Research interests:

- comparative genomics
- metagenomics
- metabolic reconstruction and functional annotation of
  genes and proteins
- identification of regulatory signals
- evolution of metabolic pathways and regulatory systems
- alternative splicing
- statistics of DNA sequences

Degrees:

2007. Professor of Bioinformatics
1998. Doctor of Science (biology / molecular biology), State Scientific Center for Biotechnology "GosNIIGenetika", Moscow. 'Computer analysis and prediction of functional features in DNA sequences'.
1993. Ph.D./Candidate of Science (mathematics / biophysics), Institute of Theoretical and Experimental Biophysics, Puschino. 'Prediction of splicing sites and protein-coding regions in DNA of higher eukaryotes'.

Awards:

2010. Academia Europaea, Member
2007 A.A.Baev Prize  in Genomics and Genoinformatics (Russian Academy of Sciences) "for work in computer comparative genomics"
December 2007. Award for the best publication in Russian scientific journals in 2005 for a series of papers in "Molecular Biology" ("Nauka/Interperiodica" publishing house)
2004. "Best Scientist of the Russian Academy of Sciences" award, Fund for Support fo the Russian Science
2000. The President of Russian Federation's Award for Young Doctors of Science
1999. A.A.Baev Prize from the Russian State Scientific Council "Human Genome"

Current grants:

2009-2011. Russian Academy of Sciences, program "Basic Sciences for Medicine", project "Age-related changes in gene expression and alternative splicing"
2009-2011. Russian Academy of Sciences, program "Genetic Diversity", project "Modeling of the interactions of an invading phage and the host's restriction-modification system"
2006-2010. Howard Hughes Medical Institute "Comparative genomics and evolution of regulatory systems" (grant 55005610, PI)
2009-2011. Russian Foundation of Basic Research (09-04-92745) "Regulation and evolution of cellular systems"
2008-2012. Russian Academy of Sciences, program "Molecular and Cellular Biology", project "Comparative genomics, reconstruction and modeling, of metabolism and regulation in bacteria and eukaryotes"
2010-2012. Russian Foundation of Basic Research (10-04-00431) "Co-evolution of DNA-binding proteins and their DNA motifs"

Editorial boards:

2009-2011. Member, Editorial Board, Journal of Bacteriology
2006-present. Member, Editorial Board, Molecular Biology (Moscow)
2006-present. Member, Editorial Board, Book Series "Bioinformatics and Molecular Biology", R&CDynamics Publishers (Izhevsk, Russia)
2005-present. Member, Editorial Board, Central European Journal of Biology
2005-2011. Member, Editorial Board, Bioinformatics
2005-present. Member, Editorial Board, Biology Direct
2005-present. Member, Editorial Board, BMC Bioinformatics
2004-present. Member, Editorial Board, Journal of Bioinformatics and Computational Biology
2003-present. Member, Editorial Board, PLoS Biology
2003-present. Member, Editorial Board, Lecture Notes in BioInformatics (LNBI), Springer-Verlag
2002-present. Member, Editorial Review Board, Archaea
2001. Guest Editor, Computerra (in Russian), special issue on Bioinformatics (#36(413))
1997-present. Associate Editor, Journal of Computational Biology
1993. Guest Editor (with P.Pevzner), BioSystems, vol. 30 "Computer Genetics"

Publications:

Ulianov S.V., Khrameeva E.E., Gavrilov A.A., Flyamer I.M., Kos P., Mikhaleva E.A., Penin A.A., Logacheva M.D., Imakaev M.V., Chertovich A., Gelfand M.S., Shevelyov Y.Y., Razin S.V. Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains. Genome Res. 2016 Jan;26(1):70-84. PubMedPDF
Ravcheev D.A., Khoroshkin M.S., Laikova O.N., Tsoy O.V., Sernova N.V., Petrova S.A., Rakhmaninova A.B., Novichkov P.S., Gelfand M.S. and Rodionov D.A. Comparative genomics and evolution of regulons of the LacI-family transcription factors. Front Microbiol. 2014 Jun 11;5:294. PubMed  PDF

Garushyants SK, Kazanov MD, Gelfand MS. Horizontal gene transfer and genome evolution in Methanosarcina.BMC Evol Biol. 2015 Jun 5;15:102.PubMed 

Denisov S.V., Bazykin G.A., Sutormin R., Favorov A.V., Mironov A.A., Gelfand M.S. and Kondrashov A.S. Weak Negative and Positive Selection and the Drift Load at Splice Sites. Genome Biol Evol. 2014 May 14;6(6):1437-47. PubMed  PDF

