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Публикации 2013

  1. Antonik A., O’Brien S.J. & Malov, S.V. Whole Genome Sequence Coverage Estimation Reexamined. In Applied Methods of Statis-tical Analysis. Applications in Survival Analysis, Reliability and Quality Control. Proceedings of the International Workshop AMSA’13 (Novosibirsk, September 25-27, 2013), 46–50, 2013.

  2. Bartha I, Carlson JM, Brumme CJ, McLaren PJ, Brumme ZL, John M, Haas DW, Martinez-Picado J, Dalmau J, López-Galíndez C, Casado C, Rauch A, Günthard HF, Bernasconi E, Vernazza P, Klimkait T, Yerly S, O’Brien SJ, Listgarten J, Pfeifer N, Lippert C, Fusi N, Kutalik Z, Allen TM, Müller V, Harrigan PR, Heckerman D, Telenti A, Fellay J. A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control. Elife. 2013 Oct 29;2:e01123. doi: 10.7554/eLife.01123.

  3. Beyersmann, Paul , Olga Chertkov, Jörn Petersen, Anne Fiebig, Amy Chen, Amrita Pati, Natalia Ivanova, Alla Lapidus, Lynne A. Goodwin, Patrick Chain, John C. Detter, Manfred Rohde, Sabine Gronow, Nikos C. Kyrpides, Tanja Woyke, Meinhard Simon, Markus Göker, Hans-Peter Klenk, Thorsten Brinkhoff. Genome sequence of Phaeobacter caeruleus type strain (DSM 24564T), a surface-associated member of the marine Roseobacter clade Standards in Genomics Sciences , Vol 8, No 3 (2013) .

  4. Chernyaeva E., E. Fedorova, G. Zhemkova, Y. Korneev, A. Kozlov . Characterization of multiple and extensively drug resistantMycobacterium tuberculosis isolates with different ofloxacin-resistance levels. Tuberculosis, Volume 93, Issue 3, May 2013, Pages 291–295.

  5. Cho, Yun Sung, Li Hu, Haolong Hou, Hang Lee, Jiaohui Xu, Soowhan Kwon, Sukhun Oh, Hak-Min Kim, Sungwoong Jho, Sangsoo Kim, Tae Hyung Kim, Shu-Jin Luo, Warren Johnson, Sunghoon Lee, Young-Ah Shin, Qian Zhou, Byung Chul Kim, Hyunmin Kim, Chang-uk Kim, Hyun-Ju Jung, Xiao Xu, Pryivrat Gadhvi, Pengwei Xu, Yingqi Xiong, Yadan Luo, Shengkai Pan, Caiyun Gou, Xiuhui Chu, Jilin Zhang, Sanyang Liu, Jing He, Ying Chen, Linfeng Yang, Yulan Yang, Jiaju He, Sha Liu, Junyi Wang, Chul Hong Kim, Jong-Soo Kim, Seungwoo Hwang, Junsu Ko, Chang-Bae Kim, Sangtae Kim, Damdin Bayarlkhagva, Woon Kee Paek, Seong-Jin Kim, Stephen J. O’Brien, Jun Wang,, and Jong Bhak,. The tiger genome and comparative analysis with other feline genomes. NATURE COMMUNICATIONS 4:2433 | DOI: 10.1038/ncomms3433 |www.nature.com/naturecommunications , 2013.

  6. Dobrynin P. , E. Matyunina, S. V. Malov, and A. P. Kozlov, “The Novelty of Human Cancer/Testis Antigen Encoding Genes in Evolution,” International Journal of Genomics, vol. 2013, Article ID 105108, 7 pages, 2013. doi:10.1155/2013/105108

  7. Davydov-Sinitsyn A.P. , O.V. Bajenova, M.A. Liskovykh, S.V. Ponomartsev, L.L. Chechik, A.N. Tomilin, E.N. Tolkunova. A comparative analysis of colorectal carcinoma cell lines that differ in metastatic potential. Tsitologia. 2013, 55 (6) : 379–387

  8. Davydov-Sinitsyn A. P. , O. V. Bajenova, M. A. Liskovykh, L. L. Chechik, S. V. Ponomartsev, A. N. Tomilin, E. N. Tolkunova IN VITRO DERIVATION AND CHARACTERIZATION OF A COLORECTAL CANCER STEM CELL SUBPOPULATION. Tsitologia. 2013, 55 (5) : 318–323.

  9. Dementyeva P., Makunin A., Graphodatsky A., Trifonov V. Genes on B chromosomes of vertebrates. Genetics and Molecular Biology (Brasil) in press 2013.

  10. Elkins JG, Hamilton-Brehm SD, Lucas S, Han J, Lapidus A, Cheng JF, Goodwin LA, Pitluck S, Peters L, Mikhailova N, Davenport KW, Detter JC, Han CS, Tapia R, Land ML, Hauser L, Kyrpides NC, Ivanova NN, Pagani I, Bruce D, Woyke T, Cottingham RW. Complete Genome Sequence of the Hyperthermophilic Sulfate-Reducing Bacterium Thermodesulfobacterium geofontis OPF15T.Genome Announc. 2013 Apr 11;1(2):e0016213.

