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Items: 1 to 50 of 82

1.

Adaptation and conservation insights from the koala genome.

Johnson RN, O'Meally D, Chen Z, Etherington GJ, Ho SYW, Nash WJ, Grueber CE, Cheng Y, Whittington CM, Dennison S, Peel E, Haerty W, O'Neill RJ, Colgan D, Russell TL, Alquezar-Planas DE, Attenbrow V, Bragg JG, Brandies PA, Chong AY, Deakin JE, Di Palma F, Duda Z, Eldridge MDB, Ewart KM, Hogg CJ, Frankham GJ, Georges A, Gillett AK, Govendir M, Greenwood AD, Hayakawa T, Helgen KM, Hobbs M, Holleley CE, Heider TN, Jones EA, King A, Madden D, Graves JAM, Morris KM, Neaves LE, Patel HR, Polkinghorne A, Renfree MB, Robin C, Salinas R, Tsangaras K, Waters PD, Waters SA, Wright B, Wilkins MR, Timms P, Belov K.

Nat Genet. 2018 Jul 2. doi: 10.1038/s41588-018-0153-5. [Epub ahead of print]

PMID:
29967444
2.

An updated genetic map of Peromyscus with chromosomal assignment of linkage groups.

Brown J, Crivello J, O'Neill RJ.

Mamm Genome. 2018 Jun;29(5-6):344-352. doi: 10.1007/s00335-018-9754-7. Epub 2018 Jun 15.

PMID:
29947964
3.

Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data.

Yang Y, Gu Q, Zhang Y, Sasaki T, Crivello J, O'Neill RJ, Gilbert DM, Ma J.

Cell Syst. 2018 Jun 18. pii: S2405-4712(18)30240-0. doi: 10.1016/j.cels.2018.05.022. [Epub ahead of print]

4.

Epigenetic maintenance of topological domains in the highly rearranged gibbon genome.

Lazar NH, Nevonen KA, O'Connell B, McCann C, O'Neill RJ, Green RE, Meyer TJ, Okhovat M, Carbone L.

Genome Res. 2018 Jul;28(7):983-997. doi: 10.1101/gr.233874.117. Epub 2018 Jun 18.

PMID:
29914971
5.

Tissue-Specific Transcriptome for Poeciliopsis prolifica Reveals Evidence for Genetic Adaptation Related to the Evolution of a Placental Fish.

Jue NK, Foley RJ, Reznick DN, O'Neill RJ, O'Neill MJ.

G3 (Bethesda). 2018 Jul 2;8(7):2181-2192. doi: 10.1534/g3.118.200270.

6.

Sex chromosome repeats tip the balance towards speciation.

O'Neill MJ, O'Neill RJ.

Mol Ecol. 2018 Apr 6. doi: 10.1111/mec.14577. [Epub ahead of print]

PMID:
29624756
7.

Replication timing kept in LINE.

O'Neill RJ, O'Neill MJ.

J Cell Biol. 2018 Feb 5;217(2):441-443. doi: 10.1083/jcb.201712173. Epub 2018 Jan 18.

PMID:
29348148
8.

Transposable elements: genome innovation, chromosome diversity, and centromere conflict.

Klein SJ, O'Neill RJ.

Chromosome Res. 2018 Mar;26(1-2):5-23. doi: 10.1007/s10577-017-9569-5. Epub 2018 Jan 13. Review.

9.

Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore.

Feigin CY, Newton AH, Doronina L, Schmitz J, Hipsley CA, Mitchell KJ, Gower G, Llamas B, Soubrier J, Heider TN, Menzies BR, Cooper A, O'Neill RJ, Pask AJ.

Nat Ecol Evol. 2018 Jan;2(1):182-192. doi: 10.1038/s41559-017-0417-y. Epub 2017 Dec 11.

PMID:
29230027
10.

Deep-targeted sequencing of endothelial nitric oxide synthase gene exons uncovers exercise intensity and ethnicity-dependent associations with post-exercise hypotension.

Pescatello LS, Schifano ED, Ash GI, Panza GA, Corso LML, Chen MH, Deshpande V, Zaleski A, Cilhoroz B, Farinatti P, Taylor BA, O'Neill RJ, Thompson PD.

Physiol Rep. 2017 Nov;5(22). pii: e13510. doi: 10.14814/phy2.13510.

11.

Healthcare costs of transarterial chemoembolization in the treatment of hepatocellular carcinoma.