Ian E., Malko D.B., Sekurova O.N., Bredholt H., Ruckert C., Borisova M.E., Albesmeier A., Kalinowski J., Gelfand M.S., Zotchev S.B. Genomics of Sponge-Associated Streptomyces spp. Closely Related to Streptomyces albus J1074: Insights into Marine Adaptation and Secondary Metabolite Biosynthesis Potential . PLoS One. 2014 May 12;9(5):e96719. PubMed 

Khrameeva EE, Bozek K, He L, Yan Z, Jiang X, Wei Y, Tang K, Gelfand MS, Prufer K, Kelso J, Paabo S, Giavalisco P, Lachmann M, Khaitovich P. Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans. Nature Communications, 2014 Apr 1. PubMed PDF

  Gogleva A.A. (prev. Nikulova), Gelfand M.S., Artamonova I.I. Comparative analysis of CRISPR cassettes from the human gut metagenomic contigs. BMC Genomics. 2014 Mar 17;15:202. PubMed 

Rossbach O, Hung LH, Khrameeva E, Schreiner S, Konig J, Curk T, Zupan B, Ule J, Gelfand MS, Bindereif A. Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L. RNA Biology, 2014 Feb 7. PubMed PDF

Belushkin AA, Vinogradov DV, Gelfand MS, Osterman AL, Cieplak P, Kazanov MD. Sequence-derived structural features driving proteolytic processing. Proteomics. 2013 Nov 13. PubMed 

Gennady V. Ponomarev, Vladimir L. Arlazarovb, Mikhail S. Gelfand, Marat D. Kazanov. ANA HEp-2 cells image classification using number, size, shape and localization of targeted cell regions ScienceDirect Available online 1 October 2013, ISSN 0031-3203. ScienceDirect  PDF

Kurmangaliyev, YZ; Sutormin, RA; Naumenko, SA; Bazykin, GA; Gelfand, MS. Functional implications of splicing polymorphisms in the human genome. Human Molecular Genetics 2013 Sep 1;22(17):3449-59. PubMed 

Rueda, S., Fathima, S., Knight, C., Yaqub, M., Papageorghiou, A., Rahmatullah, B., Foi, A., Maggioni, M., Pepe, A., Tohka, J., Stebbing, R.V., McManigle, J.E., Ciurte, A., Bresson, X., Cuadra, M.B., Sun, C., Ponomarev, G.V., Gelfand, M.S., Kazanov, M.D., Wang, C., Chen, H., Hung, C., Noble, J.A. Evaluation and Comparison of Current Fetal Ultrasound Image Segmentation Methods for Biometric Measurements: A Grand Challenge IEEE Trans Med Imaging. 2013 Aug 6. PubMed 

  Cipriano M.J., Novichkov P.N., Kazakov A.E., Rodionov D.A., Arkin A.P., Gelfand M.S., Dubchak I. RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes. BMC Genomics 2013 14(213. PubMed  PDF

Kurmangaliyev Y.Z., Sutormin R.A., Naumenko S.A., Bazykin G.A., Gelfand M.S. Functional implications of splicing polymorphisms in the human genome. Hum Mol Genet 2013 PubMed  PDF

Gordienko E.N., Kazanov M.D., Gelfand M.S. Evolution of Pan-Genomes of Escherichia coli, Shigella spp., and Salmonella enterica. J Bacteriol 2013 195(12): 2786-2792. PubMed  PDF

Kazanov M.D., Li X., Gelfand M.S., Osterman A.L., Rodionov D.A. Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum. Nucleic Acids Res 2013 41(2): 790-803. PubMed  PDF

 Tsoy O.V., Pyatnitskiy M.A., Kazanov M.D., Gelfand M.S. Evolution of transcriptional regulation in closely related bacteria. BMC Evol Biol 2012 12(1): 200. PubMed  PDF

Sernova N.V., Gelfand M.S. Comparative genomics of CytR, an unusual member of the LacI family of transcription factors. PLoS One 2012 7(9): e44194. PubMed  PDF

De Ingeniis J., Kazanov M.D., Shatalin K., Gelfand M.S., Osterman A.L., Sorci L. Glutamine versus ammonia utilization in the NAD synthetase family. PLoS One 2012 7(6): e39115. PubMed  PDF

