МЕГАГРАНТЫ

Центр геномной биоинформатики им. Ф.Г.Добржанского

О лаборатории

Наименование проекта Биоинформатическая лаборатория в СПбГУ: центр анализа данных геномики, биомедицины и сравнительной биологии.

Ссылка на официальный сайт

№ договора:
11.G34.31.0068

Наименование ВУЗа:
ФГБОУ ВПО "Санкт-Петербургский государственный университет"

Области научных исследований:
Медицинские науки и технологии

Цель проекта:
Создание центра, в котором специалисты в области генетики и биоинформатики, студенты и научные сотрудники будут разрабатывать, испытывать и внедрять инновационные компьютерные методы для сборки геномов позвоночных животных, аннотации и обнаружения генов, выявления их функций, с последующим внедрением полученных результатов в здравоохранение и охрану природы.

 

Ведущий учёный

vu mini 68 

ФИО: О'Брайен Стефан Джеймс

 

Ученые степень и звание:
Доктор наук в области генетики

Занимаемая должность:
Директор лабратории геномного разнообразия Национального ракового института Национального института здоровья

Области научных интересов:
Биология, медицинские науки и технологии

Научное признание

Стефан Джеймс О’Брайен много лет руководил лабораторией геномного разнообразия Национального ракового института Национального института здоровья (США) и получил известность как специалист в сравнительной геномике, области науки, которая изучает отличия геномов разных организмов. В 2013 году профессор О’Брайен участвовал в известном проекте по расшифровке генома амурского тигра. Доктор О Брайен был редактором шести изданий, посвященных генетическому картированию (Locus Maps of Complex Genomes, Cold Spring Harbor Laboratory Publications (1980-1993); редактором журнала «Наследственность» Американской генной ассоциации (1987-2007); редактором «Атласа хромосом млекопитающих», John Wiley Inc. NYC (2006) и автором книги «Слезы гепарда и другие рассказы о генетике», St. Martin’s Press NYC (2004). Он является адъюнкт-профессором в 12 университетах.

1. Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene
Author(s): Dean M, Carrington M, Winkler C, et al.
Source: SCIENCE Volume: 273 Issue: 5283 Pages: 1856-1862 Published: SEP 27 1996
Times Cited: 1,535

2. Molecular phylogenetics and the origins of placental mammals
Author(s): Murphy WJ, Eizirik E, Johnson WE, et al.
Source: NATURE Volume: 409 Issue: 6820 Pages: 614-618 Published: FEB 1 2001
Times Cited: 655

3. Contrasting genetic influence of CCR2 and CCR5 variants on HIV-1 infection and disease progression
Author(s): Smith MW, Dean M, Carrington M, et al.
Source: SCIENCE Volume: 277 Issue: 5328 Pages: 959-965 Published: AUG 15 1997
Times Cited: 624

4. GENETIC-BASIS FOR SPECIES VULNERABILITY IN THE CHEETAH
Author(s): OBRIEN SJ, ROELKE ME, MARKER L, et al.
Source: SCIENCE Volume: 227 Issue: 4693 Pages: 1428-1434 Published: 1985
Times Cited: 479

5. Human genes that limit AIDS
Author(s): O'Brien SJ, Nelson GW
Source: NATURE GENETICS Volume: 36 Issue: 6 Pages: 565-574 Published: JUN 2004
Times Cited: 131

6. The promise of comparative genomics in mammals
Author(s): O'Brien SJ, Menotti-Raymond M, Murphy WJ, et al.
Source: SCIENCE Volume: 286 Issue: 5439 Pages: 458-+ Published: OCT 15 1999
Times Cited: 310

7. The Late Miocene radiation of modern Felidae: A genetic assessment
Author(s): Johnson WE, Eizirik E, Pecon-Slattery J, et al.
Source: SCIENCE Volume: 311 Issue: 5757 Pages: 73-77 Published: JAN 6 2006
Times Cited: 134

8. HLA and HIV-1: Heterozygote advantage and B*35-Cw*04 disadvantage
Author(s): Carrington M, Nelson GW, Martin MP, et al.
Source: SCIENCE Volume: 283 Issue: 5408 Pages: 1748-1752
Published: MAR 12 1999
Times Cited: 591

9. Stewardship of Human Biospecimens, DNA, Genotype, and Clinical Data in the GWAS Era
Author(s): O'Brien SJ
Source: ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS Volume: 10 Pages: 193-209 Published: 2009
Times Cited:

10. Initial sequence and comparative analysis of the cat genome
Author(s): Pontius JU, Mullikin JC, Smith DR, et al.
Source: GENOME RESEARCH Volume: 17 Issue: 11 Pages: 1675-1689 Published: NOV 2007
Times Cited: 72

11. Title: Genetic Restoration of the Florida Panther
Author(s): Johnson WE, Onorato DP, Roelke ME, et al.
Source: SCIENCE Volume: 329 Issue: 5999 Pages: 1641-1645 Published: SEP 24 2010
Times Cited: 4

