МЕГАГРАНТЫ

Лаборатория эволюционной геномики ФББ МГУ

О лаборатории

Наименование проекта "Филогенетический анализ сложного отбора в молекулярной эволюции"

Ссылка на официальный сайт

Наименование ВУЗа:
ФГОУ ВПО "Московский государственный университет им. М.В. Ломоносова"

Область научных исследований:
Биология

Цель проекта:
Сопоставление геномов родственных видов и генотипов родственных особей

Основные задачи проекта:
1. Изучение сложных форм естественного отбора, характеризующихся взаимозависимостью относительных приспособленностей аллелей разных локусов;
2. Изучение феномена эпистаза в контексте как положительного отбора, благоприятствующего новым, редким фенотипам, так и отрицательного отбора, благоприятствующего предковым, частым фенотипам.

Ведущий учёный

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ФИО: Кондрашов Алексей Симонович

 

Ученые степень и звание:
Кандидат биологических наук, профессор.

Занимаемая должность:
Профессор Института биологических наук и кафедры экологии и эволюционной биологии Мичиганского университета (США).

Область научных интересов:
Эволюционная генетика

Основные научные достижения:

- детерминистская мутационная гипотеза, объясняющая поддержание полового размножения;
- работа над теорией симпатрического видообразования;
- оценка скоростей мутагенеза;
- оценка естественного отбора в нуклеотидной последовательности и белковой эволюции.

 

Kondrashov A. S. (1988). Deleterious mutations and the evolution of sexual reproduction. Nature 336, 435-440.
Kondrashov A. S. and Crow J. F. (1991). Haploidy or diploidy: which is better? Nature 351, 314-315.
Kondrashov A. S. (1994). The asexual ploidy cycle and the origin of sex. Nature 370, 213-216.
Shabalina S. A., Yampolsky L. Y. and Kondrashov A. S. (1997). Rapid decline of fitness in panmictic populations of Drosophila under relaxed selection. Proceedings of the National Academy of Sciences USA 94, 13034-13039.
Kondrashov A. S. and Kondrashov F. A. (1999). Interactions among quantitative traits in the course of sympatric speciation. Nature 400, 351- 354.
Shabalina S. A., Ogurtsov A. Y., Kondrashov V. A. and Kondrashov A. S. (2001). Selective constraint in intergenic regions of human and mouse genomes. Trends in Genetics 17, 373-376.
McCune A. R., Fuller R. C., Aquilina A. A., Dawley R. M., Fadool J. M., Houle D., Travis J. and Kondrashov A. S. (2002). A low genomic number of recessive lethals in natural populations of bluefin killifish and zebrafish. Science 296, 2398-2401.
Kondrashov A. S., Sunyaev S. and Kondrashov F. A. (2002). Dobzhansky-Muller incompatibilities in protein evolution. Proceedings of the National Academy of Sciences USA 99, 14878-14883.
Kondrashov F. A., Ogurtsov A. Y. and Kondrashov A. S. (2004). Bioinformatical assay of human gene morbidity. Nucleic Acids Research 32, 1731-1737.
Bazykin G. A., Kondrashov F. A., Sunyaev S., Ogurtsov A. Y. and Kondrashov A. S. (2004). Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. Nature 429, 558-562.

Результаты исследований

Публикации

  1. Vishnoi A, Kryazhimskiy S, Bazykin GA, Hannenhalli S, Plotkin JB. Young proteins experience more variable selection pressures than old proteins. Genome Res. 2010 Nov;20(11):1574–81. abstract+fulltext

Публикации результатов, полученных с использованием материально-технической базы лаборатории

