Marat Kazanov, PhD

Visiting Scientist

marat.kazanov@sabanciuniv.edu

Education

  • 2003-2008 Ph.D., Institute for Systems Analysis, Moscow, Russia.

    • Major: Computer Science

    • Thesis Title: Segmentation of Text and Figures in Color Magazine/Article Images

  • 1995-1997 MSc., Moscow Institute of Physics and Technology (State University), Moscow, Russia

    • Major: Applied Mathematics

  • 1991-1995 B.S., Moscow Institute of Physics and Technology (State University), Moscow, Russia

    • Major: Applied Mathematics

Work Experience

  • 2022- Visiting Researcher, Sabanci University, Istanbul, Türkiye.

  • 2017- Senior Research Scientist, Skolkovo Institute of Science and Technology, Moscow, Russia.

  • 2014- Principal Investigator, Sector of Applied Bioinformatics, IITP RAS, Moscow, Russia.

  • 2010-2014 Researcher, Research and Training Center on Bioinformatics, IITP RAS, Moscow, Russia.

  • 2008-2010 Postdoctoral Researcher, Sanford-Burnam Medical Research Institute, La Jolla, CA, USA.

  • 2007-2008 Junior Researcher, Research and Training Center on Bioinformatics, IITP RAS, Moscow, Russia.

  • 1997-2003 Software Engineer (RDBMS and Image analysis), FORS, Moscow, Russia.

Publications

  • Matveev EV, Ponomarev GV, Kazanov MD Genome-wide bioinformatics analysis of human protease capacity for proteolytic cleavage of the SARS-CoV-2 spike glycoprotein. Microbiol Spectr. 2024 Feb 6;12(2):e0353023.

  • Hibberd MC, Webber DM, Rodionov DA, Henrissat S, Chen RY, Zhou C, Lynn HM, Wang Y, Chang HW, Lee EM, Lelwala-Guruge J, Kazanov MD, Arzamasov AA, Leyn SA, Lombard V, Terrapon N, Henrissat B, Castillo JJ, Couture G, Bacalzo NP Jr, Chen Y, Lebrilla CB, Mostafa I, Das S, Mahfuz M, Barratt MJ, Osterman AL, Ahmed T, Gordon JI. Bioactive glycans in a microbiome-directed food for children with malnutrition. Nature. 2024 Jan;625(7993):157-165.

  • Hudson KM, Klimczak LJ, Sterling JF, Burkholder AB, Kazanov MD, Saini N, Mieczkowski PA, Gordenin DA. Glycidamide-induced hypermutation in yeast single-stranded DNA reveals a ubiquitous clock-like mutational motif in humans. Nucleic Acids Res. 2023 Sep 22;51(17):9075-9100.

  • Matveev EV, Safronov VV, Ponomarev GV, Kazanov MD. Predicting Structural Susceptibility of Proteins to Proteolytic Processing. Int J Mol Sci. 2023 Jun 28;24(13):10761.

  • Borkovskaia A, Bogacheva S, Konyukhova T, Dadakhanova E, Gaskova M, Soldatkina O, Dubrovina M, Popov A, Mikhailova E, Inushkina E, Kazanov M, Matveev E, Novichkova G, Maschan M, Maschan A, Olshanskaya Y, Zerkalenkova E. Molecular Heterogeneity of Pediatric AML with Atypical Promyelocytes Accumulation in Children-A Single Center Experience. Genes (Basel). 2023 Mar 8;14(3):675.

  • Ponomarev GV, Fatykhov B, Nazarov VA, Abasov R, Shvarov E, Landik NV, Denisova AA, Chervova AA, Gelfand MS, Kazanov MD. APOBEC mutagenesis is low in most types of non-B DNA structures. iScience. 2022 Jun 6;25(7):104535.

  • Semchenkova A, Mikhailova E, Komkov A, Gaskova M, Abasov R, Matveev E, Kazanov M, Mamedov I, Shmitko A, Belova V, Miroshnichenkova A, Illarionova O, Olshanskaya Y, Tsaur G, Verzhbitskaya T, Ponomareva N, Bronin G, Kondratchik K, Fechina L, Diakonova Y, Vavilova L, Myakova N, Novichkova G, Maschan A, Maschan M, Zerkalenkova E, Popov A. Lineage Conversion in Pediatric B-Cell Precursor Acute Leukemia under Blinatumomab Therapy. Int J Mol Sci. 2022 Apr 5;23(7):4019.