Результаты исследований

Публикации

An P, Winkler C, Guan L, O’Brien SJ, Zeng Z; HBV Study Consortium. A common HLA-DPA1 variant is a major determinant of hepatitis B virus clearance in Han Chinese. J Infect Dis. Apr 1;203(7):943-947. 2011.
An P, Li R, Wang JM, Yoshimura T, Takahashi M, Samudralal R, O’Brien SJ, Phair J, Goedert JJ, Kirk GD, Troyer JL, Sezgin E, Buchbinder SP, Donfield S, Nelson GW, Winkler CA. Role of exonic variation in chemokine receptor genes on AIDS: CCRL2 F167Y association with pneumocystis pneumonia. PLoS Genet. 2011 Oct;7(10):e1002328. Epub 2011 Oct 27.
Alkan, Can, M. Francesca Cardone, Francesca Antonacci1, Stephen J. O’Brien, Oliver A. Ryder, Stefania Purgato, Giuliano Della Valle, Evan E. Eichler, and Mario Ventura . Genome-wide Characterization of Centromeric Satellites from Multiple Mammalian Species .Genome Res. 2011 Jan;21(1):137-45.
Driscoll CA, Luo S, MacDonald D, Dinerstein E, Chestin I, Pereladova O, O’Brien SJ. Restoring tigers to the Caspian region. Science. 333(6044):822-3. 2011.
Driscoll C, Yamaguchi N, O’Brien SJ, Macdonald DW. A Suite of Genetic Markers Useful in Assessing Wildcat (Felis silvestris ssp.)— Domestic Cat (Felis silvestris catus) Admixture. J Hered. 102 Suppl 1:S87-90. 2011.
Guo X, Zhang Y, Li J, Ma J, Wei Z, Tan W, O’Brien SJ. Strong influence of human leukocyte antigen (HLA)-DP gene variants on development of persistent chronic hepatitis B virus carriers in the Han Chinese population. Hepatology.;53(2):422-8. 2011.
Machado , João P ,Warren E Johnson, Stephen J O’Brien, Vítor Vasconcelos and Agostinho Antunes. Adaptive evolution of the matrix extracellular phosphoglycoprotein in mammals . BMC EVOLUTIONARY BIOLOGY Volume: 11 Article Number: 342 DOI: 10.1186/1471-2148-11-342 2011
Perelman P, Johnson WE, Roos C, Seuánez HN, Horvath JE, Moreira MA, Kessing B, Pontius J, Roelke M, Rumpler Y, Schneider MP, Silva A, O’Brien SJ, Pecon-Slattery J. A molecular phylogeny of living primates. PLoS Genet. Mar;7(3):e1001342. 2011.
Sezgin E, van Natta ML, Ahuja A, Lyon A, Srivastava S, Troyer JL, O’Brien SJ, Jabs DA; Studies of the Ocular Complications of AIDS Research Group.. Association of host genetic risk factors with the course of cytomegalovirus retinitis in patients infected with human immunodeficiency virus. Am J Ophthalmol. 151(6):999-1006.e4. 2011.
Shrestha B, Reed JM, Starks PT, Kaufman GE, Goldstone JV, Roelke ME, O’Brien SJ, Koepfli KP, Frank LG, Court MH. Evolution of a major drug metabolizing enzyme defect in the domestic cat and other Felidae: phylogenetic timing and the role of hypercarnivory. PLoS One.6(3):e18046. 2011.
Troyer JL, Nelson GW, Lautenberger JA, Chinn L, McIntosh C, Johnson RC, Sezgin E, Kessing B, Malasky M, Hendrickson SL, Li G, Pontius J, Tang M, An P, Winkler CA, Limou S, Le Clerc S, Delaneau O, Zagury JF, Schuitemaker H, van Manen D, Bream JH, Gomperts ED, Buchbinder S, Goedert JJ, Kirk GD, O’Brien SJ. Genome-wide association study implicates PARD3B-based AIDS restriction.J Infect Dis.203(10):1491-502. 2011
Troyer JL, Roelke ME, Jespersen JM, Baggett N, Buckley-Beason V, Macnulty D, Craft M, Packer C, Pecon-Slattery J, O’Brien SJ. FIV diversity: FIV(Ple) subtype composition may influence disease outcome in African lions. Vet Immunol Immunopathol. 143(3-4):338-46. 2011.

