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Публикации 2016

  1. Almeida D, Maldonado E, Khan I, Silva L, Gilbert MT, Zhang G, Jarvis ED, O’Brien SJ, Johnson WE, Antunes A. Whole genome identification, phylogeny and evolution of the cytochrome P450 family 2 (CYP2) sub-families in birds. Genome Biol Evol. 2016. 8(4):1115-1131 MS810.

  2. O’Bian C, Hu Y, Ravi V, Kuznetsova IS, Shen X, Mu X, Sun Y, You X, Li J, Li X, Qiu Y, Tay BH, Thevasagayam NM, Komissarov AS, Trifonov V, Kabilov M, Tupikin A, Luo J, Liu Y, Song H, Liu C, Wang X, Gu D, Yang Y, Li W, Polgar G, Fan G, Zeng P, Zhang H, Xiong Z, Tang Z, Peng C, Ruan Z, Yu H, Chen J, Fan M, Huang Y, Wang M, Zhao X, Hu G, Yang H, Wang J, Wang J, Xu X, Song L, Xu G, Xu P, Xu J, O’Brien SJ, Orbán L, Venkatesh B, Shi Q. The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts.Sci Rep. 2016 Apr 19;6:24501. doi: 10.1038/srep24501.PMID: 27089831 MS820

  3. Kuehn, Markus H. , Koren A. Lipsett, Marilyn Menotti-Raymond, S. Scott Whitmore1,Victor A. David, Stephen J. O’Brien, Jackie K. Jens, Elizabeth M. Snella, N. Matthew Ellinwood, and Gillian J. McLellan (2016). A Mutation in LTBP2 Causes Congenital Glaucoma in Domestic Cats (Felis catus). PLoS ONE, 11(5), e0154412. http://doi.org/10.1371/journal.pone.0154412 MS818

  4. Alexey Makunin, Ilya G Kichigin, Denis M Larkin, Patricia CM O’Brien, Malcolm A Ferguson-Smith, Fengtang Yang, Anastasiya A Proskuryakova, Nadezhda V Vorobieva, Ekaterina N Chernyaeva, Stephen J O’Brien, Alexander S Graphodatsky, Vladimir A Trifonov «Contrasting origin of B chromosomes in two cervids (Siberian roe deer and grey brocket deer) unravelled by chromosome-specific DNA sequencing» BMC Genomics In Press MS809

  5. Moore AE, Cotterill FP, Winterbach CW, Winterbach HE, Antunes A, O’Brien SJ. Genetic Evidence for Contrasting Wetland and Savannah Habitat Specializations in Different Populations of Lions (Panthera leo).. J Hered. 2016;107:101-3.MS726.

  6. S.J O’Brien, W.E. Johnson, C.A. Driscoll, P. Dobrynin , and L.L. Marker. A Role for Genetic Technologies in Species Conservation- From the Cheetah to Beyond-2013. Proceedings of the Beijing Forum-2013 The Harmony of Civilizations and Prosperity for All — Retrospect and Prospect , Ed.: Academic Committee of Beijing Forum, Peking University..Peking University Press. (2015). InPress MS770

  7. Stephen J. O’Brien, Plagues-Intersecting genomics and Contagions , 2014 Darwin College Lecture Series Cambridge Univer In Press 2015. MS769

  8. Kimberly A. Terrell, Adrienne E. Crosier, David E. Wildt, Nicola M. Anthony, Steven J. O’Brien, and Warren Johnson, Laurie Marker Continued decline in genetic diversity among wild cheetahs (Acinonyx jubatus) without further loss of semen quality Biological Conservation In Press MS804 .

