Publications

2015 

1. Antontseva E.V., Matveeva M.Y., Bondar N.P., Kashina E.V., Leberfarb E.Y., Bryzgalov L.O., Gervas P.A., Ponomareva A.A., Cherdyntseva N.V., Orlov Y.L., Merkulova T.I. Regulatory single nucleotide polymorphisms at the beginning of intron 2 of the human KRAS gene // J Biosci. 2015 Dec;40(5):873-83.
2. Babenko V.N., Matvienko V.F., Safronova N.S. (2015) 19 Implication of transposons distribution on chromatin state and genome architecture in human // Journal of Biomolecular Structure and Dynamics, 33 Suppl 1:10-1. Doi:10.1080/07391102.2015.1032559.
3. Bai H., Liu H., Suyalatu S., Guo X., Chu S., Chen Y., Lan T., Borjigin B., Orlov Y.L., Posukh O.L., Yang X., Guilan G., Osipova L.P., Wu Q., Narisu N. Association Analysis of Genetic Variants with Type 2 Diabetes in a Mongolian Population in China // J Diabetes Res. 2015;2015:613236. doi: 10.1155/2015/613236.
4. Balasov M, Akhmetova K, Chesnokov I. Drosophila model of Meier-Gorlin syndrome based on the mutation in a conserved C-Terminal domain of Orc6 // Am J Med Genet A. 2015. Vol.167. P. 2533-2540. doi:10.1002/ajmg.a.37214
5. Battulin N., Fishman V.S., Mazur A.M., Pomaznoy M., Khabarova A.A., Afonnikov D.A., Prokhortchouk E.B., Serov O.L. Comparison of the 3D organization of sperm and fibroblast genomes using the Hi-C approach // Genome Biology, 2015. 16:77
6. Dobrovolskaya O., Pont C., Sibout R., Martinek P., Badaeva E., Murat F., Chosson A., Watanabe N., Prat E., Gautier N., Gautier V., Poncet C., Orlov Y.L., Krasnikov A.A., Berges H., Salina E., Laikova L., Salse J. FRIZZY PANICLE Drives Supernumerary Spikelets in Bread Wheat // Plant Physiol. 2015. 167(1):189-99. Epub 2014 Nov 14.
7. Glotov A.S., Tiys E.S., Vashukova E.S., Pakin V.S., Demenkov P.S., Saik O.V., Ivanisenko T.V., Arzhanova O.N., Mozgovaya E.V., Zainulina M.S., Kolchanov N.A., Baranov V.S., Ivanisenko V.A.Molecular association of pathogenetic contributors to pre-eclampsia (pre-eclampsia associome) // BMC Systems Biology 2015, 9(Suppl 2):S4
8. Gunbin K.V., Afonnikov D.A., Kolchanov N.A., Derevianko A.P., Rogaev E.I. The evolution of Homo sapiens denisova and Homo sapiens neanderthalensis miRNA targeting genes in the prenatal and postnatal brain BMC Genomics 2015, 16(Suppl 13):S4 ) doi:10.1186/1471-2164-16-S13-S4
9. Ivanisenko V.A., Saik O.V., Ivanisenko N.V., Tiys E.S., Ivanisenko T.V., Demenkov P.S., Kolchanov N.A. ANDSystem: an Associative Network Discovery System for automated literature mining in the field of biology // BMC Systems Biology 2015, 9(Suppl 2):S2
10. Klimenko A.I., Matushkin Y.G., Kolchanov N.A., Lashin S.A. Modeling evolution of spatially distributed bacterial communities: a simulation with the haploid evolutionary constructor // BMC Evolutionary Biology 2015, 15(Suppl 1):S3.
11. Kudryavtseva N.N., Markel A.L., Orlov Yu.L. Aggressive behavior: Genetic and physiological mechanisms // Russian Journal of Genetics: Applied Research. 2015, Volume 5, Issue 4, pp 413-429.
12. Likhoshvai V.A., Khlebodarova T.M. On the types of bacterial growth laws. Math. Biol. Bioinf. 2015;10(Suppl.):t20-t28, doi: 10.17537/2015.10.t20 Scopus (перевод статьи: Лихошвай В.А., Хлебодарова Т.М. О типах законов роста бактерий // Матем. Биол. Биоинформ., 2015, т. 10, №1, С. 154–163. doi: 10.17537/2015.10.154)
13. Likhoshvai V.A., Kogai V.V., Fadeev S. I., Khlebodarova T.M. Alternative splicing can lead to chaos // JBCB, 2015, V. 13. №1, 1540003. . doi: 10.1142/S021972001540003X
14. Medvedeva I., Demenkov P., Ivanisenko V. Computer analysis of protein functional sites projection on exon structure of genes in Metazoa. BMC Genomics 2015, 16(Suppl 13):S2 ) doi:10.1186/1471-2164-16-S13-S2 http://www.biomedcentral.com/1471-2164/16/S13/S2
15. Novoselova E.S., Mironova V.V., Khlebodarova T.M., Likhoshvai V.A. On the distribution of auxin concentrations in root horizontal layer cells // Russian Journal of Genetics: Applied Research, 2015, Vol. 5, No. 3, pp.293–299.