Abt B., Han C., Scheuner C., Lu M., Lapidus A., Nolan M., Lucas S., Hammon N., Deshpande S., Cheng J.F., Tapia R., Goodwin L.A., Pitluck S., Liolios K., Pagani I., Ivanova N., Mavromatis K., Mikhailova N., Huntemann M., Pati A., Chen A., Palaniappan K., Land M., Hauser L., Brambilla E.M., Rohde M., Spring S., Gronow S., Göker M., Woyke T., Bristow J., Eisen J.A., Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.P., Detter J.C. Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1(T)), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta. Standards in Genomic Sciences. 2012; 6(2):194-209.
Anderson I., Held B., Lapidus A., Nolan M., Lucas S., Tice H., Del Rio T.G., Cheng J.F., Han C., Tapia R., Goodwin L.A., Pitluck S., Liolios K., Mavromatis K., Pagani I., Ivanova N., Mikhailova N., Pati A., Chen A., Palaniappan K., Land M., Brambilla E.M., Rohde M., Spring S., Göker M., Detter J.C., Woyke T., Bristow J., Eisen J.A., Markowitz V., Hugenholtz P., Klenk H.P., Kyrpides N.C. Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4(T)). Standards in Genomic Sciences. 2012; 6(2):174-84.
Anderson I., Saunders E., Lapidus A., Nolan M., Lucas S., Tice H., Del Rio T.G., Cheng J.F., Han C., Tapia R., Goodwin L.A., Pitluck S., Liolios K., Mavromatis K., Pagani I., Ivanova N., Mikhailova N., Pati A., Chen A., Palaniappan K., Land M., Hauser L., Jeffries C.D., Chang Y.J., Brambilla E.M., Rohde M., Spring S., Göker M., Detter J.C., Woyke T., Bristow J., Eisen J.A., Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.P Complete genome sequence of the thermophilic sulfate-reducing ocean bacteriumThermodesulfatator indicus type strain (CIR29812(T)).. Standards in Genomic Sciences.2012; 6(2):155-64.
Anderson I., Tindall B.J., Rohde M., Lucas S., Han J., Lapidus A., Cheng J.F., Goodwin L., Pitluck S., Peters L., Pati A., Mikhailova N., Pagani I., Teshima H., Han C., Tapia R., Land M., Woyke T., Klenk H.P., Kyrpides N., Ivanova N. Complete genome sequence of Halopiger xanaduensis type strain (SH-6(T)). Standards in Genomic Sciences. 2012; 6(1):31-42.
Andronov E., Dolnik A., Tamazyan, Pershina E., Vyatkina K., Porozov Y., Pinaev A. The evolutionary space of the bacterial 16S rRNA gene. Ver. 1.0. The 14th International Symposium on Microbial Ecology (ISME 14).2012.
Bagdonavicius V., MalovV., Nikulin M. Homogeneity Tests for Related Samples Under Censoring, Communications in Statistics – Simulations and Computations 2012; 41(6): 764 – 775.
Bernardi G., Wiley E.O., Mansour H., Miller M.R., Orti G., Haussler D., O’BrienJ., Ryder O.A., Venkatesh B. The Fishes of Genome 10K. Marine Genomics 7. 2012; 3-6.
Borges R., Johnson , O’Brien S., Vasconcelos V., Antunes A. The role of gene duplication and unconstrained selective pressures in the melanopsin gene family evolution and vertebrate circadian rhythm regulation. Plosone Volume: 7 Issue: 12 Article Number: e52413 DOI: 10.1371/journal.pone.0052413 Published: Dec 2012
Bostrom M.A., Kao W.H., Li M., Abboud H.E., Adler S.G., Iyengar S.K., Kimmel P.L., Hanson R.L., Nicholas S.B., Rasooly R.S., Sedor J.R., Coresh J., Kohn O.F., Leehey D.J., Thornley-Brown D., Bottinger E.P., Lipkowitz M.S., Meoni L.A., Klag M.J., Lu L., Hicks P.J., Langefeld C.D., Parekh R.S., Bowden D.W., Freedman B.I. OBrien SJ Family Investigation of Nephropathy and Diabetes (FIND) Research Group. Genetic association and gene-gene interaction analyses in African American dialysis patients with nondiabetic nephropathy. American Journal of Kidney Diseases. 2012; 59(2):210-21
Chernyaeva, Dobrynin P., Pestova N., Matveeva N., Zhemkov V., Kozlov A. Molecular genetic analysis of Mycobacterium tuberculosis strains spread in different patient groups in St. Petersburg, Russia. European Journal Of Clinical Microbiology and Infectious Diseases 2012; 31(8): 1753-1757.
Christoph G., MalovV. Asymptotic Properties of Generalized Multivariate Rank Statistics. Communications in Statistics – Theory and Methods 2012; 41(12):2133 — 2159.
Copeland A., Gu W., Yasawong M., Lapidus A., Lucas S., Deshpande S., Pagani I., Tapia R., Cheng J.F., Goodwin L.A., Pitluck S., Liolios K., Ivanova N., Mavromatis K., Mikhailova N., Pati A., Chen A., Palaniappan K., Land M., Pan C., Brambilla E.M., Rohde M., Tindall B.J., Sikorski J., Göker M., Detter J.C., Bristow J., Eisen J.A., Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.P., Woyke T. Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1(T)) from a deep-sea hydrothermal vent chimney. Standards in Genomic Sciences. 2012; 6(1):21-30.
Copeland A., Zeytun A., Yassawong M., Nolan M., Lucas S., Hammon N., Deshpande S., Cheng J.F., Han C., Tapia R., Goodwin L.A., Pitluck S., Mavromatis K., Liolios K., Pagani I., Ivanova N., Mikhailova N., Pati A., Chen A., Palaniappan K., Land M., Hauser L., Jeffries C.D., Brambilla E.M., Rohde M., Sikorski J., Pukall R., Göker M., Detter J.C., Woyke T., Bristow J., Eisen J.A., Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.P., Lapidus Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRP(T)). Standards in Genomic Sciences. 2012; 6(2):240-50.
Copeland A., Zhang X., Misra M., Lapidus A., Nolan M., Lucas S., Deshpande S., Cheng J.F., Tapia R., Goodwin L.A., Pitluck S., Liolios K., Pagani I., Ivanova N., Mikhailova N., Pati A., Chen A., Palaniappan K., Land M., Hauser L., Pan C., Jeffries C.D., Detter J.C., Brambilla E.M., Rohde M., Djao O.D., Göker M., Sikorski J., Tindall B.J., Woyke T., Bristow J., Eisen J.A., Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.P., Mavromatis K. Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)). Standards in Genomic Sciences. 2012; 6(2):145-54.
Dolnik A., Tamazyan, Pershina E., Vyatkina K., Porozov Y., Pinaev A., Andronov E. The evolutionary space of bacterial 16S RNA gene v. 1.0 (in Russian). Sel’skokhozyaistvennaya biologiya (Agricultural biology, Russia). 2012; 5:111-120.
Driscoll C.A., Sanderson E., Christie S., Luo S.J., Seidensticker J., Miquelle D., Goodrich J., Dinerstein E., Shrethsta M., Zhuralev Y., Jhala Y.V., Yadav S.P., Pikunov D.G., Darman Y., Breitenmoser U., Chestin I., Jungius H., Yamaguchi N., Pereladova O., Wildt D.E., Macdonald D.W., O’BrienJ. A Postulate for Tiger Recovery. Journal of Threatened Taxa. 2012; 4: 2637-2643.
Göker M., Saunders E., Lapidus A., Nolan M., Lucas S., Hammon N., Deshpande S., Cheng J.F., Han C., Tapia R., Goodwin L.A., Pitluck S., Liolios K., Mavromatis K., Pagani I., Ivanova N., Mikhailova N., Pati A., Chen A., Palaniappan K., Land M., Chang Y.J., Jeffries C.D., Brambilla E.M., Rohde M., Spring S., Detter J.C., Woyke T., Bristow J., Eisen J.A., Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.P. Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314(T)). Standards in Genomic Sciences. 2012; 6(2):230-9.
Fernandez-Fueyo E., Ruiz-Dueñas F.J., Ferreira P., Floudas D., Hibbett D.S., Canessa P., Larrondo L.F., James T.Y., Seelenfreund D., Lobos S., Polanco R., Tello M., Honda Y., Watanabe T., Watanabe T., Ryu J.S., Kubicek C.P., Schmoll M., Gaskell J., Hammel K.E., St John F.J., Vanden Wymelenberg A., Sabat G., Splinter BonDurant S., Syed K., Yadav J.S., Doddapaneni H., Subramanian V., Lavín J.L., Oguiza J.A., Perez G., Pisabarro A.G., Ramirez L., Santoyo F., Master E., Coutinho P.M., Henrissat B., Lombard V., Magnuson J.K., Kües U., Hori C., Igarashi K., Samejima M., Held B.W., Barry K.W., LaButti K.M., Lapidus A., Lindquist E.A., Lucas S.M., Riley R., Salamov A.A., Hoffmeister D., Schwenk D., Hadar Y., Yarden O., de Vries R.P., Wiebenga A., Stenlid J., Eastwood D., Grigoriev I.V., Berka R.M., Blanchette R.A., Kersten P., Martinez A.T., Vicuna R., Cullen D. Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis. Proceedings of the National Academy of Sciences U S A. 2012; 109 (14) 5458-5463
