Marat Kazanov

Supervisor: Mikhail Gelfand

Marat graduated from the Applied Mathematics Department at the Moscow Institute of Physics and Technology. He defended his Candidate of Sciences thesis in Computer Science at the Laboratory of Artificial Intelligence, ISA RAS under the supervision of Professor Vladimir Arlazarov, who is known for developing the first world chess champion computer program Kaissa. Then, he spent three years as a postdoc at the laboratory of Professor Andrei Osterman at the Sanford-Burnham Medical Research Institute, La Jolla, USA, participating in the projects related to the biological regulatory network reconstruction, computational drug discovery and chemoinformatics. On his return to Moscow, he worked on various bioinformatics projects under the supervision of Professor Mikhail Gelfand. He co-authored papers in the high-impact journals including Lancet Onc., Cell Rep., NAR, Science and Nature. Marat’s current research interests include cancer bioinformatics, bacterial regulatory networks, protein structure and medical imaging.

- Cancer bioinformatics
– Structural bioinformatics
– Computational methods for drug discovery
– Biomedical imaging


41. Ludmil B. Alexandrov et al. The repertoire of mutational signatures in human cancer, Nature 578, 94-101, 2020. PMID:32025018

40. Esther Rheinbay et al. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes, Nature 578, 102-111, 2020. PMID:32025015

39. Yilong Li et al. Patterns of somatic structural variation in human cancer genomes, Nature 578, 112-121, 2020. PMID:32025012

38. Peter J. Campbell et al. Pan-cancer analysis of whole genomes, Nature 578, 82-93, 2020. PMID:32025007

37. Isidro Cortes-Ciriano et al. Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing, Nature Genetics, 1-11, 2020. PMID:32025003

36. Kadir C. Akdemir et al. Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer, Nature Genetics 1-12, 2020. PMID:32024999

35. Bernardo Rodriguez-Martin et al. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition, Nature Genetics 1-14, 2020. PMID:32024998

34. Yiqun Zhang et al. High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations, Nature Communications 11(1), 736, 2020. PMID:32024823

33. Lina Sieverling et al. Genomic footprints of activated telomere maintenance mechanisms in cancer, Nature Communications 11(1), 733, 2020. PMID:32024817


32. 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. Biochim Biophys Acta Proteins Proteom, 1867(11):140253, 2019. PMID:31330204

31. Menden M.P. et al. Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nature Communications, 10(1):2674, 2019. PMID:31209238


30. Keller A. et al. Predicting human olfactory perception from chemical features of odor molecules, Science, 355(6327), pp.820-826, 2017. PMID:28219971


29. Guinney J. et al. 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. PMID:27864015

28. 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. ScienceDirect

27. 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. (* equal contribution) PMID:26867931


26. Kazanov MD, Roberts SA, Polak P, Stamatoyannopoulos J, Klimczak LJ, Gordenin DA, Sunyaev SR. APOBEC-Induced Cancer Mutations Are Uniquely Enriched in Early-Replicating, Gene-Dense, and Active Chromatin Regions, Cell Reports, 13(6), pp.1103-1109, 2015. PMID:26527001

25. Garushyants SK, Kazanov MD, Gelfand MS. Horizontal gene transfer and genome evolution in Methanosarcina, BMC Evolutionary Biology, 15(1):102,2015. PMID:26044078

24. 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. PMID:25996941

23. 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. PMID:25631047


22. 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. PMID:25301953

21. 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. PMID:25246591

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

19. 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. PMID:24530526

18. 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. PMID:24227478

17. 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 Transactions on Medical Imaging, 33(4), pp.797-813, 2014. PMID:23934664


16. 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. PMID:24175918

15. 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. PMID:24060102

14. 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. PMID:23776507

13. 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. PMID:23585535

12. 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. PMID:23504016

11. 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. PMID:23398941

10. 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. PMID:23209028


9. Tsoy OV, Pyatnitskiy MA, Kazanov MD, Gelfand MS. Evolution of transcriptional regulation in closely related bacteria, BMC Evolutionary Biology, 12:200, 2012. PMID:23039862

8. 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. PMID:23024808

7. 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. (* equal contribution) PMID:22720044


6. 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. PMID:21810205

5. 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. PMID:21784942

4. 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. PMID:21682278

2010 and before

3. 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. PMID:21082168

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

1. Kazanov MD, Vitreschak AG, Gelfand MS. Abundance and functional diversity of riboswitches in microbial communities, BMC Genomics, 8:347, 2007. PMID:17908319