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Публикации

2018
  1. Van Trung Chu, Timm Weber, Robin Graf, Thomas Sommermann, Kerstin Petsch, Ulrike Sack, Pavel Volchkov, Klaus Rajewsky, Ralf Kühn. Efficient generation of Rosa26 knock-in mice using CRISPR/Cas9 in C57BL/6 zygotes. BMC Biotechnology, in press.

2017
  1. Gress, A., Ramensky, V., and Kalinina, O.V. (2017). Spatial distribution of disease-associated variants in three-dimensional structures of protein complexes. Oncogenesis 6, e380.
  2. Huang, A.Y., Yu, D., Davis, L.K., Sul, J.H., Tsetsos, F., Ramensky, V., Zelaya, I., Ramos, E.M., Osiecki, L., Chen, J.A., et al. (2017). Rare Copy Number Variants in NRXN1 and CNTN6 Increase Risk for Tourette Syndrome. Neuron 94, 1101–1111.e7.

  3. Jasinska A., Zelaya I., Service S., Peterson, C., et al. (2017) Genetic variation and gene expression across multiple tissues and developmental stages in a non-human primate. Nat Genet, in press. http://biorxiv.org/content/early/2016/12/09/092874

  4. Svardal, H., Jasinska A.J., Apetrei, C., Coppola G., et al. (2017) Ancient hybridization and strong adaptation to viruses across African vervet monkey populations. Nat Genet, in press

  5. Willsey, A.J., Fernandez, T.V., Yu, D., King, R.A., Dietrich, A., Xing, J., Sanders, S.J., Mandell, J.D., Huang, A.Y., Richer, P., et al. (2017). De Novo Coding Variants Are Strongly Associated with Tourette Disorder. Neuron 94, 486–499.e9.

2016
  1. Gress, A., Ramensky, V., Büch, J., Keller, A., and Kalinina, O.V. (2016). StructMAn: annotation of single-nucleotide polymorphisms in the structural context. Nucl. Acids Res. gkw364.

  2. Gaponova AVNikonova ADeneka AYKopp MCKudinov AESkobeleva NKhazak VShin Ogawa L ,Cai KQ,Duncan KEDuncan JS,Egleston BLProia DABoumber YGolemis EA., A novel HSP90 inhibitor-drug conjugate to SN38 is highly effective in small cell lung cancer (SCLC), Clinical Cancer Research. 2016 June 7 pii: clincanres.3068.2015.

2015
  1. Michael Burrows, Pavel Volchkov, Koichi Kobayashi and Alexander Chervonsky, (2015). Toll-like receptor signaling involvement in regulation of type 1 diabetes by microbiota. PNAS

  2. Oscar Simonson, Anna Domogatskaya, Pavel Volchkov and Sergey Rodin, (2015). The safety of human pluripotent stem cells in clinical treatment. Annals of Medicine. 

  3. Huang, Y.S., Ramensky, V., Service, S.K., Jasinska, A.J., Jung, Y., Choi, O.-W., Cantor, R.M., Juretic, N., Wasserscheid, J., Kaplan, J.R., et al. (2015). Sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits. BMC Biol. 13, 41.

  4. Warren, W.C., Jasinska, A.J., García-Pérez, R., Svardal, H., Tomlinson, C., Rocchi, M., Archidiacono, N., Capozzi, O., Minx, P., Montague, M.J., et al. (2015). The genome of the vervet (Chlorocebus aethiops sabaeus). Genome Res.

  5. Shagisultanova EGaponova AVGabbasov RNicolas EGolemis EA., Preclinical and clinical studies of the NEDD9 scaffold protein in cancer and other diseasesGene. 2015 Aug 1;567(1):1-11. doi: 10.1016/j.gene.2015.04.086. Epub 2015 May 9.

