Publications

All/2018/2019/2020/2021/2022/2023/2024/

Bate-Eya LT, Albayrak G, Carr SM, Shrestha A, Kanapin A, Samsonova A, La Thangue NB. Sustained cancer-relevant alternative RNA splicing events driven by PRMT5 in high-risk neuroblastoma. Mol Oncol. 2024 Jul 17. doi: 10.1002/1878-0261.13702. Epub ahead of print. PMID: 39021294.

Yuditskiy K, Bezdvornykh I, Kazantseva A, Kanapin A, Samsonova A. BSXplorer: analytical framework for exploratory analysis of BS-seq data. BMC Bioinformatics. 2024 Mar 4;25(1):96. doi: 10.1186/s12859-024-05722-9. PMID: 38438881; PMCID: PMC10913661.

Kazantseva A, Davydova Y, Enikeeva R, Mustafin R, Malykh S, Lobaskova M, Kanapin A, Prokopenko I, Khusnutdinova E. A Combined Effect of Polygenic Scores and Environmental Factors on Individual Differences in Depression Level. Genes (Basel). 2023 Jun 27;14(7):1355. doi: 10.3390/genes14071355. PMID: 37510260; PMCID: PMC10379734.

Wang RR, Dong PP, Hirata D, Abduriyim S. Mitochondrial DNA analyses revealed distinct lineages in an alpine mammal, Siberian ibex (Capra sibirica) in Xinjiang, China. Ecol Evol. 2023 Aug 2;13(8):e10288. doi: 10.1002/ece3.10288. PMID: 37539073; PMCID: PMC10396667.

Samsonova A. A., Kanapin A. A., Chernyaeva E. N., Abramov I. S., Shipulin G. A.
Genomic medicine in Russia: future perspectives.
Russian journal for personalized medicine. 2023 vol. 3, (3), pp. 99-107.

Tamazian G, Cherkasov N, Kanapin A, Samsonova A. Pygenomics: manipulating genomic intervals and data files in Python. Bioinformatics. 2023 May 25:btad346. doi: 10.1093/bioinformatics/btad346. PMID: 37228014.

Bezdvornykh I, Cherkasov N, Kanapin A, Samsonova A. A collection of read depth profiles at structural variant breakpoints. Sci Data. 2023 Apr 6;10(1):186. doi: 10.1038/s41597-023-02076-4. PMID: 37024526; PMCID: PMC10079824.

Gretsova M, Surkova S, Kanapin A, Samsonova A, Logacheva M, Shcherbakov A, Logachev A, Bankin M, Nuzhdin S, Samsonova M.
Transcriptomic Analysis of Flowering Time Genes in Cultivated Chickpea and Wild Cicer.
Int J Mol Sci. 2023 Jan 31;24(3):2692. doi: 10.3390/ijms24032692. PMID: 36769014; PMCID: PMC9916832.

Houck ML, Koepfli KP, Hains T, Khan R, Charter SJ, Fronczek JA, Misuraca AC, Kliver S, Perelman PL, Beklemisheva V, Graphodatsky A, Luo SJ, O’Brien SJ, Lim NT, Chin JSC, Guerra V, Tamazian G, Omer A, Weisz D, Kaemmerer K, Sturgeon G, Gaspard J, Hahn A, McDonough M, Garcia-Treviño I, Gentry J, Coke RL, Janecka JE, Harrigan RJ, Tinsman J, Smith TB, Aiden EL, Dudchenko O. Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity. Chromosome Res. 2023 Apr 12;31(2):13. doi: 10.1007/s10577-023-09722-y. PMID: 37043058.