  1. Abramochkin DV, Borodinova AA, Rosenshtraukh LV, Nikolsky EE. Both neuronal and non-neuronal acetylcholine take part in non-quantal acetylcholine release in the rat atrium. Life Sci. 2012 Nov 27;91(21-22):1023–6. abstract
  2. Kulakovskiy IV, Medvedeva YA, Schaefer U, Kasianov AS, Vorontsov IE, Bajic VB, et al. HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. Nucleic Acids Res. 2013 Jan;41(Database issue):D195–202. abstract+fulltext(pdf)
  3. Vorontsov IE, Kulakovskiy IV, Makeev VJ. Jaccard index based similarity measure to compare transcription factor binding site models. Algorithms Mol Biol AMB. 2013 Sep 30;8:23. abstract+fulltext(pdf) 
  4. Tyakht AV, Kostryukova ES, Popenko AS, Belenikin MS, Pavlenko AV, Larin AK, et al. Human gut microbiota community structures in urban and rural populations in Russia. Nat Commun [Internet]. 2013 Sep 16 link
  5. А.С. Розанов, Т.В. Иванисенко, А.В. Брянская, С.В. Шеховцов, М.Д. Логачева, О.В. Сайк, Т.К. Малуп, П.С. Деменков, Т.Н. Горячковская, В.А. Иванисенко, С.Е. Пельтек. Биоинформатический анализ штамма Geobacillus stearothermophilus 22, выделенного из горячего источника Гарга (Прибайкалье). Вавиловский журнал генетики и селекции, 2013 т. 17, №4/1, стр. 659-664. abstract+fulltext(pdf) 
  6. Киселева А.В. Создание геномной ВАС библиотеки Allium fistulosum L. и ее использование в молекулярно-цитогенетических исследованиях. Диссертация на соискание учѐной степени кандидата биологических наук. Москва, 2013.
  7. Гущанская Е.С. Механизмы поддержания трехмерной организации генома. Диссертация на соискание учѐной степени кандидата биологических наук. Москва, 2013.
  8. Shtratnikova VY, Bragin EY, Dovbnya DV, Pekov YA, Schelkunov MI, Strizhov N, et al. Complete Genome Sequence of Sterol-Transforming Mycobacterium neoaurum Strain VKM Ac-1815D. Genome Announc. 2014;2(1). abstract+fulltext(pdf)
  9. Shpiz S, Ryazansky S, Olovnikov I, Abramov Y, Kalmykova A. Euchromatic transposon insertions trigger production of novel Pi- and endo-siRNAs at the target sites in the drosophila germline. PLoS Genet. 2014 Feb;10(2):e1004138. abstract+fulltext
  10. Zhadan A, Vortsepneva E, Tzetlin A. Three-dimensional reconstruction of the musculature of Cossura pygodactylata Jones, 1956 (Annelida: Cossuridae). Zool Anz - J Comp Zool. 2014 Feb;253(3):181–91. abstract 
  11. Shmakov S, Savitskaya E, Semenova E, Logacheva MD, Datsenko KA, Severinov K. Pervasive generation of oppositely oriented spacers during CRISPR adaptation. Nucleic Acids Res. 2014 Apr 11; abstract+fulltext(pdf) 
  12. Gushchanskaya ES, Artemov AV, Ulyanov SV, Logacheva MD, Penin AA, Kotova ES, et al. The clustering of CpG islands may constitute an important determinant of the 3D organization of interphase chromosomes. Epigenetics Off J DNA Methylation Soc. 2014 Apr 15;9(7). abstract
  13. Safonova Y, Bankevich A, Pevzner P. dipSPAdes: assembler for highly polymorphic diploid genomes. Research in Computational Molecular Biology Lecture Notes in Computer Science Volume 8394, 2014, pp 265-279.abstract
  14. Romanova EV, Mikhailov KV, Logacheva MD, Kamaltynov RM, Aleoshin VV, Sherbakov DY. The complete mitochondrial genome of a deep-water Baikalian amphipoda Brachyuropus grewingkii (Dybowsky, 1874). Mitochondrial DNA. 2015 Jan 20:1-2.
  15. Shtratnikova VY, Schelkunov MI, Pekov YA, Fokina VV, Logacheva MD, Sokolov SL, Bragin EY, Ashapkin VV, Donova MV. Complete Genome Sequence of Steroid-Transforming Nocardioides simplex VKM Ac-2033D. Genome Announc. 2015 Jan 8;3(1). pii: e01406-14. doi: 10.1128/genomeA.01406-14.
  16. Kurmangaliyev YZ, Favorov AV, Osman NM, Lehmann KV, Campo D, Salomon MP, Tower J, Gelfand MS, Nuzhdin SV. Natural variation of gene models in Drosophila melanogaster. BMC Genomics. 2015 Mar 17;16:198. doi: 10.1186/s12864-015-1415-6.

