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Germany

USD 70 /hr

Ph.D in Genomics & Bioinformatics | Expert in data analysis & machine learning | R, Python, C++

Profile Summary

I graduated from the Applied Mathematics Department at the Moscow Institute of Physics and Technology. I defended my 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, I 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 my return to Moscow, I worked on various bioinformatics projects under the supervision of Professor Mikhail Gelfand. I co-authored papers in the high-impact journals including Lancet Onc., Cell Rep., NAR, Science and Nature. My current research interests include cancer bioinformatics, bacterial genomics, machine learning in life sciences.

Subject Matter Expertise

• ☆ Computational Biology
• ☆ Biostatistics
• ☆ Mathematical Biology
• ☆ Data Analysis
• ☆ Image Processing
• ☆ Computer Simulation/Computational Modeling
• ☆ Algorithm Design
• ☆ Predictive Modeling & Analytics
• ☆ Data Processing
• ☆ Data Exploration
• ☆ Cluster Analysis
• ☆ Data Visualization
• ☆ Big Data Analytics
• ☆ Data Management
• ☆ Data Manipulation
• ☆ Machine Learning
• ☆ Text Mining & Analytics
• ☆ Data Mining
• ☆ Data Cleaning
• ☆ Data Architecture
• ☆ Pattern Recognition
• ☆ Artificial Intelligence
• ☆ Computer Vision
• ☆ Bioinformatics
• ☆ Gene & Protein Expression Analysis
• ☆ Systems Biology
• ☆ Structural Bioinformatics
• ☆ Python
• ☆ Matlab
• ☆ SQL
• ☆ Excel
• ☆ LaTex
• ☆ R
• ☆ Scikit-learn
• ☆ Oracle

Services

• Research
• Consulting
• Data & AI

Research Scientific and Technical Research

Consulting Scientific and Technical Consulting

Data & AI Predictive Modeling, Statistical Analysis, Image Processing, Image Analysis, Algorithm Design-Non ML, Algorithm Design-ML, Data Visualization, Big Data Analytics, Text Mining & Analytics, Data Mining, Data Cleaning, Data Processing, Data Insights

Work Experience

Head of the Translational Bioinformatics Group

Institute for Information Transmission Problems

- Present

Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology

June 2019 - Present

Skolkovo Institute of Science and Technology

April 2017 - Present

Postdoc

Sanford-Burnham Medical Research Institute

2008 - 2010

Education

(Applied Mathematics)

Moscow Institute of Physics and Technology

September 1991 - May 1997

Certifications

• Certification details not provided.

Publications

PREPRINT

Fedor M Kazanov, Evgenii V Matveev, Gennady V Ponomarev, Dmitry N Ivankov, Marat D. Kazanov (2023). RNAsselem: a Python Package for Descriptive Analysis of RNA Secondary Structure Elements in Viral Genomes .

Eugenii V. Matveev, Gennady V. Ponomarev, Marat D. Kazanov (2023). Genome-wide Bioinformatics Analysis of Human Protease Specificity Identified Potential Cathepsin L Cleavage Site at K790 Position of the SARS-CoV-2 Spike Glycoprotein .

Gennady V. Ponomarev, Bulat Fatykhov, Vladimir A. Nazarov, Ruslan Abasov, Evgeny Shvarov, Nina-Vicky Landik, Alexandra A. Denisova, Almira A. Chervova, Mikhail S. Gelfand, Marat D. Kazanov(2021). APOBEC mutagenesis is low in most types of non-B DNA structures, unlike other types of cancer mutagenesis . Cold Spring Harbor Laboratory

JOURNAL ARTICLE

Kathleen M Hudson, Leszek J Klimczak, Joan F Sterling, Adam B Burkholder, Marat D Kazanov, Natalie Saini, Piotr A Mieczkowski, Dmitry A Gordenin (2023). Glycidamide-induced hypermutation in yeast single-stranded DNA reveals a ubiquitous clock-like mutational motif in humans . Nucleic Acids Research.