Khrameeva E.E., Gelfand M.S. Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments. BMC Bioinformatics 2012 13 Suppl 6:S4. PubMed  PDF

Suvorova I.A., Ravcheev D.A., Gelfand M.S. Regulation and evolution of malonate and propionate catabolism in proteobacteria. J Bacteriol 2012 194(12): 3234-3240. PubMed  PDF

Khrameeva E.E., Mironov A.A., Fedonin G.G., Khaitovich P., Gelfand M.S. Spatial proximity and similarity of the epigenetic state of genome domains. PLoS One 2012 7(4): e33947. PubMed  PDF

Gorbunov K.Y., Laikova O.N., Rodionov D.A., Gelfand M.S., Lyubetsky V.A. Evolution of regulatory motifs of bacterial transcription factors. In Silico Biol 2010 10(3): 163-183. PubMed  PDF

Pavlova O., Lavysh D., Klimuk E., Djordjevic M., Ravcheev D.A., Gelfand M.S., Severinov K., Akulenko N. Temporal regulation of gene expression of the Escherichia coli bacteriophage phiEco32. J Mol Biol 2012 416(3): 389-399. PubMed  PDF

Pervouchine D.D., Khrameeva E.E., Pichugina M.Y., Nikolaienko O.V., Gelfand M.S., Rubtsov P.M., Mironov A.A. Evidence for widespread association of mammalian splicing and conserved long-range RNA structures. Rna 2012 18(1): 1-15. PubMed  PDF

Vinogradov D.V., Tsoi O.V., Zaika A.V., Lobanov A.V., Turanov A.A., Gladyshev V.N., Gel'fand M.S. [Draft macronuclear genome of a ciliate Euplotes crassus]. Mol Biol (Mosk) 2012 46(2): 361-366. Russian. PubMed  PDF

Rodionov D.A, Novichkov P.S, Stavrovskaya E.D, Rodionova I.A, Li X, Kazanov M.D, Ravcheev D.A, Gerasimova A.V, Kazakov A.E, Kovaleva G.Y, Permina E.A, Laikova O.N, Overbeek R, Romine M.F, Fredrickson J.K, Arkin A.P, Dubchak I, Osterman A.L, Gelfand M.S. Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. BMC Genomics. 2011, 12 Suppl 1: S3. PubMed  PDF

Suvorova I.A, Tutukina M.N, Ravcheev D.A, Rodionov D.A, Ozoline O.N, Gelfand M.S. Comparative genomic analysis of the hexuronate metabolism genes and their regulation in gammaproteobacteria. J Bacteriol. 2011, 193: 3956-63. PubMed  PDF

M.S.Gelfand. Dynamic programming: one algorithmic key to several biological problems. Bioinformatics for Biologists (P.Pevzner and R.Shamir, eds.). 2011: 66-92.

Fedonin G.G., Rakhmaninova A.B., Korostelev Iu D., Laikova O.N., Gel'fand M.S. [Machine learning study of DNA binding by transcription factors from the LacI family]. Mol Biol (Mosk) 2011 45(4): 724-737. Russian. PubMed  PDF

Gerasimova A, Kazakov A.E, Arkin A.P, Dubchak I, Gelfand M.S. Comparative genomics of the dormancy regulons in mycobacteria. J Bacteriol. 2011, 193: 3446-52. PubMed  PDF

Kurmangaliyev Y.Z, Goland A., Gelfand M.S. Evolutionary patterns of phosphorylated serines. Biol Direct. 2011, s6: 8. PubMed  PDF

 Logacheva M.D, Kasianov A.S, Vinogradov D.V, Samigullin T.H, Gelfand M.S, Makeev V.J, Penin A.A. De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum). BMC Genomics. 2011, 12: 30. PubMed  PDF

Fedonin G.G, Gelfand M.S. Machine Learning Study of DNA Binding by Transcription Factors from the LacI family. 2010 Lecture Notes in Computer Science / Lecture Notes in Bioinformatics. Proceedings 5th IAPR International Conference "Pattern Recognition in Bioinformatics", PRIB 2010. 6282: 15-26. PDF

Sorokin V, Severinov K, Gelfand M.S. Large-scale identification and analysis of C-proteins. Methods Mol Biol. 2010, 674: 269-82. PubMed  PDF

Zharov I.A., Gel'fand M.S., Kazakov A.E. [Regulation of multidrug resistance genes by transcriptional factors from the BltR subfamily]. Mol Biol (Mosk) 2011 45(4): 715-723. Russian. PubMed  PDF