  6. Kolbasova Glafira D., Zalevsky Arthur O., Gafurov Azamat R., Gusev Philipp O., Ezhova Margarita A., Zheludkevich Anna A., Konovalova Olga P., Kosobokova Ksenia N., Котлов Никита Юрьевич, Lanina Natalia O., Lapashina Anna S., Medvedev Dmitry O., Nosikova Katerina S., Nuzhdina Ekaterina O., Bazykin Georgii A., Tatyana Neretina, (2015). A new species of Cyanea jellyfish sympatric to C. capillata in the White Sea. Polar Biology, Springer Verlag (Germany), с. 1-13

2014
  1. Riddell, Roi Gazit, Brian S Garrison, Guoji Guo, Assieh Saadatpour, Pankaj K Mandal, Wataru Ebina, Guo-Cheng Yuan, Pavel Volchkov, Stuart H Orkin, Derrick J Rossi, (2014). Reprogramming committed murine blood cells to induced hematopoietic stem cells with defined factors. Cell. 

  2. Service, S.K., Teslovich, T.M., Fuchsberger, C., Ramensky, V., Yajnik, P., Koboldt, D.C., Larson, D.E., Zhang, Q., Lin, L., Welch, R., et al. (2014). Re-sequencing Expands Our Understanding of the Phenotypic Impact of Variants at GWAS Loci. PLoS Genet 10.

  3. Nikonova AS, Gaponova AV, Kudinov AE, Golemis EA, (2014). CAS proteins in health and disease: an update, IUBMB Life.2014 Jun; 66(6):387-95. doi: 10.1002/iub.1282. Epub Jun 24.

2013
  1. Yurkovetskiy L, Burrows M, Khan AA, Graham L, Volchkov P, Becker L, Antonopoulos D, Umesaki Y, Chervonsky AV, (2013). Gender bias in autoimmunity is influenced by microbiota. Immunity.
2010
  1. Takatoshi Chinen, Pavel Volchkov, Alexander Chervonsky, Alexander Rudensky, (2010 Oct 25). A critical role for Treg cell-mediated control of inflammation in the absence of commensal microbiota. J. Exp. Med. 207(11): 2323-30.    

  2. Adzhubei, I.A., Schmidt, S., Peshkin, L., Ramensky, V.E., Gerasimova, A., Bork, P., Kondrashov, A.S., and Sunyaev, S.R. (2010). A method and server for predicting damaging missense mutations. Nat Meth 7, 248–249.

  3. Jordan, D.M., Ramensky, V.E., and Sunyaev, S.R. (2010). Human allelic variation: perspective from protein function, structure, and evolution. Curr Opin Struct Biol 20, 342–350.

  4. Panchin, A.Y., Gelfand, M.S., Ramensky, V.E., and Artamonova, I.I. (2010). Asymmetric and non-uniform evolution of recently duplicated human genes. Biol. Direct 5, 54.

2009
  1. Gelfand, M.S., and Ramensky, V.E. (2009). Positive Selection and Alternative Splicing in Humans. In Encyclopedia of Life Sciences, John Wiley & Sons, Ltd, ed. (Chichester, UK: John Wiley & Sons, Ltd), p.

  2. Metlitskaya, A., Kazakov, T., Vondenhoff, G.H., Novikova, M., Shashkov, A., Zatsepin, T., Semenova, E., Zaitseva, N., Ramensky, V., Van Aerschot, A., et al. (2009). Maturation of the translation inhibitor microcin C. J. Bacteriol. 191, 2380–2387.

  3. . Nikolskaya T, Nikolsky Y, Serebryiskaya T, Zvereva S, Sviridov E, Dezso Z, Rahkmatulin E, Brennan RJ, Yankovsky N, Bhattacharya SK, Agapova O, Hernandez MR, Shestopalov VI, (2009 May). Network analysis of human glaucomatous optic nerve head astrocytes. BMC Med Genomics. 9;2:24.

  4. Bureeva S, Zvereva S, Romanov V, Serebryiskaya T., (2009). Manual annotation of protein interactions. Methods Mol Biol. 563:75-95.

