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Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis.

Vara C, Paytuví-Gallart A, Cuartero Y, Le Dily F, Garcia F, Salvà-Castro J, Gómez-H L, Julià E, Moutinho C, Aiese Cigliano R, Sanseverino W, Fornas O, Pendás AM, Heyn H, Waters PD, Marti-Renom MA, Ruiz-Herrera A.

Cell Rep. 2019 Jul 9;28(2):352-367.e9. doi: 10.1016/j.celrep.2019.06.037.

Free Article

Waking the sleeping dragon: gene expression profiling reveals adaptive strategies of the hibernating reptile Pogona vitticeps.

Capraro A, O'Meally D, Waters SA, Patel HR, Georges A, Waters PD.

BMC Genomics. 2019 Jun 6;20(1):460. doi: 10.1186/s12864-019-5750-x.


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.


Monotreme sex chromosomes--implications for the evolution of amniote sex chromosomes.

Waters PD, Marshall Graves JA.

Reprod Fertil Dev. 2009;21(8):943-51. doi: 10.1071/RD09250. Review.


Physical mapping of the elephant X chromosome: conservation of gene order over 105 million years.

Delgado CL, Waters PD, Gilbert C, Robinson TJ, Graves JA.

Chromosome Res. 2009;17(7):917-26. doi: 10.1007/s10577-009-9079-1. Epub 2009 Sep 30.


Does the human X contain a third evolutionary block? Origin of genes on human Xp11 and Xq28.

Delbridge ML, Patel HR, Waters PD, McMillan DA, Marshall Graves JA.

Genome Res. 2009 Aug;19(8):1350-60. doi: 10.1101/gr.088625.108. Epub 2009 May 13.


Conservation of a chromosome arm in two distantly related marsupial species.

Mohammadi A, Delbridge ML, Waters PD, Graves JA.

Cytogenet Genome Res. 2009;124(2):147-50. doi: 10.1159/000207522. Epub 2009 May 5.


Physical map of two tammar wallaby chromosomes: a strategy for mapping in non-model mammals.

Deakin JE, Koina E, Waters PD, Doherty R, Patel VS, Delbridge ML, Dobson B, Fong J, Hu Y, van den Hurk C, Pask AJ, Shaw G, Smith C, Thompson K, Wakefield MJ, Yu H, Renfree MB, Graves JA.

Chromosome Res. 2008;16(8):1159-75. doi: 10.1007/s10577-008-1266-y. Epub 2008 Nov 8.


Target site analysis of RTE1_LA and its AfroSINE partner in the elephant genome.

Gilbert C, Pace JK 2nd, Waters PD.

Gene. 2008 Dec 1;425(1-2):1-8. doi: 10.1016/j.gene.2008.08.013. Epub 2008 Aug 28.


Identification of cryptic sex chromosomes and isolation of X- and Y-borne genes.

Waters PD, Marshall Graves JA, Thompson K, Sankovic N, Ezaz T.

Methods Mol Biol. 2008;422:239-51. doi: 10.1007/978-1-59745-581-7_15.


LINE-1 elements: analysis by fluorescence in-situ hybridization and nucleotide sequences.

Waters PD, Dobigny G, Waddell PJ, Robinson TJ.

Methods Mol Biol. 2008;422:227-37. doi: 10.1007/978-1-59745-581-7_14.


Sex determination in mammals--before and after the evolution of SRY.

Wallis MC, Waters PD, Graves JA.

Cell Mol Life Sci. 2008 Oct;65(20):3182-95. doi: 10.1007/s00018-008-8109-z. Review.


Genome analysis of the platypus reveals unique signatures of evolution.

Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, López-Otín C, Ordóñez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefèvre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Nefedov M, de Jong PJ, Renfree MB, Mardis ER, Wilson RK.

Nature. 2008 May 8;453(7192):175-83. doi: 10.1038/nature06936. Erratum in: Nature. 2008 Sep 11;455(7210):256. Nefedov, Mikhail [added]; de Jong, Pieter J [added].


Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes.

Veyrunes F, Waters PD, Miethke P, Rens W, McMillan D, Alsop AE, Grützner F, Deakin JE, Whittington CM, Schatzkamer K, Kremitzki CL, Graves T, Ferguson-Smith MA, Warren W, Marshall Graves JA.

Genome Res. 2008 Jun;18(6):965-73. doi: 10.1101/gr.7101908. Epub 2008 May 7.


Core-SINE blocks comprise a large fraction of monotreme genomes; implications for vertebrate chromosome evolution.

Kirby PJ, Greaves IK, Koina E, Waters PD, Marshall Graves JA.

Chromosome Res. 2007;15(8):975-84. doi: 10.1007/s10577-007-1187-1. Epub 2008 Jan 9.


Sex determination in platypus and echidna: autosomal location of SOX3 confirms the absence of SRY from monotremes.

Wallis MC, Waters PD, Delbridge ML, Kirby PJ, Pask AJ, Grützner F, Rens W, Ferguson-Smith MA, Graves JA.