Panchin A.Yu, Gelfand M.S, Ramensky V.E, Artamonova II. Asymmetric and non-uniform evolution of recently duplicated human genes. Biol Direct. 2010, 5: 54. PubMed  PDF

Enikeeva F.N, Severinov K.V, Gelfand M.S. Restriction-modification systems and bacteriophage invasion: who wins? J Theor Biol. 2010, 266: 550-9. 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. 2010, 5: 29. PubMed  PDF

Gelfand M.S. Introduction: 4th International Moscow Conference on Computational Molecular Biology MCCMB'09. J Bioinform Comput Biol. 2010, 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. 2010, 38: W299-307. 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. 2010, 76: 2136-44. PubMed  PDF

Kurmangaliyev, YZ; Gelfand, MS. Alternative splicing tends to involve protein phosphorylation sites. Molecular Biology 43(3), 528-530 (2009) ResearchGate  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

 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. 2010, 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

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

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

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

Kazakov A.E, Rodionov D.A, Alm E, Arkin A.P, Dubchak I, Gelfand M.S. 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

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

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

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

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

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

Artamonova II, Gelfand MS. Comparative genomics and evolution of alternative splicing: the pessimists' science. Chem Rev. 2007, 107(8):3407-30. 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

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, 73: 3440-5. 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

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

Gelfand. The view from Russia. Nature. 2006, 444:240. PubMed  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

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. 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

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

 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

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

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

Gelfand MS, Makeev VJ, Regnier M, Spirin SA. (2006) Introduction to selected papers from the 2nd international moscow conference on computational molecular biology (MCCMB'05), Moscow, Russia, July 18-21, 2005. Journal of Bioinformatics and Computational Biology. 4 (2): xi-xiv. site 

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.

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

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

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 MAGEA family of cancer/testis antigens. J.Mol.Evol. 2004, 69 (5): 620-631.

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

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

Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch? Nucleic Acids Res. 2003, 31(23):6748-57. PubMed   PDF

Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes. J Biol Chem. 2003, 278(42):41148-59 PubMed   PDF

Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL. Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol. 2003, 185(19):5673-84. PubMed   PDF

Danilova LV, Gel'fand MS, Liubetskii VA, Laikova ON. [Computer analysis of regulating metabolism of glycerol-3-phosphate in proteobacteria genome] Mol Biol (Mosk). 2003, 37(5):843-9. Russian. PubMed   PDF

Liubetskaia EV, Leont'ev LA, Gel'fand MS, Liubetskii VA. [Search for alternative secondary structures of RNA, regulating expression of bacterial genes] Mol Biol (Mosk). 2003, 37(5):834-42. Russian. PubMed

Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS. Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element. RNA. 2003, 9(9):1084-97. 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

V'iugin VV, Gel'fand MS, Liubetskii VA. [Identification of the horizontal gene transfer based on phylogenetic data] Mol Biol (Mosk). 2003, 37(4):674-87. Russian. PubMed

Nurtdinov RN, Artamonova II, Mironov AA, Gelfand MS. Low conservation of alternative splicing patterns in the human and mouse genomes. Hum Mol Genet. 2003, 12(11):1313-20. PubMed   PDF

Panina EM, Vitreschak AG, Mironov AA, Gelfand MS. Regulation of biosynthesis and transport of aromatic amino acids in low-GC Gram-positive bacteria. FEMS Microbiol Lett. 2003, 222(2):211-20. PubMed   PDF

Sutormin RA, Rakhmaninova AB, Gelfand MS. BATMAS30: amino acid substitution matrix for alignment of bacterial transporters. Proteins. 2003, 51(1):85-95. PubMed   PDF

Kriventseva EV, Koch I, Apweiler R, Vingron M, Bork P, Gelfand MS, Sunyaev S. Increase of functional diversity by alternative splicing. Trends Genet. 2003, 19(3):124-8. PubMed   PDF

Kalinina OV, Makeev VJ, Sutormin RA, Gelfand MS, Rakhmaninova AB. The channel in transporters is formed by residues that are rare in transmembrane helices. In Silico Biol. 2003, 3(1-2):197-204. PubMed

Danilova LV, Lyubetsky VA, Gelfand MS. An algorithm for identification of regulatory signals in unaligned DNA sequences, its testing and parallel implementation. In Silico Biol. 2003, 3(1-2):33-47 PubMed

