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Institution

Rachel J O'Neill PhD

TitleAssociate Professor
InstitutionUniversity of Connecticut
DepartmentMolecular and Cell Biology
AddressUNIT 2131
Beach Hall, UNIT 2131
354 Mansfield Road
Phone860-486-6031
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Chen CC, Bowers S, Lipinszki Z, Palladino J, Trusiak S, Bettini E, Rosin L, Przewloka MR, Glover DM, O'Neill RJ, Mellone BG. Establishment of Centromeric Chromatin by the CENP-A Assembly Factor CAL1 Requires FACT-Mediated Transcription. Dev Cell. 2015 Jul 6; 34(1):73-84. PMID: 26151904; PMCID: PMC4495351 [Available on 07/06/16].
    2. Itoh Y, Mackie R, Kampf K, Domadia S, Brown JD, O'Neill R, Arnold AP. Four core genotypes mouse model: localization of the Sry transgene and bioassay for testicular hormone levels. BMC Res Notes. 2015; 8:69. PMID: 25870930; PMCID: PMC4354741.
    3. Longo MS, Brown JD, Zhang C, O'Neill MJ, O'Neill RJ. Identification of a recently active mammalian SINE derived from ribosomal RNA. Genome Biol Evol. 2015 Mar; 7(3):775-88. PMID: 25637222.
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    4. O'Neill MJ, O'Neill RJ. Genomics: Something to swing about. Nature. 2014 Sep 11; 513(7517):174-5. PMID: 25209792.
      View in: PubMed
    5. Jiang Z, Sun J, Dong H, Luo O, Zheng X, Obergfell C, Tang Y, Bi J, O'Neill R, Ruan Y, Chen J, Tian XC. Transcriptional profiles of bovine in vivo pre-implantation development. BMC Genomics. 2014; 15:756. PMID: 25185836; PMCID: PMC4162962.
    6. O'Neill RJ, Vrana PB, Rosenfeld CS. Maternal methyl supplemented diets and effects on offspring health. Front Genet. 2014; 5:289. PMID: 25206362; PMCID: PMC4143751.
    7. Harris SE, O'Neill RJ, Munshi-South J. Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations. Mol Ecol Resour. 2015 Mar; 15(2):382-94. PMID: 24980186; PMCID: PMC4281516 [Available on 03/01/16].
    8. Velotta JP, McCormick SD, O'Neill RJ, Schultz ET. Relaxed selection causes microevolution of seawater osmoregulation and gene expression in landlocked Alewives. Oecologia. 2014 Aug; 175(4):1081-92. PMID: 24859345.
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    9. Kenney-Hunt J, Lewandowski A, Glenn TC, Glenn JL, Tsyusko OV, O'Neill RJ, Brown J, Ramsdell CM, Nguyen Q, Phan T, Shorter KR, Dewey MJ, Szalai G, Vrana PB, Felder MR. A genetic map of Peromyscus with chromosomal assignment of linkage groups (a Peromyscus genetic map). Mamm Genome. 2014 Apr; 25(3-4):160-79. PMID: 24445420; PMCID: PMC3961507.
    10. Harris SE, Munshi-South J, Obergfell C, O'Neill R. Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area. PLoS One. 2013; 8(8):e74938. PMID: 24015321; PMCID: PMC3756007.
    11. Earnshaw WC, Allshire RC, Black BE, Bloom K, Brinkley BR, Brown W, Cheeseman IM, Choo KH, Copenhaver GP, Deluca JG, Desai A, Diekmann S, Erhardt S, Fitzgerald-Hayes M, Foltz D, Fukagawa T, Gassmann R, Gerlich DW, Glover DM, Gorbsky GJ, Harrison SC, Heun P, Hirota T, Jansen LE, Karpen G, Kops GJ, Lampson MA, Lens SM, Losada A, Luger K, Maiato H, Maddox PS, Margolis RL, Masumoto H, McAinsh AD, Mellone BG, Meraldi P, Musacchio A, Oegema K, O'Neill RJ, Salmon ED, Scott KC, Straight AF, Stukenberg PT, Sullivan BA, Sullivan KF, Sunkel CE, Swedlow JR, Walczak CE, Warburton PE, Westermann S, Willard HF, Wordeman L, Yanagida M, Yen TJ, Yoda K, Cleveland DW. Esperanto for histones: CENP-A, not CenH3, is the centromeric histone H3 variant. Chromosome Res. 2013 Apr; 21(2):101-6. PMID: 23580138; PMCID: PMC3627038.