Baron M. and Malov S.V. Detection and estimation of multiple transient changes. Journal of Applied Statistics. 2023.doi: 10.1080/02664763.2023.2174257

Engovatova AV, Alborova IE, Mustafin KK , Lunkov VY , Lunkova YV, Kanapin AA, Samsonova AA, Mednikova MB. Ancient DNA of the Bearers of the Fatyanovo and Abashevo Cultures (Concerning Migrations of the Bronze Age people in the Forest Belt on the Russian Plain). Stratum plus. 2023. No2. doi: 10.55086/sp232207228

Yakupova A, Tomarovsky A, Totikov A, Beklemisheva V, Logacheva M, Perelman PL, Komissarov A, Dobrynin P, Krasheninnikova K, Tamazian G, Serdyukova NA, Rayko M, Bulyonkova T, Cherkasov N, Pylev V, Peterfeld V, Penin A, Balanovska E, Lapidus A, Dna Zoo Consortium, OBrien SJ, Graphodatsky A, Koepfli KP, Kliver S. Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal. Genes (Basel). 2023 Feb 28;14(3):619. doi: 10.3390/genes14030619. PMID: 36980891; PMCID: PMC10048373.

Barczak W, Carr SM, Liu G, Munro S, Nicastri A, Lee LN, Hutchings C, Ternette N, Klenerman P, Kanapin A, Samsonova A, La Thangue NB. Long non-coding RNA-derived peptides are immunogenic and drive a potent anti-tumour response. Nat Commun. 2023 Feb 25;14(1):1078. doi: 10.1038/s41467-023-36826-0. PMID: 36841868; PMCID: PMC9968330.

Kanapin A, Rozhmina T, Bankin M, Surkova S, Duk M, Osyagina E, Samsonova M. Genetic Determinants of Fiber-Associated Traits in Flax Identified by Omics Data Integration. Int J Mol Sci. 2022 Nov 22;23(23):14536. doi: 10.3390/ijms232314536. PMID: 36498863; PMCID: PMC9738745.

Levchenko A, Malov S, Antonik A, Protsvetkina A, Rybakova KV, Kanapin A, Yakovlev AN, Nenasteva AY, Nikolishin AE, Cherkasov N, Chuprova NA, Blagonravova AS, Sergeeva AV, Zhilyaeva TV, Denisenko MK, Gainetdinov RR, Kibitov AO, Krupitsky EM. A Genome-Wide Association Study Reveals a BDNF-Centered Molecular Network Associated with Alcohol Dependence and Related Clinical Measures. Biomedicines. 2022 Nov 22;10(12):3007. doi: 10.3390/biomedicines10123007. PMID: 36551763; PMCID: PMC9775455.

Rozhmina T, Samsonova A, Kanapin A, Samsonova M.
An account of Fusarium wilt resistance in flax Linum usitatissimum: The disease severity data.
Data Brief. 2022 Jan 25; 41:107869. doi:10.1016/j.dib.2022.107869. PMID: 35146091; PMCID: PMC8816659.

Duk M, Kanapin A, Rozhmina T, Bankin M, Surkova S, Samsonova A, Samsonova M.
The Genetic Landscape of Fiber Flax.
Front Plant Sci. 2021 Dec 7;
12:764612. doi:10.3389/fpls.2021.764612. PMID: 34950165; PMCID: PMC8691122.

Pavlov S, Gursky VV, Samsonova M, Kanapin A, Samsonova A.
Stochastic Effects in Retrotransposon Dynamics Revealed by Modeling under Competition for Cellular Resources.
Life (Basel). 2021 Nov 9; 11(11):1209. doi: 10.3390/life11111209.
PMID: 34833085; PMCID: PMC8625273.

Kanapin A, Bankin M, Rozhmina T, Samsonova A, Samsonova M.
Genomic Regions Associated with Fusarium Wilt Resistance in Flax.
Int J Mol Sci. 2021 Nov 17;22(22):12383. doi: 10.3390/ijms222212383. PMID: 34830265; PMCID: PMC8623186.

Rozhmina T, Bankin M, Samsonova A, Kanapin A, Samsonova M.
A comprehensive dataset of flax (Linum uitatissimum L.) phenotypes.
Data Brief. 2021 Jun 13;37:107224. doi: 10.1016/j.dib.2021.107224. PMID: 34189209; PMCID: PMC8220315.

