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Our Science – O'Brien Website

Stephen J. O'Brien, Ph.D.

Selected Publications
1)  Hendrickson SL, Hutcheson HB, Ruiz-Pesini E, Poole JC, Lautenberger J, Sezgin E, Kingsley L, Goedert JJ, Vlahov D, Donfield S, Wallace DC, O'Brien SJ.
Mitochondrial DNA Haplogroups influence AIDS Progression.
AIDS. 2008. In Press. [Journal]
2)  Antunes A, Troyer J, Roelke M, Pecon-Slattery J, Packer C, Winterbach C, Winterbach H, Hemson G, Frank L, Stander P, Siefert L, Driciru M, Funston P, Alexander K, Prager K, Mills G, Wildt D, Bush M, O'Brien S, Johnson W.
The Evolutionary History of Lion: Integrating Host/Pathogen Molecular Genetics.
PLOS Genetics. 2008. In Press. [Journal]
3)  Luo S, Johnson W, Smith J, O'Brien S.
What is a Tiger? Genetics and Phylogeny.
Tigers of the World. 2008. In Press. [Journal]
4)  Zapata B, Gonzalez J, Marin J, Cabello W, Johnson W, Skewes. O.
A case of polydactyly in a wild guanaco (Lama guanicoe). Small Ruminent Research.
Small Ruminent Research. 76: 220-222, 2008. [Journal]
5)  Fontoura-Rodrigues M, Lima-Rosa C, Rodrigues F, de Paula R, Gough M, Johnson W, Bonatto S, Eizirik E.
Cross-amplification and characterization of 13 tetranucleotide microsatellites in mulitple species of Neotropical canids.
Molecular Ecology Notes. 8: 898-900, 2008. [Journal]
6)  Trigo TC, Freitas TR, Kunzler G, Cardoso L, Silva JC, Johnson WE, O'Brien SJ, Bonatto SL, Eizirik E.
Inter-species hybridization among Neotropical cats of the genus Leopardus, and evidence for an introgressive hybrid zone between L. geoffroyi and L. tigrinus in southern Brazil.
Mol. Ecol. 2008. [Journal]
7)  Cunningham M, Brown M, Shindle D, Hayes K, Terrell S, Johnson W, Land E, Roelke M, O'Brien S.
Epizootiology of Feline Leukemia Virus in the Florida Panther.
J. Wildlife Disease. 2007. In Press. [Journal]
8)  Werdelin L, O'Brien S, Johnson W, Yamaguchi N.
Phylogeny and Evolution of Cats (Felidae) in McDonald, D. and A. Loverage (eds.).
Biology and Conservation of Wild Felids. 2007. In Press. [Journal]
9)  Waits L, Buckley-Beason V, Johnson W, Onorato D, McCarthy T.
A select panel of polymorphic microsatellite loci for individual identification of snow leopards (Panthera unica).
Molecular Ecology Notes. 7: 311-314, 2007. [Journal]
10)  Antunes A, Pontius J, Ramos M, O'Brien S, Johnson W.
Mitochondrial introgressions into the nuclear genome of the domestic cat.
J. of Heredity. 98: 414-420, 2007. [Journal]
11)  Johnson W, Perelman P.
The Alpaca Enters the Genomic Era: Development of a Radiation-Hybrid Map.
Alpaca Magazine. Autumn: 234-239, 2007. [Journal]
12)  Buckley-Beason V, Johnson W, Nash W, Menninger J, Driscoll C, Howard G, Bush M, Page J, Roelke M, Stone G, Martelli P, Wen C, Ling L, Duraisingam R, Lam P, O'Brien S.
Molecular evidence for species-level distinction in modern clouded leopards (Neofelis nebulosa).
Current Biology. 16: 2371-2376, 2006. [Journal]
13)  Carrington M, O'Brien SJ.
The influence of HLA genotype on AIDS.
Annu Rev Med. 54: 535-51, 2003. [Journal]
14)  Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, Springer MS.
Resolution of the early placental mammal radiation using Bayesian phylogenetics.
Science. 294: 2348-51, 2001. [Journal]
15)  Dean M, Carrington M, O'Brien SJ.
Balanced polymorphism selected by genetic versus infectious human disease.
Annu Rev Genomics Hum Genet. 3: 263-92, 2002. [Journal]
16)  O'Brien SJ, Menotti-Raymond M, Murphy WJ, Yuhki N.
The feline genome project.
Annu Rev Genet. 36: 657-86, 2002. [Journal]
17)  Stefanov S, Lautenberger J, Gold B.
An Analysis Pipeline for Genome-wide Association Studies.
Cancer Informatics. 2008. In Press. [Journal]
18)  Zeng Z, Guan L, An P, Sun S, O'Brien SJ, Winkler CA.
A population-based study to investigate host genetic factors associated with hepatitis B infection and pathogenesis in the Chinese population.
BMC Infect. Dis. 8: 1, 2008. [Journal]
19)  Hutcheson HB, Lautenberger JA, Nelson GW, Pontius JU, Kessing BD, Winkler CA, Smith MW, Johnson R, Stephens R, Phair J, Goedert JJ, Donfield S, O'Brien SJ.
Detecting AIDS restriction genes: From candidate genes to genome-wide association discovery.
Vaccine. 2008. [Journal]
20)  Napolitano C, Bennett M, Johnson W.
Ecological and biogeographical inferences on two sympatric and enigmatic Andean cat species using genetic identification of faecal samples.
Molecular Ecology. 17: 678-690, 2008. [Journal]
21)  Truelove AL, Oleksyk TK, Shrestha S, Thio CL, Goedert JJ, Donfield SM, Kirk GD, Thomas DL, O'Brien SJ, Smith MW.
Evaluation of IL10, IL19 and IL20 gene polymorphisms and chronic hepatitis B infection outcome.
Int. J. Immunogenet. 35: 255-64, 2008. [Journal]
22)  Pecon-Slattery J, Troyer JL, Johnson WE, O'Brien SJ.
Evolution of feline immunodeficiency virus in Felidae: Implications for human health and wildlife ecology.
Vet. Immunol. Immunopathol. 123: 32-44, 2008. [Journal]
23)  Roelke M, Johnson W, Millan J.
Exposure to disease agents in the endangered lberian lynx (Lynxpardinus).
