makeev VJ. A model of evolution with constant selective pressure for regulatory DNA sites. BMC Evol Biol. 2007, 7(1):125. PubMed PDF
Rodionov DA. Comparative Genomic Reconstruction of Transcriptional Regulatory Networks in Bacteria. Chem Rev. 2007, 107(8):3467-97. PubMed PDF
Mironov A.A. [A method for prediction of conserved RNA secondary structures]. Mol Biol (Mosk). 2007, 41: 711-8. PubMed PDF
Premkumar L, Rife CL, Sri Krishna S, McMullan D, Miller MD, Abdubek P, Ambing E, Astakhova T, Axelrod HL, Canaves JM, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Elsliger MA, Feuerhelm J, Floyd R, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kovarik JS, Kreusch A, Levin I, McPhillips TM, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rezezadeh F, Rodionov D, Schwarzenbacher R, Spraggon G, van den Bedem H, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of TM1030 from Thermotoga maritima at 2.3 A resolution reveals molecular details of its transcription repressor function. Proteins. 2007, 68(1):418-24. PubMed PDF
McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes S, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman A, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko O, Xia F, Zinner J, Overbeek R, Stevens R. The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation.Nucleic Acids Res. 2007, 35: D347-53. PubMed PDF
Kovaleva GIu, Gel'fand MS. [Regulation of methionine/cysteine biosynthesis in Corynebacterium glutamicum and related genomes]. Mol Biol (Mosk). 2007, 41(1):139-150. Russian. PubMed PDF
Gvakharia BO, Permina EA, Gelfand MS, Bottomley PJ, Sayavedra-Soto LA, Arp DJ. Global Transcriptional Response of Nitrosomonas europaea to Chloroform and Chloromethane. Appl Environ Microbiol. 2007 PubMed PDF
Rodionov DA, Kurnasov OV, Stec B, Wang Y, Roberts MF, Osterman AL. Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate. Proc Natl Acad Sci U S A. 2007, 104(11):4279-84. PubMed PDF
Johnston AW, Todd JD, Curson AR, Lei S, Nikolaidou-Katsaridou N, Gelfand MS, Rodionov DA. Living without Fur: the subtlety and complexity of iron-responsive gene regulation in the symbiotic bacterium Rhizobium and other alpha-proteobacteria. Biometals. 2007, 20(3-4):501-11 PubMed PDF
Hebbeln P, Rodionov DA, Alfandega A, Eitinger T. Biotin uptake in prokaryotes by solute transporters with an optional ATP-binding cassette-containing module. Proc Natl Acad Sci U S A. 2007 104(8):2909-14. PubMed PDF
Ravcheev DA, Gerasimova AV, Mironov AA, Gelfand MS. Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae). BMC Genomics. 2007, 8:54. PubMed PDF
Sevostyanova A, Djordjevic M, Kuznedelov K, Naryshkina T, Gelfand MS, Severinov K, Minakhin L. Temporal regulation of viral transcription during development of Thermus thermophilus bacteriophage phiYS40. J Mol Biol. 2007, 366(2):420-35. PubMed PDF
Kazakov AE, Cipriano MJ, Novichkov PS, 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, D407-12. PubMed PDF
Mamirova L, Popadin K, Gelfand MS. Purifying selection in mitochondria, free-living and obligate intracellular proteobacteria. BMC Evol Biol. 2007, 7(1):17. PubMed PDF
Kalinina OV, Russell RB, Rakhmaninova AB, Gelfand MS. [Computational method for prediction of protein functional sites using specificity determinants.] Mol Biol (Mosk). 2007, 41(1):151-162. Russian. PubMed PDF
Kovaleva GYu, Gelfand MS. [Regulation of methionine/cysteine biosynthesis in corynebacterium glutamicum and related genomes.] Mol Biol (Mosk). 2007, 41(1):139-150. Russian. PDF
Rodionov DA, Gelfand MS, Todd JD, Curson A.R.J, Johnston A.W.B. Computational Reconstruction of Iron- and Manganese-Responsive Transcriptional Networks in alfa-Proteobacteria. PLoS Comput Biol. 2006, 444:240. PubMed PDF
Gelfand. The view from Russia. Nature. 2006, 444:240. PubMed PDF
Nurtdinov RN, Neverov AD, Mal'ko DB, Kosmodem'ianskii IA, Ermakova EO, Ramenskii VE, Mironov AA, Gel'fand MS. [EDAS, databases of alternatively spliced human genes]. Biofizika. 2006, 51(4):589-92. Russian. PubMed PDF
Ermakova EO, Mal'ko DB, Gel'fand MS. [Different patterns of evolution in alternative and constitutive coding regions of Drosophila alternatively spliced genes] Biofizika. 2006 51(4):581-8. Russian. PubMed PDF
M.S. Gelfand. [Second Moscow Conference on Computational Molecular Biology MCCMB'05]. Biofizika. 2006, 51(4):675-676. Russian. PDF