  • Kovach AE, Zerkalenkova E, Zemtsova L, Borkovskaya A, Gaskova M, Kazanov M, Popov A, Baidun L, Maschan M, Maschan A, Gaynon PS, Bhojwani D, Novichkova G, Olshanskaya Y, Raca G. Acute myeloid leukemia with t(X;6)9p11;q23);MYB-GATA1 and female sex: GATA1 insufficiency may be insufficient for pathogenesis. Cancer Genet. 2022 Jan;260-261:37-40.

  • Chervova A, Fatykhov B, Koblov A, Shvarov E, Preobrazhenskaya J, Vinogradov D, Ponomarev GV, Gelfand MS, Kazanov MD. Analysis of gene expression and mutation data points on contribution of transcription to the mutagenesis by APOBEC enzymes. NAR Cancer. 2021 Jul 2;3(3):zcab025. doi: 10.1093/narcan/zcab025.

  • Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Li Y, Kelso S; MC3 Working Group; PCAWG novel somatic mutation calling methods working group, Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L; PCAWG Consortium including M.D. Kazanov. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples, Nature Communications 11(1): 4748, 2020.

  • Li CH, Prokopec SD, Sun RX, Yousif F, Schmitz N; PCAWG Tumour Subtypes and Clinical Translation, Boutros PC; PCAWG Consortium including M.D. Kazanov. Sex differences in oncogenic mutational processes, Nature Communications 11(1): 4330, 2020.

  • ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium including M.D. Kazanov. Campbell et al. Pan-cancer analysis of whole genomes, Nature 578, 82-93, 2020.

  • Alexandrov LB, Kim J, Haradhvala NJ, Huang MN, Tian Ng AW, Wu Y, Boot A, Covington KR, Gordenin DA, Bergstrom EN, Islam SMA, Lopez-Bigas N, Klimczak LJ, McPherson JR, Morganella S, Sabarinathan R, Wheeler DA, Mustonen V; PCAWG Mutational Signatures Working Group including M.D. Kazanov, Getz G, Rozen SG, Stratton MR; PCAWG Consortium. The repertoire of mutational signatures in human cancer, Nature 578, 94-101, 2020.

  • Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE, Kumar K, Khurana E, Waszak S, Korbel JO, Haber JE, Imielinski M; PCAWG Structural Variation Working Group including M.D. Kazanov, Weischenfeldt J, Beroukhim R, Campbell PJ; PCAWG Consortium. Patterns of somatic structural variation in human cancer genomes, Nature 578, 112-121, 2020.

  • Cortés-Ciriano I, Lee JJ, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang CZ, Pellman DS; PCAWG Structural Variation Working Group including M.D. Kazanov, Park PJ; PCAWG Consortium. Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing, Nature Genetics, 1-11, 2020.

  • Akdemir KC, Le VT, Chandran S, Li Y, Verhaak RG, Beroukhim R, Campbell PJ, Chin L, Dixon JR, Futreal PA; PCAWG Structural Variation Working Group including M.D. Kazanov; PCAWG Consortium. Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer, Nature Genetics 1-12, 2020.

  • Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F, Demeulemeester J, Santa-marina M, Ju YS, Temes J, Garcia-Souto D, Detering H, Li Y, Rodriguez-Castro J, Dueso-Barroso A, Bruzos AL, Dentro SC, Blanco MG, Contino G, Ardeljan D, Tojo M, Roberts ND, Zumalave S, Edwards PAW, Weischenfeldt J, Puiggròs M, Chong Z, Chen K, Lee EA, Wala JA, Raine K, Butler A, Waszak SM, Navarro FCP, Schumacher SE, Monlong J, Maura F, Bolli N, Bourque G, Gerstein M, Park PJ, Wedge DC, Beroukhim R, Torrents D, Korbel JO, Martincorena I, Fitzgerald RC, Van Loo P, Kazazian HH, Burns KH; PCAWG Structural Variation Working Group including M.D. Kazanov, Campbell PJ, Tubio JMC; PCAWG Consortium. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition, Nature Genetics 1-14, 2020.

  • Sieverling L, Hong C, Koser SD, Ginsbach P, Kleinheinz K, Hutter B, Braun DM, Cortés-Ciriano I, Xi R, Kabbe R, Park PJ, Eils R, Schlesner M; PCAWG-Structural Variation Working Group including M.D. Kazanov, Brors B, Rippe K, Jones DTW, Feuerbach L; PCAWG Consortium. Genomic footprints of activated telomere maintenance mechanisms in cancer, Nature Communications 11, 1-13, 2020.

  • Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A; PCAWG Transcriptome Working Group; PCAWG Structural Variation Working Group including M.D.Kazanov, Creighton CJ; PCAWG Consortium. High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations, Nature Communications 11, 1-14, 2020.

  • Fedonin GG, Eroshkin A, Cieplak P, Matveev EV, Ponomarev GV, Gelfand MS, Ratnikov BI, Kazanov MD. Predictive models of protease specificity based on quantitative protease-activity profiling data, Biochimica et Biophysica Acta - Proteins and Proteomics, 1867(11):140253, 2019.

  • Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M; AstraZeneca-Sanger Drug Combination DREAM Consortium including M.D. Kazanov, Jang IS, Ghazoui Z, Ahsen ME, Vogel R, Neto EC, Norman T, Tang EKY, Garnett MJ, Veroli GYD, Fawell S, Stolovitzky G, Guinney J, Dry JR, Saez-Rodriguez J. Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nature communication 10(1):2674, 2019.

  • Keller A, Gerkin RC, Guan Y, Dhurandhar A, Turu G, Szalai B, Mainland JD, Ihara Y, Yu CW, Wolfinger R, Vens C, Schietgat L, De Grave K, Norel R; DREAM Olfaction Prediction Consortium including M.D. Kazanov, Stolovitzky G, Cecchi GA, Vosshall LB, Meyer P. Predicting human olfactory perception from chemical features of odor molecules, Science, 355(6327), pp.820-826, 2017.

  • Guinney J, Wang T, Laajala TD, Winner KK, Bare JC, Neto EC, Khan SA, Peddinti G, Airola A, Pahikkala T, Mirtti T, Yu T, Bot BM, Shen L, Abdallah K, Norman T, Friend S, Stolovitzky G, Soule H, Sweeney CJ, Ryan CJ, Scher HI, Sartor O, Xie Y, Aittokallio T, Zhou FL, Costello JC; Prostate Cancer Challenge DREAM Community including M.D. Kazanov. Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data, The Lancet Oncology, 18(1), pp.132-142, 2016.

  • Ponomarev GV, Kazanov MD. Classification of ANA HEp-2 slide images using morphological features of stained patterns, Pattern Recognition Letters, 82(1), pp.79-84, 2016.

  • Pokrovsky VS, Kazanov MD, Dyakov IN, Pokrovskaya MV, Aleksandrova SS. Comparative immunogenicity and structural analysis of epitopes of different bacterial L-asparaginases, BMC Cancer, 16(1):89, 2016.

  • Kazanov MD, Roberts SA, Polak P, Stamatoyannopoulos J, Klimczak LJ, Gordenin DA, Sunyaev SR. APOBEC-induced cancer mutations are uniquely enriched in gene dense early replicating regions of active chromatin, Cell Reports, 13(6), pp.1103-1109, 2015.

  • Garushyants SK, Kazanov MD, Gelfand MS. Horizontal gene transfer and genome evolution in Methanosarcina, BMC Evolutionary Biology, 15(1):102,2015.

  • Kumar S, Ratnikov BI, Kazanov MD, Smith JW, Cieplak P. CleavPredict: a platform for reasoning about matrix metalloproteinases proteolytic events, PLoS One, 10(5):e0127877, 2015.

  • Rodionova IA, Zuccola HJ, Sorci L, Aleshin AE, Kazanov MD, Ma CT, Sergienko E, Rubin EJ, Locher CP, Osterman AL. 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 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, Journal of Biological Chemistry, 289(47), pp. 32783-32797, 2014.

  • 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. U S A, 111(40), E4148-4155, 2014.

  • Ponomarev GV, Arlazarov VL, Gelfand MS, Kazanov MD. ANA HEp-2 cells imageclassification using number, size, shape and localization of targeted cell regions, Pattern Recognition, 47 (7), pp.2360-2366, 2014.

  • 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 Letters, 588(6), pp.1016-1023, 2014.

  • Belushkin AA, Vinogradov DV, Gelfand MS, Osterman AL, Cieplak P, Kazanov MD. Sequence-derived structural features driving proteolytic processing, Proteomics, 14(1), pp.42-50, 2014.