    12. Jue NK, Murphy MB, Kasowitz SD, Qureshi SM, Obergfell CJ, Elsisi S, Foley RJ, O'Neill RJ, O'Neill MJ. Determination of dosage compensation of the mammalian X chromosome by RNA-seq is dependent on analytical approach. BMC Genomics. 2013; 14:150. PMID: 23497106; PMCID: PMC3769146.
    13. Carone DM, Zhang C, Hall LE, Obergfell C, Carone BR, O'Neill MJ, O'Neill RJ. Hypermorphic expression of centromeric retroelement-encoded small RNAs impairs CENP-A loading. Chromosome Res. 2013 Mar; 21(1):49-62. PMID: 23392618.
      View in: PubMed
    14. Sharma R, Goossens B, Kun-Rodrigues C, Teixeira T, Othman N, Boone JQ, Jue NK, Obergfell C, O'Neill RJ, Chikhi L. Two different high throughput sequencing approaches identify thousands of de novo genomic markers for the genetically depleted Bornean elephant. PLoS One. 2012; 7(11):e49533. PMID: 23185354; PMCID: PMC3504023.
    15. Lindsay J, Carone DM, Brown J, Hall L, Qureshi S, Mitchell SE, Jannetty N, Hannon G, Renfree M, Pask A, O'Neill M, O'Neill R. Unique small RNA signatures uncovered in the tammar wallaby genome. BMC Genomics. 2012; 13:559. PMID: 23075437; PMCID: PMC3576234.
    16. O'Neill RJ, Sullivan BA. Foreword: the centromere and kinetochore in creatures great and small. Chromosome Res. 2012 Jul; 20(5):461-3. PMID: 22801778.
      View in: PubMed
    17. Hall LE, Mitchell SE, O'Neill RJ. Pericentric and centromeric transcription: a perfect balance required. Chromosome Res. 2012 Jul; 20(5):535-46. PMID: 22760449.
      View in: PubMed
    18. Yu H, Lindsay J, Feng ZP, Frankenberg S, Hu Y, Carone D, Shaw G, Pask AJ, O'Neill R, Papenfuss AT, Renfree MB. Evolution of coding and non-coding genes in HOX clusters of a marsupial. BMC Genomics. 2012; 13:251. PMID: 22708672; PMCID: PMC3541083.
    19. Brown JD, Piccuillo V, O'Neill RJ. Retroelement demethylation associated with abnormal placentation in Mus musculus x Mus caroli hybrids. Biol Reprod. 2012 Mar; 86(3):88. PMID: 22116807.
      View in: PubMed
    20. Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G, Wong ES, Lefèvre CM, Nicholas KR, Kuroki Y, Wakefield MJ, Zenger KR, Wang C, Ferguson-Smith M, Nicholas FW, Hickford D, Yu H, Short KR, Siddle HV, Frankenberg SR, Chew KY, Menzies BR, Stringer JM, Suzuki S, Hore TA, Delbridge ML, Patel H, Mohammadi A, Schneider NY, Hu Y, O'Hara W, Al Nadaf S, Wu C, Feng ZP, Cocks BG, Wang J, Flicek P, Searle SM, Fairley S, Beal K, Herrero J, Carone DM, Suzuki Y, Sugano S, Toyoda A, Sakaki Y, Kondo S, Nishida Y, Tatsumoto S, Mandiou I, Hsu A, McColl KA, Lansdell B, Weinstock G, Kuczek E, McGrath A, Wilson P, Men A, Hazar-Rethinam M, Hall A, Davis J, Wood D, Williams S, Sundaravadanam Y, Muzny DM, Jhangiani SN, Lewis LR, Morgan MB, Okwuonu GO, Ruiz SJ, Santibanez J, Nazareth L, Cree A, Fowler G, Kovar CL, Dinh HH, Joshi V, Jing C, Lara F, Thornton R, Chen L, Deng J, Liu Y, Shen JY, Song XZ, Edson J, Troon C, Thomas D, Stephens A, Yapa L, Levchenko T, Gibbs RA, Cooper DW, Speed TP, Fujiyama A, M Graves JA, O'Neill RJ, Pask AJ, Forrest SM, Worley KC. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol. 2011; 12(12):414. PMID: 22212627.
