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Публикации 2015

  1. Acosta F., Sambrano D., Correa R., Goodridge A., Chernyaeva E., Rotkevich M., Mendoza L., Tarté M., Hernández H., Velazco B., de Escobar C., de Waard J.H. MYCOBACTERIUM BOVIS IN PANAMA, Emerging Infectious Diseases. 2015. Т. 21. № 6. С. 1059-1061.

  2. Bajenova, O, O’Brien, SJ Genetic factors involved in human colorectal cancer metastasis. Anticancer research: 2014 34: 5824-5825.

  3. Bajenova , O. , I. Evsyukov, S. O’Brien. Effect of carcinoembryonic antigen production by colorectal cancer cells on tumor microenvironment and cancer progression European Journal of Cancer, Supplements v 13 (2015) p 3, http://dx.doi.org/10.1016/j.ejcsup.2015.08.005.

  4. Bajenova, O. , E Tolkunova, A Davydov-Sinitsyn, A Tomilin, S Malov, P Thomas, and SJ O’Brien. The role of carcinoembryonic antigen binding protein in colorectal cancer progression. 2015 Clinical and Experimental Metastasis, CLIN-D-15-00073

  5. Borges R, Khan I, Johnson WE, Gilbert MT, Zhang G, Jarvis ED, O’Brien SJ, Antunes A. Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds. BMC Genomics. (2015) vol 16:751. doi: 10.1186/s12864-015-1924-3. MS795

  6. Borisova, Anna S , Elena V Eneyskaya, Kirill S Bobrov, Suvamay Jana, Anton Logachev, Dmitrii E Polev, Alla L Lapidus, Farid M Ibatullin, Umair Saleem, Mats Sandgren, Christina M Payne, Anna A Kulminskaya, Jerry Ståhlberg (2015). Sequencing, biochemical characterization, crystal structure and molecular dynamics of cellobiohydrolase Cel7A from Geotrichum candidum 3C. FEBS Journal, 282, №23, pp. 4515-4537, doi:10.1111/febs.13509

  7. Chung O, Jin S, Cho YS, Lim J, Kim H, Jho S, Kim HM, Jun J, Lee H, Chon A, Ko J, Edwards J, Weber JA, Han K, O’Brien SJ, Manica A, Bhak J, Paek WK. The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures.Genome Biol. 2015 Oct 21;16:215. doi: 10.1186/s13059-015-0780-4.MS789.

  8. Davydov, Sinitsyn AP Bazhenov OV Liskova MA Ponomartsev SV Rykov IV, Koshkin SA Orlova RV, Tomilin AN ., EN Tolkunova 2015. Suppression of tumor growth, obtained by xenotransplantation of cells of human colon adenocarcinoma. Cytology. 2015: 57 (4): 278-285

  9. Dobrynin P, Liu S, Tamazian G, Xiong Z, Yurchenko AA, Krasheninnikova K, Kliver S, Schmidt-Küntzel A, KP, Johnson W, Kuderna LF, García-Pérez R, Manuel Md, Godinez R, Komissarov A, Makunin A, Brukhin V, Qiu W, Zhou L, Li F, Yi J, Driscoll C, Antunes A, Oleksyk TK, Eizirik E, Perelman P, Roelke M, Wildt D, Diekhans M, Marques-Bonet T, Marker L, Bhak J, Wang J, Zhang G, O’Brien SJ. Genomic legacy of the African cheetah, Acinonyx jubatus. Genome Biol. 2015 Dec 10;16:277. doi: 10.1186/s13059-015-0837-4.MS808

  10. Garner, B. A., Brian K. Hand1*, Brett Addis2, Steve Amish1,3, Louis Bernatchez3, Jeffrey T. Foster4, Robb Leary?b4, Kristina M. Miller6, Phillip A. Morin?6b, Shawn R. Narum7, Stephen J. O’Brien, Gretchen Roffler7b, James Seeb8, Lisa Seeb8, William D. Templin9, Paul Sunnucks10, Jeffrey Strait1, Kenneth I. Warheit11, Todd R. Seamons11, John Wenburg12, Jeffrey Olsen12, Gordon Luikart1,2 2016. Genomics in conservation: case studies for bridging the gap between data and application. TRENDS IN ECOLOGY & EVOLUTION 31 : 81-83

  11. Guiblet WM, Zhao K, O’Brien SJ, Massey SE, Roca AL, Oleksyk TK. SmileFinder: a resampling-based approach to evaluate signatures of selection from genome-wide sets of matching allele frequency data in two or more diploid populations.Gigascience. 2015 Jan 14;4:1. doi: 10.1186/2047-217X-4-1. eCollection 2015. MS778