  • Rueda S, Fathima S, Knight CL, Yaqub M, Papageorghiou AT, Rahmatullah B, Foi A, Maggioni M, Pepe A, Tohka J, Stebbing RV, McManigle JE, Ciurte A, Bresson X,Cuadra MB, Sun C, Ponomarev GV, Gelfand MS, Kazanov MD, Wang CW, Chen HC, Peng CW, Hung CM, Noble JA. Evaluation and comparison of current fetal ultrasound image segmentation methods for biometric measurements: a grand challenge, IEEE Trans Med Imaging, 33(4), pp.797-813, 2014.

  • 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, 14:745, 2013.

  • 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, 14:597, 2013.

  • 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, 8(6):e65595, 2013.

  • Gordienko EN, Kazanov MD, Gelfand MS. Evolution of pan-genomes of Escherichia coli, Shigella spp., and Salmonella enterica, Journal of Bacteriology, 195(12), pp.2786-2792, 2013.

  • Leyn SA, Kazanov MD, Sernova NV, Ermakova EO, Novichkov PS, Rodionov DA. Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis, Journal of Bacteriology, 195(11), pp.2463-2473.

  • Ravcheev DA, Best AA, Sernova NV, Kazanov MD, Novichkov PS, Rodionov DA. Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria, BMC Genomics, 14:94, 2013.

  • Kazanov MD, Li X, Gelfand MS, Osterman AL, Rodionov DA. Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum, Nucleic Acids Research, 41(2), pp.790-803, 2013.

  • Tsoy OV, Pyatnitskiy MA, Kazanov MD, Gelfand MS. Evolution of transcriptional regulation in closely related bacteria, BMC Evolutionary Biology, 12:200, 2012.

  • De Ingeniis J, Ratnikov B, Richardson AD, Scott DA, Aza-Blanc P, De SK, Kazanov M, Pellecchia M, Ronai Z, Osterman AL, Smith JW. Functional specialization in proline biosynthesis of melanoma, PLoS One, 7(9):e45190, 2012.

  • De Ingeniis J, Kazanov MD, Shatalin K, Gelfand MS, Osterman AL, Sorci L. Glutamine versus ammonia utilization in the NAD synthetase family, PLoS One, 7(6):e39115, 2012.

  • Rodionov DA, Novichkov PS, Stavrovskaya ED, Rodionova IA, Li X, Kazanov MD, Ravcheev DA, Gerasimova AV, Kazakov AE, Kovaleva GY, Permina EA, Laikova ON, Overbeek R, Romine MF, Fredrickson JK, Arkin AP, Dubchak I, Osterman AL, Gelfand MS. Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus, BMC Genomics, 12 Suppl 1:S3, 2011.

  • Lazarev VN, Levitskii SA, Basovskii YI, Chukin MM, Akopian TA, Vereshchagin VV, Kostrjukova ES, Kovaleva GY, Kazanov MD, Malko DB, Vitreschak AG, Sernova NV, Gelfand MS, Demina IA, Serebryakova MV, Galyamina MA, Vtyurin NN, Rogov SI, Alexeev DG, Ladygina VG, Govorun VM. Complete genome and proteome of Acholeplasma laidlawii, Journal of Bacteriology, 193(18), pp.4943-4953, 2011.

  • Kazanov MD, Igarashi Y, Eroshkin AM, Cieplak P, Ratnikov B, Zhang Y, Li Z, Godzik A, Osterman AL, Smith JW. Structural determinants of limited proteolysis., Journal of Proteome Research, 10(8), pp.3642-3651, 2011.

  • Vakhrusheva AA, Kazanov MD, Mironov AA, Bazykin GA. Evolution of prokaryotic genes by shift of stop codons, Journal of Molecular Evolution, 72(2):138-146, 2010.

  • Arlazarov VL, Kazanov MD. Segmentation of small objects in color images, Programming and Computer Software, 34(3), pp.173-182, 2008.

  • Kazanov MD, Vitreschak AG, Gelfand MS. Abundance and functional diversity of riboswitches in microbial communities, BMC Genomics, 8:347, 2007.

Grants

  • 2024–2026 PI, TUBITAK grant #123E476.

  • 2020–2022 PI, Russian Science Foundation, grant #22-14-00132, ;

  • 2018–2020 PI, Russian Foundation for Basic Research, grant #20-04-60066.

  • 2015–2017 PI, Russian Foundation for Basic Research, grant #15-04-06861.

  • 2015–2017 PI, Russian Academy of Science, grant for new groups within the Programme of Molecular and Cellular Biology.