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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 Aug;50(8):1102-1111. doi: 10.1038/s41588-018-0153-5. Epub 2018 Jul 2.


The Methylome of Vertebrate Sex Chromosomes.

Waters SA, Capraro A, McIntyre KL, Marshall Graves JA, Waters PD.

Genes (Basel). 2018 May 1;9(5). pii: E230. doi: 10.3390/genes9050230. Review.


Landscape of DNA Methylation on the Marsupial X.

Waters SA, Livernois AM, Patel H, O'Meally D, Craig JM, Marshall Graves JA, Suter CM, Waters PD.

Mol Biol Evol. 2018 Feb 1;35(2):431-439. doi: 10.1093/molbev/msx297.


Fragile Y Chromosomes (retrospective on DOI 10.1002/bies.201500040).

Waters PD.

Bioessays. 2017 Nov;39(11). doi: 10.1002/bies.201700142. Epub 2017 Sep 15. No abstract available.


Differential intron retention in Jumonji chromatin modifier genes is implicated in reptile temperature-dependent sex determination.

Deveson IW, Holleley CE, Blackburn J, Marshall Graves JA, Mattick JS, Waters PD, Georges A.

Sci Adv. 2017 Jun 14;3(6):e1700731. doi: 10.1126/sciadv.1700731. eCollection 2017 Jun.


Evolution of the Antisense Overlap between Genes for Thyroid Hormone Receptor and Rev-erbα and Characterization of an Exonic G-Rich Element That Regulates Splicing of TRα2 mRNA.

Munroe SH, Morales CH, Duyck TH, Waters PD.

PLoS One. 2015 Sep 14;10(9):e0137893. doi: 10.1371/journal.pone.0137893. eCollection 2015.


The loss of fragile Y chromosomes (comment on 10.1002/bies.201500040).

Waters PD.

Bioessays. 2015 Sep;37(9):933. doi: 10.1002/bies.201500091. Epub 2015 Aug 10. No abstract available.


Long intervening non-coding RNA 00320 is human brain-specific and highly expressed in the cortical white matter.

Mills JD, Chen J, Kim WS, Waters PD, Prabowo AS, Aronica E, Halliday GM, Janitz M.

Neurogenetics. 2015 Jul;16(3):201-13. doi: 10.1007/s10048-015-0445-1. Epub 2015 Mar 29.


High expression of long intervening non-coding RNA OLMALINC in the human cortical white matter is associated with regulation of oligodendrocyte maturation.

Mills JD, Kavanagh T, Kim WS, Chen BJ, Waters PD, Halliday GM, Janitz M.

Mol Brain. 2015 Jan 10;8:2. doi: 10.1186/s13041-014-0091-9.


Paternal X inactivation does not correlate with X chromosome evolutionary strata in marsupials.

Rodríguez-Delgado CL, Waters SA, Waters PD.

BMC Evol Biol. 2014 Dec 24;14:267. doi: 10.1186/s12862-014-0267-z.


Origins and functional evolution of Y chromosomes across mammals.

Cortez D, Marin R, Toledo-Flores D, Froidevaux L, Liechti A, Waters PD, Grützner F, Kaessmann H.

Nature. 2014 Apr 24;508(7497):488-93. doi: 10.1038/nature13151.


Independent evolution of transcriptional inactivation on sex chromosomes in birds and mammals.

Livernois AM, Waters SA, Deakin JE, Marshall Graves JA, Waters PD.

PLoS Genet. 2013;9(7):e1003635. doi: 10.1371/journal.pgen.1003635. Epub 2013 Jul 18.


Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution.

Li G, Davis BW, Raudsepp T, Pearks Wilkerson AJ, Mason VC, Ferguson-Smith M, O'Brien PC, Waters PD, Murphy WJ.

Genome Res. 2013 Sep;23(9):1486-95. doi: 10.1101/gr.154286.112. Epub 2013 Jun 20.


Evolutionary history of novel genes on the tammar wallaby Y chromosome: Implications for sex chromosome evolution.

Murtagh VJ, O'Meally D, Sankovic N, Delbridge ML, Kuroki Y, Boore JL, Toyoda A, Jordan KS, Pask AJ, Renfree MB, Fujiyama A, Graves JA, Waters PD.

Genome Res. 2012 Mar;22(3):498-507. doi: 10.1101/gr.120790.111. Epub 2011 Nov 29.


The origin and evolution of vertebrate sex chromosomes and dosage compensation.

Livernois AM, Graves JA, Waters PD.

Heredity (Edinb). 2012 Jan;108(1):50-8. doi: 10.1038/hdy.2011.106. Epub 2011 Nov 16. Review.


A cross-species comparison of escape from X inactivation in Eutheria: implications for evolution of X chromosome inactivation.

Al Nadaf S, Deakin JE, Gilbert C, Robinson TJ, Graves JA, Waters PD.

Chromosoma. 2012 Feb;121(1):71-8. doi: 10.1007/s00412-011-0343-8. Epub 2011 Sep 27.


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].


Chromosomal evolution in Rattini (Muridae, Rodentia).

Badenhorst D, Dobigny G, Adega F, Chaves R, O'Brien PC, Ferguson-Smith MA, Waters PD, Robinson TJ.

Chromosome Res. 2011 Aug;19(6):709-27. doi: 10.1007/s10577-011-9227-2. Epub 2011 Aug 18.


Evolution from XIST-independent to XIST-controlled X-chromosome inactivation: epigenetic modifications in distantly related mammals.

Chaumeil J, Waters PD, Koina E, Gilbert C, Robinson TJ, Graves JA.

PLoS One. 2011 Apr 25;6(4):e19040. doi: 10.1371/journal.pone.0019040.


Activity map of the tammar X chromosome shows that marsupial X inactivation is incomplete and escape is stochastic.

Al Nadaf S, Waters PD, Koina E, Deakin JE, Jordan KS, Graves JA.

Genome Biol. 2010;11(12):R122. doi: 10.1186/gb-2010-11-12-r122. Epub 2010 Dec 23.

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