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


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.
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.
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.
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.


Novichkov P.S., Kazakov A., 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.
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.
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.


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.
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.
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.
De Ingeniis J., Kazanov M., Shatalin K., Gelfand M., L. Osterman A., Sorci L., Glutamine versus ammonia utilization in the NAD synthetase family


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.
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.
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.
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.


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.


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


A. Permina E., Kazakov A., V. Kalinina O., Gelfand M., "Comparative genomics of regulation of heavy metal resistance in Eubacteria." BMC Microbiol., 2006, 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.
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):981998.


Vinogradov D., ProMult: prediction of the exon-introns tructure by spliced alignment with several proteins. Biophysics (Moscow). 2003, 48 Suppl. 1, pp.68-70