  9. Vij , Shubha, Heiner Kuhl, Inna S Kuznetsova, Aleksey Komissarov, Andrey A. Yurchenko, Peter Van Heusden, Siddharth Singh, Natascha M. Thevasagayam, Prakki Sai Rama Sridatta, Kathiresan Purushothaman, Jolly M Saju, Junhui Jiang, Stanley Kimbung Mbandi, Mario Jonas, Amy Tong, Sarah Mwangi, Doreen Lau, Si Yan Ngoh, Woei Chang Liew, Xueyan Shen, Lawrence Hon, James P Drake, Matthew Boitano, Richard Hall, Jason Chin, Ramkumar Lachumanan, Jonas Korlach, Vladimir Trifonov, Marsel Kabilov, Alexey Tupikin, Darrell Green, Simon Moxon, Tyler Garvin, Fritz J. Sedlazeck, Gregory W. Vurture, Gopikrishna G, Vinaya Kumar K, Tansyn H. Noble, Vinod Scaria, Sridhar Sivasubbu, Dean R. Jerry, Michael C. Schatz, Tamás Dalmay, Steve Turner, Stephen J. O’Brien, Si Lok, Alan Christoffels, László Orbán Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding.PLoS Genet. 2016 Apr 15;12(4):e1005954. doi: 10.1371/journal.pgen.1005954. eCollection 2016. MS819.

