Публикации

2015

Казанов М.Д., 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.
Гарушянц С.К., Казанов М.Д., Гельфанд М.С., Horizontal gene transfer and genome evolution in Methanosarcina, BMC Evolutionary Biology, 15(1):102,2015.
Kumar S., Ratnikov B.I., Казанов М.Д., Smith J.W., Cieplak P., CleavPredict: a platform for reasoning about matrix metalloproteinases proteolytic events, PLoS One, 10(5):e0127877, 2015.
Родионова И.А., Zuccola H.J., Sorci L., Алешин А.Е., Казанов М.Д., 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

Pendlebury D., Wang R., Henin R.D., Hockla A., Soares A.S., Madden B.J., Казанов М.Д., 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.
Ratnikov B.I., Cieplak P., Gramatikoff K., Pierce J., Eroshkin A., Igarashi Y., Казанов М.Д., 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.
Sorci L., Brunetti L., Cialabrini L., Mazzola F., Казанов М.Д., D'Auria S., Ruggieri S., Raffaeilli N., Characterization of bacterial NMN deamidase as a Ser/Lys hydrolase expands diversity of serine amidohydrolases, FEBS Letters, 588(6), pp.1016-1023, 2014.
Belushkin A.A., Виноградов Д.В., Гельфанд М.С., Osterman A.L., Cieplak P., Казанов М.Д., Sequence-derived structural features driving proteolytic processing, Proteomics, 14(1), pp. 42-50, 2014.
Ponomarev G.V., Arlazarov V.L., Гельфанд М.С., Казанов М.Д., 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., Гельфанд М.С., Казанов М.Д., 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., Казаков А.Е., 170, Лейн С.А., Ковалева Г.Ю., Sutormin R.A., Казанов М.Д., Riehl W., Arkin A.P., Dubchak I., Родионов Д.А., RegPrecise 3.0 -- A resource for genome-scale exploration of transcriptional regulation in bacteria, BMC Genomics, 14(1):745, 2013.
Sun E.I., Лейн С.А., Казанов М.Д., Saier M.H., Родионов Д.А., Novichkov P.S., Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria, BMC Genomics, 2013, 14:597.
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.
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.
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

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., 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. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0045190
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., Kazakov A., 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
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. http://pubs.acs.org/doi/abs/10.1021/pr200271w
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. http://www.springerlink.com/content/b628621138157551/

2009

Gelfand M., Kazakov A., 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.

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
Ермакова Е.О., Ermakova EO, Nurtdinov RN, Gelfand MS. Overlapping alternative donor splice sites in the human genome. J Bioinform Comput Biol. 5(5):991-1004, 2007.
Новикова М., Метлицкая А., Даценко К., Казаков Т., Казаков А.Е., Wanner B., Северинов К., "The E. coli Yej Transporter is Required for the Uptake of Translation Inhibitor Microcin C." J Bacteriol., 2007 Nov;189(22):8361-5. http://dx.doi.org/10.1128/JB.01028-07
Северинов К., Семенова Е., Казаков А.Е., Казаков Т., Гельфанд М.С., "Low-molecular-weight post-translationally modified microcins." Mol Microbiol., 2007, 65(6):1380-94. http://dx.doi.org/10.1111/j.1365-2958.2007.05874.x
Казаков А.Е., J. Cipriano M., С. Новичков П., Minovitsky S., Виноградов Д.В., Arkin A., А. Миронов А., Л. Дубчак И., Гельфанд М.С., "RegTransBase - a database of regulatory sequences and interactions in a wide range of prokaryotic genomes." Nucleic Acids Res., 2007, 35:D407-12. http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D407

2006

А. Пермина Е., Казаков А.Е., В. Калинина О., Гельфанд М.С., "Comparative genomics of regulation of heavy metal resistance in Eubacteria." BMC Microbiol., 2006, 6:49. http://www.biomedcentral.com/1471-2180/6/49
Ермакова Е.О., Нуртдинов Р.Н., Неверов А.Д., Малько Д.Б., Космодемьянский И.А., Ермакова Е.О., Раменский В.Е., Миронов А.А., Гельфанд М.С. EDAS - база данных альтернативно сплайсированных генов человека. Биофизика 51(4): 589-592, 2006
Ермакова Е.О., Ермакова Е.О., Малько Д.Б., Гельфанд М.С. Эволюционные отличия альтернативных и постоянных белок-кодирующих участков альтернативно сплайсируемых генов Drosophila. Биофизика 51(4): 581-588, 2006
Ермакова Е.О., 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.

2003

Виноградов Д.В., ProMult: prediction of the exon-introns tructure by spliced alignment with several proteins. Биофизика (Москва). 2003, том 48 тематический выпуск 1, стр.68-70 http://www.maik.ru/contents/biophyss/biophyss1_3v48cont.pdf
Казаков А.Е., А. Шепелев В., Г. Тюменева И., А. Александров А., Б. Юров Ю., А. Александров И., "Interspersed repeats are found predominantly in the "old" alpha satellite families." Genomics, 2003, 82(6):619-27. http://dx.doi.org/10.1016/S0888-7543(03)00182-4
Казаков А.Е., Вассиева О., Остерман А., Овербек Р., Гельфанд М.С., "Bioinformatics classification and functional analysis of PhoH homologs." In Silico Biology, 2003, 3(1-2):3-15. http://www.bioinfo.de/isb/2003030002/

2001

А. Александров И., Казаков А.Е., Тюменева И., Шепелев В., Юров Ю., "Alpha-satellite DNA of primates: old and new families." Chromosoma, 2001, 110(4):253-66. http://dx.doi.org/10.1007/s004120100146

1998

Капанадзе Б., Кашуба В., Баранова А., Расул О., van Everdink W., Liu Y., Сёмов А., Corcoran M., Полтараус А., Бродянский В., Сёмова Н., Казаков А.Е., Ibbotson R., van den Berg A., Гизатуллин Р., Федорова Л., Сулимова Г., Зеленин А., Deaven L., Lehrach H., Grander D., Buys C., Oscier D., Р. Забаровский Е., Einhorn S., Янковский Н., "A cosmid and cDNA fine physical map of a human chromosome 13q14 region frequently lost in B-cell chronic lymphocytic leukemia and identification of a new putative tumor suppressor gene, Leu5." FEBS Lett., 1998, 426(2):266-70. http://dx.doi.org/10.1016/S0014-5793(98)00357-3

1997

Н. А. Малыгина, Казаков А.Е., Л. В. Дубчак, "ДНК-диагностика бульбоспинальной мышечной атрофии (болезни Кеннеди)". Журнал неврологии и психиатрии им. С. С. Корсакова, 1997, т. 97, стр. 35-38.