      View in: PubMed
    21. Brown JD, Mitchell SE, O'Neill RJ. Making a long story short: noncoding RNAs and chromosome change. Heredity (Edinb). 2012 Jan; 108(1):42-9. PMID: 22072070; PMCID: PMC3238116.
    22. Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G, Wong ES, Lefèvre CM, Nicholas KR, Kuroki Y, Wakefield MJ, Zenger KR, Wang C, Ferguson-Smith M, Nicholas FW, Hickford D, Yu H, Short KR, Siddle HV, Frankenberg SR, Chew KY, Menzies BR, Stringer JM, Suzuki S, Hore TA, Delbridge ML, Patel HR, Mohammadi A, Schneider NY, Hu Y, O'Hara W, Al Nadaf S, Wu C, Feng ZP, Cocks BG, Wang J, Flicek P, Searle SM, Fairley S, Beal K, Herrero J, Carone DM, Suzuki Y, Sugano S, Toyoda A, Sakaki Y, Kondo S, Nishida Y, Tatsumoto S, Mandiou I, Hsu A, McColl KA, Lansdell B, Weinstock G, Kuczek E, McGrath A, Wilson P, Men A, Hazar-Rethinam M, Hall A, Davis J, Wood D, Williams S, Sundaravadanam Y, Muzny DM, Jhangiani SN, Lewis LR, Morgan MB, Okwuonu GO, Ruiz SJ, Santibanez J, Nazareth L, Cree A, Fowler G, Kovar CL, Dinh HH, Joshi V, Jing C, Lara F, Thornton R, Chen L, Deng J, Liu Y, Shen JY, Song XZ, Edson J, Troon C, Thomas D, Stephens A, Yapa L, Levchenko T, Gibbs RA, Cooper DW, Speed TP, Fujiyama A, Graves JA, O'Neill RJ, Pask AJ, Forrest SM, Worley KC. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol. 2011; 12(8):R81. PMID: 21854559; PMCID: PMC3277949.
    23. Brown JD, Carone DM, Flynn BL, Finn CE, Mlynarski EE, O'Neill RJ. Centromere conversion and retention in somatic cell hybrids. Cytogenet Genome Res. 2011; 134(3):182-90. PMID: 21709412.
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    24. Heider TN, Lindsay J, Wang C, O'Neill RJ, Pask AJ. Enhancing genome assemblies by integrating non-sequence based data. BMC Proc. 2011; 5 Suppl 2:S7. PMID: 21554765; PMCID: PMC3090765.
    25. Ferreri GC, Brown JD, Obergfell C, Jue N, Finn CE, O'Neill MJ, O'Neill RJ. Recent amplification of the kangaroo endogenous retrovirus, KERV, limited to the centromere. J Virol. 2011 May; 85(10):4761-71. PMID: 21389136; PMCID: PMC3126163.
    26. Longo MS, O'Neill MJ, O'Neill RJ. Abundant human DNA contamination identified in non-primate genome databases. PLoS One. 2011; 6(2):e16410. PMID: 21358816; PMCID: PMC3040168.
    27. Mlynarski EE, Obergfell C, Dewey MJ, O'Neill RJ. A unique late-replicating XY to autosome translocation in Peromyscus melanophrys. Chromosome Res. 2010 Feb; 18(2):179-89. PMID: 20177772.
      View in: PubMed
    28. Brown JD, O'Neill RJ. Chromosomes, conflict, and epigenetics: chromosomal speciation revisited. Annu Rev Genomics Hum Genet. 2010; 11:291-316. PMID: 20438362.
