Publications

2015

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

2014

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.
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.
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

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.
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.
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.

2012

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. http://nar.oxfordjournals.org/content/early/2012/12/02/nar.gks1184.long
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. http://www.biomedcentral.com/1471-2148/12/200
De Ingeniis J., Kazanov M., Shatalin K., Gelfand M., L. Osterman A., Sorci L., Glutamine versus ammonia utilization in the NAD synthetase family http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039115

2011

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. http://www.biomedcentral.com/1471-2164/12/S1/S3
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. http://jb.asm.org/content/193/18/4943.long

2010

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, http://www.rtcb.iitp.ru/PDF/19884135.pdf
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. http://www.bioinfo.de/isb/2010/10/0012/

2009

Zhang Y., Rodionov D., Gelfand M., Gladyshev V.N., Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization. BMC Genomics. 2009, 10: 78. http://www.rtcb.iitp.ru/PDF/19208259.pdf
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 . http://nar.oxfordjournals.org/cgi/reprint/gkp407v1
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. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2677863/pdf/gkp079.pdf
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.
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. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2711938/pdf/1471%2D2148%2D9%2D142.pdf
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. http://www.rtcb.iitp.ru/PDF/19604474.pdf
Kalinina O., Gelfand M., Russell R., Combining specificity determining and conserved residues improves functional site prediction. BMC Bioinformatics. 2009, 10: 174.

2008

Kurmangaliyev Y., Gelfand M., Computational analysis of splicing errors and mutations in human transcripts. BMC Genomics. 2008, 9(1): 13. http://www.rtcb.iitp.ru/PDF/18194514.pdf
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 http://rnajournal.cshlp.org/content/14/4/717.full

2007

Kazanov M., Vitreschak A., Gelfand M., Abundance and functional diversity of riboswitches in microbial communities. BMC Genomics. 2007 Oct 1;8:347. http://www.biomedcentral.com/1471-2164/8/347
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, CPMS’2007”, November 16–19 2007, KMK Scientific Press, Moscow, pp. 30–37.
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: ÌÑÑÌÂ’07, November 2007, pp. 309–310.
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: ÌÑÑÌÂ’07, 2007, pp. 111–113.
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.

2006

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 (BGRS’2006), Novosibirsk, July 16–22 2006, V. 3, pp. 236–240. http://www.bionet.nsc.ru/meeting/bgrs_proceedings/papers/2006/BGRS_2006_V3_053.pdf
A. Permina E., 60, V. Kalinina O., Gelfand M., "Comparative genomics of regulation of heavy metal resistance in Eubacteria." BMC Microbiol., 2006, 6:49. http://www.biomedcentral.com/1471-2180/6/49
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.
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.
Ermakova E., Ermakova EO, Nurtdinov RN, Gelfand MS. Fast rate of evolution in alternatively spliced coding regions of mammalian genes. BMC Genomics 7:84, 2006. http://www.biomedcentral.com/1471-2164/7/84
Kovaleva G., Bazykin G., Brudno M., Gelfand M., Comparative genomics of transcriptional regulation in yeasts and its application to identification of a candidate alpha-isopropylmalate transporter. Journal of Bioinformatics and Computational Biology 4(5):981–998.

2005

Seliverstov A., Putzer H., Gelfand M., Lyubetsky V., “Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria” BMC Microbiology, 2005, 5:54. PMID: 16202131 http://www.biomedcentral.com/1471-2180/5/54

2004

Kusnetsov N., Gelfand M., Lyubetsky V., “Bioinformatics of Bacteria: central issues and model types” International conference “Issues of control and modeling in complex systems”, June 14–17 2004, RAS, pp. 5–11. [in Russian]
Vitreschak A., Lyubetskaya E., Shirshin M., Gelfand M., Lyubetsky V., “Attenuation regulation of amino acid biosynthetic operons in proteobacteria: comparative genomics analysis” FEMS Microbiological Letters, 2004, 234(2), pp. 357–370. PMID: 15135544 http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T2W-4C5VMJK-4&_user=10&_rdoc=1&_fmt=&_ori

2003

Vinogradov D., ProMult: prediction of the exon-introns tructure by spliced alignment with several proteins. Biophysics (Moscow). 2003, 48 Suppl. 1, pp.68-70 http://www.maik.ru/contents/biophyss/biophyss1_3v48cont.pdf
Lyubetskaya E., Leont'yev L., Gelfand M., Lyubetsky V., “Search for Alternative RNA Secondary Structures Regulating Expression of Bacterial Genes” Molecular biology, V. 37, No 5, 2003, p. 707–715. PMID 14593920
Gelfand M., Lyubetsky V., DNA: from molecules toward genomes, from biochemical breakthroughs toward algorithmic analysis. Proceedings of the RAS (Vestnik RAN), No 11, 2003, p. 963-970. [in Russian]
Danilova L., Gelfand M., Lyubetsky V., Laikova O., “Computer-Assisted Analysis of Regulation of the Glycerol-3-Phosphate Metabolism in Genomes of Proteobacteria” Molecular Biology, V. 37, No 5, 2003, ññ. 716–722. PMID 14593921
V'yugin V., Gelfand M., Lyubetsky V., “Identification of Horizontal Gene Transfer from Phylogenetic Gene Trees” Molecular biology, V. 37, No 4, 2003, p. 571-584. PMID 12942641
Danilova L., Lyubetsky V., Gelfand M., “An algorithm for identification of regulatory signals in unaligned DNA sequences, its testing and parallel implementation” In Silico Biology, V. 3, No 1,2, 2003, pp. 33–47. PMID 12762844 http://www.bioinfo.de/isb/2003/03/0004

2002

V'yugin V., Gelfand M., Lyubetsky V., “Tree Reconciliation: Reconstruction of Species Phylogeny by Phylogenetic Gene Trees” Molecular biology, 2002, V. 36, No 5, p. 650-658. PMID 12391844

2001

Danilova L., Gorbunov K., Gelfand M., Lyubetsky V., “Algorithm of Regulatory Signal Recognition in DNA Sequences” Molecular Biology, V. 35, No 6, 2001, p. 841-848. PMID 11771146
Gelfand M., V'yugin V., Lyubetsky V., An approach to infer evolutionary species tree from multiple gene data. Information processes, V. 1, No 1, 2001, p. 64-77. [in Russian]
Danilova L., Gorbunov K., Gelfand M., Lyubetsky V., An algorithm to detect regulatory signals in DNA sequence data (1). Information processes, V. 1, No 1, 2001, p. 56-63. [in Russian]