Kazakov AE, Vassieva O, Gelfand MS, Osterman A, Overbeek R. Bioinformatics classification and functional analysis of PhoH homologs. In Silico Biol. 2003, 3(1-2):3-15 PubMed

Permina EA, Gelfand MS. Heat shock (sigma32 and HrcA/CIRCE) regulons in beta-, gamma- and epsilon-proteobacteria. J Mol Microbiol Biotechnol. 2003, 6(3-4):174-81. PubMed

Holsappel S, Gagarina EIu, Poluektova EU, Hezametdinova VZ, Gel'fand MS, Prozorov AA, Bron S. [The structure of the transposable genetic element ISBsu2 in the cryptic plasmid p1516 from a soil Bacillus subtilis strain and the presence of homologues of this element in the chromosomes of various Bacillus subtilis strains] Mikrobiologiia. 2003, 72(1):70-5. Russian. PubMed

Eskin E, Keich U, Gelfand MS, Pevzner PA. Genome-wide analysis of bacterial promoter regions. Pac Symp Biocomput. 2003, 29-40. PubMed

Gerasimova AV, Gelfand MS, Makeev VYu, Mironov AA, FavorovAV. ArcA regulator of gamma-proteobacteria: identification of the binding signal and description of the regulon. Biophysics (Moscow). 2003, 48 Suppl. 1 S21-S25 PDF

Kovaleva GYu, Makeev VYu, Gelfand MS. Computer analysis of the GCN4 regulon of yeast Saccharomyces cerevisiae. Biophysics (Moscow). 2003, 48 Suppl. 1 S26-S29 PDF

Denisov S, Gelfand MS. Conservedness of the alternative splicing signal UGCAUG in the human and mouse genomes. Biophysics (Moscow). 2003, 48 Suppl. 1 S30-S35 PDF

Neverov A.D, Gelfand M.S, Mironov A.A. GipsyGene: a statistics-based gene recognizer for fungal genomes. Biophysics (Moscow), 2003, 48 Suppl. 1 S71-S75 PDF

Kalinina O.V, Gelfand M.S, Mironov A.A, Rakhmaninova A.B. Amino acid residues forming specific contacts between subunits in tetramers of the membrane channel GlpF. Biophysics (Moscow). 2003, 48 Suppl. 1 S141-S145 PDF

Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms. J Biol Chem. 2002, 277(50):48949-59 PubMed   PDF

Rodionov DA, Mironov AA, Gelfand MS. Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea. Genome Res. 2002, 12(10):1507-16. PubMed   PDF

Poluektova EU, Holsappel S, Gagarina EY, Gelfand MS, Bron S, Prozorov AA. The presence of the transposable element ISBsu2 from a cryptic plasmid in chromosomes of some Bacillus subtilis strains. Dokl Biochem Biophys. 2002, 386:275-7. PubMed

Ravcheev DA, Gel'fand MS, Mironov AA, Rakhmaninova AB. [Purine regulon of gamma-proteobacteria: a detailed description] Genetika. 2002, 38(9):1203-14. Russian. PubMed   PDF

V'iugin VV, Gel'fand MS, Liubetskii VA. [Tree reconciliation: reconstruction of species evolution by phylogenetic gene trees] Mol Biol (Mosk). 2002, 36(5):807-16. Russian. PubMed

Mirny LA, Gelfand MS. Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors. J Mol Biol. 2002, 321(1):7-20. PubMed   PDF

Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS. Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. Nucleic Acids Res. 2002, 30(14):3141-51. PubMed   PDF

Nurtdinov RN, Mironov AA, Gel'fand MS. [Is alternative splicing of mammalian genes conservative?] Biofizika. 2002, 47(4):587-94. Russian. PubMed

Kotel'nikova EA, Gel'fand MS. [Regulation of transcription in the system of genes responsible for bacteriocins production in Streptococcus equi] Genetika. 2002, 38(7):911-5. Russian. PubMed   PDF

Sadovskaya NS, Sutormin RA, Rakhmaninova AB, Gelfand MS. The comparative analysis of programs for prediction of transmembrane segments in transmembrane proteins. Information Processes. 2002, 2(1): 96-99. [The article in Russian] PDF

Permina EA, Mironov AA, Gelfand MS. Damage-repair error-prone polymerases of eubacteria: association with mobile genome elements. Gene. 2002, 293(1-2):133-40. PubMed   PDF