2008
  1. Wen L*, Ley R. E.*, Volchkov P. Y*, Stranges P. B., Avanesyan L., Stonebraker A. C., Hu C.,Wong F. S., Szot G. L., Bluestone J. A., Gordon J. I., Chervonsky A. V., (2008 Sept 21). Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature, 455(7216): 1109-13.  * Equal contribution.

  2. Lagarkova M. A., Volchkov P., Philonenko E. S., Pfannkuche K,. Prokhorovich M. A., Zabotina T., Hescheler J., Kiselev S. L., (2008 Nov 15). CD30 is a marker of undifferentiated human embryonic stem cells rather than a biomarker of transformed hESCs. Cell Cycle 7(22): 3610–12. 

  3. Lagarkova M. A., Volchkov P*., Philonenko E. S., Kiselev S. L., (2008 Sept 15). Efficient differentiation of hESCs into endothelial cells in vitro is secured by epigenetic changes. Cell Cycle, 7(18): 2929–35. * Equal contribution    

  4. Ramensky, V.E., Nurtdinov, R.N., Neverov, A.D., Mironov, A.A., and Gelfand, M.S. (2008). Positive Selection in Alternatively Spliced Exons of Human Genes. Am J Hum Genet 83, 94–98.

2007
  1. Volchkov P. Y, Lagarkova M. A., Prokhorovich M. A., Kiselev S. L., (2007). Negative control of genes during differentiation of embryonic stem cells into endothelial cells. Cellular Transplantology and Tissue Engineering, 2:51-55

  2. Ramensky, V., Sobol, A., Zaitseva, N., Rubinov, A., and Zosimov, V. (2007). A novel approach to local similarity of protein binding sites substantially improves computational drug design results. Proteins 69, 349–357.

  3. Раменский, В.Е., and Сюняев, Ш.Р. (2007). Поиск функционального полиморфизма человека с помощью метода PolyPhen. In Молекулярный Полиморфизм Человека: Структурное И Функциональное Индивидуальное Разнообразие Биомакромолекул, (РУДН Москва)

2006
  1. Lagarkova M. A., Volchkov P. Y., Lyakisheva A. V., Philonenko E. S., Kiselev S. L., (2006 Feb 15). Diverse epigenetic profile of novel human embryonic stem cell lines. Cell Cycle, 5(4). 

  2. Kiselev S. L., Volchkov P. Y, Prokhorovich M. A., Mufazalov I. A., Lyakisheva A. V., Lagarkova M. A., (2006). Molecular and cellular biology of human embryonic stem cells. Molecular Medicine, 2:6–11. 

  3. Nurtdinov, R.N., Neverov, A.D., Mal’ko, D.B., Kosmodem’ianskiĭ, I.A., Ermakova, E.O., Ramenskiĭ, V.E., Mironov, A.A., and Gel’fand, M.S. (2006). EDAS, databases of alternatively spliced human genes. Biofizika 51, 589–592.

2005
  1. Krasnov, A.N., Kurshakova, M.M., Ramensky, V.E., Mardanov, P.V., Nabirochkina, E.N., and Georgieva, S.G. (2005). A retrocopy of a gene can functionally displace the source gene in evolution. Nucleic Acids Res 33, 6654–6661.

2004
  1. Dorokhov YL, Skurat EV, Frolova OY, Gasanova TV, Smirnov AA, Zvereva SD, Ivanov PA, Ravin NV, Zamchuk LI, Atabekov IG. (2004), Reciprocal dependence between pectinmethylesterase gene expression and tobamovirus reproduction  effectiveness in Nicotiana benthamiana. Dokl Biochem Biophys. Jan-Feb;394:30-2.

  2. Zvereva SD, Ivanov PA, Skulachev MV, Klyushin AG, Dorokhov YL, Atabekov JG, (2004). Evidence for contribution of an internal ribosome entry site to intercellular transport of a tobamovirus, J Gen Virol. Jun;85 (Pt 6):1739-44. 