European Journal of Wildlife Research. 54(2): 171-178, 2008. [Journal]
24)  Troyer JL, Vandewoude S, Pecon-Slattery J, McIntosh C, Franklin S, Antunes A, Johnson W, O'Brien SJ.
FIV cross-species transmission: An evolutionary prospective.
Vet. Immunol. Immunopathol. 123: 159-66, 2008. [Journal]
25)  Münk C, Beck T, Zielonka J, Hotz-Wagenblatt A, Chareza S, Battenberg M, Thielebein J, Cichutek K, Bravo IG, O'Brien SJ, Löchelt M, Yuhki N.
Functions, structure, and read-through alternative splicing of feline APOBEC3 genes.
Genome Biol. 9: R48, 2008. [Journal]
26)  Brown MA, Cunningham MW, Roca AL, Troyer JL, Johnson WE, O'Brien SJ.
Genetic characterization of feline leukemia virus from Florida panthers.
Emerging Infect. Dis. 14: 252-9, 2008. [Journal]
27)  Pecon-Slattery J, McCracken CL, Troyer JL, VandeWoude S, Roelke M, Sondgeroth K, Winterbach C, Winterbach H, O'Brien SJ.
Genomic organization, sequence divergence, and recombination of feline immunodeficiency virus from lions in the wild.
BMC Genomics. 9: 66, 2008. [Journal]
28)  Guo X, O'Brien SJ, Zeng Y, Nelson GW, Winkler CA.
GSTM1 and GSTT1 Gene Deletions and the Risk for Nasopharyngeal Carcinoma in Han Chinese.
Cancer Epidemiol. Biomarkers Prev. 17: 1760-3, 2008. [Journal]
29)  Hendrickson SL, Jacobson LP, Nelson GW, Phair JP, Lautenberger J, Johnson RC, Kingsley L, Margolick JB, Detels R, Goedert JJ, O'Brien SJ.
Host Genetic Influences on Highly Active Antiretroviral Therapy Efficacy and AIDS-Free Survival.
J. Acquir. Immune Defic. Syndr. 2008. [Journal]
30)  Oleksyk TK, Zhao K, De La Vega FM, Gilbert DA, O'Brien SJ, Smith MW.
Identifying selected regions from heterozygosity and divergence using a light-coverage genomic dataset from two human populations.
PLoS ONE. 3: e1712, 2008. [Journal]
31)  Marker L, Wilkerson A, Sarno R.
Molecular genetic insights on cheetah (Acinonyx jubatus) ecology and conservation in Namibia.
Journal of Heredity. 99(1): 2-13, 2008. [Journal]
32)  Menotti-Raymond M, David V, Pflueger S.
Paterns of molecular genetic variation among cat breeds.
Genomics. 91: 1-11, 2008. [Journal]
33)  Yuhki N, Mullikin JC, Beck T, Stephens R, O'Brien SJ.
Sequences, annotation and single nucleotide polymorphism of the major histocompatibility complex in the domestic cat.
PLoS ONE. 3: e2674, 2008. [Journal]
34)  O'Brien SJ, Johnson W, Driscoll C, Pontius J, Pecon-Slattery J, Menotti-Raymond M.
State of cat genomics.
Trends Genet. 24: 268-79, 2008. [Journal]
35)  Luo SJ, Johnson WE, Martenson J, Antunes A, Martelli P, Uphyrkina O, Traylor-Holzer K, Smith JL, O'Brien SJ.
Subspecies genetic assignments of worldwide captive tigers increase conservation value of captive populations.
Curr. Biol. 18: 592-6, 2008. [Journal]
36)  da Fonseca RR, Johnson WE, O'Brien SJ, Ramos MJ, Antunes A.
The adaptive evolution of the mammalian mitochondrial genome.
BMC Genomics. 9: 119, 2008. [Journal]
37)  Nash W, Menninger J, Padilla-Nash H.
The ancestral carnivore karyotype (2n=38) lives today in ringtails.
Journal of Heredity. 99 (3): 241-253, 2008. [Journal]
38)  O'Brien SJ.
The platypus genome unraveled.
Cell. 133: 953-5, 2008. [Journal]
39)  Menotti-Raymond M, O'Brien S.
The domestic cat, Felis catus, as a model of hereditary and infectious disease. In: Sourcebook of Models for Biomedical Research. Volume .
Totowa, NJ: Humana Press, Inc.; 2007. In Press. [Book Chapter]
40)  Menotti-Raymond M, David V, O'Brien S.
STR based forensic analysis of felid samples from domestic and exotic cats. In: Non-Human DNA Typing: Theory and Casework Applications. Volume .
Boca Raton, FL: Taylor and Francis Group, LLC; 2007. p. 69-86 [Book Chapter]
41)  Murphy W, Davis B, David V, Agarwala R, Schaffer A, Wilkerson A, Neelam B, O'Brien S, Menotti-Raymond M.
A 1.5-Mb-resolution radiation hybrid map of the cat genome and comparative analysis with the canine and human genomes.
Genomics. 89 (2): 189-96, 2007. [Journal]
42)  Miller-Butterworth C, Murphy W, O'Brien S, Jacobs D, Springer M, Teeling E.
A Family Matter: Conclusive Resolution of the Taxonomic Position of the Long-fingered Bats, Miniopterus.
Mol Biol Evol. Epub ahead of print, 2007. [Journal]
43)  Martin MP, Pascal V, Yeager M, Phair J, Kirk GD, Hoots K, O'brien SJ, Anderson SK, Carrington M.
A mutation in KIR3DS1 that results in truncation and lack of cell surface expression.
Immunogenetics. 2007. [Journal]
44)  Wilting A, Buckley-Beason V, Feldhaar H, Gadau J, O'Brien S, Linsenmair K.
Clouded leopard phylogeny revisited: support for species recognition and population division between Borneo and Sumatra.
Front Zool. 4: 15, 2007. [Journal]
45)  Yuhki N, Beck T, Stephens R, Neelam B, O'Brien S.
Comparative genomic structure of human, dog, and cat MHC: HLA, DLA, and FLA.
Journal of Heredity. 98: 390-399, 2007. Full Text Article. [Journal]
46)  Roca AL, Georgiadis N, O'Brien SJ.
Cyto-nuclear genomic dissociation and the African elephant species question.