 

  1. Bazykin GA, Kondrashov AS. Detecting Past Positive Selection through Ongoing Negative Selection. Genome Biol Evol. 2011 Jan 1;3:1006–13. abstract+fulltext(pdf)
  2. Logacheva MD, Kasianov AS, Vinogradov DV, Samigullin TH, Gelfand MS, Makeev VJ, et al. De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum). BMC Genomics. 2011 Jan 13;12(1):30. abstract+fulltext(pdf)
  3. Logacheva MD, Schelkunov MI, Penin AA. Sequencing and analysis of plastid genome in mycoheterotrophic orchid Neottia nidus-avis. Genome Biol Evol. 2011;3:1296–303. abstract+fulltext(pdf)
  4. Shnol EE, Ermakova EA, Kondrashov AS. On the relationship between the load and the variance of relative fitness. Biol Direct. 2011 Apr 14;6(1):20. fulltext
  5. Vakhrusheva AA, Kazanov MD, Mironov AA, Bazykin GA. Evolution of prokaryotic genes by shift of stop codons. J Mol Evol. 2011 Feb;72(2):138–46. abstract
  6. Kryazhimskiy S, Dushoff J, Bazykin GA, Plotkin JB. Prevalence of epistasis in the evolution of influenza A surface proteins. PLoS Genet. 2011 Feb;7(2):e1001301. abstract+fulltext
  1. Leushkin EV, Bazykin GA, Kondrashov AS. Insertions and deletions trigger adaptive walks in Drosophila proteins. Proc Biol Sci. 2012 Aug 7;279(1740):3075–82. abstract+fulltext(pdf)
  2.  Garlitska L, Neretina T, Schepetov D, Mugue N, De Troch M, Baguley JG, et al. Cryptic diversity of the “cosmopolitan” harpacticoid copepod Nannopus palustris: genetic and morphological evidence. Mol Ecol. 2012 Nov;21(21):5336–47. abstract
  1. Naumenko SA, Kondrashov AS. Rate and breadth of protein evolution are only weakly correlated. Biol Direct. 2012;7:8. fulltext(pdf)
  2. Seplyarskiy VB, Kharchenko P, Kondrashov AS, Bazykin GA. Heterogeneity of the transition/transversion ratio in Drosophila and Hominidae genomes. Mol Biol Evol. 2012 Aug;29(8):1943–55. abstract+fulltext(pdf)
  3. Bazykin GA, Kondrashov AS. Major role of positive selection in the evolution of conservative segments of Drosophila proteins. Proc Biol Sci. 2012 Sep 7;279(1742):3409–17. abstract+fulltext(pdf)
  4. Naumenko SA, Kondrashov AS, Bazykin GA. Fitness conferred by replaced amino acids declines with time. Biol Lett. 2012 Oct 23;8(5):825–8. abstract+fulltext(pdf)
  5. Popadin KY, Nikolaev SI, Junier T, Baranova M, Antonarakis SE. Purifying selection in mammalian mitochondrial protein-coding genes is highly effective and congruent with evolution of nuclear genes. Mol Biol Evol. 2013 Feb;30(2):347–55. abstract+fulltext(pdf)
  6. Iles WJD, Rudall PJ, Sokoloff DD, Remizowa MV, Macfarlane TD, Logacheva MD, et al. Molecular phylogenetics of Hydatellaceae (Nymphaeales): sexual-system homoplasy and a new sectional classification. Am J Bot. 2012 Apr;99(4):663–76. abstract+fulltext(pdf)
  7. Demidenko NV, Penin AA. Comparative analysis of gene expression level by quantitative real-time PCR has limited application in objects with different morphology. PloS One. 2012;7(5):e38161. abstract+fulltext
  1. Fantin YS, Neverov AD, Favorov AV, Alvarez-Figueroa MV, Braslavskaya SI, Gordukova MA, et al. Base-calling algorithm with vocabulary (BCV) method for analyzing population sequencing chromatograms. PloS One. 2013;8(1):e54835. abstract+fulltext
  2. Leushkin EV, Bazykin GA, Kondrashov AS. Strong mutational bias toward deletions in the Drosophila melanogaster genome is compensated by selection. Genome Biol Evol. 2013;5(3):514–24. abstract+fulltext(pdf) 