Evgenii V. Matveev, Vyacheslav V. Safronov, Gennady V. Ponomarev, Marat D. Kazanov (2023). Predicting Structural Susceptibility of Proteins to Proteolytic Processing . International Journal of Molecular Sciences.

Marat Kazanov, Evgenii V. Matveev, Vyacheslav V. Safronov, Gennady V. Ponomarev (2023). Predicting Structural Susceptibility of Proteins to Proteolytic Processing . International Journal of Molecular Sciences.

Borkovskaia A, Bogacheva S, Konyukhova T, Dadakhanova E, Gaskova M, Soldatkina O, Dubrovina M, Popov A, Mikhailova E, Inushkina E, et al.(2023). Molecular Heterogeneity of Pediatric AML with Atypical Promyelocytes Accumulation in Children-A Single Center Experience . Genes.

Gennady V. Ponomarev, Bulat Fatykhov, Vladimir A. Nazarov, Ruslan Abasov, Evgeny Shvarov, Nina-Vicky Landik, Alexandra A. Denisova, Almira A. Chervova, Mikhail S. Gelfand, Marat D. Kazanov (2022). APOBEC mutagenesis is low in most types of non-B DNA structures . iScience.

Zerkalenkova E, Lebedeva S, Borkovskaia A, Menchits Y, Gaskova M, Itov A, Matveev E, Kazanov M, Olshanskaya Y(2022). PB1799: KMT2A-REARRANGED PEDIATRIC ACUTE MYELOID LEUKEMIA . HemaSphere.

Marat Kazanov, Alexandra Semchenkova, Ekaterina Mikhailova, Alexander Komkov, Marina Gaskova, Ruslan Abasov, Evgenii Matveev, Ilgar Mamedov, Anna Shmitko, Vera Belova, et al.(2022). Lineage Conversion in Pediatric B-Cell Precursor Acute Leukemia under Blinatumomab Therapy . International Journal of Molecular Sciences. 23. (7). p. 4019. {MDPI} {AG}

Marat Kazanov, Alexandra Semchenkova, Ekaterina Mikhailova, Alexander Komkov, Marina Gaskova, Ruslan Abasov, Evgenii Matveev, Ilgar Mamedov, Anna Shmitko, Vera Belova, et al. (2022). Lineage Conversion in Pediatric B-Cell Precursor Acute Leukemia under Blinatumomab Therapy . International Journal of Molecular Sciences.

Kovach AE, Zerkalenkova E, Zemtsova L, Borkovskaya A, Gaskova M, Kazanov M, Popov A, Baidun L, Maschan M, Maschan A, et al.(2021). Acute myeloid leukemia with t(X;6)9p11;q23);MYB-GATA1 and female sex: GATA1 insufficiency may be insufficient for pathogenesis . Cancer genetics.

Almira Chervova, Bulat Fatykhov, Alexander Koblov, Evgeny Shvarov, Julia Preobrazhenskaya, Dmitry Vinogradov, Gennady V Ponomarev, Mikhail S Gelfand, Marat D Kazanov(2021). Analysis of gene expression and mutation data points on contribution of transcription to the mutagenesis by APOBEC enzymes . NAR Cancer. 3. (3). Oxford University Press ({OUP})

Shuai S, PCAWG Drivers and Functional Interpretation Working Group, Gallinger S, Stein LD, PCAWG Consortium(2020). Combined burden and functional impact tests for cancer driver discovery using DriverPower . Nature communications.

Yuan Y, Ju YS, Kim Y, Li J, Wang Y, Yoon CJ, Yang Y, Martincorena I, Creighton CJ, Weinstein JN, et al.(2020). Comprehensive molecular characterization of mitochondrial genomes in human cancers . Nature genetics.

Bhandari V, Li CH, Bristow RG, Boutros PC, PCAWG Consortium(2020). Divergent mutational processes distinguish hypoxic and normoxic tumours . Nature communications.

PCAWG Transcriptome Core Group, Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, et al.(2020). Genomic basis for RNA alterations in cancer . Nature.

