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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
Pendlebury D, Wang R, Henin RD, Hockla A, Soares AS, Madden BJ, Kazanov MD, Radisky ES. Sequence and Conformational Specificity in Substrate Recognition: Several Human Kunitz Protease Inhibitor Domains Are Specific Substrates of Mesotrypsin. J Biol Chem 2014 Oct 9PubMed 

Ratnikov BI, Cieplak P, Gramatikoff K, Pierce J, Eroshkin A, Igarashi Y, Kazanov M, Sun Q, Godzik A, Osterman A, Stec B, Strongin A, Smith JW Basis for substrate recognition and distinction by matrix metalloproteinases. Proc Natl Acad Sci USA 2014 Oct 7PubMed 

Гущанская Е.С., Артемов А.А., Ульянов С.В., Пенин А.А., Логачева М.Д., Разин С.В., Гаврилов А.А. Пространственная организация генов домашнего хозяйства в интерфазных ядрах Молекулярная биология 2014, т. 48, №6:1008-1018   PDF

Gushchanskaya E.S., Artemov A.V., Ulyanov S.V., Logacheva M.D., Penin A.A., Kotova E.S., Akopov S.B., Nikolaev L.G., Iarovaia O.V., Sverdlov E.D., Gavrilov A.A., Razin S.V. The clustering of CpG islands may constitute an important determinant of the 3D organization of interphase chromosomes. Epigenetics. 2014 Jul;9(7):951-63. PubMed  PDF

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

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

Sorci L, Brunetti L, Cialabrini L, Mazzola F, Kazanov MD, D'Auria S, Ruggieri S, Raffaelli N. Characterization of bacterial NMN deamidase as a Ser/Lys hydrolase expands diversity of serine amidohydrolases. FEBS Lett. 2014 Mar 18PubMed 

  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 

Novichkov PS, Kazakov AE, Ravcheev DA, Leyn SA, Kovaleva GY, Sutormin RA, Kazanov MD, Riehl W, Arkin AP, Dubchak I, Rodionov DA. RegPrecise 3.0 -- A resource for genome-scale exploration of transcriptional regulation in bacteria. BMC Genomics. 2013 Nov 1;14(1):745. PubMed  PDF

Gorbachev AY, Fisunov GY, Izraelson M, Evsyutina DV, Mazin PV, Alexeev DG, Pobeguts OV, Gorshkova TN, Kovalchuk SI, Kamashev DE, Govorun VM. DNA repair in Mycoplasma gallisepticum.BMC Genomics. 2013 Oct 23;14:726. 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

Sun EI, Leyn SA, Kazanov MD, Saier MH Jr, Novichkov PS, Rodionov DA. Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria. BMC Genomics. 2013 Sep 2;14:597.PubMed  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 

Cialabrini L, Ruggieri S, Kazanov MD, Sorci L, Mazzola F, Orsomando G, Osterman AL, Raffaelli N. Genomics-guided analysis of NAD recycling yields functional elucidation of COG1058 as a new family of pyrophosphatases. PLoS One. 2013 Jun 12;8(6):e65595.PubMed  PDF

  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

Leyn S.A., Kazanov M.D., Sernova N.V., Ermakova E.O., Novichkov P.S., Rodionov D.A. Genomic Reconstruction of the Transcriptional Regulatory Network in Bacillus subtilis. J Bacteriol 2013 195(11): 2463-2473. PubMed  PDF

Ravcheev D.A., Best A.A., Sernova N.V., Kazanov M.D., Novichkov P.S., Rodionov D.A. Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria. BMC Genomics 2013 14(94. 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

De Ingeniis J., Ratnikov B., Richardson A.D., Scott D.A., Aza-Blanc P., De S.K., Kazanov M., Pellecchia M., Ronai Z., Osterman A.L., Smith J.W. Functional specialization in proline biosynthesis of melanoma. PLoS One 2012 7(9): e45190. 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

Favorov A., Mularoni L., Cope L.M., Medvedeva Y., Mironov A.A., Makeev V.J., Wheelan S.J. Exploring massive, genome scale datasets with the GenometriCorr package. PLoS Comput Biol 2012 8(5): e1002529. PubMed  PDF