  3. Vakhrusheva OA, Bazykin GA, Kondrashov AS. Genome-Level Analysis of Selective Constraint without Apparent Sequence Conservation. Genome Biol Evol. 2013;5(3):532–41. abstract+fulltext(pdf)
  4. Kolbasova GD, Tzetlin AB, Kupriyanova EK. Biology of Pseudopotamilla reniformis (Müller 1771) in the White Sea, with description of asexual reproduction. Invertebr Reprod Dev. 2013;57(4):264–75. abstract 
  5. Terekhanova NV, Bazykin GA, Neverov A, Kondrashov AS, Seplyarskiy VB. Prevalence of multinucleotide replacements in evolution of primates and Drosophila. Mol Biol Evol. 2013 Jun;30(6):1315–25. abstract+fulltext(pdf)
  6. Leushkin EV, Bazykin GA. Short indels are subject to insertion-biased gene conversion. Evolution 2013 Sep;67(9):2604–13. abstract
  7. Kurmangaliyev YZ, Sutormin RA, Naumenko SA, Bazykin GA, Gelfand MS. Functional implications of splicing polymorphisms in the human genome. Hum Mol Genet. 2013 Sep 1;22(17):3449–59. abstract
  8. Stupnikova AN, Molodtsova TN, Mugue NS, Neretina TV. Genetic variability of the Metridia lucens complex (Copepoda) in the Southern Ocean. J Mar Syst. 2013 Dec;128:175–84. abstract
  9. Flegontov P, Votýpka J, Skalický T, Logacheva MD, Penin AA, Tanifuji G, Onodera NT, Kondrashov AS, Volf P, Archibald JM, Lukes J. Paratrypanosoma is a novel early-branching trypanosomatid. Curr Biol CB. 2013 Sep 23;23(18):1787–93. abstract
  10. Leushkin EV, Sutormin RA, Nabieva ER, Penin AA, Kondrashov AS, Logacheva MD. The miniature genome of a carnivorous plant Genlisea aurea contains a low number of genes and short non-coding sequences. BMC Genomics. 2013 Jul 15;14(1):476. abstract+fulltext(pdf)
  11. Flot JF, ..., Bazykin GA, ..., Kondrashov AS, ..., Vakhrusheva OA et al. (39 co-authors). Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga. Nature. 2013 Aug 22;500(7463):453–7. fulltext(pdf)
  12. Kulagin DN, Stupnikova AN, Neretina TV, Mugue NS. Spatial genetic heterogeneity of the cosmopolitan chaetognath Eukrohnia hamata (Möbius, 1875) revealed by mitochondrial DNA. Hydrobiologia. 2014 Jan 1;721(1):197–207. abstract
  13. Temereva EN, Neretina TV. A distinct phoronid larva: morphological and molecular evidence. Invertebr Syst. 2013;27(6):622–33. abstract
  1. Neverov AD, Lezhnina KV, Kondrashov AS, Bazykin GA. Intrasubtype Reassortments Cause Adaptive Amino Acid Replacements in H3N2 Influenza Genes. PLoS Genet. 2014;10(1):e1004037. abstract+fulltext
  2. Spiridonov VA, Neretina TV, Schepetov D. Morphological characterization and molecular phylogeny of Portunoidea Rafinesque, 1815 (Crustacea Brachyura): implications for understanding evolution of swimming capacity and revision of the family-level classification. Zool Anz - J Comp Zool. 2014;253(5):404-429. full text
  3. Kolbasova GD, Tzetlin AB, Kupriyanova EK. Chaetal loss and replacement in Pseudopotamilla reniformis (Sabellida, Annelida). Invertebrate Biology. 2014;133(3):261–273. abstract
  4. Арифулов РНПопова НВНауменко СА. Оптимизация потоков данных в центре обработки геномных данных при помощи распределенной файловой системы Lustre. Информационные технологии и вычислительные системы 2014, N.1, с.35–45. Abstract Препринт
  5. Logacheva MD, Schelkunov MI, Nuraliev MS, Samigullin TH, Penin AA. The plastid genome of mycoheterotrophic monocot Petrosavia stellaris exhibits both gene losses and multiple rearrangements. Genome Biol Evol. 2014;6(1):238–46. abstract+fulltext(pdf)