      View in: PubMed
    29. Mlynarski EE, Obergfell CJ, O'Neill MJ, O'Neill RJ. Divergent patterns of breakpoint reuse in Muroid rodents. Mamm Genome. 2010 Feb; 21(1-2):77-87. PMID: 20033182.
      View in: PubMed
    30. Longo MS, Carone DM. Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty. BMC Genomics. 2009; 10:334. PMID: 19630942; PMCID: PMC2736999.
    31. Brown JD, O'Neill RJ. The mysteries of chromosome evolution in gibbons: methylation is a prime suspect. PLoS Genet. 2009 Jun; 5(6):e1000501. PMID: 19557194; PMCID: PMC2695000.
    32. O'Neill RJ, Carone DM. The role of ncRNA in centromeres: a lesson from marsupials. Prog Mol Subcell Biol. 2009; 48:77-101. PMID: 19521813.
      View in: PubMed
    33. Carone DM, Longo MS, Ferreri GC, Hall L, Harris M, Shook N, Bulazel KV, Carone BR, Obergfell C, O'Neill MJ, O'Neill RJ. A new class of retroviral and satellite encoded small RNAs emanates from mammalian centromeres. Chromosoma. 2009 Feb; 118(1):113-25. PMID: 18839199.
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    34. Mlynarski EE, Obergfell CJ, Rens W, O'Brien PC, Ramsdell CM, Dewey MJ, O'Neill MJ, O'Neill RJ. Peromyscus maniculatus--Mus musculus chromosome homology map derived from reciprocal cross species chromosome painting. Cytogenet Genome Res. 2008; 121(3-4):288-92. PMID: 18758174.
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    35. Lawton BR, Carone BR, Obergfell CJ, Ferreri GC, Gondolphi CM, Vandeberg JL, Imumorin I, O'Neill RJ, O'Neill MJ. Genomic imprinting of IGF2 in marsupials is methylation dependent. BMC Genomics. 2008; 9:205. PMID: 18454865; PMCID: PMC2386826.
    36. Ramsdell CM, Lewandowski AA, Glenn JL, Vrana PB, O'Neill RJ, Dewey MJ. Comparative genome mapping of the deer mouse (Peromyscus maniculatus) reveals greater similarity to rat (Rattus norvegicus) than to the lab mouse (Mus musculus). BMC Evol Biol. 2008; 8:65. PMID: 18302785; PMCID: PMC2266908.
    37. Brown JD, Golden D, O'Neill RJ. Methylation perturbations in retroelements within the genome of a Mus interspecific hybrid correlate with double minute chromosome formation. Genomics. 2008 Mar; 91(3):267-73. PMID: 18226492.
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    38. Metcalfe CJ, Bulazel KV, Ferreri GC, Schroeder-Reiter E, Wanner G, Rens W, Obergfell C, Eldridge MD, O'Neill RJ. Genomic instability within centromeres of interspecific marsupial hybrids. Genetics. 2007 Dec; 177(4):2507-17. PMID: 18073443; PMCID: PMC2219476.
    39. O'Neill MJ, Lawton BR, Mateos M, Carone DM, Ferreri GC, Hrbek T, Meredith RW, Reznick DN, O'Neill RJ. Ancient and continuing Darwinian selection on insulin-like growth factor II in placental fishes. Proc Natl Acad Sci U S A. 2007 Jul 24; 104(30):12404-9. PMID: 17636118; PMCID: PMC1941482.
    40. Smilowitz HM, Weissenberger J, Weis J, Brown JD, O'Neill RJ, Laissue JA. Orthotopic transplantation of v-src-expressing glioma cell lines into immunocompetent mice: establishment of a new transplantable in vivo model for malignant glioma. J Neurosurg. 2007 Apr; 106(4):652-9. PMID: 17432718.
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    41. Ambrosi DJ, Tanasijevic B, Kaur A, Obergfell C, O'Neill RJ, Krueger W, Rasmussen TP. Genome-wide reprogramming in hybrids of somatic cells and embryonic stem cells. Stem Cells. 2007 May; 25(5):1104-13. PMID: 17272499.