  10. PGD: a pangolin genome hub for the research community
    Tze King Tan, Ka Yun Tan, Ranjeev Hari, Aini Mohamed Yusoff, Guat Jah Wong, Cheuk Chuen Siow, Naresh V.R. Mutha, Mike Rayko, Aleksey Komissarov, Pavel Dobrynin, Ksenia Krasheninnikova, Gaik Tamazian, Ian C. Paterson, Wesley C. Warren, Warren E. Johnson, Stephen J. O’Brien, Siew Woh Choo
    Database (Oxford) 2016; 2016: baw063. Published online 2016 Sep 11. doi: 10.1093/database/baw063
    PMCID: PMC5018392
  11. The Genome-Wide Analysis of Carcinoembryonic Antigen Signaling by Colorectal Cancer Cells Using RNA Sequencing
    Olga Bajenova, Anna Gorbunova, Igor Evsyukov, Michael Rayko, Svetlana Gapon, Ekaterina Bozhokina, Alexander Shishkin, Stephen J. O’Brien
    PLoS One. 2016; 11(9): e0161256. Published online 2016 Sep 1. doi: 10.1371/journal.pone.0161256
    PMCID: PMC5008809
  12. Pangolin genomes and the evolution of mammalian scales and immunity
    Siew Woh Choo, Mike Rayko, Tze King Tan, Ranjeev Hari, Aleksey Komissarov, Wei Yee Wee, Andrey A. Yurchenko, Sergey Kliver, Gaik Tamazian, Agostinho Antunes, Richard K. Wilson, Wesley C. Warren, Klaus-Peter Koepfli, Patrick Minx, Ksenia Krasheninnikova, Antoinette Kotze, Desire L. Dalton, Elaine Vermaak, Ian C. Paterson, Pavel Dobrynin, Frankie Thomas Sitam, Jeffrine J. Rovie-Ryan, Warren E. Johnson, Aini Mohamed Yusoff, Shu-Jin Luo, Kayal Vizi Karuppannan, Gang Fang, Deyou Zheng, Mark B. Gerstein, Leonard Lipovich, Stephen J. O’Brien, Guat Jah Wong
    Genome Res. 2016 Oct; 26(10): 1312–1322. doi: 10.1101/gr.203521.115
    PMCID: PMC5052048
  13. De novo sequencing, assembly and analysis of eight different transcriptomes from the Malayan pangolin
    Aini Mohamed Yusoff, Tze King Tan, Ranjeev Hari, Klaus-Peter Koepfli, Wei Yee Wee, Agostinho Antunes, Frankie Thomas Sitam, Jeffrine Japning Rovie-Ryan, Kayal Vizi Karuppannan, Guat Jah Wong, Leonard Lipovich, Wesley C. Warren, Stephen J. O’Brien, Siew Woh Choo
    Sci Rep. 2016; 6: 28199. Published online 2016 Sep 13. doi: 10.1038/srep28199
    PMCID: PMC5020319
  14. The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts
    Chao Bian, Yinchang Hu, Vydianathan Ravi, Inna S. Kuznetsova, Xueyan Shen, Xidong Mu, Ying Sun, Xinxin You, Jia Li, Xiaofeng Li, Ying Qiu, Boon-Hui Tay, Natascha May Thevasagayam, Aleksey S. Komissarov, Vladimir Trifonov, Marsel Kabilov, Alexey Tupikin, Jianren Luo, Yi Liu, Hongmei Song, Chao Liu, Xuejie Wang, Dangen Gu, Yexin Yang, Wujiao Li, Gianluca Polgar, Guangyi Fan, Peng Zeng, He Zhang, Zijun Xiong, Zhujing Tang, Chao Peng, Zhiqiang Ruan, Hui Yu, Jieming Chen, Mingjun Fan, Yu Huang, Min Wang, Xiaomeng Zhao, Guojun Hu, Huanming Yang, Jian Wang, Jun Wang, Xun Xu, Linsheng Song, Gangchun Xu, Pao Xu, Junmin Xu, Stephen J. O’Brien, László Orbán, Byrappa Venkatesh, Qiong Shi
    Sci Rep. 2016; 6: 24501. Published online 2016 Apr 19. doi: 10.1038/srep24501
    PMCID: PMC4835728
  15. Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly
    Soonok Kim, Yun Sung Cho, Hak-Min Kim, Oksung Chung, Hyunho Kim, Sungwoong Jho, Hong Seomun, Jeongho Kim, Woo Young Bang, Changmu Kim, Junghwa An, Chang Hwan Bae, Youngjune Bhak, Sungwon Jeon, Hyejun Yoon, Yumi Kim, JeHoon Jun, HyeJin Lee, Suan Cho, Olga Uphyrkina, Aleksey Kostyria, John Goodrich, Dale Miquelle, Melody Roelke, John Lewis, Andrey Yurchenko, Anton Bankevich, Juok Cho, Semin Lee, Jeremy S. Edwards, Jessica A. Weber, Jo Cook, Sangsoo Kim, Hang Lee, Andrea Manica, Ilbeum Lee, Stephen J. O’Brien, Jong Bhak, Joo-Hong Yeo
    Genome Biol. 2016; 17: 211. Published online 2016 Oct 11. doi: 10.1186/s13059-016-1071-4
    PMCID: PMC5090899
  16. Koalas (Phascolarctos cinereus) From Queensland Are Genetically Distinct From 2 Populations in Victoria
    Christina T. Ruiz-Rodriguez, Yasuko Ishida, Neil D. Murray, Stephen J. O’Brien, Jennifer A. M. Graves, Alex D. Greenwood, Alfred L. Roca
    J Hered. 2016; 107(7): 573–580. Published online 2016 Aug 11. doi: 10.1093/jhered/esw049
    PMCID: PMC5063317
  17. Contrasting origin of B chromosomes in two cervids (Siberian roe deer and grey brocket deer) unravelled by chromosome-specific DNA sequencing
    Alexey I. Makunin, Ilya G. Kichigin, Denis M. Larkin, Patricia C. M. O’Brien, Malcolm A. Ferguson-Smith, Fengtang Yang, Anastasiya A. Proskuryakova, Nadezhda V. Vorobieva, Ekaterina N. Chernyaeva, Stephen J. O’Brien, Alexander S. Graphodatsky, Vladimir A. Trifonov
    BMC Genomics. 2016; 17: 618. Published online 2016 Aug 11. doi: 10.1186/s12864-016-2933-6
    PMCID: PMC4982142
  18. Genome Sequencing and Comparative Analysis of Saccharomyces cerevisiae Strains of the Peterhof Genetic Collection
    Polina B. Drozdova, Oleg V. Tarasov, Andrew G. Matveenko, Elina A. Radchenko, Julia V. Sopova, Dmitrii E. Polev, Sergey G. Inge-Vechtomov, Pavel V. Dobrynin
    PLoS One. 2016; 11(5): e0154722. Published online 2016 May 6. doi: 10.1371/journal.pone.0154722
    PMCID: PMC4859572
  19. Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding
    Shubha Vij, Heiner Kuhl, Inna S. Kuznetsova, Aleksey Komissarov, Andrey A. Yurchenko, Peter Van Heusden, Siddharth Singh, Natascha M. Thevasagayam, Sai Rama Sridatta Prakki, Kathiresan Purushothaman, Jolly M. Saju, Junhui Jiang, Stanley Kimbung Mbandi, Mario Jonas, Amy Hin Yan Tong, Sarah Mwangi, Doreen Lau, Si Yan Ngoh, Woei Chang Liew, Xueyan Shen, Lawrence S. Hon, James P. Drake, Matthew Boitano, Richard Hall, Chen-Shan Chin, Ramkumar Lachumanan, Jonas Korlach, Vladimir Trifonov, Marsel Kabilov, Alexey Tupikin, Darrell Green, Simon Moxon, Tyler Garvin, Fritz J. Sedlazeck, Gregory W. Vurture, Gopikrishna Gopalapillai, Vinaya Kumar Katneni, Tansyn H. Noble, Vinod Scaria, Sridhar Sivasubbu, Dean R. Jerry, Stephen J. O’Brien, Michael C. Schatz, Tamás Dalmay, Stephen W. Turner, Si Lok, Alan Christoffels, László Orbán
    PLoS Genet. 2016 Apr; 12(4): e1005954. Published online 2016 Apr 15. doi: 10.1371/journal.pgen.1005954Correction in: PLoS Genet. 2016 Dec; 12(12): e1006500.
    PMCID: PMC4833346
  20. Draft genome of Prochlorothrix hollandica CCAP 1490/1T (CALU1027), the chlorophyll a/b-containing filamentous cyanobacterium
    Natalia Velichko, Mikhail Rayko, Ekaterina Chernyaeva, Alla Lapidus, Alexander Pinevich
    Stand Genomic Sci. 2016; 11: 82. Published online 2016 Oct 18. doi: 10.1186/s40793-016-0204-4
    PMCID: PMC5069947
  21. Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences
    Gaik Tamazian, Pavel Dobrynin, Ksenia Krasheninnikova, Aleksey Komissarov, Klaus-Peter Koepfli, Stephen J. O’Brien
    Gigascience. 2016; 5(1): 38. Published online 2016 Aug 22. doi: 10.1186/s13742-016-0141-6
    PMCID: PMC4994284
  22. Bone-associated gene evolution and the origin of flight in birds
    João Paulo Machado, Warren E. Johnson, M. Thomas P. Gilbert, Guojie Zhang, Erich D. Jarvis, Stephen J. O’Brien, Agostinho Antunes
    BMC Genomics. 2016; 17: 371. Published online 2016 May 18. doi: 10.1186/s12864-016-2681-7
    PMCID: PMC4870793