  6. Denisov SV, Bazykin GA, Sutormin R, Favorov AV, Mironov AA, Gelfand MS, Kondrashov AS. Weak negative and positive selection and the drift load at splice sites. Genome Biol Evol 2014;6(6):1437-47. doi: 10.1093/gbe/evu100. full text
  7. Seplyarskiy VB, Logacheva MDPenin AABaranova MALeushkin EVDemidenko NVKlepikova AV, Kondrashov FA, Kondrashov AS, James TY. Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. Mol Biol Evol 2014;31(11):3016–25. doi: 10.1093/molbev/msu242. full text
  8. Gusev O, Suetsugu Y, Cornette R, Kawashima T, Logacheva MDKondrashov ASPenin AA, Hatanaka R, Kikuta S, Shimura S, Kanamor Hi, Katayose Y, Matsumoto T, Shagimardanova E, Alexeev D, Govorun V, Wisecaver J, Mikheyev A, Koyanagi R, Fujie M, Nishiyama T, Shigenobu S, Shibata TF, Golygina V, Hasebe M, Okuda T, Satoh N, Kikawada T. Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge. Nature Communications 5, Article number: 4784 doi:10.1038/ncomms5784  full text
  9. Terekhanova NV, Logacheva MD, Penin AA, Neretina TV, Barmintseva AE, Bazykin GA, Kondrashov AS, Mugue NS. Fast evolution from precast bricks: genomics of young freshwater populations of threespine stickleback Gasterosteus aculeatus. PLoS Genetics 2014;10(10):e1004696. doi: 10.1371/journal.pgen.10046964. full text.
  10. Popadin KY, Gutierrez-Arcelus M, Lappalainen T, Buil A, Steinberg J, Nikolaev SI, Lukowski SW, Bazykin GA, Seplyarskiy VB et al. Gene Age Predicts the Strength of Purifying Selection Acting on Gene Expression Variation in Humans. Am J Hum Genet. 2014;95(6):660–74. doi: 10.1016/j.ajhg.2014.11.003. abstract+fulltext
  11. Petrunina A.S., Neretina T.V., Mugue N.S., Kolbasov G.A. Tantulocarida versus Thecostraca: inside or outside? First attempts to resolve phylogenetic position of Tantulocarida using gene sequences. Journal of Zoological Systematics and Evolutionary Research. 2014;52(2):100–108. 
  12. Radashevsky VI, Neretina TV, Pankova VV, Tzetlin AB, Jin-Woo C. Molecular identity, morphology and taxonomy of the Rhynchospio glutaea complex with a key to Rhynchospio species (Annelida, Spionidae). Systematics and Biodiversity 2014;12:424–433.
  13. Evstafieva AG, Garaeva AA, Khutornenko AA, Klepikova AVLogacheva MDPenin AA, Novakovsky GA, Kovaleva IE, Chumakov PM. A sustained deficiency of mitochondrial respiratory complex III induces an apoptotic cell death through the p53-mediated inhibition of pro-survival activities of the Activating Transcription Factor 4. Cell Death & Disease. 2014;5:e1511. doi: 10.1038/cddis.2014.469.
  14. Romanova EV, Mikhailov KV, Logacheva MD, Kamaltynov RM, Aleoshin VV, Sherbakov DY. The complete mitochondrial genome of Baikalian amphipoda Eulimnogammarus vittatus Dybowsky, 1874. Mitochondrial DNA. 2014; Sep 29:1–3. abstract 
  1. Schelkunov MIShtratnikova VYu, Nuraliev MS, Selosse M-A, Penin AALogacheva MD. Exploring the limits for reduction of plastid genomes: a case study of the mycoheterotrophic orchids Epipogium aphyllum and Epipogium roseum. Genome Biol Evol. 2015 Jan 28;7(4):1179-91. doi: 10.1093/gbe/evv019.  full text
  2. Borisanova AO, Chernyshev AV, Neretina TVStupnikova AN. Description and phylogenetic position of the first abyssal solitary kamptozoan species from the Kuril-Kamchatka trench area: Loxosomella profundorum sp. nov. (Kamptozoa: Loxosomatidae). Deep Sea Research Part II: Topical Studies in Oceanography 2015;111:351-356. doi: 10.1016/j.dsr2.2014.07.016. full text