Baytaluk MV, Gelfand MS, Mironov AA. Exact mapping of prokaryotic gene starts. Brief Bioinform. 2002, 3(2):181-94. PubMed   PDF

Kotel'nikova EA, Gel'fand MS. [Production of bacteriocins by gram-positive bacteria and the mechanisms of transcriptional regulation] Genetika. 2002, 38(6):758-72. Russian. PubMed

Mirny LA, Gelfand MS. Structural analysis of conserved base pairs in protein-DNA complexes. Nucleic Acids Res. 2002, 30(7):1704-11. PubMed   PDF

Baitaliuk MV, Gel'fand MS, Mironov AA. [Comparative approach to correction of annotated gene starts in complete bacterial genomes] Biofizika. 2002, 47(2):197-203. Russian. PubMed

Mirny LA, Gelfand MS. Using orthologous and paralogous proteins to identify specificity determining residues. Genome Biol. 2002, 3(3): PREPRINT0002. PubMed   PDF

Ponomarenko JV, Orlova GV, Frolov AS, Gelfand MS, Ponomarenko MP. SELEX_DB: a database on in vitro selected oligomers adapted for recognizing natural sites and for analyzing both SNPs and site-directed mutagenesis data. Nucleic Acids Res. 2002, 30(1):195-9. PubMed   PDF

Sze SH, Gelfand MS, Pevzner PA. Finding weak motifs in DNA sequences. Pac Symp Biocomput. 2002, 235-46. PubMed

Laikova ON, Mironov AA, Gelfand MS. Computational analysis of the transcriptional regulation of pentose utilization systems in the gamma subdivision of Proteobacteria. FEMS Microbiol Lett. 2001, 205(2):315-22. PubMed   PDF

Rodionov DA, Mironov AA, Gelfand MS. Transcriptional regulation of pentose utilisation systems in the Bacillus/Clostridium group of bacteria. FEMS Microbiol Lett. 2001, 205(2):305-14. PubMed   PDF

Panina EM, Mironov AA, Gelfand MS. Comparative analysis of FUR regulons in gamma-proteobacteria. Nucleic Acids Res. 2001, 29(24):5195-206. PubMed   PDF

Novichkov PS, Gelfand MS, Mironov AA. Gene recognition in eukaryotic DNA by comparison of genomic sequences. Bioinformatics. 2001, 17(11):1011-8. PubMed   PDF

Danilova LV, Gorbunov KIu, Gel'fand MS, Liubetskii VA. [Algorithms for isolating regulatory signals in DNA sequences] Mol Biol (Mosk). 2001, 35(6):987-95. Russian. PubMed   PDF

Sadovskaya NS, Laikov ON, Mironov AA, Gel'fand MS. [Study on regulation of long-chain fatty acid metabolism with the use of computer analysis of complete bacterial genomes] Mol Biol (Mosk). 2001, 35(6):1010-4. Russian. PubMed   PDF

Gerasimova AV, Rodionov DA, Mironov AA, Gel'fand MS. [Computer analysis of regulatory signals in bacterial genomes. Fnr binding segments] Mol Biol (Mosk). 2001, 35(6):1001-9. Russian. PubMed   PDF

Panina EM, Vitreschak AG, Mironov AA, Gelfand MS. Regulation of aromatic amino acid biosynthesis in gamma-proteobacteria. J Mol Microbiol Biotechnol. 2001, 3(4):529-43. PubMed   PDF

Brudno M, Gelfand MS, Spengler S, Zorn M, Dubchak I, Conboy JG. Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing. Nucleic Acids Res. 2001, 29(11):2338-48. PubMed   PDF

Rodionov DA, Gelfand MS, Mironov AA, Rakhmaninova AB. Comparative approach to analysis of regulation in complete genomes: multidrug resistance systems in gamma-proteobacteria. J Mol Microbiol Biotechnol. 2001, 3(2):319-24. PubMed   PDF

Mironov AA, Novichkov PS, Gelfand MS. Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors. Bioinformatics. 2001, 17(1):13-5. PubMed   PDF

Makarova KS, Mironov AA, Gelfand MS. Conservation of the binding site for the arginine repressor in all bacterial lineages. Genome Biol. 2001, 2(4):RESEARCH0013 PubMed   PDF

Gelfand MS, Novichkov PS, Novichkova ES, Mironov AA. Comparative analysis of regulatory patterns in bacterial genomes. Brief Bioinform. 2000, 1(4):357-71. PubMed