Quaternary international : the journal of the International Union for Quaternary Research. 169-170: 4-16, 2007. [Journal]
47)  Luo S, Johnson W, David V, Menotti-Raymond M, Stanyon R, Cai Q, Beck T, Yuhki N, Pecon-Slattery J, Smith J, O'Brien S.
Development of Y Chromosome Intraspecific Polymorphic Markers in the Felidae.
J Hered. 98(5): 400-13, 2007. [Journal]
48)  King V, Goodfellow P, Pearks-Wilkerson A, Johnson W, O'Brien S, Pecon-Slattery J.
Evolution of the male-determining gene SRY within the cat family Felidae.
Genetics. 175: 1855-1867, 2007. [Journal]
49)  Kehler J, David V, Schaffer A, Eizirik E, Ryugo D, Hannah S, O'Brien S, Menotti-Raymond M.
Four separate mutations in the feline fibroblast growth factor 5 gene are responsible for long hair in the domestic cat.
Journal of Heredity. 98(6): 555-566, 2007. [Journal]
50)  Vàzquez-Salat N, Yuhki N, Beck T, O'Brien SJ, Murphy WJ.
Gene conversion between mammalian CCR2 and CCR5 chemokine receptor genes: a potential mechanism for receptor dimerization.
Genomics. 90: 213-24, 2007. [Journal]
51)  Thio C, Astemborski J, Bashirova A, Mosbruger T, Greer S, Witt M, Goedert J, Hilgartner M, Majeske A, O'Brien S, Thomas D, Carrington M.
Genetic protection against hepatitis B virus conferred by CCR5 Delta 32: Evidence that CCR5 contributes to viral persistence.
J Virol. 81 (2): 441-5, 2007. [Journal]
52)  Pontius J, O'Brien S.
Genome Annotation Resource Fields - GARFIELD: a genome browser for felis catus.
J hered. 98 (5): 386-389, 2007. [Journal]
53)  Wetzel T, Gao X, Pfeiffer R, Martin M, O'Brien S, Goedert J, Carrington M, O'Brien T.
HLA-B Bw4 alleles and HIV-1 transmission in heterosexual couples.
AIDS. 21 (2): 225-9, 2007. [Journal]
54)  Martin MP, Qi Y, Gao X, Yamada E, Martin JN, Pereyra F, Colombo S, Brown EE, Shupert WL, Phair J, Goedert JJ, Buchbinder S, Kirk GD, Telenti A, Connors M, O'Brien SJ, Walker BD, Parham P, Deeks SG, McVicar DW, Carrington M.
Innate partnership of HLA-B and KIR3DL1 subtypes against HIV-1.
Nat. Genet. 39: 733-40, 2007. [Journal]
55)  Luo S, Cai Q, David V, Zang L, Martelli P, Lim NT, Ferrand N, Chin S, Gaubert P, Ramos MJ, O'Brien SJ, Antunes A, Johnson W.
Isolation and characterization of microsatellite markers in pangolins (Mammalia, Pholidota, Manis spp.).
Molecular Ecology Notes. 7 (2): 269-272, 2007. Full Text Article. [Journal]
56)  Menotti-Raymond M, David V, Schaffer A, Stephens R, Wells D, Kumar-Singh R, O'Brien S, Narfstrom K.
Mutation in CEP290 discovered for cat model of human retinal degeneration.
Journal of Heredity. 98: 211-220, 2007. [Journal]
57)  Menotti-Raymond M, David V, Pflueger S, O'Brien S, Johnson W.
Patterns of molecular genetic variation among cat breeds.
Genomics. 91(1): 1-11, 2007. [Journal]
58)  Ping A, Duggal P, Wang LH, O'Brien SJ, Donfield S, Goedert JJ, Phair J, Buchbinder S, Kirk G, Winkler C.
Polymorphisms of CUL5 are associated with CD4(+) T cell loss in HIV-1 infected individuals.
Plos Genetics. 3 (1): e19, 2007. [Journal]
59)  O'Brien SJ.
Q&A: Stephen J. O'Brien.
Curr. Biol. 17 (5): R152-4, 2007. [Journal]
60)  An P, Wang LH, Hutcheson-Dilks H, Nelson G, Donfield S, Goedert JJ, Rinaldo CR, Buchbinder S, Kirk GD, O'Brien SJ, Winkler CA.
Regulatory polymorphisms in the cyclophilin A gene, PPIA, accelerate progression to AIDS.
PLoS Pathog. 3: e88, 2007. [Journal]
61)  Pontius J, Mullikin J, Smith D, Agencourt Sequencing Team , Lindblad-Toh K, Gnerre S, Clamp M, Chang J, Stephens R, Neelam B, Volfovsky N, Schaffer A, Agarwala R, Narfstrom K, Murphy W, Giger U, Roca A, Antunes A, Menotti-Raymond M, Yuhki N, Pecon-Slattery J, Johnson W, Bourque G, Tesler G, O'Brien S.
The domestic cat genome sequence: annotation and comparative inferences.
Genome Research. 17: 1675-1689, 2007. [Journal]
62)  O'Brien SJ, Johnson WE.
The Evolution of the Cats.
Scientific American. 297: 68-75, 2007. [Journal]
63)  Driscoll CA, Menotti-Raymond M, Roca AL, Hupe K, Johnson WE, Geffen E, Harley EH, Delibes M, Pontier D, Kitchener AC, Yamaguchi N, O'brien SJ, Macdonald DW.
The Near Eastern origin of cat domestication.
Science. 317: 519-23, 2007. [Journal]
64)  Coomber N, David VA, O'brien SJ, Menotti-Raymond M.
Validation of a short tandem repeat multiplex typing system for genetic individualization of domestic cat samples.
Croat. Med. J. 48: 547-55, 2007. [Journal]
65)  Murphy WJ, David B, David VA, Agarwala R, Schaffer AA, Pearks-Wilkerson AJ, Neelam B, O'Brien SJ, Menotti-Raymond M.
A 1.5 megabase resolution radiation hybrid map of the cat genome and comparative analysis with the canine and human genomes.
Genomics. 89(2): 189-196, 2006. [Journal]
66)  Ishida Y, David VA, Eizirik E, Schaffer AA, Neelam BA, Roelke ME, Hannah SS, O'Brien SJ, Menotti-Raymond M.