  23. Response to Comment by Faurby, Werdelin and Svenning
    Stephen J. O’Brien, Klaus Peter Koepfli, Eduardo Eizirik, Warren Johnson, Carlos Driscoll, Agostinho Antunes, Anne Schmidt-Kuntzel, Laurie Marker, Pavel Dobrynin
    Genome Biol. 2016; 17: 90. Published online 2016 May 5. doi: 10.1186/s13059-016-0942-z
    PMCID: PMC4858819
  24. A Mutation in LTBP2 Causes Congenital Glaucoma in Domestic Cats (Felis catus)
    Markus H. Kuehn, Koren A. Lipsett, Marilyn Menotti-Raymond, S. Scott Whitmore, Todd E. Scheetz, Victor A. David, Stephen J. O’Brien, Zhongyuan Zhao, Jackie K. Jens, Elizabeth M. Snella, N. Matthew Ellinwood, Gillian J. McLellan
    PLoS One. 2016; 11(5): e0154412. Published online 2016 May 5. doi: 10.1371/journal.pone.0154412Correction in: PLoS One. 2016; 11(8): e0161517.
    PMCID: PMC4858209
  25. A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination
    Gang Li, LaDeana W. Hillier, Robert A. Grahn, Aleksey V. Zimin, Victor A. David, Marilyn Menotti-Raymond, Rondo Middleton, Steven Hannah, Sher Hendrickson, Alex Makunin, Stephen J. O’Brien, Pat Minx, Richard K. Wilson, Leslie A. Lyons, Wesley C. Warren, William J. Murphy
    G3 (Bethesda) 2016 Jun; 6(6): 1607–1616. Published online 2016 Mar 29. doi: 10.1534/g3.116.028746
    PMCID: PMC4889657
  26. Whole-Genome Identification, Phylogeny, and Evolution of the Cytochrome P450 Family 2 (CYP2) Subfamilies in Birds
    Daniela Almeida, Emanuel Maldonado, Imran Khan, Liliana Silva, M. Thomas P. Gilbert, Guojie Zhang, Erich D. Jarvis, Stephen J. O’Brien, Warren E. Johnson, Agostinho Antunes
    Genome Biol Evol. 2016 Apr; 8(4): 1115–1131. Published online 2016 Mar 14. doi: 10.1093/gbe/evw041
    PMCID: PMC4860681
  27. The Population Origins and Expansion of Feral Cats in Australia
    Peter B.S. Spencer, Andrey A. Yurchenko, Victor A. David, Rachael Scott, Klaus-Peter Koepfli, Carlos Driscoll, Stephen J. O’Brien, Marilyn Menotti-Raymond
    J Hered. 2016 Mar; 107(2): 104–114. Published online 2015 Dec 7. doi: 10.1093/jhered/esv095
    PMCID: PMC4757960