Rodionov DA, Mironov AA, Rakhmaninova AB, Gelfand MS. Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria. Mol Microbiol. 2000, 38(4):673-83. PubMed   PDF

Kreneva RA, Gel'fand MS, Mironov AA, Iomantas IuA, Kozlov IuI, Mironov AS, Perumov DA. [Study of the phenotypic occurrence of ura gene inactivation in Bacillus subtilis] Genetika. 2000, 36(8):1166-8. Russian. PubMed

Vitreshchak AG, Gel'fand MS. [Computer analysis of signals of regulation in bacterial genomes. Attenuators of operons of aromatic amino acids metabolism] Mol Biol (Mosk). 2000, 34(4):545-52. Russian. PubMed

Mironov AA, Vinokurova NP, Gel'fand MS. [Software for analyzing bacterial genomes] Mol Biol (Mosk). 2000, 34(2):253-62. Russian. PubMed

Panina EM, Mironov AA, Gel'fand MS. [Statistical analysis of complete bacterial genomes: palindromes and systems of restriction-modification] Mol Biol (Mosk). 2000, 34(2):246-52. Russian. PubMed

Novichkov PS, Gel'fand MS, Mironov AA. [Prediction of the exon-intron structure by comparing nucleotide sequences from various genomes] Mol Biol (Mosk). 2000, 34(2):230-6. Russian. PubMed

Gelfand MS, Koonin EV, Mironov AA. Prediction of transcription regulatory sites in Archaea by a comparative genomic approach. Nucleic Acids Res. 2000, 28(3):695-705. PubMed   PDF

Dralyuk I, Brudno M, Gelfand MS, Zorn M, Dubchak I. ASDB: database of alternatively spliced genes. Nucleic Acids Res. 2000, 28(1):296-7. PubMed   PDF

Peshkin L, Gelfand MS. Segmentation of yeast DNA using hidden Markov models. Bioinformatics. 1999, 15(12):980-6. PubMed   PDF

Mironov AA, Fickett JW, Gelfand MS. Frequent alternative splicing of human genes. Genome Res. 1999, 9(12):1288-93. PubMed   PDF

Gel'fand MS, Mironov AA. [Computational biology at the turn of the decade] Mol Biol (Mosk). 1999, 33(6):969-84. Russian. PubMed

Gelfand MS. Recognition of regulatory sites by genomic comparison. Res Microbiol. 1999, 150(9-10):755-71. PubMed

Gelfand MS, Mironov AA, Jomantas J, Kozlov YI, Perumov DA. A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes. Trends Genet. 1999, 15(11):439-42. PubMed   PDF

Kriventseva EV, Gelfand MS. Statistical analysis of the exon-intron structure of higher and lower eukaryote genes. J Biomol Struct Dyn. 1999, 17(2):281-8. PubMed

Gel'fand MS, Mironov AA. [Computer analysis of regulatory signals in complete bacterial genomes. Participation of LexA and DinR binding] Mol Biol (Mosk). 1999, 33(5):772-8. Russian. PubMed

Mironov AA, Koonin EV, Roytberg MA, Gelfand MS. Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes. Nucleic Acids Res. 1999, 27(14):2981-9. PubMed   PDF

Borovina TA, Nazipova NN, Overbik R, Gel'fand MS. [Statistical analysis and prediction of bacterial sites for ribosomal binding] Biofizika. 1999, 44(4):611-9. Russian. PubMed

Vitreshchak A, Bansal AK, Titov II, Gel'fand MS. [Computer analysis of regulatory signals in complete bacterial genomes. Translation initiation of ribosomal protein operons] Biofizika. 1999, 44(4):601-10. Russian. PubMed

Kriventseva EV, Makeev VIu, Gel'fand MS. [Statistical analysis of the exon-intron structure of higher eukaryote genes] Biofizika. 1999, 44(4):595-600. Russian. PubMed

Mironov AA, Frishman D, Gelfand MS. [Computer analysis of regulatory signals in complete bacterial genomes. Participation of ribosome binding] Mol Biol (Mosk). 1999, 33(1):133-40. Russian. PubMed

Mironov AA, Gel'fand MS. [Computer analysis of regulatory signals in complete bacterial genomes. Participation of PurR binding] Mol Biol (Mosk). 1999, 33(1):127-32. Russian. PubMed

Gelfand MS, Dubchak I, Dralyuk I, Zorn M. ASDB: database of alternatively spliced genes. Nucleic Acids Res. 1999, 27(1):301-2. PubMed   PDF