Fateen W, Khan F, O'Neill RJ, James MW, Ryder SD, Aithal GP.

J Hepatocell Carcinoma. 2017 Oct 16;4:123-130. doi: 10.2147/JHC.S144068. eCollection 2017.

12.

RNA-dependent stabilization of SUV39H1 at constitutive heterochromatin.

Johnson WL, Yewdell WT, Bell JC, McNulty SM, Duda Z, O'Neill RJ, Sullivan BA, Straight AF.

Elife. 2017 Aug 1;6. pii: e25299. doi: 10.7554/eLife.25299.

13.

Transcriptomic imprints of adaptation to fresh water: parallel evolution of osmoregulatory gene expression in the Alewife.

Velotta JP, Wegrzyn JL, Ginzburg S, Kang L, Czesny S, O'Neill RJ, McCormick SD, Michalak P, Schultz ET.

Mol Ecol. 2017 Feb;26(3):831-848. doi: 10.1111/mec.13983. Epub 2017 Jan 27.

PMID:
28012221
14.

Rapid Evolutionary Rates and Unique Genomic Signatures Discovered in the First Reference Genome for the Southern Ocean Salp, Salpa thompsoni (Urochordata, Thaliacea).

Jue NK, Batta-Lona PG, Trusiak S, Obergfell C, Bucklin A, O'Neill MJ, O'Neill RJ.

Genome Biol Evol. 2016 Oct 30;8(10):3171-3186.

15.

The repetitive DNA element BncDNA, enriched in the B chromosome of the cichlid fish Astatotilapia latifasciata, transcribes a potentially noncoding RNA.

Ramos É, Cardoso AL, Brown J, Marques DF, Fantinatti BE, Cabral-de-Mello DC, Oliveira RA, O'Neill RJ, Martins C.

Chromosoma. 2017 Mar;126(2):313-323. doi: 10.1007/s00412-016-0601-x. Epub 2016 May 12.

PMID:
27169573
16.

Establishment of Centromeric Chromatin by the CENP-A Assembly Factor CAL1 Requires FACT-Mediated Transcription.

Chen CC, Bowers S, Lipinszki Z, Palladino J, Trusiak S, Bettini E, Rosin L, Przewloka MR, Glover DM, O'Neill RJ, Mellone BG.

Dev Cell. 2015 Jul 6;34(1):73-84. doi: 10.1016/j.devcel.2015.05.012.

17.

Identification of a recently active mammalian SINE derived from ribosomal RNA.

Longo MS, Brown JD, Zhang C, O'Neill MJ, O'Neill RJ.

Genome Biol Evol. 2015 Jan 29;7(3):775-88. doi: 10.1093/gbe/evv015.

18.

Genomics: Something to swing about.

O'Neill MJ, O'Neill RJ.

Nature. 2014 Sep 11;513(7517):174-5. doi: 10.1038/513174a. No abstract available.

PMID:
25209792
19.

Maternal methyl supplemented diets and effects on offspring health.

O'Neill RJ, Vrana PB, Rosenfeld CS.

Front Genet. 2014 Aug 26;5:289. doi: 10.3389/fgene.2014.00289. eCollection 2014. Review.

20.

Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations.

Harris SE, O'Neill RJ, Munshi-South J.

Mol Ecol Resour. 2015 Mar;15(2):382-94. doi: 10.1111/1755-0998.12301. Epub 2014 Jul 16.

21.

Relaxed selection causes microevolution of seawater osmoregulation and gene expression in landlocked Alewives.

Velotta JP, McCormick SD, O'Neill RJ, Schultz ET.

Oecologia. 2014 Aug;175(4):1081-92. doi: 10.1007/s00442-014-2961-3. Epub 2014 May 24.

PMID:
24859345
22.

A genetic map of Peromyscus with chromosomal assignment of linkage groups (a Peromyscus genetic map).

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.

Mamm Genome. 2014 Apr;25(3-4):160-79. doi: 10.1007/s00335-014-9500-8. Epub 2014 Jan 21.

23.

Esperanto for histones: CENP-A, not CenH3, is the centromeric histone H3 variant.

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.

Chromosome Res. 2013 Apr;21(2):101-6. doi: 10.1007/s10577-013-9347-y. Epub 2013 Apr 12.

24.

Determination of dosage compensation of the mammalian X chromosome by RNA-seq is dependent on analytical approach.