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    42. Lawton BR, Obergfell C, O'Neill RJ, O'Neill MJ. Physical mapping of the IGF2 locus in the South American opossum Monodelphis domestica. Cytogenet Genome Res. 2007; 116(1-2):130-1. PMID: 17268191.
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    43. Duselis AR, Obergfell C, Mack JA, O'Neill MJ, Nguyen QK, O'Neill RJ, Vrana PB. Changes in cell cycle and extracellular matrix gene expression during placental development in deer mouse (Peromyscus) hybrids. Reprod Fertil Dev. 2007; 19(5):695-708. PMID: 17601418.
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    44. Bulazel KV, Ferreri GC, Eldridge MD, O'Neill RJ. Species-specific shifts in centromere sequence composition are coincident with breakpoint reuse in karyotypically divergent lineages. Genome Biol. 2007; 8(8):R170. PMID: 17708770; PMCID: PMC2375000.
    45. Kronforst MR, Young LG, Kapan DD, McNeely C, O'Neill RJ, Gilbert LE. Linkage of butterfly mate preference and wing color preference cue at the genomic location of wingless. Proc Natl Acad Sci U S A. 2006 Apr 25; 103(17):6575-80. PMID: 16611733; PMCID: PMC1458925.
    46. Bulazel K, Metcalfe C, Ferreri GC, Yu J, Eldridge MD, O'Neill RJ. Cytogenetic and molecular evaluation of centromere-associated DNA sequences from a marsupial (Macropodidae: Macropus rufogriseus) X chromosome. Genetics. 2006 Feb; 172(2):1129-37. PMID: 16387881; PMCID: PMC1456211.
    47. Ford KK, Mack JA, O'Neill RJ. Multiple independent pseudogene derivations indicate increased instability of the Mdm2 locus in Mus caroli. Mol Biol Rep. 2005 Jun; 32(2):95-101. PMID: 16022282.
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    48. Lawton BR, Sevigny L, Obergfell C, Reznick D, O'Neill RJ, O'Neill MJ. Allelic expression of IGF2 in live-bearing, matrotrophic fishes. Dev Genes Evol. 2005 Apr; 215(4):207-12. PMID: 15654625.
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    49. Ferreri GC, Liscinsky DM, Mack JA, Eldridge MD, O'Neill RJ. Retention of latent centromeres in the Mammalian genome. J Hered. 2005 May-Jun; 96(3):217-24. PMID: 15653556.
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    50. Wilder JA, Dyreson EG, O'Neill RJ, Spangler ML, Gupta R, Wilder AS, Hollocher H. Contrasting modes of natural selection acting on pigmentation genes in the Drosophila dunni subgroup. J Exp Zool B Mol Dev Evol. 2004 Sep 15; 302(5):469-82. PMID: 15384167.
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    51. O'Neill RJ, Eldridge MD, Metcalfe CJ. Centromere dynamics and chromosome evolution in marsupials. J Hered. 2004 Sep-Oct; 95(5):375-81. PMID: 15388765.
      View in: PubMed
    52. Carvalho-Silva DR, O'Neill RJ, Brown JD, Huynh K, Waters PD, Pask AJ, Delbridge ML, Graves JA. Molecular characterization and evolution of X and Y-borne ATRX homologues in American marsupials. Chromosome Res. 2004; 12(8):795-804. PMID: 15702418.
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    53. Ferreri GC, Marzelli M, Rens W, O'Neill RJ. A centromere-specific retroviral element associated with breaks of synteny in macropodine marsupials. Cytogenet Genome Res. 2004; 107(1-2):115-8. PMID: 15305065.
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    54. Wilder JA, Diaz T, O'Neill RJ, Kenney J, Hollocher H. Characterization and isolation of novel microsatellites from the Drosophila dunni subgroup. Genet Res. 2002 Dec; 80(3):177-85. PMID: 12688656.