A homozygous single-base deletion in MLPH causes the dilute coat color phenotype in the domestic cat.
Genomics. 88(6): 698-705, 2006. [Journal]
67)  Capelli C, Macphee R, Roca A, Brisighelli F, Georgiadis N, O'Brien S, Greenwood A.
A nuclear DNA phylogeny of the woolly mammoth (Mammuthus primigenius).
Mol Phylogenet Evol. 40(2): 620-7, 2006. [Journal]
68)  Menotti-Raymond M, Fyfe JC, David VA, Brichta L, Schaffer AA, Agarwala R, Murphy WJ, Wedemeyer WJ, Drummond MC, Buzzell BG, Gregory BL, Wirth B, O'Brien SJ.
An ~140 kb deletion associated with feline spinal muscular atrophy implies an essential LIX1 function for motor neuron survival.
Genome Research. 16(9): 1084-1090, 2006. [Journal]
69)  Guo X, O'Brien S, Winkler C, Scott K, Hutcheson H, David V, Kessing B, Zheng Y, Liao J, Lui Y, Guy de T, Zeng Y.
Association study of chromosome 4 STRs polymorphisms with nasopharyngeal carcinoma.
Yi Chuan. 28(7): 783-90. Chinese, 2006. [Journal]
70)  Shrestha S, Strathdee S, Galai N, Oleksyk T, Fallin M, Mehta S, Schaid D, Vlahov D, O'Brien S, Smith M.
Behavioral risk exposure and host genetics of susceptibility to HIV-1.
J Infect Dis. 193(1):: 16-26, 2006. [Journal]
71)  Bashirova A, Bleiber G, Qi Y, Hutcheson H, Yamashita T, Johnson R, Cheng J, Alter G, Goedert J, Buchbinder S, Hoots K, Vlahov D, May M, Maldarelli F, Jacobson L, O'Brien S, Telenti A, Carrington M.
Consistent effects of TSG101 genetic variability on multiple outcomes of exposure to human immunodeficiency virus type 1.
J Virol. 80(14): 6757-63, 2006. [Journal]
72)  Baker C, Vant M, Dalebout M, Lento G, O'Brien S, Yuhki N.
Diversity and duplication of DQB and DRB-like genes of the MHC in baleen whales.
Immunogenetics. 58(4): 283-96, 2006. [Journal]
73)  Gao X, Single R, Karacki P, Marti D, O'Brien S, Carrington M.
Diversity of MICA and linkage disequilibrium with HLA-B in two North American.
Hum Immunol. 67(3): 152-8, 2006. [Journal]
74)  Javanbakht H, An P, Gold B, Peterson D, O'hUigin C, Nelson G, O'Brien S, Kirk G, Detels R, Buchbinder S, Donfield S, Shulenin S, Song B, Perron M, Stremlau M, Sodroski J, Dean M, Winkler C.
Effects of human TRIM5a1pha polymorphisms on antiretroviral function and susceptibility to human immunodeficiency virus infection.
Virology. 354(1): 15-27, 2006. [Journal]
75)  Lind J, Hutcheson-Dilks H, Williams S, Moore J, Essex M, Ruiz-Pesini E, Wallace D, Tishkoff S, O'Brien S, Smith M.
Elevated male European and female African contributions to the genomes of African American individuals.
Hum Genet. 120(5): 713-22, 2006. [Journal]
76)  Kim J, Antunes A, Luo S, Menninger J, Nash WG, O'Brien SJ, Johnson WE.
Evolutionary analysis of a large mtDNA translocation (numt) into the nuclear genome of the Panthera genus species.
Gene. 366(2):: 292-302, 2006. [Journal]
77)  Guo X, Scott K, Liu Y, Dean M, David V, Nelson G, Johnson R, Dilks H, Lautenberger J, Kessing B, Martenson J, Guan L, Sun S, Deng H, Zheng Y, de The G, Liao J, Zeng Y, O'Brien S, Winkler C.
Genetic factors leading to chronic Epstein-Barr virus infection and nasopharyngeal carcinoma in South East China: study design, methods and feasibility.
Hum Genomics. 2(6): 365-75, 2006. [Journal]
78)  Modi W, Lautenberger J, An P, Scott K, Goedert J, Kirk G, Buchbinder S, Phair J, Donfield S, O'Brien S, Winkler C.
Genetic Variation in the CCL18-CCL3-CCL4 Chemokine Gene Cluster Influences HIV.
Am J Hum Genet. 79(1): 120-8, 2006. [Journal]
79)  Qi Y, Martin M, Gao X, Jacobson L, Goedert J, Buchbinder S, Kirk G, O'Brien S, Trowsdale J, Carrington M.
KIR/HLA Pleiotropism: Protection against both HIV and Opportunistic Infections.
PLoS Pathog. 8: e79, 2006. [Journal]
80)  Buckley-Beason VA, Johnson WE, Nash WG, Stanyon R, Menninger JC, Driscoll CA, Howard J, Bush M, Page JE, Roelke ME, Stone G, Martelli PP, Wen C, Ling L, Duraisingam RK, Lam PV, O'Brien SJ.
Molecular evidence for species-level distinctions in clouded leopards.
Curr. Biol. 16: 2371-6, 2006. [Journal]
81)  O'Brien SJ, Troyer JL, Roelke M, Marker L, Pecon-Slattery J.
Plagues and adaptation: Lessions from the Felidae models for SARS and AIDS.
Biological Conservation. 131, Issue 2: 255-265, 2006. [Journal]
82)  Roelke ME, Pecon-Slattery J, Taylor S, Citino S, Brown E, Packer C, Vandewoude S, O'Brien SJ.
T-lymphocyte profiles in FIV-infected wild lions and pumas reveal CD4 depletion.
J. Wildl. Dis. 42: 234-48, 2006. [Journal]
83)  Johnson W, Eizirik E, Pecon-Slattery J, Murphy W, Antunes A, Teeling E, O'Brien S.
The late Miocene radiation of modern Felidae: a genetic assessment.
Science. 311(5757):: 73-7, 2006. [Journal]
84)  Nelson G, O'Brien S.
Using Mutual Information to Measure the Impact of Multiple Genetic Factors on.