Nikulova A.A., Polishchuk M.S., Tumanian V.G., Makeev V., Mironov A.A., Favorov A.V. [Correlations between clusters of protein-DNA binding sites and the binding experimental data allow to predict a structure of regulatory modules]. Biofizika 2012 57(2): 212-214. 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

Nikulova A.A., Favorov A.V., Sutormin R.A., Makeev V.J., Mironov A.A. CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation. Nucleic Acids Res 2012 40(12): e93. 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

Ravcheev D.A., Li X., Latif H., Zengler K., Leyn S.A., Korostelev Y.D., Kazakov A.E., Novichkov P.S., Osterman A.L., Rodionov D.A. Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor Rex. J Bacteriol 2012 194(5): 1145-1157. 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

Chursov A., Walter M.C., Schmidt T., Mironov A., Shneider A., Frishman D. Sequence-structure relationships in yeast mRNAs. Nucleic Acids Res 2012 40(3): 956-962. PubMed  PDF

F. Smedile, E. Messina, V. La Cono, O. Tsoy, L.S. Monticelli, M. Borghini, L. Giuliano, P.N. Golyshin, A. Mushegian, M.M. Yakimov. Metagenomic analysis of hadopelagic microbial assemblages thriving at the deepest part of Mediterranean Sea, Matapan-Vavilov Deep. Environ Microbiol. 2012, PubMed  PDF

Д. В. Виноградов, О. В. Цой, А. В. Заика, А. В. Лобанов, А. А. Туранов, В. Н. Гладышев, М. C. Гельфанд. Предварительная версия генома макронуклеуса инфузории Euplotes crassus. Молекулярная биология. 2012, 46(2): 361-366. 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

Khrameeva E.E., Mironov A.A., Gelfand M.S. The impact of interchromosomal associations on the functional state of the human genome. J. Biomol. Struct. Dynam. 2011, 28: 112.

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

Федонин Г.Г., Рахманинова А.Б., Коростелев Ю.Д., Лайкова О.Н., Гельфанд М.С. Изучение связывания ДНК факторами транскрипции LacI семейства методами машинного обучения. Молекулярная биология 2011 45(4): 724-737. Russian. PubMed  PDF

Leyn S.A., Li X., Zheng Q., Novichkov P.S., Reed S., Romine M.F., Fredrickson J.K., Yang C., Osterman A.L., Rodionov D.A. Control of proteobacterial central carbon metabolism by the HexR transcriptional regulator: a case study in Shewanella oneidensis. J Biol Chem 2011 286(41): 35782-35794. PubMed  PDF

Bonchuk A., Denisov S., Georgiev P., Maksimenko O. Drosophila BTB/POZ domains of "ttk group" can form multimers and selectively interact with each other. J Mol Biol 2011 412(3): 423-436. PubMed  PDF

Lazarev V.N., Levitskii S.A., Basovskii Y.I., Chukin M.M., Akopian T.A., Vereshchagin V.V., Kostrjukova E.S., Kovaleva G.Y., Kazanov M.D., Malko D.B., Vitreschak A.G., Sernova N.V., Gelfand M.S., Demina I.A., Serebryakova M.V., Galyamina M.A., Vtyurin N.N., Rogov S.I., Alexeev D.G., Ladygina V.G., Govorun V.M. Complete genome and proteome of Acholeplasma laidlawii. J Bacteriol 2011 193(18): 4943-4953. PubMed  PDF

Kazanov M.D., Igarashi Y., Eroshkin A.M., Cieplak P., Ratnikov B., Zhang Y., Li Z., Godzik A., Osterman A.L., Smith J.W. Structural determinants of limited proteolysis. J Proteome Res 2011 10(8): 3642-3651. 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, 6: 8. PubMed  PDF

Blaby-Haas C.E, Furman R, Rodionov D.A, Artsimovitch I, de Crecy-Lagard V. Role of a Zn-independent DksA in Zn homeostasis and stringent response. Mol Microbiol. 2011, 79: 700-15. PubMed  PDF

Kurmangaliyev, YZ; Goland, A; Gelfand, MS. Evolutionary patterns of phosphorylated serines Biology Direct 2011 Feb 9;6:8. PubMed 