Sadovskaya NS, Sutormin RA, Gelfand MS. Recognition of transmembrane segments in proteins: review and consistency-based benchmarking of internet servers. J Bioinform Comput Biol. 2006, 4(5): 1033-56. PubMed PDF
Kovaleva GY, Bazykin GA, Brudno M, Gelfand MS. Comparative genomics of transcriptional regulation in yeasts and its application to identification of a candidate alpha-isopropylmalate transporter. J Bioinform Comput Biol. 2006, 4(5): 981-98. PubMed PDF
Lyubetskaya AV, Rubanov LI, Gelfand MS. [Use of the Flux Model of Amino Acid Metabolism of Escherichia coli.] Biochemistry (Mosk). 2006, 71(11): 1256-1260. Russian. PubMed PDF
Doroshchuk NA, Gelfand MS, Rodionov DA. Regulation of nitrogen metabolism in gram-positive bacteria. Molecular Biology. 2006, 40 (5): 829-836
Gelfand MS. [Bacterial cis-regulatory RNA structures]. Mol Biol (Mosk). 2006, 40(4): 609-19. Russian. PubMed PDF
Sutormin RA, Mironov AA. [Membrane probability profile construction based on amino acids sequences multiple alignment]. Mol Biol (Mosk). 2006, 40(3):541-5. Russian. PubMed PDF
Yang C, Rodionov DA, Li X, Laikova ON, Gelfand MS, Zagnitko OP, Romine MF, Obraztsova AY, Nealson KH, Osterman AL. Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. J Biol Chem. 2006, 281(40):29872-85. PubMed PDF
Danilova L.V, Pervouchine D.D, Favorov A.V, Mironov A.A. RNAKinetics: a web server that models secondary structure kinetics of an elongating RNA. J Bioinform Comput Biol. 2006, 4: 589-96. PubMed PDF
Kucherov G, Mironov AA, Roytberg MA. An overview of the algorithmic session of MCCMB'05. JBCB. 2006, 4(2): xv-xvi. site
Gelfand MS, Makeev VJ, Regnier M, Spirin SA. Introduction to selected papers from the 2nd international moscow conference on computational molecular biology (MCCMB'05), Moscow, Russia, July 18-21, 2005. JBCB. 2006, 4(2): xi-xiv. site
Kalinina OV, Gelfand MS. Amino acid residues that determine functional specificity of NADP- and NAD-dependent isocitrate and isopropylmalate dehydrogenases. Proteins. 2006, 64(4):1001-9 PubMed PDF Supplementary material
Merkeev IV, Novichkov PS, Mironov AA. PHOG: a database of supergenomes built from proteome complements. BMC Evol Biol. 2006, 6(1):52 PubMed PDF
Merkeev I, Mironov AA. PHOG-BLAST - a new generation tool for fast similarity search of protein families. BMC Evol Biol. 2006, 6(1):51 PubMed PDF
Permina EA, Kazakov AE, Kalinina OV, Gelfand MS. Comparative genomics of regulation of heavy metal resistance in Eubacteria. BMC Microbiology 2006, 6:49 PubMed PDF
Spirin V, Gelfand MS, Mironov AA, Mirny LA. A metabolic network in the evolutionary context: Multiscale structure and modularity. Proc Natl Acad Sci U S A. 2006, 103(23):8774-9 PubMed PDF
Gelfand MS. Evolution of transcriptional regulatory networks in microbial genomes. Curr Opin Struct Biol. 2006 Jun;16(3):420-9. PubMed PDF
Todd JD, Sawers G, Rodionov DA, Johnston AW. The Rhizobium leguminosarum regulator IrrA affects the transcription of a wide range of genes in response to Fe availability. Mol Genet Genomics. 2006, 275(6):564-77. PubMed PDF
Litvinov II, Lobanov MIu, Mironov AA, Finkel'shtin MA. [Information about the protein secondary structure improves quality of an alignment of protein sequences] Mol Biol (Mosk). 2006, 40(3):533-40. Russian. PubMed
Feklistov A, Barinova N, Sevostyanova A, Heyduk E, Bass I, Vvedenskaya I, Kuznedelov K, Merkiene E, Stavrovskaya E, Klimasauskas S, Nikiforov V, Heyduk T, Severinov K, Kulbachinskiy A. A basal promoter element recognized by free RNA polymerase sigma subunit determines promoter recognition by RNA polymerase holoenzyme. Mol Cell. 2006, 23(1):97-107. PubMed PDF
Stavrovskaya ED, Makeev VYu, Mironov AA. [ClusterTree-RS: A Binary Tree Algorithm Identifying Coregulated Genes by Clustering Regulatory Signals] Mol Biol (Mosk). 2006, 40(3): 465-473. Russian. PubMed
Giel JL, Rodionov DA, Liu M, Blattner FR, Kiley PJ. IscR-dependent gene expression links iron-sulphur cluster assembly to the control of O2-regulated genes in Escherichia coli. Molecular Microbiology. 2006, 60(4):1058-75 PubMed PDF
Malko DB, Makeev VJ, Mironov AA, Gelfand MS. Evolution of exon-intron structure and alternative splicing in fruit flies and malarial mosquito genomes. Genome Res. 2006, 16(4):505-9 PubMed PDF Supplementary material
Ermakova EO, Nurtdinov RN, Gelfand MS. Fast rate of evolution in alternatively spliced coding regions of mammalian genes. BMC Genomics. 2006, 7(1):84 PubMed PDF
Gelfand MS. Interview to Polit.Ru Feb. 27th 2006.