Han C., Kotsyurbenko O., Chertkov O., Held B., Lapidus A., Nolan M., Lucas S., Hammon N., Deshpande S., Cheng J.F., Tapia R., Goodwin L.A., Pitluck S., Liolios K., Pagani I., Ivanova N., Mavromatis K., Mikhailova N., Pati A., Chen A., Palaniappan K., Land M., Hauser L., Chang Y.J., Jeffries C.D., Brambilla E.M., Rohde M., Spring S., Sikorski J., Göker M., Woyke T., Bristow J., Eisen J.A., Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.P., Detter J.C. Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1(T)). Standards in Genomic Sciences. 2012; 6(1):94-103.
Hostetler J.A., Onorato D.P., Bolker B.M., Johnson W.E., O’BrienJ., Jansen D., Oli M. Does genetic introgression improve female reproductive performance? A test on the endangered Florida panther. Oecologia 2012; 168(1):289-300.
Huntemann M., Teshima H., Lapidus A., Nolan M., Lucas S., Hammon N., Deshpande S., Cheng J.F., Tapia R., Goodwin L.A., Pitluck S., Liolios K., Pagani I., Ivanova N., Mavromatis K., Mikhailova N., Pati A., Chen A., Palaniappan K., Land M., Hauser L., Pan C., Brambilla E.M., Rohde M., Spring S., Göker M., Detter J.C., Bristow J., Eisen J.A., Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.P., Woyke T. Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1(T)). Standards in Genomic Sciences. 2012; 6(2):185-93.
Ilina E.L., LogachovA., Laplaze L., Demchenko N.P., Pawlowski K., Demchenko K.N. Composite Cucurbita pepo plants with transgenic roots as a tool to study root development. Annals of botany, 2012; 110(2):479–89.
Johnson WE, Onorato DP, Roelke ME,and O’Brien SJ. Genetic Future for Florida Panthers SCIENCE Volume: 330 : 1744-1744 2012
Kaelin C.B., Xu X., Hong L.Z., David V.A., McGowan K.A., Schmidt-Küntzel A., Roelke M.E., Pontius J., Cooper G.M., Marker H., Harper C.K., van Dyk A., Yue B., Mullikin J.C., Warren W.C., Eizirik E., O’BrienJ., Barsh G.S., Menotti-Raymond M. Specifying and sustaining pigmentation patterns in domestic and wild cats. Science 2012; 337:1536-1541.(2012)
Klenk H.P., Held B., Lucas S., Lapidus A., Copeland A., Hammon N., Pitluck S., Goodwin L.A., Han C., Tapia R., Brambilla E.M., Pötter G., Land M., Ivanova N., Rohde M., Göker M., Detter J.C., Kyrpides N.C., Woyke T. Genome sequence of the soil bacterium Saccharomonospora azurea type strain (NA-128(T)). Standards in Genomic Sciences. 2012; 6(2):220-9.
Klenk H.P., Lu M., Lucas S., Lapidus A., Copeland A., Pitluck S., Goodwin L.A., Han C., Tapia R., Brambilla E.M., Pötter G., Land M., Ivanova N., Rohde M., Göker M., Detter J.C., Li W.J., Kyrpides N.C., Woyke T. Genome sequence of the ocean sediment bacterium Saccharomonospora marina type strain (XMU15(T)). Standards in Genomic Sciences. 2012; 6(2):265-75.
KozlovP., Zabezhinskiĭ M.A., Popovich I.G., Polev D.E., Shilov E.S., Muriashev B.V. Hyperplastic skin growth on the head of goldfish—comparative oncology aspects. Voprosy Onkologii. 2012; 58(3):387-93.
Lee M.Y., Hyun J.Y., Lee S.J., An J., Lee E., Min M.S., Kimura J., Kawada S., Kurihara N., Luo S.J., O’BrienJ., Johnson W.E., Lee H. Subspecific Status of the Korean Tiger Inferred by Ancient DNA Analysis Animal Systematics, Evolution and Diversity. 2012; 28(1): 48-53.
Limou S., Delaneau O., van Manen D., An P., Sezgin E., Le Clerc S., Coulonges C., Troyer J.L., Veldink J.H., van den Berg L.H., Spadoni J.L., Taing L., Labib T., Montes M., Delfraissy J.F., Schachter F., O’BrienJ., Buchbinder S., van Natta M.L., Jabs D.A., Froguel P., Schuitemaker H., Winkler C.A., Zagury J.F. Multicohort Genomewide Association Study Reveals a New Signal of Protection Against HIV-1 Acquisition. J Infectious Diseases. 2012; 205:1155-62.
Lucas S., Han J., Lapidus A., Cheng J.F., Goodwin L.A., Pitluck S., Peters L., Mikhailova N., Teshima H., Detter J.C., Han C., Tapia R., Land M., Hauser L., Kyrpides N.C., Ivanova N., Pagani I., Vannier P., Oger P., Bartlett D.H., Noll K.M., Woyke T., Jebbar M. Complete Genome Sequence of the Thermophilic, Piezophilic, Heterotrophic Bacterium Marinitoga piezophila KA3. Journal of Bacteriology. 2012; 194(21):5974-5.
Mavromatis K., Chertkov O., Lapidus A., Nolan M., Lucas S., Tice H., Del Rio T.G., Cheng J.F., Han C., Tapia R., Bruce D., Goodwin L.A., Pitluck S., Huntemann M., Liolios K., Pagani I., Ivanova N., Mikhailova N., Pati A., Chen A., Palaniappan K., Land M., Brambilla E.M., Rohde M., Spring S., Göker M., Detter J.C., Bristow J., Eisen J.A., Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.P., Woyke T. Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (= HR1). Standards in Genomic Sciences. 2012 ;6(2):210-9.
Meincke L., Copeland A., Lapidus A., Lucas S., Berry K.W., Del Rio T.G., Hammon N., Dalin E., Tice H., Pitluck S., Richardson P., Bruce D., Goodwin L., Han C., Tapia R., Detter J.C., Schmutz J., Brettin T., Larimer F., Land M., Hauser L., Kyrpides N.C., Ivanova N., Göker M., Woyke T., Wu Q.L., Pöckl M., Hahn M.W., Klenk H.P. Complete genome sequence of Polynucleobacter necessarius subsp. asymbioticus type strain (QLW-P1DMWA-1(T)). Standards in Genomic Sciences. 2012 ;6(1):74-83.
Menotti-Raymond M., David V.A., Weir B.S., O’Brien S.J. A Population Genetic Database of Cat Breeds Developed in Coordination with a Domestic Cat STR Multiplex Journal of Forensic Sciences 2012; 57:596-601.
Morin E., Kohler A., Baker A.R., Foulongne-Oriol M., Lombard V., Nagy L.G., Ohm R.A., Patyshakuliyeva A., Brun A., Aerts A.L., Bailey A.M., Billette C., Coutinho P.M., Deakin G., Doddapaneni H., Floudas D., Grimwood J., Hildén K., Kües U., Labutti K.M., Lapidus A., Lindquist E.A., Lucas S.M., Murat C., Riley R.W., Salamov A.A., Schmutz J., Subramanian V., Wösten H.A., Xu J., Eastwood D.C., Foster G.D., Sonnenberg A.S., Cullen D., de Vries R.P., Lundell T., Hibbett D.S., Henrissat B., Burton K.S., Kerrigan R.W., Challen M.P., Grigoriev I.V., Martin F. Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proceedings of the National Academy of Sciences U S A. 2012; 109(43):17501-6.
Murashev B.V., Nazarenko O.V., Akulova E.B., Artemyeva A.K., Verevochkin S.V., Shaboltas A.V., Skochilov R.V., Toussova O.V., KozlovP. The High Frequency of HIV Type 1-Specific Cellular Immune Responses in Seronegative Individuals with Parenteral and/or Heterosexual HIV Type 1 Exposure. AIDS Research and Human Retroviruses. 2012; 28(12):1598-605.
Neupane S., Högberg N., Alström S., Lucas S., Han J., Lapidus A., Cheng J.F., Bruce D., Goodwin L., Pitluck S., Peters L., Ovchinnikova G., Lu M., Han C, Detter JC, Tapia R, Fiebig A., Land M., Hauser L., Kyrpides N.C., Ivanova N., Pagani I., Klenk H.P., Woyke T., Finlay R.D. Complete genome sequence of the rapeseed plant-growth promoting Serratia plymuthica strain AS9. Standards in Genomic Sciences. 2012; 6(1):54-62.