Jiao W, Atwal G, Polak P, Karlic R, Cuppen E, PCAWG Tumor Subtypes and Clinical Translation Working Group, Danyi A, de Ridder J, van Herpen C, PCAWG Consortium(2020). A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns . Nature communications.

Cmero M, Yuan K, Ong CS, Schröder J, PCAWG Evolution and Heterogeneity Working Group, Corcoran NM, Papenfuss T, Hovens CM, Markowetz F, Macintyre G, et al.(2020). Inferring structural variant cancer cell fraction . Nature communications.

Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC, PCAWG Drivers and Functional Interpretation Working Group, PCAWG Consortium(2020). Integrative pathway enrichment analysis of multivariate omics data . Nature communications.

Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, et al.(2020). Pathway and network analysis of more than 2500 whole cancer genomes . Nature communications.

Rubanova Y, Shi R, Harrigan CF, Li R, Wintersinger J, Sahin N, Deshwar AG, PCAWG Evolution and Heterogeneity Working Group, Morris QD, PCAWG Consortium(2020). Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig . Nature communications.

Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, et al.(2020). The evolutionary history of 2,658 cancers . Nature.

Carlevaro-Fita J, Lanzós A, Feuerbach L, Hong C, Mas-Ponte D, Pedersen JS, PCAWG Drivers and Functional Interpretation Group, Johnson R, PCAWG Consortium(2020). Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis . Communications biology.

Yakneen S, Waszak SM, PCAWG Technical Working Group, Gertz M, Korbel JO, PCAWG Consortium(2020). Butler enables rapid cloud-based analysis of thousands of human genomes . Nature biotechnology.

Li, C.H., Prokopec, S.D., Sun, R.X., Yousif, F., Schmitz, N., Al-Shahrour, F., Atwal, G., Bailey, P.J., Biankin, A.V., Boutros, P.C., et al.(2020). Sex differences in oncogenic mutational processes . Nature Communications. 11. (1).

Cortés-Ciriano, I., Lee, J.J.-K., Xi, R., Jain, D., Jung, Y.L., Yang, L., Gordenin, D., Klimczak, L.J., Zhang, C.-Z., Pellman, D.S., et al.(2020). Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing . Nature Genetics. 52. (3). p. 331-341.

Akdemir, K.C., Le, V.T., Chandran, S., Li, Y., Verhaak, R.G., Beroukhim, R., Campbell, P.J., Chin, L., Dixon, J.R., Futreal, P.A., et al.(2020). Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer . Nature Genetics. 52. (3). p. 294-305.

Sieverling, L., Hong, C., Koser, S.D., Ginsbach, P., Kleinheinz, K., Hutter, B., Braun, D.M., Cortés-Ciriano, I., Xi, R., Kabbe, R., et al.(2020). Genomic footprints of activated telomere maintenance mechanisms in cancer . Nature Communications. 11. (1).

Rheinbay, E., Nielsen, M.M., Abascal, F., Wala, J.A., Shapira, O., Tiao, G., Hornshøj, H., Hess, J.M., Juul, R.I., Lin, Z., et al.(2020). Analyses of non-coding somatic drivers in 2,658 cancer whole genomes . Nature. 578. (7793). p. 102-111.

Zhang, Y., Chen, F., Fonseca, N.A., He, Y., Fujita, M., Nakagawa, H., Zhang, Z., Brazma, A., Amin, S.B., Awadalla, P., et al.(2020). High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations . Nature Communications. 11. (1).

Rodriguez-Martin, B., Alvarez, E.G., Baez-Ortega, A., Zamora, J., Supek, F., Demeulemeester, J., Santamarina, M., Ju, Y.S., Temes, J., Garcia-Souto, D., et al.(2020). Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition . Nature Genetics. 52. (3). p. 306-319.

Li, Y., Roberts, N.D., Wala, J.A., Shapira, O., Schumacher, S.E., Kumar, K., Khurana, E., Waszak, S., Korbel, J.O., Haber, J.E., et al.(2020). Patterns of somatic structural variation in human cancer genomes . Nature. 578. (7793). p. 112-121.