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    55. Pask AJ, Harry JL, Graves JA, O'Neill RJ, Layfield SL, Shaw G, Renfree MB. SOX9 has both conserved and novel roles in marsupial sexual differentiation. Genesis. 2002 Jul; 33(3):131-9. PMID: 12124946.
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    56. Brown JD, Strbuncelj M, Giardina C, O'Neill RJ. Interspecific hybridization induced amplification of Mdm2 on double minutes in a Mus hybrid. Cytogenet Genome Res. 2002; 98(2-3):184-8. PMID: 12698001.
      View in: PubMed
    57. O'Neill RJ, Eldridge MD, Graves JA. Chromosome heterozygosity and de novo chromosome rearrangements in mammalian interspecies hybrids. Mamm Genome. 2001 Mar; 12(3):256-9. PMID: 11252178.
      View in: PubMed
    58. O'Neill MJ, O'Neill RJ. Whatever happened to SRY? Cell Mol Life Sci. 1999 Dec; 56(11-12):883-93. PMID: 11212323.
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    59. Roemer I, Grützner F, Winking H, Haaf T, Orth A, Skidmore L, Antczak D, Fundele R. Genome evolution. Global methylation in eutherian hybrids. Nature. 1999 Sep 9; 401(6749):131-2. PMID: 10490019.
      View in: PubMed
    60. O'Neill RJ, Eldridge MD, Toder R, Ferguson-Smith MA, O'Brien PC, Graves JA. Chromosome evolution in kangaroos (Marsupialia: Macropodidae): cross species chromosome painting between the tammar wallaby and rock wallaby spp. with the 2n = 22 ancestral macropodid karyotype. Genome. 1999 Jun; 42(3):525-30. PMID: 10382300.
      View in: PubMed
    61. O'Neill RJ, O'Neill MJ, Graves JA. Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid. Nature. 1998 May 7; 393(6680):68-72. PMID: 9590690.
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    62. O'Neill RJ, Brennan FE, Delbridge ML, Crozier RH, Graves JA. De novo insertion of an intron into the mammalian sex determining gene, SRY. Proc Natl Acad Sci U S A. 1998 Feb 17; 95(4):1653-7. PMID: 9465071; PMCID: PMC19134.
    63. Graves JA, O'Neill RJ. Sex chromosome evolution and Haldane's rule. J Hered. 1997 Sep-Oct; 88(5):358-60. PMID: 9378909.
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    64. Toder R, O'Neill RJ, Wienberg J, O'Brien PC, Voullaire L, Marshall-Graves JA. Comparative chromosome painting between two marsupials: origins of an XX/XY1Y2 sex chromosome system. Mamm Genome. 1997 Jun; 8(6):418-22. PMID: 9166586.
      View in: PubMed
    65. O'Neill RJ, Eldridge MD, Crozier RH, Graves JA. Low levels of sequence divergence in rock wallabies (Petrogale) suggest a lack of positive directional selection in SRY. Mol Biol Evol. 1997 Mar; 14(3):350-3. PMID: 9066801.
      View in: PubMed
    66. Delbridge ML, Harry JL, Toder R, O'Neill RJ, Ma K, Chandley AC, Graves JA. A human candidate spermatogenesis gene, RBM1, is conserved and amplified on the marsupial Y chromosome. Nat Genet. 1997 Feb; 15(2):131-6. PMID: 9020837.
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    67. Watson CM, Johnston PG, Rodger KA, McKenzie LM, O'Neill RJ, Cooper DW. SRY and karyotypic status of one abnormal and two intersexual marsupials. Reprod Fertil Dev. 1997; 9(2):233-41. PMID: 9208434.
      View in: PubMed
    68. Pamilo P, O'Neill RJ. Evolution of the Sry genes. Mol Biol Evol. 1997 Jan; 14(1):49-55. PMID: 9000753.
      View in: PubMed
    69. Martin J, Herniou E, Cook J, Waugh O'Neill R, Tristem M. Human endogenous retrovirus type I-related viruses have an apparently widespread distribution within vertebrates. J Virol. 1997 Jan; 71(1):437-43. PMID: 8985368; PMCID: PMC191069.
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