Jue NK, Murphy MB, Kasowitz SD, Qureshi SM, Obergfell CJ, Elsisi S, Foley RJ, O'Neill RJ, O'Neill MJ.

BMC Genomics. 2013 Mar 6;14:150. doi: 10.1186/1471-2164-14-150.

25.

Hypermorphic expression of centromeric retroelement-encoded small RNAs impairs CENP-A loading.

Carone DM, Zhang C, Hall LE, Obergfell C, Carone BR, O'Neill MJ, O'Neill RJ.

Chromosome Res. 2013 Mar;21(1):49-62. doi: 10.1007/s10577-013-9337-0. Epub 2013 Feb 8.

PMID:
23392618
26.

Two different high throughput sequencing approaches identify thousands of de novo genomic markers for the genetically depleted Bornean elephant.

Sharma R, Goossens B, Kun-Rodrigues C, Teixeira T, Othman N, Boone JQ, Jue NK, Obergfell C, O'Neill RJ, Chikhi L.

PLoS One. 2012;7(11):e49533. doi: 10.1371/journal.pone.0049533. Epub 2012 Nov 21. Erratum in: PLoS One. 2013;8(7). doi: 10.1371/annotation/8aaa2a9c-9c15-4214-808d-db8b0bd8ab88.

27.

Foreword: the centromere and kinetochore in creatures great and small.

O'Neill RJ, Sullivan BA.

Chromosome Res. 2012 Jul;20(5):461-3. doi: 10.1007/s10577-012-9303-2. No abstract available.

PMID:
22801778
28.

Pericentric and centromeric transcription: a perfect balance required.

Hall LE, Mitchell SE, O'Neill RJ.

Chromosome Res. 2012 Jul;20(5):535-46. doi: 10.1007/s10577-012-9297-9. Review.

PMID:
22760449
29.

Retroelement demethylation associated with abnormal placentation in Mus musculus x Mus caroli hybrids.

Brown JD, Piccuillo V, O'Neill RJ.

Biol Reprod. 2012 Mar 30;86(3):88. doi: 10.1095/biolreprod.111.095273. Print 2012 Mar.

PMID:
22116807
30.

Making a long story short: noncoding RNAs and chromosome change.

Brown JD, Mitchell SE, O'Neill RJ.

Heredity (Edinb). 2012 Jan;108(1):42-9. doi: 10.1038/hdy.2011.104. Epub 2011 Nov 9. Review.

31.

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.

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 Biol. 2011 Aug 29;12(8):R81. doi: 10.1186/gb-2011-12-8-r81. Erratum in: Genome Biol. 2011;12(12):414. Patel, Hardip R [added].

32.

Centromere conversion and retention in somatic cell hybrids.

Brown JD, Carone DM, Flynn BL, Finn CE, Mlynarski EE, O'Neill RJ.

Cytogenet Genome Res. 2011;134(3):182-90. doi: 10.1159/000328830. Epub 2011 Jun 29.

PMID:
21709412
33.

Enhancing genome assemblies by integrating non-sequence based data.

Heider TN, Lindsay J, Wang C, O'Neill RJ, Pask AJ.

BMC Proc. 2011 May 28;5 Suppl 2:S7. doi: 10.1186/1753-6561-5-S2-S7.

34.

Recent amplification of the kangaroo endogenous retrovirus, KERV, limited to the centromere.

Ferreri GC, Brown JD, Obergfell C, Jue N, Finn CE, O'Neill MJ, O'Neill RJ.

J Virol. 2011 May;85(10):4761-71. doi: 10.1128/JVI.01604-10. Epub 2011 Mar 9.

35.

Abundant human DNA contamination identified in non-primate genome databases.

Longo MS, O'Neill MJ, O'Neill RJ.

PLoS One. 2011 Feb 16;6(2):e16410. doi: 10.1371/journal.pone.0016410.

36.

Differential modes of DNA binding by mismatch uracil DNA glycosylase from Escherichia coli: implications for abasic lesion processing and enzyme communication in the base excision repair pathway.

Grippon S, Zhao Q, Robinson T, Marshall JJ, O'Neill RJ, Manning H, Kennedy G, Dunsby C, Neil M, Halford SE, French PM, Baldwin GS.

Nucleic Acids Res. 2011 Apr;39(7):2593-603. doi: 10.1093/nar/gkq913. Epub 2010 Nov 25.

37.

Chromosomes, conflict, and epigenetics: chromosomal speciation revisited.