Alexandrov, L.B., Kim, J., Haradhvala, N.J., Huang, M.N., Tian Ng, A.W., Wu, Y., Boot, A., Covington, K.R., Gordenin, D.A., Bergstrom, E.N., et al.(2020). The repertoire of mutational signatures in human cancer . Nature. 578. (7793). p. 94-101.

Campbell, P.J., Getz, G., Korbel, J.O., Stuart, J.M., Jennings, J.L., Stein, L.D., Perry, M.D., Nahal-Bose, H.K., Ouellette, B.F.F., Li, C.H., et al.(2020). Pan-cancer analysis of whole genomes . Nature. 578. (7793). p. 82-93.

Bailey, M.H., Meyerson, W.U., Dursi, L.J., Wang, L.-B., Dong, G., Liang, W.-W., Weerasinghe, A., Li, S., Kelso, S., Akbani, R., et al.(2020). Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples . Nature Communications. 11. (1).

Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R, et al.(2019). Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen . Nature communications.

Fedonin, G.G., Eroshkin, A., Cieplak, P., Matveev, E.V., Ponomarev, G.V., Gelfand, M.S., Ratnikov, B.I., Kazanov, M.D.(2019). Predictive models of protease specificity based on quantitative protease-activity profiling data . Biochimica et Biophysica Acta - Proteins and Proteomics. 1867. (11).

Menden, M.P., Wang, D., Mason, M.J., Szalai, B., Bulusu, K.C., Guan, Y., Yu, T., Kang, J., Jeon, M., Wolfinger, R., et al.(2019). Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen . Nature Communications. 10. (1).

(2017). Predicting human olfactory perception from chemical features of odor molecules . Science (New York, N.Y.).

Keller, A., Gerkin, R.C., Guan, Y., Dhurandhar, A., Turu, G., Szalai, B., Mainland, J.D., Ihara, Y., Yu, C.W., Wolfinger, R., et al.(2017). Predicting human olfactory perception from chemical features of odor molecules . Science. 355. (6327). p. 820-826.

Seyednasrollah, F., Koestler, D.C., Wang, T., Piccolo, S.R., Vega, R., Greiner, R., Fuchs, C., Gofer, E., Kumar, L., Wolfinger, R.D., et al.(2017). A DREAM challenge to build prediction models for short-term discontinuation of docetaxel in metastatic castration- resistant prostate cancer . JCO Clinical Cancer Informatics. 2017. (1). p. 1-15.

Guinney, Justin, Wang, Tao, Laajala, Teemu D., Winner, Kimberly Kanigel, Bare, J. Christopher, Neto, Elias Chaibub, Khan, Suleiman A., Peddinti, Gopal, Airola, Antti, Pahikkala, Tapio, et al.(2017). 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 . Lancet Oncology. 18. (1). p. 132-142.

Guinney J, Wang T, Laajala TD, Winner KK, Bare JC, Neto EC, Khan SA, Peddinti G, Airola A, Pahikkala T, et al.(2016). 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.

Gennady V. Ponomarev, Marat D. Kazanov(2016). Classification of ANA HEp-2 slide images using morphological features of stained patterns . Pattern Recognition Letters. 82. p. 79--84. Elsevier {BV}

Ponomarev, G.V., Kazanov, M.D.(2016). Classification of ANA HEp-2 slide images using morphological features of stained patterns . Pattern Recognition Letters. 82. p. 79-84.

Pokrovsky, V.S., Kazanov, M.D., Dyakov, I.N., Pokrovskaya, M.V., Aleksandrova, S.S.(2016). Comparative immunogenicity and structural analysis of epitopes of different bacterial L-asparaginases . BMC Cancer. 16. (1).

Kazanov MD, Roberts SA, Polak P, Stamatoyannopoulos J, Klimczak LJ, Gordenin DA, Sunyaev SR, Cell reports, 2015, vol. 13, no. 6, pp. 1103-1109 .