Samsonova A, Kanapin A, Bankin M, Logachev A, Gretsova M, Rozhmina T,
Samsonova M.
A Genomic Blueprint of Flax Fungal Parasite Fusarium oxysporum f. sp. lini.
Int J Mol Sci. 2021 Mar 6;22(5):2665. doi:10.3390/ijms22052665. PMID: 33800857; PMCID: PMC7961770.

Blaszczak W, Liu G, Zhu H, Barczak W, Shrestha A, Albayrak G, Zheng S, Kerr D, Samsonova A, La Thangue NB.
Immune modulation underpins the anti-cancer activity of HDAC inhibitors. Mol Oncol. 2021 Dec;15(12):3280-3298. doi:10.1002/1878-0261.12953. Epub 2021 May 1. PMID: 33773029; PMCID: PMC8637571.

2021

Levchenko A, Kanapin A, Samsonova A, Fedorenko OY, Kornetova EG, Nurgaliev T, Mazo GE, Semke AV, Kibitov AO, Bokhan NA, Gainetdinov RR, Ivanova SA.
A genome-wide association study identifies a gene network associated with paranoid schizophrenia and antipsychotics-induced tardive dyskinesia. Prog Neuropsychopharmacol Biol Psychiatry. 2021 Mar 8;105:110134. doi:
10.1016/j.pnpbp.2020.110134. Epub 2020 Oct 13. PMID: 33065217.

2021

Shevchenko AK, Zhernakova DV, Malov SV, Komissarov A, Kolchanova SM, Tamazian G, Antonik A, Cherkasov N, Kliver S, Turenko A, Rotkevich M, Evsyukov I, Vlahov D, Thami PK, Gaseitsiwe S, Novitsky V, Essex M, O’Brien SJ.
Genome-wide association study reveals genetic variants associated with HIV-1C infection in a Botswana study population.
Proc Natl Acad Sci U S A. 2021 Nov 23;118(47):e2107830118.
doi: 10.1073/pnas.2107830118. PMID: 34782459; PMCID:PMC8672799.

2021

Tamazian G, Dobrynin P, Zhuk A, Zhernakova DV, Perelman PL, Serdyukova NA, Graphodatsky AS, Komissarov A, Kliver S, Cherkasov N, Scott AF, Mohr DW, Koepfli KP, O’Brien SJ, Krasheninnikova K.
Draft de novo Genome Assembly of the Elusive Jaguarundi, Puma yagouaroundi.
J Hered. 2021 Nov 1;112(6):540-548. doi:
10.1093/jhered/esab036. PMID: 34146095; PMCID: PMC8558579.

Duk MA, Gursky VV, Samsonova MG, Surkova SY.
Application of Domain- and Genotype- Specific Models to Infer Post Transcriptional Regulation of Segmentation Gene Expression in Drosophila. Life (Basel). 2021 Nov 13;11(11):1232. doi: 10.3390/life11111232. PMID: 34833107; PMCID: PMC8618293.

Malov, S.V.
Uniform convergence rate of the nonparametric maximum likelihood estimator for current status data with competing risks.
Statistics 55(1),2021, 155-172, doi: 10.1080/02331888.2020.1811281.

Zhernakova DV, Brukhin V, Malov S, Oleksyk TK, Koepfli KP, Zhuk A, Dobrynin P, Kliver S, Cherkasov N, Tamazian G, Rotkevich M, Krasheninnikova K, Evsyukov I, Sidorov S, Gorbunova A, Chernyaeva E, Shevchenko A, Kolchanova S, Komissarov A, Simonov S, Antonik A, Logachev A, Polev DE, Pavlova OA, Glotov AS, Ulantsev V, Noskova E, Davydova TK, Sivtseva TM, Limborska S, Balanovsky O, Osakovsky V, Novozhilov A, Puzyrev V, O’Brien SJ.
Genome-wide sequence analyses of ethnic populations across Russia.
Genomics. 2020 Jan;112(1):442-458.
doi: 10.1016/j.ygeno.2019.03.007. Epub 2019 Mar 19. PMID: 30902755.