Eitinger T, Rodionov D.A, Grote M, Schneider E. Canonical and ECF-type ATP-binding cassette importers in prokaryotes: diversity in modular organization and cellular functions. FEMS Microbiol Rev. 2011, 35: 3-67. 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

Vakhrusheva A.A, Kazanov M.D, Mironov A.A, Bazykin G.A. Evolution of prokaryotic genes by shift of stop codons. J Mol Evol. 2011, 72: 138-46. 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

Жаров И.А, Гельфанд М.С, Казаков А.Е. Регуляция генов множественной лекарственной устойчивости транскрипционными факторами подсемейства BltR. Молекулярная биология, 2011 45(4): 715-723. 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

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

P.V. Mazin, M.S. Gelfand, A.A. Mironov, A.B. Rakhmaninova, A.R. Rubinov, R.B. Russell, O.V. Kalinina. 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

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

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. 2010, 11: 255. PubMed  PDF

J. Schroder, N. Jochmann, D.A. Rodionov, A. Tauch. The Zur regulon of Corynebacterium glutamicum ATCC 13032. BMC Genomics. 2010, 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. 2010, 107: 10573-7. PubMed  PDF

Е.У. Полуэктова, Е.Ю. Гагарина, В.З. Незаметдинова, И.П. Шиловский, С.А. Родионова, А.А. Прозоров. Характеристика определяющего конъюгативный перенос tra-района плазмиды р19 их почвенного штамма Bacillus subtilis. Генетика. 2010, 45(1), 33-43

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. 2010, 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. 2010, 38: D111-8. PubMed  PDF

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

Ракитин Д.И, Гельфанд М.С. Совместная метаболическая активность тли Acyrthosiphon pisum и симбиотической бактерии Buchnera aphidicola STR APS Молекулярная биология. 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

М.С. Гельфанд. Геномы и эволюция. Вестник РАН, 2009, 79(5) 411-418. PDF

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

Eudes A., Erkens G.B, Slotboom D.J, Rodionov D.A, Naponelli V, Hanson A.D. 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, 106: 2874-9. 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

Е.Ж. Курмангалиев, М.С. Гельфанд. Сайты фосфорилирования тяготеют к альтернативно сплайсируемым областям белков. Молекулярная биология, 2009 , 43(3):572-4 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

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

Е.У. Полуэктова, Е.Ю, Гагарина, И.П. Шиловский, Е.А. Федорина, В.З. Незаметдинова, С.А. Родионова, А.А. Прозоров. Молекулярный анализ некоторых генов плазмиды p19 из почвенного штамма Bacillus subtilis 19, участвующих в процессе конъюгации. Молекулярная генетика, 2008, 44(5): 623-630 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

Л.В. Сычева, Е.А. Пермина, М.С. Гельфанд. Таксон-специфичная регуляция SOS-ответа у гамма-протеобактерий. Мол. Биол. 2007, 41(5): 908-917. PubMed  PDF

М.О. Цыганова, М.С.Гельфанд, Д.А.Равчеев. Регуляция дыхания у энтеробактерий: сопоставление данных по экспрессии на биочипах и сравнительно-геномного анализа. Мол. Биол. 2007, 41(3): 556-571. 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

АА. Миронов. Метод поиска консервативных структур РНК. Молекулярная биология. 2007, 41:(4) 711-718. 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

О.В. Калинина, Р.Б. Рассел, А.Б. Рахманинова, М.С. Гельфанд. Вычислительный метод для предсказания функциональных сайтов белка с использованием детерминант специфичности. Мол. биол. 2007, 41(1):151-162. PubMed   PDF

Г.Ю. Ковалева, М.С. Гельфанд. Регуляция биосинтеза метионина/цистеина в Corynebacterium glutamicum и родственных организмах. Мол. биол. 2007, 41(1):139-150. 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

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

Deev, I E; Vasilenko, K P; Kurmangaliev, E Zh; Serova, O V; Popova, N V; Galagan, Yu S; Burova, E B; Zozulya, S A; Nikol'skii, N N; Petrenko, A G. Effect of changes in ambient pH on phosphorylation of cellular proteins. Doklady. Biochemistry and biophysics 408, 184 (2006). PubMed 

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

Г.Ю. Ковалева, М.С. Гельфанд (2006) Способ исследования и прогнозирования пути биосинтеза метионина в родственных геномах коринебактерий. Патент 2006127265/13 (вх. 029629).