Rodionova IA, Zuccola HJ, Sorci L, Aleshin AE, Kazanov MD, Ma CT, Sergienko E, Rubin EJ, Locher CP, Osterman AL, The Journal of biological chemistry, 2015, vol. 290, no. 12, pp. 7693-7706 .

Rodionova, I.A., Zuccola, H.J., Sorci, L., Aleshin, A.E., Kazanov, M.D., Ma, C.-T., Sergienko, E., Rubin, E.J., Locher, C.P., Osterman, A.L.(2015). Mycobacterial Nicotinate Mononucleotide Adenylyltransferase structure, mechanism, and implications for drug discovery . Journal of Biological Chemistry. 290. (12). p. 7693-7706.

Kumar S, Ratnikov BI, Kazanov MD, Smith JW, Cieplak P, PloS one, 2015, vol. 10, no. 5, pp. e0127877 .

Kumar, S., Ratnikov, B.I., Kazanov, M.D., Smith, J.W., Cieplak, P.C.(2015). CleavPredict: A platform for reasoning about matrix metalloproteinases proteolytic events . PLoS ONE. 10. (5).

Pokrovsky VS, Kazanov MD, Dyakov IN, Pokrovskaya MV, Aleksandrova SS, BMC cancer, 2015, vol. 16, no. 1, pp. 89 .

Garushyants SK, Kazanov MD, Gelfand MS, BMC evolutionary biology, 2015, vol. 15, pp. 102 .

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

Kazanov, M.D., Roberts, S.A., Polak, P., Stamatoyannopoulos, J., Klimczak, L.J., Gordenin, D.A., Sunyaev, S.R.(2015). APOBEC-Induced Cancer Mutations Are Uniquely Enriched in Early-Replicating, Gene-Dense, and Active Chromatin Regions . Cell Reports. 13. (6). p. 1103-1109.

Kumar, S., Ratnikov, B.I., Kazanov, M.D., Smith, J.W., Cieplak, P.(2015). Erratum: CleavPredict: A platform for reasoning about matrix metalloproteinases proteolytic events (PLoS ONE (2015) 10: 5 (e0127877) DOI: 10.1371/journal.pone.0127877) . PLoS ONE. 10. (6).

Pendlebury D, Wang R, Henin RD, Hockla A, Soares AS, Madden BJ, Kazanov MD, Radisky ES, The Journal of biological chemistry, 2014, vol. 289, no. 47, pp. 32783-32797 .

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, Proceedings of the National Academy of Sciences of the United States of America, 2014, vol. 111, no. 40, pp. E4148-55 .

Sorci, L., Brunetti, L., Cialabrini, L., Mazzola, F., Kazanov, M.D., D'Auria, S., Ruggieri, S., Raffaelli, N.(2014). Characterization of bacterial NMN deamidase as a Ser/Lys hydrolase expands diversity of serine amidohydrolases . FEBS Letters. 588. (6). p. 1016-1023.

Rueda, Sylvia, Fathima, Sana, Knight, Caroline L, Yaqub, Mohammad, Papageorghiou, Aris T, Rahmatullah, Bahbibi, Foi, Alessandro, Maggioni, Matteo, Pepe, Antonietta, Tohka, Jussi, et al.(2014). Evaluation and comparison of current fetal ultrasound image segmentation methods for biometric measurements: a grand challenge . IEEE transactions on medical imaging. 33. (4). p. 797-813.

Rueda, S., Fathima, S., Knight, C.L., Yaqub, M., Papageorghiou, A.T., Rahmatullah, B., Foi, A., Maggioni, M., Pepe, A., Tohka, J., et al.(2014). Evaluation and comparison of current fetal ultrasound image segmentation methods for biometric measurements: A grand challenge . IEEE Transactions on Medical Imaging. 33. (4). p. 797-813.

Belushkin, A.A., Vinogradov, D.V., Gelfand, M.S., Osterman, A.L., Cieplak, P., Kazanov, M.D.(2014). Sequence-derived structural features driving proteolytic processing . Proteomics. 14. (1). p. 42-50.