Neupane S., Finlay R.D., Alström S., Goodwin L., Kyrpides N.C., Lucas S., Lapidus, Bruce D., Pitluck S., Peters L., Ovchinnikova G., Chertkov O., Han J., Han C., Tapia R., Detter J.C., Land M., Hauser L., Cheng J.F., Ivanova N., Pagani I., Klenk H.P., Woyke T., Högberg N. Complete genome sequence of Serratia plymuthica strain AS12. Standards in Genomic Sciences. 2012; 6(2):165-73.
O’Brien J. Redefining Tiger Subspecies In Fierce Beauty: Preserving the World of Wild Cats. A Bhagavan, T Flach, B Bland, and R Duvall Mandala Publ. 2012; 324.
O’BrienJ., Troyer J.L., Brown M.A., Johnson W.E., Antunes A., Roelke M.E., Pecon-Slattery J. Emerging Viruses in the Felidae: Shifting Paradigms Viruses 2012; 4(2): 236-257.
O’BrienJ. Genome empowerment for the Puerto Rican parrot – Amazona vittata GigaScience 2012; 1:13-16.
Padamsee M., Kumar T.K., Riley R., Binder M., Boyd A., Calvo A.M., Furukawa K., Hesse C., Hohmann S., James T.Y., LaButti K., Lapidus A., Lindquist E., Lucas S., Miller K., Shantappa S., Grigoriev I.V., Hibbett D.S., McLaughlin D.J., Spatafora J.W., Aime M.C. The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction. Fungal Genetics and Biology. 2012; 49(3):217-26.
Pershina E., Tamazian G., Dolnik A., Vyatkina K., Porozov Y., Pinaev A., Andronov E. . Study of saline solt microbial coenosis structure using efficient sequencing (in Russian). Ekologicheskaya genetika (Ecological Genetics, Russia). 2012; X,(2): 32–39.
Pester M., Brambilla E., Alazard D., Rattei T., Weinmaier T., Han J., Lucas S., Lapidus A., Cheng J.F., Goodwin L., Pitluck S., Peters L., Ovchinnikova G., Teshima H., Detter J.C., Han C.S., Tapia R., Land M.L., Hauser L., Kyrpides N.C., Ivanova N.N., Pagani I., Huntmann M., Wei C.L., Davenport K.W., Daligault H., Chain P.S., Chen A., Mavromatis K., Markowitz V., Szeto E., Mikhailova N., Pati A., Wagner M., Woyke T., Ollivier B., Klenk H.P., Spring S., Loy A. Complete Genome Sequences of Desulfosporosinus orientis DSM765T, Desulfosporosinus youngiae DSM17734T, Desulfosporosinus meridiei DSM13257T, and Desulfosporosinus acidiphilus DSM22704T. Journal of Bacteriology. 2012; 194(22):6300-1.
Philip, S, Machado JP, Maldonado E, Vasconcelos V, O’Brien SJ, Johnson WE, Antunes A. Fish lateral line innovation: insights into the evolutionary genomic dynamics of a unique mechanosensory organ. Mol Biol Evol. 2012 29(12):3887-98.
Roberts J.L., Buckley R.H., Luo B., Pei J., Lapidus A., Peri S., Wei Q., Shin J., Parrott R.E., Dunbrack R.L. Jr, Testa J.R., Zhong X.P., Wiest D.L. CD45-deficient severe combined immunodeficiency caused by uniparental disomy. Proceedings of the National Academy of SciencesU S A. 2012; 109(26):10456-61.
Schneider, A , David, VA; Johnson, WE ; O’Brien, SJ; Barsh, GS; Menotti-Raymond, M, Eizirik, E. >How the Leopard Hides Its Spots: ASIP Mutations and Melanism in Wild Cats PLOS ONE Volume: 7 Issue: 12 Article Number: e50386 DOI: 10.1371/journal.pone.0050386 2012
Siddaramappa S., Challacombe J.F., Delano S.F., Green L.D., Daligault H., Bruce D., Detter C., Tapia R., Han S., Goodwin L., Han J., Woyke T., Pitluck S., Pennacchio L., Nolan M., Land M., Chang Y.J., Kyrpides N.C., Ovchinnikova G., Hauser L., Lapidus A., Yan J., Bowman K.S., da Costa M.S., Rainey F.A., Moe W.M. Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9(T)) and comparison to «Dehalococcoides» strains. Standards in Genomic Sciences. 2012; 6(2):251-64.
Sunagar K., Johnson W.E., O’Brien S.J., Vasconcelos V., Antunes A. Evolution of CRISPs associated with toxicoferan-reptilian venom and mammalian reproduction. Molecular Biology and Evolution. 2012; 29:1807-1822
Susanti D., Johnson E.F., Rodriguez J.R., Anderson I., Perevalova A.A., Kyrpides N., Lucas S., Han J., Lapidus A., Cheng J.F., Goodwin L., Pitluck S., Mavrommatis K., Peters L., Land M.L., Hauser L., Gopalan V., Chan P.P., Lowe T.M., Atomi H., Bonch-Osmolovskaya E.A., Woyke T., Mukhopadhyay B. Complete Genome Sequence of Desulfurococcus fermentans, a Hyperthermophilic Cellulolytic Crenarchaeon Isolated from a Freshwater Hot Spring in Kamchatka, Russia. Journal of Bacteriology. 2012; 194(20):5703-4.
Suzuki H., Macdonald J., Syed K., Salamov A., Hori C., Aerts A., Henrissat B., Wiebenga A., Vankuyk P.A., Barry K., Lindquist E., Labutti K., Lapidus A., Lucas S., Coutinho P., Gong Y., Samejima M., Mahadevan R., Abou-Zaid M., de Vries R.P., Igarashi K., Yadav J.S., Grigoriev I.V., Master E.R. Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize. BMC Genomics. 2012; 13:444.
Tang M., Lautenberger J.A., Gao X., Sezgin E., Hendrickson S.L., Troyer J.L., David V.A., Guan L., Mcintosh C.E., Guo X., Zheng Y., Liao J., Deng H., Malasky M., Kessing B., Winkler C.A., Carrington M., Guy de´ T, Zeng Y., O’Brien S.J. The Principal Genetic Determinants for Nasopharyngeal Carcinoma in China Involve the HLA Class I Antigen Recognition Groove PLOS Genetics: 2012; 8(11):e1003103.
Tamazian G. A variation of the pure adaptive random search // Proceedings of the 3rd International Conference on Optimization Methods and Software. 2012:93.
Troyer J.L., Roelke M.E., Jespersen J.M., Baggett N., Buckley-Beason V., MacNulty D., Craft M., Packer C., Pecon-Slattery J., O’Brien S.J..FIV diversity: FIVPle subtype composition may influence disease outcome in African lions: Veterinary Immunology And Immunopathology- SI 2012; 143: 338-346.
Wester C.W., Eden S.K., Shepherd B.E., Bussmann H., Novitsky V., Samuels D.C., Hendrickson S.L., Winkler C.A., O’Brien S.J., Essex M., D’Aquila R.T., Degruttola V., Marlink R.G. Risk Factors for Symptomatic Hyperlactatemia and Lactic Acidosis Among Combination Antiretroviral Therapy-Treated Adults in Botswana: Results from a Clinical Trial. AIDS Research and Human Retroviruses. 2012; 28:759-765.
de Wit P.J.G.M., Van der Burgt A., Okmen B., Stergiopoulos I., Abd-.‐Elsalam K.A., Aerts A.L., Bahkali A.H., Beenen H.G., Chettri P., Cox M.P., Datema E., de Vries R.P., Dhillon B., Ganley A.R., Griffiths S.A., Guo Y., Hamelin R.C., Henrissat B., Kabir M.S., Jashni M.K., Kema G., Klaubauf S., Lapidus A., Levasseur A., Lindquist E., Mehrabi R., Ohm R.A., Owen T.J., Salamov A., Schwelm A., Schijlen E., Sun H., Van den Burg H.A., Van Ham R.C.H.J., Zhang S., Goodwin S.B., Grigoriev I.V., Collemare J., Bradshaw R.E.The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothisstroma Septosporum Reveal adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry. PLOS Genetics. 2012;11.
Wong P., Wiley E., Johnson W, Ryder O., O’Brien S., Haussler D., Koepfli K., Houck M., Perelman P., Mastromonaco G., Bentley A., Venkatesh B., Zhang Y., Murphy R., Genome 10 K Community of Scientists Tissue sampling and standards for vertebrate genomics GigaScience 2012;1:8-20.
Zhan W., Hansen N.B., Shaboltas A.V., Skochilov R.V., Kozlov A.P., Krasnoselskikh T.V., Abdala N. Partner violence perpetration and victimization and HIV risk behaviors in St. Petersburg, Russia. Journal of Traumatic Stress. 2012; 25(1):86-93.
Zhan W., Krasnoselskikh T.V., Golovanov S., Kozlov A.P., Abdala N. Gap between consecutive sexual partnerships and sexually transmitted infections among STI clinic patients in St Petersburg, Russia. AIDS and Behavior. 2012;16(2):334-9.
Zhan W., Shaboltas A.V., Skochilov R.V., Kozlov A.P., Krasnoselskikh T.V., Abdala N. Depressive symptoms and unprotected sex in St. Petersburg, Russia. Journal of Psychosomatic Research. 2012; 72(5):371-5.