Р.Н. Нуртдинов, А.Д. Неверов, Д.Б. Малько, И.А. Космодемьянский, Е.О. Ермакова, В.Е. Раменский, А.А. Миронов, М.С. Гельфанд. EDAS - база данных альтернативно сплайсированных генов человека. Биофизика. 2006, 51(4):589-92. PubMed  PDF

Е.О. Ермакова, Д.Б. Малько, М.С. Гельфанд. Эволюционные отличия альтернативных и постоянных белок-кодирующих участков альтернативно сплайсируемых генов Drosophila. Биофизика. 2006, 51(4)581-588. PubMed  PDF

АА. Миронов, ЕД. Ставровская, ВЮ. Макеев. (2006) Способ исследования совместной регуляции генов бактерий и прогнозирования содержания новых регулонов и функций генов. Патент 2006127264/13 (вх. 029628).

Г.Ю. Ковалева, М.С. Гельфанд (2006) Способ исследования и прогнозирования пути биосинтеза метионина в родственных геномах коринебактерий. Патент 2006127265/13 (вх. 029629).

М.С. Гельфанд. Вторая Московская конференция по вычислительной молекулярной биологии МССМВ'05. Биофизика. 2006, 51(4):765-766. 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

А.В. Любецкая, Л.И. Рубанов, М.С. Гельфанд. Потоковая модель метаболизма аминокислот кишечной палочки. Биохимия. 2006, 71(11): 1544-1549. PubMed  PDF

Н.А. Дорощук, М.С. Гельфанд, Д.А. Родионов. Регуляция метаболизма азота у грамположительных бактерий. Молекулярная биология. 2006, 40 (5): 919-926

РА. Сутормин, АА. Миронов. Вероятностный метод предсказания трансмембранных участков по множественным выравниваниям аминокислотных последовательностей. Молекулярная биология. 2006, 40:(3) 541-545. PubMed  PDF

МС. Гельфанд. Что можно сказать о бактерии, зная только её геном (и геномы ещё нескольких сотен бактерий). Знание-Сила. 2006, 8(950): 64-68

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 

МС. Гельфанд. Цис-регуляторные структуры РНК бактерий. Молекулярная биология. 2006, 40(4):609-19. PubMed  PDF

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

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

Литвинов ИИ, Лобанов МЮ, Миронов АА, Финкельштейн АВ, Ройтберг МА. Информация о вторичной структуре белка улучшает качество выравнивания. Молекулярная биология. 2006, 40(3):533-40. PubMed 

ЕД. Ставровская, ВЮ. Макеев, АА. Миронов ClusterTree-RS: алгоритм кластеризации регуляторных сигналов с помощью бинарного дерева. Молекулярная биология. 2006, 40(3): 465-473 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

Герасимова А.В. Анализ регуляции транскрипции генов дыхания в гамма-протеобактериях методами сравнительной геномики. Москва - 2006 Автореферат диссертации на соискание ученой степени к.б.н.

Пермина Е.А. Изучение регулонов бактериального стресса методами сравнительной геномики. Москва - 2006 Автореферат диссертации на соискание ученой степени к.б.н.

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

М.С. Гельфанд Интервью ПОЛИТ.РУ  27 февраля 2006 г.

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

Д.А. Равчеев, А.Б. Рахманинова, А.А. Миронов, М.С. Гельфанд. Регуляция нитрат-нитритного дыхания гамма-протеобактерий: исследование методами сравнительной геномики. Мол. биол., 2005, 39(5): 832-46 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.

М.С. Гельфанд. Апология биоинформатики. Биофизика. 2005, 50(4): 752-766. PubMed  PDF

М.С. Гельфанд. Регуляция экспрессии генов и электронные модели живой клетки Информационные процессы. 2005, 5(1): 33-39

М.С. Гельфанд. Ремонтировать – не значит ломать. Поиск. 25.3.2005, 12 (826) 4 PDF

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 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

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