  12. Iyengar SK, Sedor JR, Freedman BI, Kao WH, Kretzler M, Keller BJ, Abboud HE, Adler SG, Best LG, Bowden DW, Burlock A, Chen YD, Cole SA, Comeau ME, Curtis JM, Divers J, Drechsler C, Duggirala R, Elston RC, Guo X, Huang H, Hoffmann MM, Howard BV, Ipp E, Kimmel PL, Klag MJ, Knowler WC, Kohn OF, Leak TS, Leehey DJ, Li M, Malhotra A, März W, Nair V, Nelson RG, Nicholas SB, O’Brien SJ, Pahl MV, Parekh RS, Pezzolesi MG, Rasooly RS, Rotimi CN, Rotter JI, Schelling JR, Seldin MF, Shah VO, Smiles AM, Smith MW, Taylor KD, Thameem F, Thornley-Brown DP, Truitt BJ, Wanner C, Weil EJ, Winkler CA, Zager PG, Igo RP Jr, Hanson RL, Langefeld CD; Genome-Wide Association and Trans-ethnic Meta-Analysis for Advanced Diabetic Kidney Disease: Family Investigation of Nephropathy and Diabetes (FIND). Family Investigation of Nephropathy and Diabetes (FIND). PLoS Genet. 2015 Aug 25;11(8):e1005352. doi: 10.1371/journal.pgen.1005352. MS798

  13. Khan I, Yang Z, Maldonado E, Li C, Zhang G, Gilbert MT, Jarvis ED, O’Brien SJ, Johnson WE, Antunes A. Olfactory Receptor Subgenomes Linked with Broad Ecological Adaptations in Sauropsida.Mol Biol Evol. 2015 Nov;32(11):2832-43. doi: 10.1093/molbev/msv155. Epub 2015 Jul 28. MS792

  14. Klaus-Peter, John Pollinger, Jacqueline Robinson, Amanda Lea, Sarah Hendricks, Rena Schweizer, Olaf Thalmann, Pedro Silva, Zhenxin Fan, Andrey Yurchenko, Pavel Dobrynin, Alexei Makunin, James A. Cahill, Beth Shapiro, Eli Geffen, Frank Zachos, Raquel Godinho, Jennifer A. Leonard, Warren E. Johnson, Stephen J. O’Brien, Blaire Van Valkenburgh, and. Robert K. Wayne. Genome-wide Evidence Reveals that African and Eurasian Golden Jackals Are Distinct SpeciesCurrent Biol Volume: 25 Issue: 16 Pages: 2158-2165. MS801

  15. Klaus-Peter Todd Castoe2, Andrew Crawford3, Dent Earl4, Matt Fujita2, Tony Gamble5,6, Arthur Georges7, Richard E. Green8, David Haussler4, Glenn Hickey8, Erich Jarvis9, Warren Johnson10, Ian Korf11, Robert Murphy12, Benedict Paten4, Oliver Ryder13, Beth Shapiro14, Jose Lopez, Dan Distel, Huanming Yang, Harris Lewin, Cynthia Steiner13, Bryappa Venkatesh15, Edward Wiley16, Guojie Zhang17,18, and Stephen J. O’Brien1. The Genome 10K Project: A Way Forward . Ann Rev An. Biosci. 2015 . 3:57-211. MS754.

  16. Koczkodaj, W.W., Mikhailov, L., Redlarski, G., Soltys, M., Szybowski, J., Tamazian G., Wajch, E. and Yuen. K.K.F., 2015. Improtant facts and observations about pairwise comparisons. Fundamenta Informaticae, In Press.

  17. Koshkin; Sergey Anna Danilova; Grigory Raskin; Nikolai Petrov; Olga Bajenova, Stephen J O’Brien; Alexey Tomilin, Elena Tolkunova Primary cultures of human colon cancer as a model to study cancer stem cells. Experimental Cell Research: ECR-15-806

  18. Machado JP, Johnson WE, Gilbert MTP, Zhang G, Jarvis ED, O’Brien SJ, Antunes A. (2014) Bone-associated gene evolution and the origin of flight in birds» BMC Genomics In Press MS790.