Chromosome Res. 2007;15(8):949-59. doi: 10.1007/s10577-007-1185-3. Epub 2008 Jan 9.


Dissection of a Y-autosome translocation in Cryptomys hottentotus (Rodentia, Bathyergidae) and implications for the evolution of a meiotic sex chromosome chain.

Deuve JL, Bennett NC, Ruiz-Herrera A, Waters PD, Britton-Davidian J, Robinson TJ.

Chromosoma. 2008 Apr;117(2):211-7. Epub 2007 Dec 20.


Sex chromosomes of basal placental mammals.

Waters PD, Ruiz-Herrera A, Dobigny G, Garcia Caldès M, Robinson TJ.

Chromosoma. 2007 Dec;116(6):511-8. Epub 2007 Jun 30.


Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences.

Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SM, Sharpe T, Baker ML, Batzer MA, Benos PV, Belov K, Clamp M, Cook A, Cuff J, Das R, Davidow L, Deakin JE, Fazzari MJ, Glass JL, Grabherr M, Greally JM, Gu W, Hore TA, Huttley GA, Kleber M, Jirtle RL, Koina E, Lee JT, Mahony S, Marra MA, Miller RD, Nicholls RD, Oda M, Papenfuss AT, Parra ZE, Pollock DD, Ray DA, Schein JE, Speed TP, Thompson K, VandeBerg JL, Wade CM, Walker JA, Waters PD, Webber C, Weidman JR, Xie X, Zody MC; Broad Institute Genome Sequencing Platform; Broad Institute Whole Genome Assembly Team, Graves JA, Ponting CP, Breen M, Samollow PB, Lander ES, Lindblad-Toh K.

Nature. 2007 May 10;447(7141):167-77.


Mammalian sex--Origin and evolution of the Y chromosome and SRY.

Waters PD, Wallis MC, Marshall Graves JA.

Semin Cell Dev Biol. 2007 Jun;18(3):389-400. Epub 2007 Feb 24. Review.


Evolutionary history of LINE-1 in the major clades of placental mammals.

Waters PD, Dobigny G, Waddell PJ, Robinson TJ.

PLoS One. 2007 Jan 17;2(1):e158.


Absence of hypomethylation and LINE-1 amplification in a white x black rhinoceros hybrid.

Dobigny G, Waters PD, Robinson TJ.

Genetica. 2006 May;127(1-3):81-6.


Autosomal location of genes from the conserved mammalian X in the platypus (Ornithorhynchus anatinus): implications for mammalian sex chromosome evolution.

Waters PD, Delbridge ML, Deakin JE, El-Mogharbel N, Kirby PJ, Carvalho-Silva DR, Graves JA.

Chromosome Res. 2005;13(4):401-10.


Molecular characterization and evolution of X and Y-borne ATRX homologues in American marsupials.

Carvalho-Silva DR, O'Neill RJ, Brown JD, Huynh K, Waters PD, Pask AJ, Delbridge ML, Graves JA.

Chromosome Res. 2004;12(8):795-804.


LINE-1 amplification accompanies explosive genome repatterning in rodents.

Dobigny G, Ozouf-Costaz C, Waters PD, Bonillo C, Coutanceau JP, Volobouev V.

Chromosome Res. 2004;12(8):787-93.


LINE-1 distribution in Afrotheria and Xenarthra: implications for understanding the evolution of LINE-1 in eutherian genomes.

Waters PD, Dobigny G, Pardini AT, Robinson TJ.

Chromosoma. 2004 Sep;113(3):137-44. Epub 2004 Jul 29.


Assignment of the thymosin beta 4 X/Y chromosome (TMSB4X/Y) gene to tammar wallaby chromosome 5p by fluorescence in situ hybridisation.

Waters PD, Sankovic N, Kirby PJ, Delbridge ML, Graves JA.

Cytogenet Genome Res. 2003;103(1-2):203F. No abstract available.


Assignment of the protocadherin 20 (PCDH20) gene to tammar wallaby chromosome 6q by fluorescence in situ hybridisation.

Waters PD, Kirby PJ, Graves JA.

Cytogenet Genome Res. 2002;98(4):311D. No abstract available.


Cloning and mapping of platypus SOX2 and SOX14: insights into SOX group B evolution.

Kirby PJ, Waters PD, Delbridge M, Svartman M, Stewart AN, Nagai K, Graves JA.

Cytogenet Genome Res. 2002;98(1):96-100.


Assignment of the SMARCF1 gene to tammar wallaby chromosome 5q by fluorescence in situ hybridisation.

Waters PD, Kirby PJ, Graves JA.

Cytogenet Cell Genet. 2001;93(3-4):315-6. No abstract available.


The human Y chromosome derives largely from a single autosomal region added to the sex chromosomes 80-130 million years ago.

Waters PD, Duffy B, Frost CJ, Delbridge ML, Graves JA.

Cytogenet Cell Genet. 2001;92(1-2):74-9.


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