Brown JD, O'Neill RJ.

Annu Rev Genomics Hum Genet. 2010;11:291-316. doi: 10.1146/annurev-genom-082509-141554. Review.

PMID:
20438362
38.

A unique late-replicating XY to autosome translocation in Peromyscus melanophrys.

Mlynarski EE, Obergfell C, Dewey MJ, O'Neill RJ.

Chromosome Res. 2010 Feb;18(2):179-89. doi: 10.1007/s10577-010-9113-3. Epub 2010 Feb 23.

PMID:
20177772
39.

Divergent patterns of breakpoint reuse in Muroid rodents.

Mlynarski EE, Obergfell CJ, O'Neill MJ, O'Neill RJ.

Mamm Genome. 2010 Feb;21(1-2):77-87. doi: 10.1007/s00335-009-9242-1. Epub 2009 Dec 22.

PMID:
20033182
40.

Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty.

Longo MS, Carone DM; NISC Comparative Sequencing Program, Green ED, O'Neill MJ, O'Neill RJ.

BMC Genomics. 2009 Jul 24;10:334. doi: 10.1186/1471-2164-10-334.

41.

The mysteries of chromosome evolution in gibbons: methylation is a prime suspect.

Brown JD, O'Neill RJ.

PLoS Genet. 2009 Jun;5(6):e1000501. doi: 10.1371/journal.pgen.1000501. Epub 2009 Jun 26. No abstract available.

42.

The role of ncRNA in centromeres: a lesson from marsupials.

O'Neill RJ, Carone DM.

Prog Mol Subcell Biol. 2009;48:77-101. doi: 10.1007/978-3-642-00182-6_4. Review.

PMID:
19521813
43.

A new class of retroviral and satellite encoded small RNAs emanates from mammalian centromeres.

Carone DM, Longo MS, Ferreri GC, Hall L, Harris M, Shook N, Bulazel KV, Carone BR, Obergfell C, O'Neill MJ, O'Neill RJ.

Chromosoma. 2009 Feb;118(1):113-25. doi: 10.1007/s00412-008-0181-5. Epub 2008 Oct 7.

PMID:
18839199
44.

Peromyscus maniculatus--Mus musculus chromosome homology map derived from reciprocal cross species chromosome painting.

Mlynarski EE, Obergfell CJ, Rens W, O'Brien PC, Ramsdell CM, Dewey MJ, O'Neill MJ, O'Neill RJ.

Cytogenet Genome Res. 2008;121(3-4):288-92. doi: 10.1159/000138900. Epub 2008 Aug 29.

PMID:
18758174
45.

Genomic imprinting of IGF2 in marsupials is methylation dependent.

Lawton BR, Carone BR, Obergfell CJ, Ferreri GC, Gondolphi CM, Vandeberg JL, Imumorin I, O'Neill RJ, O'Neill MJ.

BMC Genomics. 2008 May 2;9:205. doi: 10.1186/1471-2164-9-205.

46.

Comparative genome mapping of the deer mouse (Peromyscus maniculatus) reveals greater similarity to rat (Rattus norvegicus) than to the lab mouse (Mus musculus).

Ramsdell CM, Lewandowski AA, Glenn JL, Vrana PB, O'Neill RJ, Dewey MJ.

BMC Evol Biol. 2008 Feb 26;8:65. doi: 10.1186/1471-2148-8-65.

47.

Methylation perturbations in retroelements within the genome of a Mus interspecific hybrid correlate with double minute chromosome formation.

Brown JD, Golden D, O'Neill RJ.

Genomics. 2008 Mar;91(3):267-73. doi: 10.1016/j.ygeno.2007.12.001. Epub 2008 Jan 15.

48.

Genomic instability within centromeres of interspecific marsupial hybrids.

Metcalfe CJ, Bulazel KV, Ferreri GC, Schroeder-Reiter E, Wanner G, Rens W, Obergfell C, Eldridge MD, O'Neill RJ.

Genetics. 2007 Dec;177(4):2507-17.

49.
50.

Ancient and continuing Darwinian selection on insulin-like growth factor II in placental fishes.

O'Neill MJ, Lawton BR, Mateos M, Carone DM, Ferreri GC, Hrbek T, Meredith RW, Reznick DN, O'Neill RJ.

Proc Natl Acad Sci U S A. 2007 Jul 24;104(30):12404-9. Epub 2007 Jul 16.

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