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.

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.

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) .

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.

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.

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

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

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.

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

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.

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

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.

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

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.

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)

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).

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.

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

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.

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.

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

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

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.

Bajenova O, Chaika N, Tolkunova E, Davydov-Sinitsyn A, Gapon S, Thomas P, O’Brien S. Carcinoembryonic antigen promotes colorectal cancer progression by targeting adherens junction complexes. Exp Cell Res. 2014;324:115-23. doi: 10.1016/j.yexcr.2014.04.007.

Bajenova, O.; O’Brien, S. J. GENETIC FACTORS INVOLVED IN HUMAN COLORECTAL CANCER METASTASIS. ANTICANCER RESEARCH : 34 : 5824-5825 2014

Chernyaeva, E. , M. Shulgina, M.Rotkevich, P. Dobrynin, S. Simonov, E. Shitikov, D. Ischenko, I. Karpova, E. Kostryukova, E. Ilina, V. Govorun, V. Zhuravlev, O. Manicheva, P. Yablonsky, Y. Isaeva, E. Nosova, I. Mokrousov, O. Narvskaya, A. Vyazovaya, A. Lapidus, S. J. O’Brien Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology BMC GENOMICS Volume: 15 Article Number: 308 . 2014

David, Victor A. , Marilyn Menotti-Raymond, Andrea Coots Wallace, Melody Roelke, James Kehler‡, Robert Leighty, Eduardo Eizirik, Steven S. Hannah, George Nelson, Alejandro A. Schäffer, Catherine J. Connelly, Stephen J. O’Brien, David K. Ryugo Endogenous Retrovirus Insertion in KIT Oncogene Determines White , White Spotted and White Deafness in Domestic cats . G3-Genes Genomes Genetics: 4:1881-1891 2014

A. P. Davydov-Sinitsyn, O. V. Bajenova, M.A. Liskova, S.V. Ponomartsev., I.V.Rykov, S.A.Koshkin, A.N. Tomilin, E.N. Tolkunova. Подавление роста опухолей , полученных при ксенотрансплантации клеток аденокарциномы толстой кишки человека Tsitologia

GIGA-Community of Scientists*, Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes Submitted Jour Heredity 2014, 105: 1-18 .