Frishman D, Mironov A, Gelfand M. Starts of bacterial genes: estimating the reliability of computer predictions. Gene. 1999, 234(2):257-65. PubMed   PDF

Frishman D, Mironov A, Mewes H.-W, Gelfand M. Combining diverse evidence for gene recognition in completely sequenced bacterial genomes. Nucleic Acids Research. 1998, 26(12):2941-7. PubMed   PDF

Mironov AA, Roytberg MA, Pevzner PA, Gelfand MS. Performance-guarantee gene predictions via spliced alignment. Genomics. 1998, 51(3):332-9. PubMed   PDF

Sze SH, Roytberg MA, Gelfand MS, Mironov AA, Astakhova TV, Pevzner PA. Algorithms and software for support of gene identification experiments. Bioinformatics. 1998, 14(1):14-9. PubMed   PDF

Gel'fand MS. [Computer analysis of DNA sequences] Mol Biol (Mosk). 1998, 32(1):103-20. Russian. PubMed

Gelfand MS, Koonin EV. Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes. Nucleic Acids Res. 1997, 25(12):2430-9. Erratum in: Nucleic Acids Res 1997, 25(24):5135-6. PubMed   PDF

Gel'fand MS, Pugachev VV, Evgrafov OV. [A new member of the MER2 repeat family is detected in the promoter region of the human X11 gene] Dokl Akad Nauk. 1997, 354(5):690-5. Russian. PubMed

Shchepetkova IL, Gel'fand MS. [Statistical characteristics of splicing sites in vertebrates and invertebrates] Biofizika. 1997, 42(1):82-91. Russian. PubMed

Roytberg MA, Astakhova TV, Gelfand MS. Combinatorial approaches to gene recognition. Comput Chem. 1997, 21(4):229-35. PubMed   PDF

Roitberg MA, Astakhova TV, Gel'fand MS. [A combinatorial algorithm for highly specific recognition of protein-coding regions in DNA sequences from higher eukaryotes] Mol Biol (Mosk). 1997, 31(1):25-31. Russian. PubMed

Gelfand MS, Mironov AA, Pevzner PA. Gene recognition via spliced sequence alignment. Proc Natl Acad Sci U S A. 1996, 93(17):9061-6. PubMed   PDF

Gelfand MS, Podolsky LI, Astakhova TV, Roytberg MA. Recognition of genes in human DNA sequences. J Comput Biol. 1996, 3(2):223-34. PubMed

Gelfand MS. FANS-REF: a bibliography on statistics and functional analysis of nucleotide sequences. Comput Appl Biosci. 1995, 11(5):541. PubMed

Razgulyaev O, Rubinov A, Gelfand M, Chetverin A. Sequencing potential of nested strand hybridization. J Comput Biol. 1995, 2(2):383-95. PubMed

Rubinov AR, Gelfand MS. Reconstruction of a string from substring precedence data. J Comput Biol. 1995, 2(2):371-81. PubMed

Gelfand MS. Prediction of function in DNA sequence analysis. J Comput Biol. 1995, 2(1):87-115. PubMed

Gelfand MS. Genetic language: metaphore or analogy? Biosystems. 1993, 30(1-3):277-88. PubMed

Gelfand MS, Roytberg MA. Prediction of the exon-intron structure by a dynamic programming approach. Biosystems. 1993, 30(1-3):173-82. PubMed

Gelfand MS. Statistical analysis and prediction of the exonic structure of human genes. J Mol Evol. 1992, 35(3):239-52. PubMed

Gelfand MS, Kozhukhin CG, Pevzner PA. Extendable words in nucleotide sequences. Comput Appl Biosci. 1992, 8(2):129-35. PubMed

Gelfand MS. Computer prediction of the exon-intron structure of mammalian pre-mRNAs. Nucleic Acids Res. 1990, 18(19):5865-9.PubMed   PDF

Gel'fand MS. [Statistical analysis of splicing sites in mammals] Mol Biol (Mosk). 1989, 23(5):1428-39. Russian. PubMed

Gelfand MS. Statistical analysis of mammalian pre-mRNA splicing sites. Nucleic Acids Res. 1989, 17(15):6369-82. PubMed   PDF

Gelfand MS, Goncharov AB. Spatial rotational alignment of identical particles in the case of (almost) coaxial projections. Ultramicroscopy. 1989, 27(3):301-6. PubMed