J Acquir Immune Defic Syndr. 42(3): 347-54, 2006. [Journal]
85)  Teeling EC, Springer MS, Madsen O, Bates P, O'brien SJ, Murphy WJ.
A molecular phylogeny for bats illuminates biogeography and the fossil record.
Science. 307: 580-4, 2005. [Journal]
86)  Menotti-Raymond MA, David VA, Wachter LL, Butler JM, O'Brien SJ.
An STR forensic typing system for genetic individualization of domestic cat (Felis catus) samples.
J. Forensic Science. 50: 1061-70, 2005. [Journal]
87)  O'Brien SJ, Johnson WE.
Big cat genomics.
Annual review of genomics and human genetics. 6: 407-29, 2005. [Journal]
88)  Roca AL, Georgiadis N, O'Brien SJ.
Cytonuclear genomic dissociation in African elephant species.
Nat Genet. 37: 96-100, 2005. [Journal]
89)  Murphy WJ, Larkin DM, Everts-van der Wind A, Bourque G, Tesler G, Auvil L, Beever JE, Chowdhary BP, Galibert F, Gatzke L, Hitte C, Meyers SN, Milan D, Ostrander EA, Pape G, Parker HG, Raudsepp T, Rogatcheva MB, Schook LB, Skow LC, Welge M, Womack JE, O'brien SJ, Pevzner PA, Lewin HA.
Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps.
Science. 309: 613-617, 2005. [Journal]
90)  He Q, Lowrie C, Shelton GD, Castellani RJ, Menotti-Raymond M, Murphy W, O'Brien SJ, Swanson WF, Fyfe JC.
Inherited motor neuron disease in domestic cats: a model of spinal muscular atrophy.
Pediatr. Res. 57: 324-30, 2005. [Journal]
91)  Roca AL, Nash WG, Menninger JC, Murphy WJ, O'Brien SJ.
Insertional polymorphisms of endogenous feline leukemia viruses.
J Virol. 79: 3979-86, 2005. [Journal]
92)  Troyer JL, Pecon-Slattery J, Roelke ME, Johnson W, VandeWoude S, Vazquez-Salat N, Brown M, Frank L, Woodroffe R, Winterbach C, Winterbach H, Hemson G, Bush M, Alexander KA, Revilla E, O'Brien SJ.
Seroprevalence and Genomic Divergence of Circulating Strains of Feline Immunodeficiency Virus among Felidae and Hyaenidae Species.
J. Virol. 79: 8282-94, 2005. [Journal]
93)  Donfield SM, Kirk GD, Thomas DL, O'Brien SJ, Smith MW, Oleksyk TK, Thio CL, Truelove AL, Goedert JJ.
Single nucleotide polymorphisms and haplotypes in the IL10 region associated with HCV clearance.
Genes Immun. 6: 347-57, 2005. [Journal]
94)  Duggal P, Winkler CA, An P, Yu XF, Farzadegan H, O'Brien SJ, Beaty TH, Vlahov D.
The effect of RANTES chemokine genetic variants on early HIV-1 plasma RNA among African American injection drug users.
J Acquir Immune Defic Syndr. 38: 584-9, 2005. [Journal]
95)  Beck TW, Menninger J, Murphy WJ, Nash WG, O'brien SJ, Yuhki N.
The feline major histocompatibility complex is rearranged by an inversion with a breakpoint in the distal class I region.
Immunogenetics. 56: 702-9, 2005. [Journal]
96)  De La Vega FM, Isaac H, Hunkapiller MW, Spier EG, Gilbert DA, Collins A, Scafe CR, Halldórsson BV, Su X, Lippert RA, Wang Y, Laig-Webster M, Koehler RT, Ziegle JS, Wogan LT, Stevens JF, Leinen KM, Olson SJ, Guegler KJ, You X, Xu LH, Hemken HG, Kalush F, Itakura M, Zheng Y, de Thé G, O'Brien SJ, Clark AG, Istrail S.
The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern.
Genome Res. 15: 454-62, 2005. [Journal]
97)  Schmidt-Küntzel A, Eizirik E, O'Brien SJ, Menotti-Raymond M.
Tyrosinase and Tyrosinase Related Protein 1 Alleles Specify Domestic Cat Coat Color Phenotypes of the albino and brown Loci.
J. Hered. 289-301, 2005. [Journal]
98)  Patterson N, Hattangadi N, Lane B, Lohmueller KE, Hafler DA, Hauser SL, Smith M, O'Brien SJ, Altshuler D, Daly M, Reich D.
Methods for high density admixture mapping of disease genes.
Am. J. Hum. Gen. . 74: 979-1000, 2004.. [Journal]
99)  Smith MW, Patterson N, Sninsky JJ, Hafler DA, Altshuler D, Gilbert DA, O'Brien SJ, Reich D, Lautenberger JA, Truelove AL, McDonald GJ, Waliszewska A, Kessing BD, Malasky MJ, Scafe C, Le E, De Jager PL, Mignault AA, Yi Z, De The G, Essex M, Sankale JL, Moore JH, Poku K, Phair JP, Goedert JJ, Vlahov D, Williams SM, Tishkoff SA, Winkler CA, De La Vega FM, Woodage T.
A high-density admixture map for disease gene discovery in African Americans.
Am. J. Hum. Genet. 74: 1001-13, 2004. [Journal]
100)  Pearks Wilkerson AJ, Teeling EC, Troyer JL, Bar-Gal GK, Roelke M, Marker L, Pecon-Slattery J, O'Brien SJ.
Coronavirus outbreak in cheetahs: Lessons for SARS.
Curr Biol. 14: R227-8, 2004. [Journal]
101)  Johnson WE.
Evaluating and Predicting the Impacts of Exploitation and Trade on Canid Populations.
In Canids: foxes, wolfes, jackals and dogs. Status survey and conservation action plan. IUCN/SSC Canid Specialist Group: Gland, Switzerland, 2004. [Journal]
102)  Silverberg MJ, Smith MW, Chmiel JS, Detels R, Margolick JB, Rinaldo CR, O'Brien SJ, Muñoz A.
Fraction of cases of acquired immunodeficiency syndrome prevented by the interactions of identified restriction gene variants.
Am J Epidemiol. 159: 232-41, 2004. [Journal]
103)  Roca AL, Pecon-Slattery J, O'Brien SJ.