Levchenko A, Kanapin A, Samsonova A, Fedorenko OY, Kornetova EG, Nurgaliev T, Mazo GE, Semke AV, Kibitov AO, Bokhan NA, Gainetdinov RR, Ivanova SA.
A genome-wide association study identifies a gene network associated with paranoid schizophrenia and antipsychotics-induced tardive dyskinesia. Prog Neuropsychopharmacol Biol Psychiatry. 2021 Mar 8;105:110134. doi:
10.1016/j.pnpbp.2020.110134. Epub 2020 Oct 13. PMID: 33065217.

Barczak W, Jin L, Carr SM, Munro S, Ward S, Kanapin A, Samsonova A, La Thangue NB.
PRMT5 promotes cancer cell migration and invasion through the E2F pathway.
Cell Death Dis. 2020 Jul 24;11(7):572. doi: 10.1038/s41419-020-02771-9.
PMID: 32709847; PMCID: PMC7382496.

Kanapin A, Samsonova A, Rozhmina T, Bankin M, Logachev A, Samsonova M.
The Genome Sequence of Five Highly Pathogenic Isolates of Fusarium oxysporum f. sp. lini.
Mol Plant Microbe Interact. 2020 Sep;33(9):1112-1115.
doi: 10.1094/MPMI-05-20-0130-SC. Epub 2020 Jul 22. PMID: 32568599.

Levchenko A, Nurgaliev T, Kanapin A, Samsonova A, Gainetdinov RR.
Current challenges and possible future developments in personalized psychiatry with an emphasis on psychotic disorders.
Heliyon. 2020 May 20;6(5):e03990.
doi:10.1016/j.heliyon.2020.e03990. PMID: 32462093; PMCID: PMC7240336.

Tatkiewicz W, Dickie J, Bedford F, Jones A, Atkin M, Kiernan M, Maze EA, Agit B, Farnham G, Kanapin A, Belshaw R.
Characterising a human endogenous retrovirus(HERV)-derived tumour-associated antigen: enriched RNA-Seq analysis of HERV-K(HML-2) in mantle cell lymphoma cell lines.
Mob DNA. 2020 Feb 7;11:9.
doi: 10.1186/s13100-020-0204-1. Erratum in: Mob DNA. 2020 Nov 30; 11(1):31. PMID: 32055257; PMCID: PMC7007669.

Gooley RM, Tamazian G, Casta?eda-Rico S, Murphy KR, Dobrynin P, Ferrie GM,Haefele H, Maldonado JE, Wildt DE, Pukazhenthi BS, Edwards CW, Koepfli KP.
Comparison of genomic diversity and structure of sable antelope (Hippotragus niger) in zoos, conservation centers, and private ranches in North America.
Evol Appl. 2020 Apr 27;13(8):2143-2154. doi: 10.1111/eva.12976. PMID: 32908610;PMCID: PMC7463370.

Humble E, Dobrynin P, Senn H, Chuven J, Scott AF, Mohr DW, Dudchenko O, Omer AD, Colaric Z, Lieberman Aiden E, Al Dhaheri SS, Wildt D, Oliaji S, Tamazian G, Pukazhenthi B, Ogden R, Koepfli KP.
Chromosomal-level genome assembly of the scimitar-horned oryx: Insights into diversity and demography of a species extinct in the wild.
Mol Ecol Resour. 2020 Nov;20(6):1668-1681. Epub 2020 Jun 7. Erratum in: Mol Ecol Resour. 2021
Apr;21(3):999.
doi: 10.1111/1755-0998.13181.
PMID: 32365406.

Malov, S.V., Antonik, A. & Shevchenko, A.K. (2020)
On region based inference in genome wide association study.
Abstracts of the Twelfth International Multiconference “Bioinformatics of
Genome Regulation and Structure/Systems Biology (BGRS/SB-2020)” (06–10 July 2020, Novosibirsk, Russia), 177–178. DOI: 10.18699/BGRS/SB-2020-111.