Neverov AD., Mironov AA., Gelfand MS. Similarity-based gene recognition. Handbook of Computational Molecular Biology (Chapman & Hall/CRC). Ed. Alluru S. 2006, 2-1–2-18
Gelfand MS. Computational analysis of alternative splicing. Handbook of Computational Molecular Biology (Chapman & Hall/CRC). Ed. Alluru S. 2006, 16-1–16-33.
Rodionov DA, Gelfand MS. Computational identification of BioR, a transcriptional regulator of biotin metabolism in alpha-proteobacteria, and of its binding signal. FEMS Microbiol Lett. 2006, 255(1):102-7. PubMed PDF
Rodionov DA, Hebbeln P, Gelfand MS, Eitinger T. Comparative and Functional Genomic Analysis of Prokaryotic Nickel and Cobalt Uptake Transporters: Evidence for a Novel Group of ATP-Binding Cassette Transporters. J Bacteriol. 2006, 188(1):317-27. PubMed PDF
Artamonova II, Frishman G, Gelfand MS, Frishman D. Mining sequence annotation databanks for association patterns. Bioinformatics. 2005, 21: iii49-iii57 PubMed PDF
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Ruckert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V.
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.
Nucleic Acids Res. 2005 Oct 7;33(17):5691-702. Print 2005. PubMed PDF
Rodionov D.A, Dubchak I.L, Arkin A.P, Alm E.J, Gelfand M.S. Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks. PLoS Comput Biol. 2005, 1(5):e55. PubMed PDF
Neverov A.D, Artamonova I.I, Nurtdinov R.N, Frishman D, Gelfand M.S, Mironov A.A. Alternative splicing and protein function. BMC Bioinformatics. 2005, 6(1):266 PubMed PDF
Ravcheev DA, Rakhmaninova AB, Mironov AA, Gel'fand MS. [Comparative genomics analysis of nitrate and nitrite respiration in gamma proteobacteria.] Mol Biol (Mosk). 2005, 39(5):832-46. Russian. PubMed PDF
Seliverstov AV, Gelfand MS, Lyubetsky VA. Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria. BMC Microbiol. 2005. 5: 54. PubMed PDF
Oparina NJ, Kalinina OV, Gelfand MS, Kisselev LL. Common and specific amino acid residues in the prokaryotic release factors RF1 and RF2: possible functional implications. Nucleic Acids Res. 2005. 33(16): 5226-5234. PubMed PDF
Fededa JP, Petrillo E, Gelfand MS, Neverov AD, Kadener S, Nogues G, Pelisch F, Baralle FE, Muro A, Kornblihtt AR. A polar mechanism coordinates different regions of alternative splicing within a single gene. Molecular Cell. 2005, 19 (3): 393-404. PubMed PDF
Gerasimova AV, Gelfand MS. Evolution of the NadR regulon in Enterobacteriaceae. Journal of Bioinformatics and Computational Biology. 2005, 3 (4): 1007-1019. PubMed PDF
Rodionov DA, Gelfand MS. Identification of a Bacterial Regulatory System for Ribonucleotide Reductases by Phylogenetic Profiling. Trends in.Genetics. 2005, 21 (7): 385-389. PubMed PDF
Kotelnikova EA, Makeev VYu, Gelfand MS. Evolution of transcription factor DNA binding sites. Gene. 2005, 347 (2): 255-263. PubMed PDF
Gelfand MS, Gerasimova AV, Kotelnikova EA, Laikova ON, Makeev VY, Mironov AA, Panina EM, Ravcheev DA, Rodionov DA, Vitreschak AG
Comparative genomics and evolution of bacterial regulatory systems.