  3. Ekimova I,  Korshunova T, Sсhepetov D, Neretina T, Sanamyan N, Martynov A. Integrative systematics of Northern and Arctic nudibranchs of the genus Dendronotus (Mollusca, Gastropoda) with descriptions of three new species. Zoological Journal of the Linnean Society 2015;173(4):841-886. full text
  4. Polishchuk LV, Popadin KY, Baranova MAKondrashov AS. A genetic component of extinction risk in mammals. Oikos. 2015 Aug, 124(8): 983-93. full text 
  5. Anosov SE, Spiridonov VA, Neretina TV, Uryupova EF, Schepetov D. King crabs of the western Atlantic sector of Antarctic and adjacent areas: new records, molecular barcode data and distribution (Crustacea: Decapoda: Lithodidae). Polar Biology 2015;38(2):231-249. full text
  6. Kolbasova GD, Zalevsky AO, Gafurov AR, Gusev PO, Ezhova MA, Zheludkevich AA, Konovalova OP, Kotlov NU, Lanina NO, Lapashina AS, Medvedev DO, Nosikova KS, Nuzhdina EO, Bazykin GA, Neretina TV. A new species of Cyanea jellyfish sympatric to C. capillata in the White Sea. Polar Biology. 2015 Sep, 38(9):1439-51. full text 
  7. Leushkin EV, Logacheva MDPenin AA, Sutormin RA, Gerasimov ES, Kochkina GA, Ivanushkina NE, Vasilenko OV, Kondrashov AS, Ozerskaya SM. Comparative genome analysis of Pseudogymnoascus spp. reveals primarily clonal evolution with small genome fragments exchanged between lineages. BMC Genomics 2015, 16:400 doi:10.1186/s12864-015-1570-9 full text
  8. Hayward AD, Lummaa V, Bazykin GA. Fitness Consequences of Advanced Ancestral Age over Three Generations in Humans. PLoS One. 2015 Jun 1;10(6):e0128197. doi: 10.1371/journal.pone.0128197. eCollection 2015. full text
  9. Klepikova AVLogacheva MD, Dmitriev SE, Penin AA. RNA-seq analysis of an apical meristem time series reveals a critical point in Arabidopsis thaliana flower initiation. BMC Genomics, 2015, 16:466 doi:10.1186/s12864-015-1688-9. full text
  10. Baranova MALogacheva MDPenin AASeplyarskiy VB, Safonova YY, Naumenko SAKlepikova AVGerasimov ESBazykin GA, James TY, Kondrashov AS. Extraordinary genetic diversity in a wood decay mushroom. Mol Biol Evol. 2015 Oct;32(10):2775-83. doi: 10.1093/molbev/msv153. Epub 2015 Jul 10. full text
  11. Neverov AD, Kryazhimskiy S, Plotkin JP, Bazykin GA. Coordinated evolution of Influenza A surface proteins. PLoS Genetics, 11(8): e1005404. doi:10.1371/journal.pgen.1005404. full text 
  12. Budaeva N, Schepetov D, Zanol J, Neretina T, Willassen E. When molecules support morphology: Phylogenetic reconstruction of the family Onuphidae (Eunicida, Annelida) based on 16S rDNA and 18S rDNA. Mol Phylogenet Evol. 2015 Oct 21. pii: S1055-7903(15)00314-0. doi: 10.1016/j.ympev.2015.10.011. full text 
  13. Bazykin GA. Changing preferences: deformation of single position amino acid fitness landscapes and evolution of proteins. Biol Lett. 2015 Oct;11(10). pii: 20150315. doi: 10.1098/rsbl.2015.0315. Review. full text
  14. Seplyarskiy VB, Bazykin GA, Soldatov RA. Polymerase ζ Activity Is Linked to Replication Timing in Humans: Evidence from Mutational Signatures. Mol Biol Evol. 2015 Dec;32(12):3158-72. doi: 10.1093/molbev/msv184. Epub 2015 Sep 15. full text
  15. Denisov SV, Bazykin GA, Favorov AV, Mironov AA, Gelfand MS. Correlated evolution of nucleotide positions within splice sites in mammals. PLOS One. 2015;10(12):e0144388. doi: 10.1371/journal.pone.0144388. full text