Guo, Xiuchan, Cheryl A. Winkler, Ji Li, Li Guan, Minzhong Tang, Jian Liao, Hong Deng, Guy de Thé, Yi Zeng and Stephen J. OʹBrien . Evaluation and integration of genetic signature for Prediction Risk of Nasopharyngeal Carcinoma in Southern China. BIOMED RESEARCH INTERNATIONAL Article Number: 434072, 2014.

Jarvis, Erich D.,et al Whole Genome Analyses Resolve the Early Branches in the Tree of Life of Modern Birds. Science In press. 2014.

Jiang X, Peery A, Hall AB, Sharma A, Chen X, Waterhouse RM, Komissarov A, Riehle MM, Shouche Y, Sharakhova MV, Lawson D, Pakpour N, Arensburger P, Davidson V, Eiglmeier K, Emrich S, George P, Kennedy R, Mane SP, Maslen G, Oringanje C, Qi Y, Settlage R, Tojo M, Tubio JM, Unger M, Wang B, Vernick KD, Ribeiro JM, James AA, Michel K, Riehle MA, Luckhart S, Sharakhov IV, Tu Z. Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi Genome Biology 2014, 15:459 doi:10.1186/s13059-014-0459-2

Khan, Imran , Emanuel Maldonado, Vítor Vasconcelos, Stephen J. O’Brien,Warren E. Johnson and Agostinho Antunes. Mammalian keratin associated proteins (KRTAPs)subgenomes: disentangling hair diversity and adaptation to terrestrial and aquatic environments. BMC Genomic: 15: Article Number: UNSP 779. 2014.

Kuznetsova IS, Thevasagayam NM, Sridatta PS, Komissarov AS, Saju JM, Ngoh SY, Jiang J, Shen X, Orban L.Primary analysis of repeat elements of the Asian seabass (Lates calcarifer) transcriptome and genome. Front Genet. 2014 Jul 25;5:223. doi: 10.3389/fgene.2014.00223.

Liang Y, Tang W, Huang T, Gao Y, Tan A, Yang X, Zhang H, Hu Y, Qin X, Li S, Zhang S, Mo L, Liang Z, Shi D, Huang Z, Guan Y, Zhou J, Winkler C, O’Brien SJ, Xu J, Mo Z, Peng T. Genetic variations affecting serum carcinoembryonic antigen levels and status of regional lymph nodes in patients with sporadic colorectal cancer from Southern China. PLoS One. 2014 Jun 18;9(6):e97923.

Luo SJ, Zhang Y, Johnson WE, Miao L, Martelli P, Antunes A, Smith JL, O’Brien SJ. Sympatric Asian felid phylogeography reveals a major Indochinese-Sundaic divergence. Mol Ecol. 2014 Apr;23(8):2072-92. doi: 10.1111/mec.12716.PMID: 24629132
Malov S.V., Shevchenko, A.K. & O’Brien S.J. (2013) Genome associations discovering. Part 1: Statistical methods (in Russian). Komputerniye instrumenti v obrazovanii, Computer Tools in Education v. 5, pp 17 – 32.

Malov S.V., Shevchenko, A.K. & O’Brien S.J. (2013). Genome associations discovering. Part 2: Multiple testing problem, Computer Tools and Applications (in Russian). Komputerniye instrumenti v obrazovanii, Computer Tools in Education v. 6, pp. 3-17

Menotti-Raymond, M., David, A. V., O´Brien, S. J., Kanthaswamy, S., Projić, P., Škaro V., Lauc, G., “STR Based Forensic Animal DNA Analysis”, Chapt. 11 , Forensic DNA Applications: An Interdisciplinary Perspective. Editors. Dragan Primorac and Moses Schanfield, CRC Press Taylor and Francis, 2014

Morris KM, Kirby K, Beatty JA, Barrs VR, Cattley S, David V, O’Brien SJ, Menotti-Raymond M, Belov K. Development of MHC-linked microsatellite markers in the domestic cat and their use to evaluate MHC diversity in Domestic cats, cheetahs and Gir lions. Jour Heredity 105:493-505, 2014

Montague, Michael J. , Gang Li, Barbara Gandolfi, Razib Khan, Bronwen Aken, Steve Searle, Patrick Minx, LaDeana Hillier, Dan Kolboldt, Brian W. Davis, Carlos A. Driscoll , Christina Barr, Kevin Blackistone, Javier Quilez Oliete7, Maria Belen Lorente Galdos, Tomas Marques-Bonet, Can Alkan , Gregg W.C. Thomas, Matthew W. Hahn, Marilyn Menotti-Raymond, Stephen J. O’Brien, Leslie A. Lyons, William J. Murphy, Richard K. Wilson, Wesley C. Warren. Comparative analysis of the domestic cat genome reveals genetic signatures of selection underlying feline biology and domestication. Proc Natl Acad Sci 111: 17230-17235.

Napolitano, Constanza ,Warren E. Johnson, Jim Sanderson, Stephen J. O’Brien, A. Rus Hoelzel, Rachel Freer, Nigel Dunstone, Kermit Ritland, Carol E. Ritland, Elie Poulin Phylogeography and population history of Leopardus guigna, the smallest American felid. Conservation Genetics 15: 631-653 2014.

O’Brien, Stephen J . ,Anton Svitin, Sergey Malov, Nikolay Cherkazov Pavel Dobrynin, Paul Geerts, Jennifer Troyer, Sher Hendrickson-Lambert, Efe Sezgin, Holli Hutcheson.Gene Discovery and Data Sharing in Genome Wide Association Analyses: lessons form AIDS genetic restriction genes-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES Volume: 65 Supplement: 2 Pages: 59-59 2014

O’Brien, SJ, The “Exotic Aliens” Controversy- A View from Afar. Journal of the Bombay Natural History Society 110:108-113 2014.