Bioinformatics of Genome Regulation and Structure II (Springer Science+Business Media, Inc.) P. 111-119 (2005)
Eds. Kolchanov N. and Hofestaedt R.
Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Regnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z. Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol. 2005, 23(1):137-44. PubMed PDF
Favorov AV, Gelfand MS, Gerasimova AV, Ravcheev DA, Mironov AA, Makeev VYu. A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length. Bioinformatics. 2005, 21(10):2240-5. PubMed PDF
Rakhmaninova AB, Kalinina OV, Minin VV. Discriminative sites in the conserved core of various annexin families from vertebrates. Annexins. 2004, 1(2): S137-S142
Gelfand MS. Computational genomics: from the wet lab to computer and back. In: Biomediale: Contemporary Society and Genomic Culture. Ed. Dmitry Bulatov (National Centre for Contemporary Art, Kaliningrad brach). 2004, 28-39.
Artamonova II, Gelfand MS. Evolution of the exon-intron structure and alternative splicing of the MAGE-A family of cancer/testis antigens. J.Mol.Evol. 2004, 69 (5): 620-631. PubMed PDF
K. Popadin, L. Mamirova. [The history of a single chromosome]. Priroda. 2004, 9: 11-16. Russian. PDF
Gelfand MS. Doing science in uncertain times. PloS Biology. 2004, 2(7): 0886-0891. PubMed PDF
Permina EA, Gelfand MS Heat Shock (sigma32 and HrcA/CIRCE) regulons in beta-, gamma and epsilon-proteobacteria. J Mol Microbiol Biotechnol. 2004, 6(3-4): 174-181.
Rodionov DA, Gelfand MS, Hugouvieux-Cotte-Pattat N. Comparative genomics of the KdgR regulon in Erwinia chrysanthemi 3937 and other gamma-proteobacteria. Microbiology. 2004, 150(Pt 11):3571-90. PubMed PDF
Novichkov PS, Omelchenko MV, Gelfand MS, Mironov AA, Wolf YI, Koonin EV. Genome-wide molecular clock and horizontal gene transfer in bacterial evolution. J Bacteriol. 2004, 186(19):6575-85. PubMed PDF
Rouanet C, Reverchon S, Rodionov DA, Nasser W. Definition of a consensus DNA-binding site for PecS, a global regulator of virulence gene expression in Erwinia chrysanthemi and identification of new members of the PecS regulon. J Biol Chem. 2004, 279(29):30158-67 PubMed PDF
Zinin NV, Serkina AV, Gelfand MS, Shevelev AB, Sineoky SP. Gene cloning, expression and characterization of novel phytase from Obesumbacterium proteus. FEMS Microbiol Lett. 2004, 236(2):283-90. PubMed PDF
Kalinina OV, Novichkov PS, 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, 32(Web Server issue):W424-8. PubMed PDF
Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems. Nucleic Acids Res. 2004, 32(11):3340-53. Print 2004. PubMed PDF
Vitreschak AG, Lyubetskaya EV, Shirshin MA, Gelfand MS, Lyubetsky VA. Attenuation regulation of amino acid biosynthetic operons in proteobacteria: comparative genomics analysis. FEMS Microbiol Lett. 2004,234(2):357-70. PubMed PDF
Offman MN, Nurtdinov RN, Gelfand MS, Frishman D. No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions. BMC Bioinformatics. 2004, 5(1):41. PubMed PDF
Kalinina OV, Mironov AA, Gelfand MS, Rakhmaninova AB. Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families. Protein Sci. 2004, 13(2):443-56. PubMed PDF
Rodionov DA, Dubchak I, Arkin A, Alm E, Gelfand MS. Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria. Genome Biol. 2004; 5(11):R90 PubMed PDF
Mironov AA, Gel'fand MS. [Prediction and computer analysis of the exon-intron structure of human genes] Mol Biol (Mosk). 2004, 38(1):82-91. Russian. PubMed PDF
Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS. Riboswitches: the oldest mechanism for the regulation of gene expression? Trends Genet. 2004, 20(1):44-50. PubMed PDF
Panina EM, Mironov AA, Gelfand MS. Comparative genomics of bacterial zinc regulons: enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins.Proc Natl Acad Sci U S A. 2003, 100(17):9912-7. PubMed PDF