  28. Genetic Ancestry of the Extinct Javan and Bali Tigers
    Hao-Ran Xue, Nobuyuki Yamaguchi, Carlos A. Driscoll, Yu Han, Gila Kahila Bar-Gal, Yan Zhuang, Ji H. Mazak, David W. Macdonald, Stephen J. O’Brien, Shu-Jin Luo
    J Hered. 2015 May-Jun; 106(3): 247–257. Published online 2015 Mar 8. doi: 10.1093/jhered/esv002
    PMCID: PMC4406268
  29. X Chromosome Evolution in Cetartiodactyla
    Anastasia A. Proskuryakova, Anastasia I. Kulemzina, Polina L. Perelman, Alexey I. Makunin, Denis M. Larkin, Marta Farré, Anna V. Kukekova, Jennifer Lynn Johnson, Natalya A. Lemskaya, Violetta R. Beklemisheva, Melody E. Roelke-Parker, June Bellizzi, Oliver A. Ryder, Stephen J. O’Brien, Alexander S. Graphodatsky
    Genes (Basel) 2017 Sep; 8(9): 216. Published online 2017 Aug 31. doi: 10.3390/genes8090216
    PMCID: PMC5615350

  30. Perspectives provided by leopard and other cat genomes: how diet determined the evolutionary history of carnivores, omnivores, and herbivores
    Soonok Kim, Yun Sung Cho, Jong Bhak, Stephen J. O’Brian, Joo-Hong Yeo
    BMB Rep. 2017; 50(1): 3–4. Published online 2017 Jan 31. doi: 10.5483/BMBRep.2017.50.1.002
    PMCID: PMC5319657
  31. Submitted in 2016