  19. Malov, S.V. (2015) Copula process, Archimedean. Wiley StatsRef: Statistics Reference Online. pp. 1–7.

  20. Malov, S.V. & O’Brien, S.J. (2015) On survival categorical methods based on an extended actuarial estimator. In Applied Methods of Statistical Analysis. Nonparametric Approach. Proceedings of the International Workshop AMSA’15 (Novosibirsk-Belokuriha, September 14-19, 2015), 169–175. MS811

  21. Malov, S.V. & O’Brien, S.J. (2015) On an extended actuarial estimator. In Abstracts of 8-th International Workshop on Simulations, Vienna, September, 21-25 (eds. D.Rasch, V.Melas, J.Pils, K.Moder & B.Spangl).

  22. Igor Mokrousov, Anna Vyazovaya, Natalia Solovieva, Tatiana Sunchalina, Yuri Markelov, Ekaterina Chernyaeva, Natalia Melnikova, Marine Dogonadze, Daria Starkova, Nela Vasilieva, Alena Gerasimova, Yulia Kononenko, Viacheslav Zhuravlev, Olga Narvskaya. Trends in molecular epidemiology of drug-resistant tuberculosis in Republic of Karelia, Russian Federation. BMC Microbiol. 2015; 15: 279. Published online 2015 December 18. doi: 10.1186/s12866-015-0613-3 PMCID: PMC4683759

  23. OBrien, S.J.Can Genomics Empower Conservation? Woodland- Native Woodland Trust (2015) 20:24-26 MS799.

  24. Oleksyk , Taras K., Vladimir Brukhin, and Stephen J O’Brien The Genome Russia Project :Closing The Largest Remaining Omission on the World Genome Map. (2015) GigaScience 4:53DOI 10.1186/s13742-015-0095-0 MS813

  25. Oleksyk , Taras K., Vladimir Brukhin, and Stephen J O’Brien 2015. Putting Russia on the Genome Map Science 350:747. MS812

  26. Ostromyshenskii, DI. IS Kuznetsova, AS Komissarov, IV Kartavtseva, OI Podgornaya. Tandem repeats in the rodent genome and their mapping (2015) Cell and Tissue Biology 9 (3), 217-225.

  27. Schneider A, Henegar C, Day K, Absher D, Napolitano C, Silveira L, David VA, O’Brien SJ, Menotti-Raymond M, Barsh GS, Eizirik E. Recurrent evolution of melanism in South American felids. PLoS Genet. 2015 Feb 19;11(2):e1004892. doi: 10.1371/journal.pgen.1004892. eCollection 2015 Feb. Erratum in: PLoS Genet. 2015 Apr;11(4):e1005126.MS793

  28. Spencer PB, Yurchenko AA, David VA, Scott R, KP, Driscoll C, O’Brien SJ, Menotti-Raymond M. The Population Origins and Expansion of Feral Cats in Australia. J Hered. 2015, 1–11 doi:10.1093/jhered/esv095 MS772

  29. Starostina E, Tamazian G, Dobrynin PV, O’Brien SJ, Komissarov A. «Cookiecutter: a tool for kmer-based read filtering and extraction.» bioRxiv (2015): 02679. doi: http://dx.doi.org/10.1101/024679 MS817.

  30. Velichko N, Chernyaeva E, Averia S, Gavrilova O, Lapidus A, Pinevich A. Consortium of the ‘bichlorophyllous’ cyanobacterium Prochlorothrix hollandica and chemoheterotrophic partner bacteria: culture and metagenome based description. Environ Microbiol Rep. 2015 May 20. doi: 10.1111/1758-2229.12298. [Epub ahead of print] PubMed PMID: 25990300.

  31. Volobuev, Sergey Anton Logachev, Nikolay Mushnikov, Mikhail Okun (2015). New records of aphyllophoroid fungi (Agaricomycetes, Basidiomycota) from the Les na Vorskle area of the Belogor’e Nature Reserve (Belgorod Region, Russia). Folia Cryptogamica Estonica, 52, pp. 89-93, doi:10.12697/fce.2015.52.11

  32. Xue, Hao-Ran; Yamaguchi, Nobuyuki; Driscoll, Carlos A.; et al. Genetic Ancestry of the Extinct Javan and Bali Tigers JOURNAL OF HEREDITY 106: 247-257 2015. (MS785).

  33. Zimenkov DV, Kulagina EV, Antonova OV, Krasnova MA, Chernyaeva EN, Zhuravlev VY, Kuz’min AV, Popov SA, Zasedatelev AS, Gryadunov DA. Evaluation of a low-density hydrogel microarray technique for mycobacterial species identification. J Clin Microbiol. 2015 Apr;53(4):1103-14. doi: 10.1128/JCM.02579-14. Epub 2015 Jan 21. PubMed PMID: 25609722; PubMed Central PMCID: PMC4365248.