  11. Hoffman I.F., Latkin C.A., Kukhareva P.V., Malov S.V., Batluk J.V., Shaboltas A.V., Skochilov R.V., Sokolov N.V., Verevochkin S.V., Hudgens M.G. & Kozlov A.P. (2013). A Peer-Educator Network HIV Prevention Intervention Among Injection Drug Users: Results of a Randomized Controlled Trial in St. Petersburg, Russia. AIDS and Behavior, Vol. 17, Issue 7, pp 2510-2520

  12. Kits KD, Kalyuzhnaya MG, Klotz MG, Jetten MS, Op den Camp HJ, Vuilleumier S, Bringel F, Dispirito AA, Murrell JC, Bruce D, Cheng JF, Copeland A, Goodwin L, Hauser L, Lajus A, Land ML, Lapidus A, Lucas S, Médigue C, Pitluck S, Woyke T, Zeytun A, Stein LY. Genome Sequence of the Obligate Gammaproteobacterial Methanotroph Methylomicrobium album Strain BG8. Genome Announc. 2013 Apr 11;1(2):e0017013.

  13. Lu-Nan , Le-Qun Li, Yuan-Yuan Chen , Zhao-Hong Chen , Tao Bai , Bang-De Xiang, Xiao Qin ,Kai-Yin Xiao , Min-Hao Peng , Zhi-Ming Liu, Tang-Wei Liu , Xue Qin , Shan Li , Ze-Guang Han5 , Zeng-Nan Mo, Regina M. Santella , Cheryl A. Winkler , Stephen J. O’Brien, Tao Peng Genome-Wide and Differential Proteomic Analysis of Hepatitis B Virus and Aflatoxin B1 Related HepatocellularCarcinoma in Guangxi, China. PLOS ONE | 2013 | Volume 8 | Issue 12 | e83465

  14. Malov S.V. & O’Brien S.J. On Survival Categorical Methods with Applications in Epidemiology and AIDS Research. In “Applied Methods of Statistical Analysis. Applications in Survival Analysis, Reliability and Quality Control”, Proceedings of the International Workshop (Novosibirsk, September 25-27, 2013), 173—180.

  15. Malov S.V, A.K. Shevchenko & S.J. O’Brien (2013) Genome associations discovering. Part 1: Statistical methods (in Russian). Komputerniye instrumenti v obrazovanii, v. 5, pp 17 – 32. (Title in Russian: Малов С.В., Шевченко А.К. & О’Брайен С.Д. Поиск генетических закономерностей. Часть 1: Статистические методы. Компьютерные инструмен-ты в образовании 5, 2013, 17-32) (Computer Tools in Education 5, 2013, 17-32) (MS757)

  16. Malov S.V., A.K. Shevchenko & S.J. O’Brien (2013) Genome associations discovering. Part 2: Multiple testing problem, computer tools and applications (in Russian). Komputerniye instrumenti v obrazovanii, v. 6, pp. 3-17. (Title in Russian: Малов С.В., Шевченко А.К. & О’Брайен С.Д. Поиск генетических закономерностей. Часть 2: Проблема интерпретации результатов множества тестов, компьютерные инструменты и приложения, Компьютерные инструмен-ты в образовании 6, 2013, 3-1 (Computer Tools in Education 6,2013,3-1).

  17. Makunin A.I. , V.A. Trifonov. 2013. Contemporary approaches to B chromosome analysis. Tsitologiya. 55 (3) : 148–152 (Макунин А.И., Трифонов В.А. Современные методы анализа добавочных хромосом. Цитология 55 (3): 148-152) 2013.

  18. Matte EM, Castilho CS, Miotto RA3, Sana DA, Johnson WE, O’Brien SJ, de Freitas TR, Eizirik E. Molecular evidence for a recent demographic expansion in the puma (Puma concolor) (Mammalia, Felidae). Genet Mol Biol. 2013 36:586-97. doi: 10.1590/S1415-47572013000400018

  19. McLaren, Paul J, Cédric Coulonges, Stephan Ripke, Leonard van den Berg, Susan Buchbinder, Mary Carrington, Andrea Cossarizza, Olivier Delaneau, Andrea De Luca, James Goedert, David Haas, Joshua Herbeck, Sekar Kathiresan, Gregory Kirk, Olivier Lambotte, Ma Luo, Simon Mallal, Danielle van Manen, Javier Martinez-Picado, Laurence Meyer, José M Miro, Jim Mullins, Niels Obel, Stephen J O’Brien, Florencia Pereyra, Guido Poli, Ying Qi, Manj Sandhu, Patrick Shea, Hanneke Shuitemaker, Ioannis Theodorou, Fredrik Vannberg, Jan Veldink, Amy Weintrob, Cheryl Winkler, Steven Wolinsky, Amalio Telenti, David B Goldstein, Paul IW de Bakker, Jean-François Zagury, Jacques Fellay on behalf of the International Collaboration for the Genomics of HIV** Genome-wide association study of HIV-1 acquisition in 6,500 infected cases and 7,200 controls. PLoS Pathog. 2013 Jul;9(7):e1003515. doi: 10.1371/j.

  20. Nurk S., Bankevich A., Antipov D., Gurevich A., Korobeynikov A., Lapidus A., Prjibelsky A., Pyshkin A., Sirotkin A., Sirotkin Y., Stepanauskas R., McLean J., Lasken R., Tesler G., Alekseyev M., Pevzner P., “Assembling Genomes and Multigenomes from Highly Chimeric Reads”. RECOMB 2013, The 17th Annual International Conference on Research in Computational Molecular Biology. Beijing, April 7-10, 2013.

  21. O’Brien SJ and Hendrickson ,S. Host Genomic Influences on HIV/AIDS. Genome Biology Genome Biology, 14:201-214. 2013

  22. O’Brien SJ, Koepfli KP. Evolution: a new cat species emerges.Curr Biol. 2013 Dec 16;23(24):R1103-5. doi: 10.1016/j.cub.2013.10.074. PMID: 24355788 MS766

  23. Simonov, Serguei, Alex Makunin, Stephen O’Brien Browser for a genome. In: Computer tools in education (magazine) (http://ipo.spb.ru/journal/index.php?magazines/2013/) 2013.