16. Olga V Arkova, Mikhail P Ponomarenko, Dmitry A Rasskazov, Irina A Drachkova, Tatjana V Arshinova, Petr M Ponomarenko, Ludmila K Savinkova and Nikolay A Kolchanov Obesity-related known and candidate SNP markers can significantly change affinity of TATA-binding protein for human gene promoters. BMC Genomics 2015, 16(Suppl 13):S5 ) doi:10.1186/1471-2164-16-S13-S5
17. Orlov Y.L., Hofestadt R.M., Kolchanov N.A. (2015) Introductory note for BGRS\SB-2014 special issue. J Bioinform Comput Biol. 13(1):1502001. doi: 10.1142/S0219720015020011
18. Ovchinnikov V.Y., Dmitry A. Afonnikov, Gennady V. Vasiliev, Elena V. Kashina, Banchob Sripa, Viacheslav A. Mordvinov, Alexey V. Katokhin Identification of microRNA Genes in Three Opisthorchiids // PLOS, April 21, 2015. 9(4)
19. Pomaznoy M.Y., Logacheva M.D., Young N.D., Penin A.A., Ershov N.I., Katokhin A.V., Mordvinov V.A. Whole transcriptome profiling of adult and infective stages of the trematode Opisthorchis felineus // Parasitol Int. 2016 Feb;65(1):12-9. doi: 10.1016/j.parint.2015.09.002.
20. Ponomarenko M, Rasskazov D, Arkova O, Ponomarenko P, Suslov V, Savinkova L, et al. How to use SNP_TATA_Comparator to find a significant change in gene expression caused by the regulatory SNP of this gene’s promoter via a change in affinity of the TATA-binding protein for this promoter. Hindawi Publishing Corporation BioMed Research International, Volume 2015, Article ID 359835, 17 pages. http://dx.doi.org/10.1155/2015/359835
21. Ponomarenko PM, Ponomarenko MP. Sequence-based prediction of transcription up-regulation by auxin in plants. // J Bioinform Comput Biol. 2015. V.13. N. 1. P. 1540009.
22. Safronova N.S., Babenko V.N., Orlov Y.L. 117 Analysis of SNP containing sites in human genome using text complexity estimates // Journal of Biomolecular Structure and Dynamics, 2015 33:sup1, 73-74, DOI:10.1080/07391102.2015.1032750
23. Smagin D.A., Kovalenko I.L., Galyamina A.G., Bragin A.O., Orlov Yu.L., Kudryavtseva N.N. (2015) Dysfunction in ribosomal gene expression in the hypotalamus and hyppocampus following chronic social defeat stress in male mice as revealed by RNA-seq. Neural plasticity. Article ID 769835 (http://www.hindawi.com/journals/np/aa/769835/)
24. Sokolov V.S., Zuraev B.S., Lashin S.A., Matushkin Yu.G. EloE: web application for estimation of gene translation elongation efficiency // Russian Journal of Genetics: Applied Research, 2015, Vol. 5, No. 4, pp. 335–339.
25. Turnaev I.I., Gunbin K.V., Afonnikov D.A. Plant auxin biosynthesis did not originate in charophytes Trends in Plant Science August 2015, Vol. 20, No. 8
26. Turnaev II, Gunbin KV, Afonnikov DA. Plant auxin biosynthesis did not originate in charophytes. Trends Plant Sci. 2015 Aug;20(8):463-5. doi: 10.1016/j.tplants.2015.06.004.
27. Ustyantsev Kirill, Novikova Olga, Blinov Alexander, Smyshlyaev Georgy. 2015. Convergent Evolution of Ribonuclease H in LTR Retrotransposons and Retroviruses // Mol. Biol, Evol., 32(5):1197-207.
28. Zaytseva O.O., Gunbin K.V., Mglinets A.V., Kosterin O.E. Divergence and population traits in evolution of the genus Pisum L. as reconstructed using genes of two histone H1 subtypes showing different phylogenetic resolution // Gene. 2015 Feb 10;556(2):235-44. doi: 10.1016/j.gene.2014.11.062.
29. Akhmetova, K.; Dorogova, N.; Chesnokov, I.; Fedorova, S. Analysis of peanut gene RNAi in drosophila oogenesis. Russian Journal of Genetics;Sep2015, Vol. 51 Issue 9, p847. DOI: 10.1134/S1022795415090021