    • Antonik, A., Berred, A., Malov, S. V. Coverage Problem revisited, The Annals of Applied Probability Submitted.
    • Olga Bajenova, Elena Tolkunova, Alexander Davydov-Sinitsyn, Peter Thomas, Stephen O’Brien. The role of carcinoembryonic antigen binding protein (CEAR) in colorectal cancer cells tumorigenesis. Submitted. Clinical and Experimental metastasis MS745.
    • Olga Bajenova, Anna Gorbunova, Igor Evsyukov, Michael Rayko, Katya Bozhokina and Stephen O’Brien. Analysis of carcinoembryonic antigen signaling by colorectal cancer cells using RNA-sequencing Submitted
    • Rui BORGES, Warren E. JOHNSON, Stephen J. O’BRIEN, Christopher P. HEESY, and Agostinho ANTUNES Patterns of Opsin Gene Evolution Reflect Adaptation of Early Mammals to Nocturnal Environments Submitted GBE (MS774).
    • Borisova, Anna; Eneyskaya, Elena; Bobrov, Kirill; Jana, Suvamay; Logachev, Anton; Polev, Dmitrii; Lapidus, Alla; Ibatullin, Farid; Saleem, Umair; Sandgren, Mats; Payne, Christina; Kulminskaya, Anna; Ståhlberg, Jerry. Sequencing, biochemical characterization, crystal structure and molecular dynamics of Cellobiohydrolase Cel7A from Geotrichum candidum 3C. Submitted
    • Choo Siew Woh, Tze King Tan, Ranjeev Hari, Agostinho Antunes, Klaus-Peter , Jessica Alfoldi, Lindblad-Toh Kerstin, Ian C. Paterson, Wong Guat Jah, Gang Fang, Frankie Thomas Sitam, Kayal Vizi Karuppannan, Jeffrine Rovie Ryan Japning, Deyou Zheng, Mark B. Gerstein, Leonard Lipovich, Spephen J O’Brien Comparative genome analysis provides insights into the evolutionary adaptations of pangolins . Submitted MS807
    • Machado, João Paulo, Siby Philip, Emanuel Maldonado, Stephen J O’Brien, Warren E Johnson and Agostinho Antunes Positive selection and recent gene duplication linked with generation of novel mammalian dentition patterns. Submitted MS806
    • Lopez et al Leveraging the Power of Community Cooperation to Advance Invertebrate Genomics — Updates from the GIGA consortium Submitted
    • Malov S.V. & O’Brien S.J. (2016). Signal localization: a new approach in signal discovery. Submitted to Biometrical Journal (second round).
    • Malov S.V. & O’Brien S.J. (2016). Life Table Estimator Revisited. Submitted to Statistics & Probability Letters (first round).
    • O’Leary, C.A. , L, Balme, M. Menotti-Raymond, V.A. David, S.J. O’Brien , B. Penglis, S. Hendrikson, M. Reeves-Johnson, S. Gottlieb, L. Fleeman, D. Vankan, G. Morahan, J. Rand. Genetic Risk Factors Contributing to High Diabetes Mellitus Incidence in Australian-bred Burmese Cats Map to Feline Chromosomes C2, A3 and C1 Submitted MS805
    • Philip S, Johnson WE, Gilbert MTP, Zhang G, Jarvis ED, O’Brien SJ, Antunes A. (2014) Did adaptive evolution of avian Superoxide Dismutases (SOD) improve flight efficiency and lengthen life-expectancy in birds (Submitted to Genome Biology and Evolution).(MS791)
    • Tamazian, Gaik , Pavel Dobrynin, Aleksey Komissarov, Klaus-Peter and Stephen J. O’Brien. Chromosomer: a reference-assisted assembly tool for producing draft chromosome sequences. Submitted. MS787
    • Wen Xie, Denis Agniel, Andrey Shevchenko, Sergey V. Malov, Anton Svitin Nikolay Cherkasov , Vladimir Novitsky, Marianna Baum, Adriana Campa, Hermann Bussmann, Joe Makhema, Richard Marlink, Tun-Hou Lee, Tianxi Cai, Stephen J. O’Brien, Myron Essex. Genome-wide Analyses Reveals Gene Influence on AIDS progression and HIV-1C acquisition in Southern Africa Submitted MS794.
    • Kozlov A.P., Skochilov R.V., Toussova O.V., Verevochkin S.V., Krasnoselskikh T.V., Malov S.V., Shaboltas A.V. (2016) HIV incidence and behavioral correlates of HIV acquisition in a cohort of injection drug users in St Petersburg, Russia. Medicine 95(44), e5238, DOI:10.1097/MD.0000000000005238