Ponomarev, G.V., Arlazarov, V.L., Gelfand, M.S., Kazanov, M.D.(2014). ANA HEp-2 cells image classification using number, size, shape and localization of targeted cell regions . Pattern Recognition. 47. (7). p. 2360-2366.

Pendlebury, D., Wang, R., Henin, R.D., Hockla, A., Soares, A.S., Madden, B.J., Kazanov, M.D., Radisky, E.S.(2014). Sequence and conformational specificity in substrate recognition: Several human Kunitz protease inhibitor domains are specific substrates of mesotrypsin . Journal of Biological Chemistry. 289. (47). p. 32783-32797.

Sorci, Leonardo, Brunetti, Lucia, Cialabrini, Lucia, Mazzola, Francesca, Kazanov, Marat D., D'Auria, Sabato, Ruggieri, Silverio, Raffaelli, Nadia(2014). Characterization of bacterial NMN deamidase as a Ser/Lys hydrolase expands diversity of serine amidohydrolases . Febs Letters. 588. (6). p. 1016-1023.

Ratnikov, B.I., Cieplak, P., Gramatikoff, K., Pierce, J., Eroshkin, A., Igarashi, Y., Kazanov, M., Sun, Q., Godzik, A., Osterman, A., et al.(2014). Basis for substrate recognition and distinction by matrix metalloproteinases . Proceedings of the National Academy of Sciences of the United States of America. 111. (40). p. E4148-E4155.

Belushkin, Alexander A., Vinogradov, Dmitry V., Gelfand, Mikhail S., Osterman, Andrei L., Cieplak, Piotr, Kazanov, Marat D.(2014). Sequence-derived structural features driving proteolytic processing . Proteomics. 14. (1). p. 42-50.

Gelfand, Mikhail S., Gordienko, Evgeny N., Kazanov, Marat D.(2013). Evolution of Pan-Genomes of Escherichia coli, Shigella spp., and Salmonella enterica . Journal of Bacteriology. 195. (12). p. 2786-2792.

Gordienko, E.N., Kazanov, M.D., Gelfand, M.S.(2013). Evolution of pan-genomes of Escherichia coli, Shigella spp., and Salmonella enterica . Journal of Bacteriology. 195. (12). p. 2786-2792.

Gelfand, Mikhail S., Kazanov, Marat D., Li, Xiaoqing, Osterman, Andrei L., Rodionov, Dmitry A.(2013). Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum . Nucleic Acids Research. 41. (2). p. 790-803.

Kazanov, M.D., Li, X., Gelfand, M.S., Osterman, A.L., Rodionov, D.A.(2013). Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum . Nucleic Acids Research. 41. (2). p. 790-803.

Leyn, S.A., Kazanov, M.D., Sernova, N.V., Ermakova, E.O., Novichkov, P.S., Rodionova, D.A.(2013). Genomic reconstruction of the transcriptional regulatory network in bacillus subtilis . Journal of Bacteriology. 195. (11). p. 2463-2473.

Best, Aaron A., Kazanov, Marat D., Novichkov, Pavel S., Ravcheev, Dmitry A., Rodionov, Dmitry A., Sernova, Natalia V.(2013). Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria . Bmc Genomics. 14.

Sun, Eric I., Leyn, Semen A., Kazanov, Marat D., Saier, Milton H., Jr., Novichkov, Pavel S., Rodionov, Dmitry A.(2013). Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria . Bmc Genomics. 14.

Sun, E.I., Leyn, S.A., Kazanov, M.D., Saier, M.H., Novichkov, P.S., Rodionov, D.A.(2013). Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria . BMC Genomics. 14. (1).

Ravcheev, D.A., Best, A.A., Sernova, N.V., Kazanov, M.D., Novichkov, P.S., Rodionov, D.A.(2013). Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria . BMC Genomics. 14. (1).

