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2015 year
Authors: Kazanov M., Roberts S.A., Polak P., Stamatoyannopoulos J., Klimczak L.J., Gordenin D.A., Sunyaev S.R.

APOBEC-Induced Cancer Mutations Are Uniquely Enriched in Early-Replicating, Gene-Dense, and Active Chromatin Regions, Cell Reports 13(6), pp.1103-1109, 2015.

2015 year
Authors: Garushyants S., Kazanov M., Gelfand M.

Horizontal gene transfer and genome evolution in Methanosarcina, BMC Evolutionary Biology, 15(1):102,2015.

2015 year
Authors: Kumar S., Ratnikov B.I., Kazanov M., Smith J.W., Cieplak P.

CleavPredict: a platform for reasoning about matrix metalloproteinases proteolytic events, PLoS One, 10(5):e0127877, 2015.

2015 year
Authors: Rodionova I.A., Zuccola H.J., Sorci L., Aleshin A.E., Kazanov M., Ma C.T., Sergienko E., Rubin E.J., Locher C.P., Osterman A.L.

Mycobacterial Nicotinate Mononucleotide Adenylyltransferase: Structure, Mechanism, and Implications for Drug Discovery, Journal of Biological Chemistry, 290(12), pp. 7693-7706, 2015.

2014 year
Authors: Pendlebury D., Wang R., Henin R.D., Hockla A., Soares A.S., Madden B.J., Kazanov M., Radisky E.S.

Sequence and Conformational Specificity in Substrate Recognition: Several Human Kunitz Protease Inhibitor Domains are Specific Substrates of Mezotrypsin, Journal of Biological Chemistry, 289(47), pp.32783-32797, 2014.

2014 year
Authors: Ratnikov B.I., Cieplak P., Gramatikoff K., Pierce J., Eroshkin A., Igarashi Y., Kazanov M., Sun Q, Godzik A., Osterman A., Stec B., Strongin A., Smith J.W.

Basis for substrate recognition and distinction by matrix metalloproteinases, PNAS, 111(40), E4148-4155, 2014.

2014 year
Authors: Sorci L., Brunetti L., Cialabrini L., Mazzola F., Kazanov M., D'Auria S., Ruggieri S., Raffaelli N.

Characterization of bacterial NMN deamidase as a Ser/Lys hydrolase expands diversity of serine amidohydrolases, FEBS Letters, 588(6), pp.1016-1023, 2014.

2014 year
Authors: Belushkin A.A., Vinogradov D., Gelfand M., Osterman A.L., Cieplak P., Kazanov M.

Sequence-derived structural features driving proteolytic processing, Proteomics, 14(1), pp. 42-50, 2014.

2014 year
Authors: Ponomarev G.V., Arlazarov V.L., Gelfand M., Kazanov M.

ANA HEp-2 cells image classification using number, size, shape and localization of targeted cell regions, Pattern Recognition, 47(7), pp. 2360-2366, 2014.

2014 year
Authors: 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., Kazanov M., 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 Transactions on Medical Imaging, 33(4), pp.797-813, 2014.

2013 year
Authors: Novichkov P.S., 60, 170, Leyn S., Kovaleva G., Sutormin R.A., Kazanov M., Riehl W., Arkin A.P., Dubchak I., Rodionov D.

RegPrecise 3.0 -- A resource for genome-scale exploration of transcriptional regulation in bacteria, BMC Genomics, 14(1):745, 2013.

2013 year
Authors: Sun E.I., Leyn S., Kazanov M., Saier M.H., Rodionov D., Novichkov P.S.

Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria, BMC Genomics, 2013, 14:597.

2013 year
Authors: Cialabrini L., Ruggieri S., Kazanov M., Sorci L., Mazzola F., Orsomando G., Osterman A.L., 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.

2013 year
Authors: Gordienko E.N., Kazanov M., Gelfand M.

Evolution of pan-genomes of Escherichia coli, Shigella spp., and Salmonella enterica, J Bacteriol. 2013 Jun;195(12):2786-92.

2013 year
Authors: Leyn S., Kazanov M., Sernova N.V., Ermakova E., Novichkov P.S., Rodionov D.

Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis, J Bacteriol. 2013 Jun;195(11):2463-73.

2013 year
Authors: 170, Best A.A., Sernova N.V., Kazanov M., Novichkov P.S., Rodionov D.

Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria, BMC Genomics. 2013 Feb 12;14:94.

2012 year
Authors: Kazanov M., Li X., Gelfand M., L. Osterman A., Rodionov D.

Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum. Nucleic Acids Res. 2012 Dec 2.
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2012 year
Authors: Tsoy O., A. Pyatnitskiy M., Kazanov M., Gelfand M.

Evolution of transcriptional regulation in closely related bacteria. BMC Evol Biol. 2012 Oct 6;12:200.
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2012 year
Authors: De Ingeniis J., Ratnikov B., D. Richardson A., A. Scott D., Aza-Blanc P., De K., Kazanov M., Pellecchia M., Ronai Z., L. Osterman A., W. Smith J.

Functional specialization in proline biosynthesis of melanoma. PLoS One. 2012;7(9):e45190.
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2012 year
Authors: De Ingeniis J., Kazanov M., Shatalin K., Gelfand M., L. Osterman A., Sorci L.

Glutamine versus ammonia utilization in the NAD synthetase family
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2011 year
Authors: Rodionov D., Novichkov P.S., Stavrovskaya E., Rodionova I.A., Li X, Kazanov M., 170, Gerasimova A.V., 60, Kovaleva G., Permina E.A., Laikova O.N., Overbeek R, Romine M.F., Fredrickson J.K., Arkin A.P., Dubchak I, Osterman A.L., Gelfand M.

Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. BMC Genomics. 2011 Jun 15;12 Suppl 1:S3.
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2011 year
Authors: Lazarev V.N., Levitskii S.A., Basovskii Y.I., Chukin M.M., Akopian T.A., Vereshchagin V.V., Kostrjukova E.S., Kovaleva G., Kazanov M., Malko D.B., Vitreschak A., Sernova N.V., Gelfand M., 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. Journal of Bacteriology 2011 Sep;193(18):4943-4953.
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2011 year
Authors: Kazanov M., 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. Journal of Proteome Research 2011 Aug 5;10(8):3642-3651.
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2011 year
Authors: Vakhrusheva A.A., Kazanov M., Mironov A.A., Bazykin G.

Evolution of prokaryotic genes by shift of stop codons. Journal of Molecular Evolution 2011 Feb;72(2):138-146.
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2010 year
Authors: Novichkov P.S., Laikova O., Novichkova E., Gelfand M., Arkin A., Dubchak I., Rodionov D.

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res. 2010,
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2010 year
Authors: Gorbunov K., Laikova O.N., Rodionov D., Gelfand M., Lyubetsky V.

Evolution of regulatory motifs of bacterial transcription factors In Silico Biology, 2010, 10, 0012.
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2009 year
Authors: Zhang Y., Rodionov D., Gelfand M., Gladyshev V.N.

Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization. BMC Genomics. 2009, 10: 78.
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2009 year
Authors: Raker V., Mironov A., Gelfand M., Pervouchine D.

Modulation of alternative splicing by long-range RNA structures in Drosophila. Nucleic Acids Res. 2009, 37(14):4533-44 .
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2009 year
Authors: Desai T., Rodionov D., Gelfand M., Alm E.J., Rao C.

Engineering transcription factors with novel DNA-binding specificity using comparative genomics. Nucleic Acids Res. 2009, 37: 2493-503.
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2009 year
Authors: Gelfand M., 60, Korostelev Y., Laikova O., Mironov A., Rakhmaninova A., 170, Rodionov D., Vitreschak A.

Evolution of Regulatory Systems in Bacteria. Lecture Notes in Bioinformatics. 2009; 5542 (ISBRA 2009): 1-4.

2009 year
Authors: Nurtdinov R., Mironov A., Gelfand M.

Rodent-specific alternative exons are more frequent in rapidly evolving genes and in paralogs. BMC Evol Biol. 2009, 9: 142.
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2009 year
Authors: Huang N., De Ingeniis J., Galeazzi L., Mancini C., Korostelev Y.D., Rakhmaninova A., Gelfand M., Rodionov D., Raffaelli N., Zhang H.

Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism. Structure. 2009, 17: 939-51.
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2009 year
Authors: Kalinina O., Gelfand M., Russell R.

Combining specificity determining and conserved residues improves functional site prediction. BMC Bioinformatics. 2009, 10: 174.

2008 year
Authors: Kurmangaliyev Y., Gelfand M.

Computational analysis of splicing errors and mutations in human transcripts. BMC Genomics. 2008, 9(1): 13.
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2008 year
Authors: Vitreschak A., Mironov A., Lyubetsky V., Gelfand M.

Comparative genomic analysis of T-box regulatory systems in bacteria Ribonucleic acids molecular biology (RNA), V. 14, No. 4, April 2008, pp. 717-735. PMID: 18359782
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2007 year
Authors: Kazanov M., Vitreschak A., Gelfand M.

Abundance and functional diversity of riboswitches in microbial communities. BMC Genomics. 2007 Oct 1;8:347.
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2007 year
Authors: Vitreschak A., Lyubetsky V., Gelfand M.

Analysis of evolution of T-box regulatory elements prediction of amino acid transporters and other amino acid related genes Proceedings of the international scientific conference Computational Phylogenetics and Molecular Systematics, CPMS2007, November 1619 2007, KMK Scientific Press, Moscow, pp. 3037.

2007 year
Authors: Vitreschak A., Mironov A., Lyubetsky V., Gelfand M.

Function and evolutionary analysis of the T-box regulon in bacteria Proceedings of International Moscow Conference on Computational Molecular Biology: ’07, November 2007, pp. 309310.

2007 year
Authors: Gorbunov K., Radionov D., Laikova O., Gelfand M., Lyubetsky V.

Reconstruction of ancestral regulatory signal along a phylogeny Proceedings of International Moscow Conference on Computational Molecular Biology: ’07, 2007, pp. 111113.

2007 year
Authors: Ermakova E.

Ermakova EO, Nurtdinov RN, Gelfand MS. Overlapping alternative donor splice sites in the human genome. J Bioinform Comput Biol. 5(5):991-1004, 2007.
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2006 year
Authors: Vitreschak A., Lyubetsky V., Gelfand M.

Evolutional and Functional Analysis of T-box Regulon in Bacteria: Identification of new Genes Involved in Amino Acid Metabolism Proceedings of The Fifth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS2006), Novosibirsk, July 1622 2006, V. 3, pp. 236240.
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2006 year
Authors: A. Permina E., 60, V. Kalinina O., Gelfand M.

"Comparative genomics of regulation of heavy metal resistance in Eubacteria." BMC Microbiol., 2006, 6:49.
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2006 year
Authors: Ermakova E.

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 51(4):589-592, 2006.
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2006 year
Authors: Ermakova E.

Ermakova EO, Mal"ko DB, Gel"fand MS. [Different patterns of evolution in alternative and constitutive coding regions of Drosophila alternatively spliced genes] Biofizika 51(4):581-588, 2006.
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