 

  1. Flegontov P, Changmai P, Zidkova A, Logacheva MD, Flegontova O, Gelfand MS, Gerasimov ES, Khrameeva EV, Konovalova OPNeretina TV, Nikolsky YV, Starostin G, Stepanova VV, Travinsky IV, Tříska M, Tříska P, Tatarinova TV. Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry. Scientific Reports 6, Article number: 20768 (2016) abstract
  2. Sarkisyan KS, Bolotin DA, Meer MV, Usmanova DR, Mishin AS, Sharonov GV, Ivankov DN, Bozhanova NG, Baranov MS, Soylemez O, Bogatyreva NS, Vlasov PK, Egorov ES, Logacheva MDKondrashov AS, Chudakov DM, Putintseva EV, Mamedov IZ, Tawfik DS, Lukyanov KA, Kondrashov FA. Local fitness landscape of the green fluorescent protein. Nature. 2016 May 11;533(7603):397-401. abstract
  3. Klepikova AVKasianov ASGerasimov ESLogacheva MDPenin AA. A High Resolution Map of the Arabidopsis thaliana Developmental Transcriptome Based on RNA-seq Profiling. Plant J Cell Mol Biol. 2016 Aug 23; abstract
  4. Radashevsky VI, Pankova V V, Neretina TV., Tzetlin A. B. 2016 Molecular analysis of the Pygospio elegans group of species (Annelida: Spionidae). Zootaxa. 2016 4083(2):239. abstract
  5. Temereva EN, Neretina TV, Stupnikova A.  The fauna of the South China Sea include unknown phoronid species: new records of larvae and adults. Systematics and Biodiversity. 2016 14(5):509-523. abstract
  6. Fedyaeva MA, Neretina TV, Konovalova OP, Tchesunov AV.  Two known and one new species of Draconematidae and Epsilonematidae (Nematoda, Desmodorida) from the White Sea, North Russia. Zootaxa. 2016 4121(4): 383-411. abstract
  7. Popova EV, Petrusek A. Korinek V., Mergeay J., Bekker EI, Karabanov DP, Galimov YR, Neretina TV, Taylor DJ & Kotov AA. Revision of the Old World Daphnia (Stenodaphnia) similis group (Cladocera: Daphniidae). Zootaxa. 2016 4161 (1):001-040. abstract
  8. Temereva EN, Neretina TV, Stupnikova A. An original description of the larval stages of Phoronis australis Haswell, 1883 and an analysis of the world fauna of phoronid larvae. Russian Journal of Marine Biology 2016 42(2) 128-138. abstract
  9. Seplyarskiy VB, Soldatov RA, Popadin KY, Antonarakis SE, Bazykin GA, Nikolaev SI. APOBEC-induced mutations in human cancers are strongly enriched on the lagging DNA strand during replication. Genome Res. 2016 Feb;26(2):174–82. full_text
  10. Zolotarev N, Fedotova A, Kyrchanova O, Bonchuk A, Penin AA, Lando AS, et al. Architectural proteins Pita, Zw5,and ZIPIC contain homodimerization domain and support specific long-range interactions in Drosophila. Nucleic Acids Res. 2016 May 2;gkw371. full_text
  11. Logacheva MDSchelkunov MIShtratnikova VY, Matveeva MV, Penin AA. Comparative analysis of plastid genomes of non-photosynthetic Ericaceae and their photosynthetic relatives. Sci Rep [Internet]. 2016 Jul 25 [cited 2016 Oct 24];6. full_text
  12. Samigullin TH, Logacheva MDPenin AA, Vallejo-Roman CM. Complete Plastid Genome of the Recent Holoparasite Lathraea squamaria Reveals Earliest Stages of Plastome Reduction in Orobanchaceae. PloS One. 2016;11(3):e0150718. full_text
  13. Kainov YA, Aushev VN, Naumenko SA, Tchevkina EM, Bazykin GA. Complex Selection on Human Polyadenylation Signals Revealed by Polymorphism and Divergence Data. Genome Biol Evol. 2016 Jul 2;8(6):1971–9. full_text
  14. Popova OV, Mikhailov KV, Nikitin MA, Logacheva MDPenin AA, Muntyan MS, et al. Mitochondrial Genomes of Kinorhyncha: trnM Duplication and New Gene Orders within Animals. PloS One. 2016;11(10):e0165072. full_text
  15. Mikhailov KV, Slyusarev GS, Nikitin MA, Logacheva MDPenin AA, Aleoshin VV, et al. The Genome of Intoshia linei Affirms Orthonectids as Highly Simplified Spiralians. Curr Biol CB. 2016 Jul 11;26(13):1768–74. abstract
  16. Pomaznoy MY, Logacheva MD, Young ND, Penin AA, Ershov NI, Katokhin AV, et al. Whole transcriptome profiling of adult and infective stages of the trematode Opisthorchis felineus. Parasitol Int. 2016 Feb;65(1):12–9. abstract

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  1. Naumenko S, Logacheva M, Popova N, Klepikova A, Penin A, Bazykin G, Etingova A, Mugue N, Kondrashov A, Yampolsky L. Transcriptome-based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection. Molecular Ecology  2017 26(2): 536-553 abstract 
  2. Terekhanova NV, Seplyarskiy VB, Soldatov RA, Bazykin GA. Evolution of local mutation rate and its determinants. Molecular Biology and Evolution 2017 full text

 

 

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