Kaito Mizumachi, Sergei V. Gorbunov, Alexander A. Vasilevski, Tetsuya Amano, Hiroko Ono, Pavel A. Kosintsev, Daisuke Hirata, Yoshinori Nishita, Ryuichi Masuda. (2020).
Phylogenetic relationships of ancient brown bears (Ursus arctos) on Sakhalin Island, revealed by APLP and PCR-direct sequencing analyses of mitochondrial DNA.
Mammal Research. 66:95-102.

Kaito Mizumachi, Nikolai Spassov, Dimitar Kostov, Evgeniy G Raichev, Stanislava Peeva, Daisuke Hirata, Yoshinori Nishita, Yayoi Kaneko, Ryuichi Masuda. (2020).
Mitochondrial haplogrouping of the ancient brown bears (Ursus arctos) in Bulgaria, revealed by the APLP method.
Mammal Research. 65: 413-421.

Roworth AP, Carr SM, Liu G, Barczak W, Miller RL, Munro S, Kanapin A,
Samsonova A, La Thangue NB.
Arginine methylation expands the regulatory mechanisms and extends the genomic landscape under E2F control.
Sci Adv. 2019 Jun 26;5(6):eaaw4640. doi: 10.1126/sciadv.aaw4640. PMID: 31249870; PMCID: PMC6594773.

Koepfli KP, Tamazian G, Wildt D, Dobrynin P, Kim C, Frandsen PB, Godinho R, Yurchenko AA, Komissarov A, Krasheninnikova K, Kliver S, Kolchanova S, Gon?alves M, Carneiro M, Pinto PV, Ferrand N, Maldonado JE, Ferrie GM, Chemnick L, Ryder OA, Johnson WE, Comizzoli P, O’Brien SJ, Pukazhenthi BS.
Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger): A Resource for Monitoring Diversity in ex Situ and in Situ Populations.
G3(Bethesda). 2019 Jun 5;9(6):1785-1793. doi: 10.1534/g3.119.400084. PMID:31000506; PMCID: PMC6553546.

Makashov, A., Malov, S.V. & Kozlov, A.P. (2019)
Oncogenes, tumor suppressor and differentiation genes represent the oldest human gene classes and evolve concurrently. Scientific Reports 9:16410, DOI: 10.1038/s41598-019-52835-w

Malova, I.Yu., Malov, S.V. (2019)
On estimation algorithms in nonparametric analysis of the current status right-censored data. In Applied Methods of Statistical Analysis. Statistical Computation and Simulation.
Proceedings of the International Workshop AMSA’19 (Novosibirsk, September 18-20, 2019), 74–84.

2019

Malov, S.V. (2019).
Nonparametric estimation for a current status right-censored data model.
Statistica Neerlandica 73(4), 475-495, DOI: 10.1111/stan.12180.

Robbe P, Popitsch N, Knight SJL, Antoniou P, Becq J, He M, Kanapin A,
Samsonova A, Vavoulis DV, Ross MT, Kingsbury Z, Cabes M, Ramos SDC, Page S, Dreau H, Ridout K, Jones LJ, Tuff-Lacey A, Henderson S, Mason J, Buffa FM, Verrill C, Maldonado-Perez D, Roxanis I, Collantes E, Browning L, Dhar S, Damato S, Davies S, Caulfield M, Bentley DR, Taylor JC, Turnbull C, Schuh A;
100,000 Genomes Project. Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project.
Genet Med. 2018 Oct;20(10):1196-1205. doi: 10.1038/gim.2017.241.
Epub 2018 Feb 1.
PMID: 29388947; PMCID: PMC6520241.

Levchenko A, Kanapin A, Samsonova A, Gainetdinov RR.
Human Accelerated Regions and Other Human-Specific Sequence Variations in the Context of Evolution and Their Relevance for Brain Development. Genome Biol Evol. 2018 Jan 1; 10(1):166-188. doi: 10.1093/gbe/evx240. PMID: 29149249; PMCID: PMC5767953.