2003
  1. Buzdin A., Gogvadze E., Kovalskaya E., Volchkov P., Ustyugova S., Illarionova A., Fushan A., Vinogradova T., Sverdlov E., (2003 Aug 1). The human genome contains many types of chimeric retrogenes generated through in vivo RNA recombination. Nucleic Acids Research, 31(15):4385–90.    

  2. Sunyaev, S., Kondrashov, F.A., Bork, P., and Ramensky, V. (2003). Impact of selection, mutation rate and genetic drift on human genetic variation. Hum. Mol. Genet. 12, 3325–3330.

  3. S.I. Malyshenko, L.G. Tyul'kina, S.D. Zvereva, G.N. Raldugina, (March 2003). Transgenic Brassica campestris Plants Expressing the gfp Gene. Russian Journal of Plant Physiology 50(2):276-281.

  4. Tony Wahlroos, Petri Susi, Lidia Tylkina, Svetlana Malyshenko, Svetlana Zvereva, Timo Korpela, (September 2003). Agrobacterium–mediated transformation and stable expression of the green fluorescent protein in Brassica rapa. Plant Physiology and Biochemistry 41(9):773-778

  5. Мильчевский, Ю.В., Раменский, В.Е., Жоров, Б.С., Котовская, Е.С., Есипова, Н.Г., and Туманян (2003). Молекулярное моделирование коллагена II человека в связи с болезнями, ассоциированными с аминокислотными заменами. Аллергия, Астма И Клиническая Иммунология 7, 27–32.

2002
  1. Ramensky, V., Bork, P., and Sunyaev, S. (2002). Human non-synonymous SNPs: server and survey. Nucleic Acids Res 30, 3894–3900.

  2. Dorokhov YL, Skulachev MV, Ivanov PA, Zvereva SD, Tjulkina LG, Merits A, Gleba YY, Hohn T, Atabekov JG, (2002). Polypurine (A)-rich sequences promote cross-kingdom conservation of internal ribosome entry. Proc Natl Acad Sci U S A. Apr 16;99(8):5301-6. 

2001
  1. Makeev, V., Ramensky, V., Gelfand, M., Roytberg, M., and Tumanyan, V. (2001). Bayesian Approach to DNA Segmentation into Regions with Different Average Nucleotide Composition. In Computational Biology, (Springer, Berlin, Heidelberg), pp. 57–73.

  2. Milchevsky, J.V., Ramensky, V.E., Esipova, N.G., Tumanyan, V.G., and Zorov, B.S. (2001). Molecular modelling of disease-causing single-nucleotide polymorphisms in collagen. SAR QSAR Environ Res 12, 383–399.
  3. Ramensky, V.E., Makeev, V.J., Roytberg, M.A., and Tumanyan, V.G. (2001). Segmentation of long genomic sequences into domains with homogeneous composition with BASIO software. Bioinformatics 17, 1065–1066.

  4. Sunyaev, S., Ramensky, V., Koch, I., Lathe, W., Kondrashov, A.S., and Bork, P. (2001). Prediction of deleterious human alleles. Hum. Mol. Genet 10, 591–597.

2000
  1. Ramenskiĭ, V.E., Vlasov, P.K., Siuniaev, S.R., and Tumanian, V.G. (2000). How do point amino acid substitutions affect the protein structure? Biofizika 45, 220–227.

  2. S. Zvereva, G.A. Romanov, (May 2000) . Reporter genes for plant genetic engineering: Characteristics and detection, Russian Journal of Plant Physiology 47(3):424-432.

  3. Ramensky, V.E., Makeev VJu, Roytberg, M.A., and Tumanyan, V.G. (2000). DNA segmentation through the Bayesian approach. J. Comput. Biol 7, 215–231.

  4. Sunyaev, S., Ramensky, V., and Bork, P. (2000a). Towards a structural basis of human non-synonymous single nucleotide polymorphisms. Trends Genet 16, 198–200.

  5. Sunyaev, S.R., Lathe, W.C., Ramensky, V.E., and Bork, P. (2000b). SNP frequencies in human genes an excess of rare alleles and differing modes of selection. Trends Genet 16, 335–337.

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