Kazanov Lab

Publications

2026

  1. Lyskova AO, Abasov RKh, Pavlova A, Matveev EV, Madorskaya AV, Kazanov FM, Garshina DV, Smolnikova AE, Ponomarev GV, Sharova EI, Ivankov DN, Adebali O, Gelfand MS, Kazanov MD. MPXV RNA-seq Data Provide Evidence for Protection of Viral Transcripts from APOBEC3 Editing. Journal of Virology, 2026.

2025

  1. Madorskaya AV, Kazanov FM, Ponomarev GV, Smolnikova A, Garshina D, Matveev EV, Abasov RKh, Ivankov DN, Gelfand MS, Kazanov MD. Comment on "Inverted repeats in the monkeypox virus genome are hot spots for mutation". bioRxiv 2025.08.19.670320.
  2. Arzamasov AA, Rodionov DA, Hibberd MC, Guruge JL, Kent JE, Kazanov MD, Leyn SA, Elane ML, Sejane K, Furst A, Bode L, Barratt MJ, Gordon JI, Osterman AL. Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria. Nat Microbiol. 2025 Aug;10(8):2031–2047.

2024

  1. Kazanov FM, Matveev EV, Ponomarev GV, Ivankov DN, Kazanov MD. Analysis of the abundance and diversity of RNA secondary structure elements in RNA viruses using the RNAsselem Python package. Sci Rep. 2024 Nov 19;14(1):28587.
  2. Arzamasov AA, Rodionov DA, Hibberd MC, Guruge JL, Kazanov MD, Leyn SA, Kent JE, Sejane K, Bode L, Barratt MJ, Gordon JI, Osterman AL. Integrative genomic reconstruction of carbohydrate utilization networks in bifidobacteria: global trends, local variability, and dietary adaptation. bioRxiv [Preprint]. 2024 Jul 7:2024.07.06.602360.
  3. 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.
  4. 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.

2023

  1. Hudson K, Klimczak L, Sterling J, Burkholder A, Kazanov M, Saini N, Mieczkowski P, Gordenin D. Glycidamide-induced hypermutation in yeast single-stranded DNA reveals a ubiquitous clock-like mutational motif in humans. Nucleic Acids Research, gkad611, 2023.
  2. Matveev EV, Safronov VV, Ponomarev GV, Kazanov MD. Predicting Structural Susceptibility of Proteins to Proteolytic Processing. Int. J. Mol. Sci. 24, 10761, 2023.
  3. 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.

2022

  1. Ponomarev GV, Fatykhov B, Nazarov VA, Abasov R, Shvarov E, Landik N-V, Denisova AA, Chervova AA, Gelfand MS, Kazanov MD. APOBEC mutagenesis is low in most types of non-B DNA structures, unlike other types of cancer mutagenesis. iScience 25(7):104535, 2022.
  2. 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. 23(7):4019, 2022.

2021

  1. 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)(p11;q23); MYB-GATA1 and female sex: GATA1 insufficiency may be insufficient for pathogenesis. Cancer Genetics, 260–261:37–40, 2021.
  2. 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 3(3):zcab025, 2021.

2020

  1. Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Li Y, Kelso S; MC3 Working Group; 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.
  2. Li CH, Prokopec SD, Sun RX, Yousif F, Schmitz N; PCAWG Consortium (including M.D. Kazanov). Sex differences in oncogenic mutational processes. Nature Communications 11(1):4330, 2020.
  3. 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.
  4. 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.
  5. Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L et al.; PCAWG Drivers and Functional Interpretation Working Group; PCAWG Consortium (including M.D. Kazanov). Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature 578, 102–111, 2020.
  6. 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); PCAWG Consortium. Patterns of somatic structural variation in human cancer genomes. Nature 578, 112–121, 2020.
  7. 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); PCAWG Consortium. Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nature Genetics, 1–11, 2020.
  8. 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.
  9. Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F et al.; PCAWG Structural Variation Working Group (including M.D. Kazanov); PCAWG Consortium. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nature Genetics 1–14, 2020.
  10. 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); PCAWG Consortium. Genomic footprints of activated telomere maintenance mechanisms in cancer. Nature Communications 11, 1–13, 2020.
  11. Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A; PCAWG Transcriptome Working Group; PCAWG Consortium (including M.D. Kazanov). 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.

2019

  1. 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.
  2. Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y et al.; AstraZeneca-Sanger Drug Combination DREAM Consortium (including M.D. Kazanov). Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nature Communications 10(1):2674, 2019.

2017

  1. 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):820–826, 2017.

2016

  1. Guinney J, Wang T, Laajala TD, Winner KK, Bare JC, Neto EC et al.; 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):132–142, 2016.
  2. Ponomarev GV, Kazanov MD. Classification of ANA HEp-2 slide images using morphological features of stained patterns. Pattern Recognition Letters, 82(1):79–84, 2016.
  3. 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)

2015

  1. 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):1103–1109, 2015.
  2. Garushyants SK, Kazanov MD, Gelfand MS. Horizontal gene transfer and genome evolution in Methanosarcina. BMC Evolutionary Biology, 15(1):102, 2015.
  3. 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.
  4. 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):7693–7706, 2015.

2014

  1. 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):32783–32797, 2014.
  2. 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. USA, 111(40):E4148–4155, 2014.
  3. 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):2360–2366, 2014.
  4. 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):1016–1023, 2014.
  5. Belushkin AA, Vinogradov DV, Gelfand MS, Osterman AL, Cieplak P, Kazanov MD. Sequence-derived structural features driving proteolytic processing. Proteomics, 14(1):42–50, 2014.
  6. 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):797–813, 2014.

2013

  1. 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.
  2. 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.
  3. 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.
  4. Gordienko EN, Kazanov MD, Gelfand MS. Evolution of pan-genomes of Escherichia coli, Shigella spp., and Salmonella enterica. Journal of Bacteriology, 195(12):2786–2792, 2013.
  5. 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):2463–2473, 2013.
  6. 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.
  7. 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):790–803, 2013.

2012

  1. Tsoy OV, Pyatnitskiy MA, Kazanov MD, Gelfand MS. Evolution of transcriptional regulation in closely related bacteria. BMC Evolutionary Biology, 12:200, 2012.
  2. 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.
  3. 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)

2011

  1. 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.
  2. 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):4943–4953, 2011.
  3. 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):3642–3651, 2011.

2010 and before

  1. 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.
  2. Arlazarov VL, Kazanov MD. Segmentation of small objects in color images. Programming and Computer Software, 34(3):173–182, 2008.
  3. Kazanov MD, Vitreschak AG, Gelfand MS. Abundance and functional diversity of riboswitches in microbial communities. BMC Genomics, 8:347, 2007.