Genomically intact endogenous feline leukemia viruses of recent origin.
J Virol. 78: 4370-5, 2004. [Journal]
104)  O'Brien SJ, Nelson GW.
Human Genes that limit AIDS.
Nature Genetics. 36: 565-574, 2004. [Journal]
105)  Murphy WJ, Pevzner P, O'Brien SJ.
Mammalian phylogenetics comes of age.
Trends in Genetics. In press, 2004. [Journal]
106)  Karacki PS, Gao X, Thio CL, Thomas DL, Goedert JJ, Vlahov D, Kaslow RA, Strathdee S, Hilgartner MW, O'Brien SJ, Carrington M.
MICA and recovery from hepatitis C virus and hepatitis B virus infections.
Genes Immun. 2004. [Journal]
107)  Eizirik E, Murphy WJ, Springer MS, O'Brien SJ.
Molecular phylogeny and dating of early primate divergences.
In Anthropoid Origins, New Visions. In Press, 2004. [Journal]
108)  Yamaguchi N, Sarno RJ, Johnson WE, O'Brien SJ, MacDonald DW.
Multiple paternity and reproductive tactics of free-ranging American mink, Mustela vison.
Journal of Mammalogy. 85: 432-439, 2004. [Journal]
109)  Kehler J, Tolkunova E, Koschorz B, Pesce M, Gentile L, Boiani M, Lomelí H, Nagy A, McLaughlin KJ, Schöler HR, Tomilin A.
Oct4 is required for primordial germ cell survival.
EMBO Reports. 5(11):: 1078-83., 2004. [Journal]
110)  Winkler C, An P, O'Brien SJ.
Patterns of ethnic diversity among the genes that influence AIDS.
Hum Mol Genet. 13 Suppl 1: R9-R19, 2004. [Journal]
111)  Troyer JL, Pecon-Slattery J, Roelke ME, Black L, Packer C, O'Brien SJ.
Patterns of feline immunodeficiency virus multiple infection and genome divergence in a free-ranging population of African lions.
J Virol. 78: 3777-91, 2004. [Journal]
112)  Johnson WE, Godoy JA, Palomares F, Delibes M, Fernandes M, Revilla E, O'Brien SJ.
Phylogenetic and phylogeographic analysis of Iberian lynx populations.
Journal of Heredity. 95: 19-28, 2004. [Journal]
113)  Pecon-Slattery J, Peark-Wilkerson AJ, Murphy WJ, O'Brien SJ.
Phylogenetic Assessment of Introns and SINEs within the Y-chromosome Using the Cat Family Felidae as a Species Tree.
Mol. Biol. Evol. 21: 1-11, 2004. [Journal]
114)  Luo SJ, Kim JH, Johnson WE, van der Walt J, Martenson J, Yuhki N, Miquelle DG, Uphyrkina O, Goodrich JM, Quigley HB, Tilson R, Brady G, Martelli P, Subramaniam V, McDougal C, Hean S, Huang SQ, Pan W, Karanth UK, Sunquist M, Smith JL, O'Brien SJ.
Phylogeography and genetic ancestry of tigers (Panthera tigris ).
PLoS Biology. 2: 2275-2293, 2004. [Journal]
115)  Kikuchi Y, Chomel BB, Kasten RW, Martenson JS, Swift PK, O'Brien SJ.
Seroprevalence of Toxoplasma gondii in American free-ranging or captive pumas (Felis concolor) and bobcats (Lynx rufus).
Vet Parasitol. 120: 1-9, 2004. [Journal]
116)  Menotti-Raymond M, David V, O'Brien SJ.
STR based forensic analysis of felid samples from domestic and exotic cats.
Non-human DNA Typing (book). In press, 2004. [Journal]
117)  Beck TW, Menninger J, Murphy WJ, Nash WG, O'Brien SJ, Yuhki N.
The feline major histocompatibility complex is rearranged by an inversion with a breakpoint in the distal class I region.
Immunogenetics. In press, 2004. [Journal]
118)  Menotti-Raymond M, David VA, O'Brien SJ.
The generation of an STR forensic typing system for the genetic individualization of domestic cat (Felis catus) samples.
http://www.ojp.usdoj.gov/nih. Final Report 1999-IJ-R-A079, 2004. [Journal]
119)  Vila C, Leonard JA, Iriarte A, O'Brien SJ, Johnson WE, Wayne RK.
Vanishing populations of the highly endangered Darwin's fox Pseudalopex fulvipes.
Animal Conservation. 7: 147-153, 2004. [Journal]
120)  O'Brien SJ, Murphy WJ.
A dog's breakfast?.
Science. 301: 1854-1855, 2003. [Journal]
121)  An P, Vlahov D, Margolick JB, Phair J, O'Brien TR, Lautenberger J, O'Brien SJ, Winkler CA.
A tumor necrosis factor-alpha-inducible promoter variant of interferon-gamma accelerates CD4+ T cell depletion in human immunodeficiency virus-1-infected individuals.
J Infect Dis. 188: 228-31, 2003. [Journal]
122)  Modi WS.
CCL3L1 and CCL4L1 chemokine genes are located in a segmental duplication at chromosome 17q12.
Genomics. 2003. [Journal]
123)  Modi WS, Serdyukova NA, Vorobieva NV, Graphodatsky AS.
Chromosomal localization of six repeated DNA sequences among species of Microtus (Rodentia).
Chromosome Research. 11: 705-713, 2003. [Journal]
124)  Yuhki N, Beck T, Stephens RM, Nishigaki Y, Newmann K, O'Brien SJ.
Comparative Genome Organization of Human, Murine, and Feline MHC Class II Region.
Genome Res. 13: 1169-79, 2003. [Journal]
125)  Modi WS, O'Brien TR, Vlahov D, Buchbinder S, Gomperts E, Phair J, O'Brien SJ, Winkler C.
Haplotype diversity in the interleukin-4 gene is not associated with HIV-1 transmission and AIDS progression.
Immunogenetics. 55: 157-164, 2003. [Journal]
126)  Kuznetsov S, Matveeva NM, Murphy WJ, O'Brien SJ, Serov OL.
Mapping of 53 loci in American mink (Mustela vision).