OBrien , Stephen J., David Haussler and Oliver Ryder . The Birds of Genome10K GigaScience 2014, 3:32 http://www.gigasciencejournal.com/content/3/1/32.

Pereira , J ,Johnson W., O’Brien S., Jarvis E., Zhang G., Gilbert M., Vasconcelos V., Antunes A. Evolutionary Genomics and Adaptive Evolution of the Hedgehog Gene Family (SHH, IHH AND dHH) in Vertebrates. PLOSONE 2014 Volume: 9 Issue: 12 Article Number: e74132 Published: DEC 30 2014.

Pershina, E. V., A. S. Dolnik, G. S. Tamazyan, K. V. Vyatkina, Y. B. Porozov, A. G. Pinaev, S. O. Karimov, N. A. Provorov, and E. E. Andronov. «The Evolutionary Space Model to be Used for the Metagenomic Analysis of Molecular and Adaptive Evolution in the Bacterial Communities.» In Evolutionary Biology: Genome Evolution, Speciation, Coevolution and Origin of Life, pp. 339-355. Springer International Publishing, 2014.

Svitin Anton, Malov Sergey, Cherkasov Nikolay, Geerts Paul, Rotkevich Mikhail, Dobrynin Pavel, Shevchenko Andrey, Guan Li, Troyer Jennifer, Hendrickson Sher, Hutcheson Dilks Holli, Oleksyk K. Taras, Donfield Sharyne, Gomperts Edward, Jabs A. Douglas, Sezgin Efe, Van Natta Mark, Harrigan P. Richard, Brumme L. Zabrina, O’Brien Stephen J. GWATCH: a web platform for automated gene association discovery analysis. (2014 ) GigaScience 3:18.

Tamazian, T; Simonov, S; Dobrynin, P; Makunin, A; Logachev, A; Komissarov, A; Shevchenko, A; Brukhin, V; Cherkasov, N; Svitin, A; Koepfli, KP; Pontius, J; Driscoll, CA; Blackistone, K; Barr, C; Goldman, D; Antunes, A; Quilez, J; Lorente-Galdos, B; Alkan, C; Marques-Bonet, T; Menotti-Raymond, M; David, V; Narfstrom, K; O’Brien, SJ (2014): Annotated Features of the Domestic Cat (Felis catus) Genome. GigaScience 3:13 . doi:10.1186/2047-217X-3-13
http://www.gigasciencejournal.com/content/3/1/13 2014

Vasilyeva I.N., Bespalov V.G., Semenov A.L., Ivanov S.D., Komissarov A.S., Podgornaya O.I. Секвенирование внеклеточной нуклеосомной ДНК крови облученных крыс. Molekulyarnaya diagnostika 2014, 2014, p. 278

Walters-Conte KB, Johnson DL, Johnson WE, O’Brien SJ, Pecon-Slattery J. The dynamic proliferation of CanSINEs mirrors the complex evolution of Feliforms. BMC Evol Biol. 2014. 14:137.

Xue, Hao-Ran Nobuyuki Yamaguchi, Carlos A. Driscoll, Yu Han, Gila Kahila Bar-Gal, Yan Zhuang, David W. Macdonald, Stephen J. O’Brien, Shu-Jin Luo, Genetic Ancestry of the Presumed Extinct Javan and Balinese Tigers Inform a Refinement of Tiger Subspecies Taxonomy PLOS-Biology Submitted Journal of Hered. 2014

124. Yim HS, Cho YS, Guang X, Kang SG, Jeong JY, Cha SS, Oh HM, Lee JH, Yang EC, Kwon KK, Kim YJ, Kim TW, Kim W, Jeon JH, Kim SJ, Choi DH, Jho S, Kim HM, Ko J, Kim H, Shin YA, Jung HJ, Zheng Y, Wang Z, Chen Y, Chen M, Jiang A, Li E, Zhang S, Hou H, Kim TH, Yu L, Liu S, Ahn K, Cooper J, Park SG, Hong CP, Jin W, Kim HS, Park C, Lee K, Chun S, Morin PA, O’Brien SJ, Lee H, Kimura J, Moon DY, Manica A, Edwards J, Kim BC, Kim S, Wang J, Bhak J, Lee HS, Lee JH. Minke whale genome and aquatic adaptation in cetaceans. Nat Genet. 46:88-92.( 2014). doi: 10.1038/ng.2835.

125. Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Ödeen A, Cui J, Zhou Q, Xu L, Pan H, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, Zeng Y, Xiong Z, Liu S, Zhou L, Huang Z, An N, Wang J, Zheng Q, Xiong Y, Wang G, Wang B, Wang J, Fan Y, da Fonseca RR, Alfaro-Núñez A, Schubert M, Orlando L, Mourier T, Howard JT, Ganapathy G, Pfenning A, Whitney O, Rivas MV, Hara E, Smith J, Farré M, Narayan J, Slavov G, Romanov MN, Borges R, Machado JP, Khan I, Springer MS, Gatesy J, Hoffmann FG, Opazo JC, Håstad O, Sawyer RH, Kim H, Kim KW, Kim HJ, Cho S, Li N, Huang Y, Bruford MW, Zhan X, Dixon A, Bertelsen MF, Derryberry E, Warren W, Wilson RK, Li S, Ray DA, Green RE, O’Brien SJ, Griffin D, Johnson WE, Haussler D, Ryder OA, Willerslev E, Graves GR, Alström P, Fjeldså J, Mindell DP, Edwards SV, Braun EL, Rahbek C, Burt DW, Houde P, Zhang Y, Yang H, Wang J; Avian Genome Consortium, Jarvis ED, Gilbert MT, Wang J. Comparative genomics reveals insights into avian genome evolution and adaptation. Science. 2014 Dec 12;346(6215):1311-20. doi: 10.1126/science.1251385. Epub 2014 Dec 11.MS782

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.

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

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.

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

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

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

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.

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

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

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

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

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

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

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

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.

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.

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

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.

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

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

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).

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

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

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

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

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.

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

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

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.

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.

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

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).

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.


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.

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

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

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

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.

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

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

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 .

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.

Back to top