Ermakova, Ekaterina O., Kazanov, Marat D., Leyn, Semen A., Novichkov, Pavel S., Rodionov, Dmitry A., Sernova, Natalia V.(2013). Genomic Reconstruction of the Transcriptional Regulatory Network in Bacillus subtilis . Journal of Bacteriology. 195. (11). p. 2463-2473.

Cialabrini, Lucia, Kazanov, Marat D., Mazzola, Francesca, Orsomando, Giuseppe, Osterman, Andrei L., Raffaelli, Nadia, Ruggieri, Silverio, Sorci, Leonardo(2013). Genomics-Guided Analysis of NAD Recycling Yields Functional Elucidation of COG1058 as a New Family of Pyrophosphatases . Plos One. 8. (6).

Cialabrini, L., Ruggieri, S., Kazanov, M.D., Sorci, L., Mazzola, F., Orsomando, G., Osterman, A.L., Raffaelli, N.(2013). Genomics-Guided Analysis of NAD Recycling Yields Functional Elucidation of COG1058 as a New Family of Pyrophosphatases . PLoS ONE. 8. (6).

Novichkov, Pavel S., Kazakov, Alexey E., Ravcheev, Dmitry A., Leyn, Semen A., Kovaleva, Galina Y., Sutormin, Roman A., Kazanov, Marat D., Riehl, William, Arkin, Adam P., Dubchak, Inna, et al.(2013). RegPrecise 3.0-A resource for genome-scale exploration of transcriptional regulation in bacteria . Bmc Genomics. 14.

Novichkov, P.S., Kazakov, A.E., Ravcheev, D.A., Leyn, S.A., Kovaleva, G.Y., Sutormin, R.A., Kazanov, M.D., Riehl, W., Arkin, A.P., Dubchak, I., et al.(2013). RegPrecise 3.0 - A resource for genome-scale exploration of transcriptional regulation in bacteria . BMC Genomics. 14. (1).

Gelfand, Mikhail S., Kazanov, Marat D., Pyatnitskiy, Mikhail A., Tsoy, Olga V.(2012). Evolution of transcriptional regulation in closely related bacteria . Bmc Evolutionary Biology. 12.

Tsoy, O.V., Pyatnitskiy, M.A., Kazanov, M.D., Gelfand, M.S.(2012). Evolution of transcriptional regulation in closely related bacteria . BMC Evolutionary Biology. 12. (1).

Kazanov, Marat, Aza-Blanc, Pedro, De Ingeniis, Jessica, De, Surya K., Osterman, Andrei L., Pellecchia, Maurizio, Ratnikov, Boris, Richardson, Adam D., Ronai, Ze'ev, Scott, David A., et al.(2012). Functional Specialization in Proline Biosynthesis of Melanoma . Plos One. 7. (9).

de Ingeniis, J., Ratnikov, B., Richardson, A.D., Scott, D.A., Aza-Blanc, P., De, S.K., Kazanov, M., Pellecchia, M., Ronai, Z., Osterman, A.L., et al.(2012). Functional Specialization in Proline Biosynthesis of Melanoma . PLoS ONE. 7. (9).

De Ingeniis, Jessica, Gelfand, Mikhail S., Kazanov, Marat D., Osterman, Andrei L., Shatalin, Konstantin, Sorci, Leonardo(2012). Glutamine versus Ammonia Utilization in the NAD Synthetase Family . Plos One. 7. (6).

de Ingeniis, J., Kazanov, M.D., Shatalin, K., Gelfand, M.S., Osterman, A.L., Sorci, L.(2012). Glutamine versus ammonia utilization in the NAD synthetase family . PLoS ONE. 7. (6).

Arkin, Adam P., Dubchak, Inna, Fredrickson, James K., Gelfand, Mikhail S., Gerasimova, Anna V., Kazakov, Alexey E., Kazanov, Marat D., Kovaleva, Galina Yu, Laikova, Olga N., Li, Xiaoqing, et al.(2011). Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus . Bmc Genomics. 12.