Psallidas I, Kanellakis NI, Gerry S, Th?z?nas ML, Charles PD, Samsonova A, Schiller HB, Fischer R, Asciak R, Hallifax RJ, Mercer R, Dobson M, Dong T, Pavord ID, Collins GS, Kessler BM, Pass HI, Maskell N, Stathopoulos GT, Rahman NM.
Development and validation of response markers to predict survival and pleurodesis success in patients with malignant pleural effusion (PROMISE): a multicohort analysis.
Lancet Oncol. 2018 Jul;19(7):930-939. doi: 10.1016/S1470-2045(18)30294-8. Epub 2018 Jun 13. PMID: 29908990.

Papaspyropoulos A, Bradley L, Thapa A, Leung CY, Toskas K, Koennig D, Pefani DE, Raso C, Grou C, Hamilton G, Vlahov N, Grawenda A, Haider S, Chauhan J, Buti L, Kanapin A, Lu X, Buffa F, Dianov G, von Kriegsheim A, Matallanas D, Samsonova A, Zernicka-Goetz M, O’Neill E.
RASSF1A uncouples Wnt from Hippo signalling and promotes YAP mediated differentiation via p73.
Nat Commun. 2018 Jan 30;9(1):424.
doi: 10.1038/s41467-017-02786-5. PMID: 29382819; PMCID: PMC5789973.

Schwerd T, Bryant RV, Pandey S, Capitani M, Meran L, Cazier JB, Jung J, Mondal K, Parkes M, Mathew CG, Fiedler K, McCarthy DJ; WGS500 Consortium; Oxford IBD cohort study investigators; COLORS in IBD group investigators; UK IBD Genetics Consortium, Sullivan PB, Rodrigues A, Travis SPL, Moore C, Sambrook J, Ouwehand WH, Roberts DJ, Danesh J; INTERVAL Study, Russell RK, Wilson DC, Kelsen JR, Cornall R, Denson LA, Kugathasan S, Knaus UG, Serra EG, Anderson CA, Duerr RH, McGovern DP, Cho J, Powrie F, Li VS, Muise AM, Uhlig HH.
NOX1 loss-of-function genetic variants in patients with inflammatory bowel disease.
Mucosal Immunol. 2018 Mar;11(2):562-574. doi: 10.1038/mi.2017.74. Epub 2017 Nov 1. PMID: 29091079; PMCID: PMC5924597.

Zhernakova DV, Kliver S, Cherkasov N, Tamazian G, Rotkevich M,
Krasheninnikova K, Evsyukov I, Sidorov S, Dobrynin P, Yurchenko AA, Shimansky V, Shcherbakova IV, Glotov AS, Valle DL, Tang M, Shin E, Schwarz KB, O’Brien SJ.
Analytical “bake-off” of whole genome sequencing quality for the Genome Russia project using a small cohort for autoimmune hepatitis. PLoS One. 2018 Jul 11;13(7):e0200423.
doi: 10.1371/journal.pone.0200423. PMID: 29995946; PMCID:PMC6040705.

Harper C, Ludwig A, Clarke A, Makgopela K, Yurchenko A, Guthrie A, Dobrynin P, Tamazian G, Emslie R, van Heerden M, Hofmeyr M, Potter R, Roets J, Beytell P, Otiende M, Kariuki L, du Toit R, Anderson N, Okori J, Antonik A, Koepfli KP, Thompson P, O’Brien SJ.
Robust forensic matching of confiscated horns to individual poached African rhinoceros.
Curr Biol. 2018 Jan 8;28(1):R13-R14. doi:10.1016/j.cub.2017.11.005. PMID: 29316411.

Malov, S.V., O’Brien S.J. (2018)
Life Table Estimator Revisited. Communications in Statistics – Theory
and Methods, 47(9), 2126-2133, DOI:
10.1080/03610926.2017.1335418.

Barbitoff YA, Bezdvornykh IV, Polev DE, Serebryakova EA, Glotov AS, Glotov OS, Predeus AV.
Catching hidden variation: systematic correction of reference minor allele annotation in clinical variant calling.
Genet Med. 2018 Mar;20(3):360-364. doi: 10.1038/gim.2017.168. Epub 2017 Oct 26. PMID: 29155419.