Journal of Heredity. 94: 386-391, 2003. [Journal]
127)  Modi WS, Goedert JJ, Strathdee S, Buchbinder S, Detels R, Donfield S, Brien SJ, Winkler C.
MCP-1 – MCP-3 – Eotaxin Gene cluster influences HIV-1 transmission.
AIDS. 2003. [Journal]
128)  Eizirik E, Yuhki N, Johnson WE, Menotti-Raymond M, Hannah SS, O'Brien SJ.
Molecular genetics and evolution of melanism in the cat family.
Curr Biol. 13: 448-53, 2003. [Journal]
129)  Teeling EC, Madsen O, Murphy WJ, Springer MS, O'Brien SJ.
Nuclear gene sequences confirm an ancient link between New Zealand's short-tailed bat and South American noctilionoid bats.
Molecular Phylogenetics and Evolution. 28: 208-319, 2003. [Journal]
130)  Springer MS, Murphy WJ, Eizirik E, O'Brien SJ.
Placental mammal diversification and the K-T boundary.
Proceedings of the National Academy of Sciences. 100: 1056-1061, 2003. [Journal]
131)  Menotti-Raymond M, David V, Wachter L, Yuhki N, O'Brien SJ.
Quantitative polymerase chain reaction-based assay for estimating DNA yield extracted from domestic cat specimens.
Croatian Medical Journal. 44(3): 327-331, 2003. [Journal]
132)  Menotti-Raymond M, David VA, Agarwala R, Schäffer AA, Stephens R, O'Brien SJ, Murphy WJ.
Radiation hybrid mapping of 304 novel microsatellites in the domestic cat genome.
Cytogenetics & Genome Research. 2003. [Journal]
133)  Murphy WJ, Bourque G, Tesler G, Pevzner P, O'Brien SJ.
Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps.
Human Genomics. 1: 30-40, 2003. [Journal]
134)  Swanson WF, Johnson WE, Cambre RC, Citino SB, Quigley KB, Brousset D, Morais RN, Moreira N, O'Brien SJ, Wildt DE.
Reproductive status of endemic felid species in Latin American Zoos and implications for ex situ conservation.
Zoo Biology. 22: 421-441, 2003. [Journal]
135)  Menotti-Raymond M, David VA, Roelke ME, Chen ZQ, Menotti KA, Sun S, Schäffer AA, Tomlin JF, Agarwala R, O'Brien SJ, Murphy WJ.
Second-Generation Integrated Genetic Linkage/Radiation Hybrid Maps of the Domestic Cat (Felis catus).
J Hered. 94: 95-106, 2003. [Journal]
136)  Murphy WJ, Froenicke L, O'Brien SJ, Stanyon R.
The origin of human chromosome 1 and its homologues in placental mammals.
Genome Research. 13: 1880-1888, 2003. [Journal]
137)  Martinez-Cruz B, David VA, Godoy JA, Negro JJ, Johnson WE, O'Brien SJ.
18 polymorphic microsatellite markers for the highly endangered Spanish Imperial Eagle (Aquila adalberti) and cross amplification in other raptor species.
Molecular Ecology Notes. 2: 323-326, 2002. [Journal]
138)  Uphyrkina O, Miquelle D, Quigley H, Driscoll C, O'Brien SJ.
Conservation genetics of the Far Eastern leopard (Panthera pardus orientalis).
J Hered. 93: 303-11, 2002. [Journal]
139)  Martin MP, Gao X, Lee JH, Nelson GW, Detels R, Goedert JJ, Buchbinder S, Hoots K, Vlahov D, Trowsdale J, Wilson M, O'Brien SJ, Carrington M.
Epistatic interaction between KIR3DS1 and HLA-B delays the progression to AIDS.
Nat Genet. 31: 429-34, 2002. [Journal]
140)  Palomares F, Godoy JA, Piriz A, O'Brien SJ, Johnson WE.
Fecal genetic analysis to determine the presence and distribution of elusive carnivores: design and feasibility for the Iberian Lynx.
Molecular Ecology. 11: 2171-2182, 2002. [Journal]
141)  Driscoll CA, Menotti-Raymond M, Nelson G, Goldstein D, O'Brien SJ.
Genomic microsatellites as evolutionary chronometers: a test in wild cats.
Genome Res. 12: 414-23, 2002. [Journal]
142)  Copeland NG, Jenkins NA, O'Brien SJ.
Genomics. Mmu 16--comparative genomic highlights.
Science. 296: 1617-8, 2002. [Journal]
143)  Harty LC, Lin AY, Goldstein AM, Jaffe ES, Carrington M, Tucker MA, Modi WS.
HLA-DR, HLA-DQ, and TAP genes in familial Hodgkin disease.
Blood. 99: 690-693, 2002. [Journal]
144)  An P, Nelson GW, Wang L, Donfield S, Goedert JJ, Phair J, Vlahov D, Buchbinder S, Farrar WL, Modi W, O'Brien SJ, Winkler CA.
Modulating influence on HIV/AIDS by interacting RANTES gene variants.
Proc Natl Acad Aci USA. 99: 1002-1007, 2002. [Journal]
145)  Butler JM, David VA, Menotti-Raymond M.
The "MeowPlex:" A new DNA test using tetranucleotide STR markers for the domestic cat.
Profiles in DNA. 5(2): 7-10, 2002. [Journal]
146)  Murphy WJ, Page JE, Smith C, Desrosiers RC, O'Brien SJ.
A radiation hybrid mapping panel for the rhesus macaque.
J Hered. 92: 516-9, 2001. [Journal]
147)  O'Brien SJ.
Cell culture forensics.
Proc Natl Acad Sci U S A. 98: 7656-8, 2001. [Journal]
148)  Beck TW, Menninger J, Voigt G, Newmann K, Nishigaki Y, Nash WG, Stephens RM, Wang Y, de Jong PJ, O'Brien SJ, Yuhki N.
Comparative feline genomics: a BAC/PAC contig map of the major histocompatibility complex class II region.
Genomics. 71: 282-95, 2001. [Journal]
149)  Gao X, Nelson GW, Karacki P, Martin MP, Phair J, Kaslow R, Goedert JJ, Buchbinder S, Hoots K, Vlahov D, O'Brien SJ, Carrington M.
Effect of a single amino acid change in MHC class I molecules on the rate of progression to AIDS.
