Artyom Kasyanov

The main scientific interests lie in the development of algorithms for the analysis of biological sequences. Key projects include the development of software and algorithms for cross-species comparison of expression profiles using machine learning, indexes for mapping to genomic graphs, and annotation algorithms.

1. Liang R, Arif T, Kalmykova S, Kasianov A, Lin M, Menon V, Qiu J, Bernitz JM, Moore K, Lin F, Benson DL, Tzavaras N, Mahajan M, Papatsenko D, Ghaffari S. Restraining Lysosomal Activity Preserves Hematopoietic Stem Cell Quiescence and Potency. Cell Stem Cell. 2020 Mar 5;26(3):359-376.e7. doi: 10.1016/j.stem.2020.01.013. Epub 2020 Feb 27. PMID: 32109377; PMCID: PMC8075247.

2. FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmidl C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M, Severin J, Semple C, Ishizu Y, Young RS, Francescatto M, Alam I, Albanese D, Altschuler GM, Arakawa T, Archer JA, Arner P, Babina M, Rennie S, Balwierz PJ, Beckhouse AG, Pradhan-Bhatt S, Blake JA, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Burroughs AM, Califano A, Cannistraci CV, Carbajo D, Chen Y, Chierici M, Ciani Y, Clevers HC, Dalla E, Davis CA, Detmar M, Diehl AD, Dohi T, Drabløs F, Edge AS, Edinger M, Ekwall K, Endoh M, Enomoto H, Fagiolini M, Fairbairn L, Fang H, Farach-Carson MC, Faulkner GJ, Favorov AV, Fisher ME, Frith MC, Fujita R, Fukuda S, Furlanello C, Furino M, Furusawa J, Geijtenbeek TB, Gibson AP, Gingeras T, Goldowitz D, Gough J, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Harbers M, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto T, Herlyn M, Hitchens KJ, Ho Sui SJ, Hofmann OM, Hoof I, Hori F, Huminiecki L, Iida K, Ikawa T, Jankovic BR, Jia H, Joshi A, Jurman G, Kaczkowski B, Kai C, Kaida K, Kaiho A, Kajiyama K, Kanamori-Katayama M, Kasianov AS, Kasukawa T, Katayama S, Kato S, Kawaguchi S, Kawamoto H, Kawamura YI, Kawashima T, Kempfle JS, Kenna TJ, Kere J, Khachigian LM, Kitamura T, Klinken SP, Knox AJ, Kojima M, Kojima S, Kondo N, Koseki H, Koyasu S, Krampitz S, Kubosaki A, Kwon AT, Laros JF, Lee W, Lennartsson A, Li K, Lilje B, Lipovich L, Mackay-Sim A, Manabe R, Mar JC, Marchand B, Mathelier A, Mejhert N, Meynert A, Mizuno Y, de Lima Morais DA, Morikawa H, Morimoto M, Moro K, Motakis E, Motohashi H, Mummery CL, Murata M, Nagao-Sato S, Nakachi Y, Nakahara F, Nakamura T, Nakamura Y, Nakazato K, van Nimwegen E, Ninomiya N, Nishiyori H, Noma S, Noma S, Noazaki T, Ogishima S, Ohkura N, Ohimiya H, Ohno H, Ohshima M, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov DA, Pain A, Passier R, Patrikakis M, Persson H, Piazza S, Prendergast JG, Rackham OJ, Ramilowski JA, Rashid M, Ravasi T, Rizzu P, Roncador M, Roy S, Rye MB, Saijyo E, Sajantila A, Saka A, Sakaguchi S, Sakai M, Sato H, Savvi S, Saxena A, Schneider C, Schultes EA, Schulze-Tanzil GG, Schwegmann A, Sengstag T, Sheng G, Shimoji H, Shimoni Y, Shin JW, Simon C, Sugiyama D, Sugiyama T, Suzuki M, Suzuki N, Swoboda RK, 't Hoen PA, Tagami M, Takahashi N, Takai J, Tanaka H, Tatsukawa H, Tatum Z, Thompson M, Toyodo H, Toyoda T, Valen E, van de Wetering M, van den Berg LM, Verado R, Vijayan D, Vorontsov IE, Wasserman WW, Watanabe S, Wells CA, Winteringham LN, Wolvetang E, Wood EJ, Yamaguchi Y, Yamamoto M, Yoneda M, Yonekura Y, Yoshida S, Zabierowski SE, Zhang PG, Zhao X, Zucchelli S, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y. A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. doi: 10.1038/nature13182. PMID: 24670764; PMCID: PMC4529748.

3. Klepikova AV, Kasianov AS, Gerasimov ES, Logacheva MD, Penin AA. A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profiling. Plant J. 2016 Dec;88(6):1058-1070. doi: 10.1111/tpj.13312. Epub 2016 Nov 19. PMID: 27549386.

4. Morozova I, Kasianov A, Bruskin S, Neukamm J, Molak M, Batieva E, Pudło A, Rühli FJ, Schuenemann VJ. New ancient Eastern European Yersinia pestis genomes illuminate the dispersal of plague in Europe. Philos Trans R Soc Lond B Biol Sci. 2020 Nov 23;375(1812):20190569. doi: 10.1098/rstb.2019.0569. Epub 2020 Oct 5. PMID: 33012225; PMCID: PMC7702796.

5. Kasianov AS, Klepikova AV, Kulakovskiy IV, Gerasimov ES, Fedotova AV, Besedina EG, Kondrashov AS, Logacheva MD, Penin AA. High-quality genome assembly of Capsella bursa-pastoris reveals asymmetry of regulatory elements at early stages of polyploid genome evolution. Plant J. 2017 Jul;91(2):278-291. doi: 10.1111/tpj.13563. Epub 2017 Jun 12. PMID: 28387959.

6. Klepikova AV, Kulakovskiy IV, Kasianov AS, Logacheva MD, Penin AA. An update to database TraVA: organ-specific cold stress response in Arabidopsis thaliana. BMC Plant Biol. 2019 Feb 15;19(Suppl 1):49. doi: 10.1186/s12870-019-1636-y. PMID: 30813912; PMCID: PMC6393959.

7. Ivanov M, Ivanov M, Kasianov A, Rozhavskaya E, Musienko S, Baranova A, Mileyko V. Novel bioinformatics quality control metric for next-generation sequencing experiments in the clinical context. Nucleic Acids Res. 2019 Dec 2;47(21):e135. doi: 10.1093/nar/gkz775. PMID: 31511888; PMCID: PMC6868350.