Rodionov, D.A., Novichkov, P.S., Stavrovskaya, E.D., Rodionova, I.A., Li, X., Kazanov, M.D., Ravcheev, D.A., Gerasimova, A.V., Kazakov, A.E., Kovaleva, G.Y., et al.(2011). Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus . BMC Genomics. 12. (SUPPL. 1).

Akopian, T. A., Alexeev, D. G., Basovskii, Y. I., Chukin, M. M., Demina, I. A., Galyamina, M. A., Gelfand, M. S., Govorun, V. M., Kazanov, M. D., Kostrjukova, E. S., et al.(2011). Complete Genome and Proteome of Acholeplasma laidlawii . Journal of Bacteriology. 193. (18). p. 4943-4953.

Lazarev, V.N., Levitskii, S.A., Basovskii, Y.I., Chukin, M.M., Akopian, T.A., Vereshchagin, V.V., Kostrjukova, E.S., Kovaleva, G.Y., Kazanov, M.D., Malko, D.B., et al.(2011). Complete genome and proteome of Acholeplasma laidlawii . Journal of Bacteriology. 193. (18). p. 4943-4953.

Bazykin, Georgii A., Kazanov, Marat D., Mironov, Andrey A., Vakhrusheva, Anna A.(2011). Evolution of Prokaryotic Genes by Shift of Stop Codons . Journal of Molecular Evolution. 72. (2). p. 138-146.

Vakhrusheva, A.A., Kazanov, M.D., Mironov, A.A., Bazykin, G.A.(2011). Evolution of prokaryotic genes by shift of stop codons . Journal of Molecular Evolution. 72. (2). p. 138-146.

Dontsova, O., Kazanov, M., Osterman, I., Sergiev, P.(2011). New class of Escherichia coli small RNAs - tRNA associated RNAs (TARs). Febs Journal. 278. p. 471.

Cieplak, Piotr, Eroshkin, Alexey M., Godzik, Adam, Igarashi, Yoshinobu, Kazanov, Marat D., Li, Zhanwen, Osterman, Andrei L., Ratnikov, Boris, Smith, Jeffrey W., Zhang, Ying(2011). Structural Determinants of Limited Proteolysis . Journal of Proteome Research. 10. (8). p. 3642-3651.

Kazanov, M.D., Igarashi, Y., Eroshkin, A.M., Cieplak, P., Ratnikov, B., Zhang, Y., Li, Z., Godzik, A., Osterman, A.L., Smith, J.W.(2011). Structural determinants of limited proteolysis . Journal of Proteome Research. 10. (8). p. 3642-3651.

Arlazarov, V. L., Kazanov, M. D.(2008). Segmentation of small objects in color images . Programming and Computer Software. 34. (3). p. 173-182.

Arlazarov, V.L., Kazanov, M.D.(2008). Segmentation of small objects in color images . Programming and Computer Software. 34. (3). p. 173-182.

Gelfand, Mikhail S., Kazanov, Marat D., Vitreschak, Alexey G.(2007). Abundance and functional diversity of riboswitches in microbial communities . Bmc Genomics. 8.

Kazanov, M.D., Vitreschak, A.G., Gelfand, M.S.(2007). Abundance and functional diversity of riboswitches in microbial communities . BMC Genomics. 8.

OTHER

Almira Chervova, Bulat Fatykhov, Alexander Koblov, Evgeny Shvarov, Julia Preobrazhenskaya, Dmitry Vinogradov, Gennady V. Ponomarev, Mikhail S. Gelfand, Marat D. Kazanov(2021). Analysis of gene expression and mutation data points on contribution of transcription to the mutagenesis by APOBEC enzymes . Cold Spring Harbor Laboratory

CONFERENCE PAPER

Kazanov, M.(2004). A new color image segmentation algorithm based on watershed transformation . Proceedings - International Conference on Pattern Recognition. 2. p. 590-593.

Kazanov, M.(2004). Modification of watershed transformation for images, containing small objects . Proceedings - International Conference on Pattern Recognition. 1. p. 612-615.

WORKING PAPER

RNAsselem: a Python Package for Descriptive Analysis of RNA Secondary Structure Elements in Viral Genomes .