N Engl J Med. 344: 1668-75, 2001. [Journal]
150)  Murphy WJ, Stanyon R, O'Brien SJ.
Evolution of mammalian genome organization inferred from comparative gene mapping.
Genome Biol. 2: REVIEWS0005, 2001. [Journal]
151)  Roca AL, Georgiadis N, Pecon-Slattery J, O'Brien SJ.
Genetic evidence for two species of elephant in Africa.
Science. 293: 1473-7, 2001. [Journal]
152)  O'Brien SJ, Eizirik E, Murphy WJ.
Genomics. On choosing mammalian genomes for sequencing.
Science. 292: 2264-6, 2001. [Journal]
153)  Sun S, Murphy WJ, Menotti-Raymond M, O'Brien SJ.
Integration of the feline radiation hybrid and linkage maps.
Mamm Genome. 12: 436-41, 2001. [Journal]
154)  Smith MW, Lautenberger JA, Shin HD, Chretien JP, Shrestha S, Gilbert DA, O'Brien SJ.
Markers for mapping by admixture linkage disequilibrium in African American and Hispanic populations.
Am J Hum Genet. 69: 1080-94, 2001. [Journal]
155)  Eizirik E, Murphy WJ, O'Brien SJ.
Molecular dating and biogeography of the early placental mammal radiation.
J Hered. 92: 212-9, 2001. [Journal]
156)  Murphy WJ, Eizirik E, Johnson WE, Zhang YP, Ryder OA, O'Brien SJ.
Molecular phylogenetics and the origins of placental mammals.
Nature. 409: 614-8, 2001. [Journal]
157)  Uphyrkina O, Johnson WE, Quigley H, Miquelle D, Marker L, Bush M, O'Brien SJ.
Phylogenetics, genome diversity and origin of modern leopard, Panthera pardus.
Mol Ecol. 10: 2617-33, 2001. [Journal]
158)  Eizirik E, Kim JH, Menotti-Raymond M, Crawshaw PG, O'Brien SJ, Johnson WE.
Phylogeography, population history and conservation genetics of jaguars (Panthera onca, Mammalia, Felidae).
Mol Ecol. 10: 65-79, 2001. [Journal]
159)  Sarno RJ, David VA, Franklin WL, O'Brien SJ, Johnson WE.
Development of microsatellite markers in the guanaco, Lama guanicoe: utility for South American camelids.
Mol Ecol. 9: 1922-4, 2000. [Journal]
160)  Pecon-Slattery J, Sanner-Wachter L, O’Brien SJ.
Directed gene conversion occurs between mammalian X and Y homologues outside the pseudoautosomal region.
Proc. Natl. Acad. Sci. USA,97: 5307-5312, 2000. [Journal]
161)  Shin HD, Winkler C, Stephens JC, Bream J, Young H, Goedert JJ, O'Brien TR, Vlahov D, Buchbinder S, Giorgi J, Rinaldo C, Donfield S, Willoughby A, O'Brien SJ, Smith MW.
Genetic restriction of HIV-1 pathogenesis to AIDS by promoter alleles of IL10.
Proc Natl Acad Sci U S A. 97: 14467-72, 2000. [Journal]
162)  An P, Martin MP, Nelson GW, Carrington M, Smith MW, Gong K, Vlahov D, O'Brien SJ, Winkler CA.
Influence of CCR5 promoter haplotypes on AIDS progression in African-Americans.
AIDS. 14: 2117-22, 2000. [Journal]
163)  Pecon-Slattery J, Murphy WI, O’Brien SJ.
Monophyletic origin of SINE retroposons located on the Y chromosome in Felidae (Mammalia).
Mol. Biol. Evol. 17: 825-829, 2000. [Journal]
164)  O'Brien SJ, Nelson GW, Winkler CA, Smith MW.
Polygenic and multifactorial disease gene association in man: Lessons from AIDS.
Annu Rev Genet. 34: 563-591, 2000. [Journal]
165)  O'Brien SJ, Moore JP.
The effect of genetic variation in chemokines and their receptors on HIV transmission and progression to AIDS.
Immunol Rev. 177: 99-111, 2000. [Journal]
166)  Johnson WE, Slattery JP, Eizirik E, Kim JH, Raymond MM, Bonacic C, Cambre R, Crawshaw P, Nunes A, Seuánez HN, Moreira MA, Seymour KL, Simon F, Swanson W, O'Brien SJ.
Disparate phylogeographic patterns of mitochondrial DNA variation in four closely related South American small cat species.
Mol. Biol. Evol. 8: S79-S94, 1999. [Journal]
167)  McKenzie LM, Pecon-Slattery J, Carrington M, O'Brien SJ.
Taxonomic hierarchy of HLA class I allele sequences.
Genes Immun. 1: 120-9, 1999. [Journal]
168)  Yuhki N, Beck T, Stephens R, Neelam B, O'brien SJ.
Comparative Genomic Structure of Human, Dog, and Cat MHC: HLA, DLA, and FLA.
J. Hered. 98: 390-9, , ,. [Journal]
169)  Pontius JU, O'brien SJ.
Genome Annotation Resource Fields GARFIELD: A Genome Browser for Felis catus.
J. Hered. 98: 386-9, , ,. [Journal]
170)  Antunes A, Faria R, Johnson WE, Guyomard R, Alexandrino P.
Life on the edge: the long-term persistence and contrasting spatial genetic structure of distinct brown trout life histories at their ecological limits.
J. Hered. 97: 193-205, , ,. [Journal]
171)  Antunes A, Pontius J, Ramos MJ, O'brien SJ, Johnson WE.
Mitochondrial introgressions into the nuclear genome of the domestic cat.
J. Hered. 98: 414-20, , ,. [Journal]
172)  Menotti-Raymond M, David VA, Schäffer AA, Stephens R, Wells D, Kumar-Singh R, O'Brien SJ, Narfström K.
Mutation in CEP290 discovered for cat model of human retinal degeneration.
J. Hered. 98: 211-20, , ,. [Journal]
173)  Nash WG, Menninger JC, Padilla-Nash HM, Stone G, Perelman PL, O'Brien SJ.
The ancestral carnivore karyotype (2n = 38) lives today in ringtails.
J. Hered. 99: 241-53, , ,. [Journal]

This page was last updated on 9/29/2008.