Select Publications

Books

Deakin JE; Waters PD; Graves JAM, 2010, Marsupial genetics and genomics, http://dx.doi.org/10.1007/978-90-481-9023-2

Waters PD, 2010, Part IV: Marsupial sex chromosomes, http://dx.doi.org/10.1007/978-90-481-9023-2

Waters PD, 2010, Part V: Marsupial epigenetics, http://dx.doi.org/10.1007/978-90-481-9023-2

Waters PD; Deakin JE, 2010, Part VIII: Marsupial genes and gene evolution, http://dx.doi.org/10.1007/978-90-481-9023-2

Deakin JE; Waters PD; Graves JAM, 2010, Preface, http://dx.doi.org/10.1007/978-90-481-9023-2

Book Chapters

McIntyre K; Waters S; Waters P, 2018, 'Sex Chromosomes', in Skinner MK (ed.), Encyclopedia of Reproduction, edn. 2, Academic Press, pp. 238 - 244, http://dx.doi.org/10.1016/B978-0-12-801238-3.64459-8

Murtagh VJ; Waters PD; Marshall Graves JA, 2010, 'Compact but complex - The marsupial Y chromosome', in Marsupial Genetics and Genomics, pp. 207 - 228, http://dx.doi.org/10.1007/978-90-481-9023-2_11

Al Nadaf S; Waters PD; Deakin JE; Graves JAM, 2010, 'Marsupial genetics reveals insights into evolution of mammalian X chromosome inactivation', in Marsupial Genetics and Genomics, pp. 259 - 280, http://dx.doi.org/10.1007/978-90-481-9023-2_13

Journal articles

Waters PD; Ruiz-Herrera A, 2020, 'Meiotic Executioner Genes Protect the Y from Extinction', Trends in Genetics, vol. 36, pp. 728 - 738, http://dx.doi.org/10.1016/j.tig.2020.06.008

Sarma RR; Edwards RJ; Crino OL; Eyck HJF; Waters PD; Crossland MR; Shine R; Rollins LA, 2020, 'Do epigenetic changes drive corticosterone responses to alarm cues in larvae of an invasive amphibian?', Integr Comp Biol, http://dx.doi.org/10.1093/icb/icaa082

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, 2019, 'Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis', Cell Reports, vol. 28, pp. 352 - 367.e9, http://dx.doi.org/10.1016/j.celrep.2019.06.037

Waters S; Waters P; Capraro A, 2019, 'Waking the sleeping dragon: gene expression profiling reveals adaptive strategies of the hibernating reptile Pogona vitticeps', BMC Genomics, http://dx.doi.org/10.1186/s12864-019-5750-x

Sprague D; Waters SA; Kirk JM; Wang JR; Samollow PB; Waters PD; Calabrese JM, 2019, 'Nonlinear sequence similarity between the Xist and Rsx long noncoding RNAs suggests shared functions of tandem repeat domains', RNA, vol. 25, pp. 1004 - 1019, http://dx.doi.org/10.1261/rna.069815.118

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 AYY; 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, 2018, 'Adaptation and conservation insights from the koala genome', Nature Genetics, vol. 50, pp. 1102 - 1111, http://dx.doi.org/10.1038/s41588-018-0153-5

Waters SA; Capraro A; McIntyre KL; Graves JAM; Waters PD, 2018, 'The methylome of vertebrate sex chromosomes', Genes, vol. 9, http://dx.doi.org/10.3390/genes9050230

Waters SA; Livernois AM; Patel H; O’Meally D; Craig JM; Marshall Graves JA; Suter CM; Waters PD, 2018, 'Landscape of DNA methylation on the marsupial x', Molecular Biology and Evolution, vol. 35, pp. 431 - 439, http://dx.doi.org/10.1093/molbev/msx297

Waters PD, 2017, 'Fragile Y Chromosomes (retrospective on DOI 10.1002/bies.201500040)', BioEssays, vol. 39, http://dx.doi.org/10.1002/bies.201700142

Deveson IW; Holleley CE; Blackburn J; Marshall Graves JA; Mattick JS; Waters PD; Georges A, 2017, 'Differential intron retention in Jumonji chromatin modifier genes is implicated in reptile temperature-dependent sex determination', Science Advances, vol. 3, http://dx.doi.org/10.1126/sciadv.1700731

Munroe SH; Morales CH; Duyck TH; Waters PD, 2015, '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', PLoS ONE, vol. 10, http://dx.doi.org/10.1371/journal.pone.0137893

Mills JD; Chen J; Kim WS; Waters PD; Prabowo AS; Aronica E; Halliday GM; Janitz M, 2015, 'Long intervening non-coding RNA 00320 is human brain-specific and highly expressed in the cortical white matter', Neurogenetics, vol. 16, pp. 201 - 213, http://dx.doi.org/10.1007/s10048-015-0445-1

Mills JD; Kavanagh T; Kim WS; Chen BJ; Waters PD; Halliday GM; Janitz M, 2015, 'High expression of long intervening non-coding RNA OLMALINC in the human cortical white matter is associated with regulation of oligodendrocyte maturation', Molecular brain, vol. 8, pp. 2, http://dx.doi.org/10.1186/s13041-014-0091-9

Georges A; Li Q; Lian J; O'Meally D; Deakin J; Wang Z; Zhang P; Fujita M; Patel HR; Holleley CE; Zhou Y; Zhang X; Matsubara K; Waters P; Graves JAM; Sarre SD; Zhang G, 2015, 'High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps', GigaScience, vol. 4, http://dx.doi.org/10.1186/s13742-015-0085-2

Waters SA; Waters PD, 2015, 'Imprinted X chromosome inactivation: evolution of mechanisms in distantly related mammals', AIMS GENETICS, vol. 2, pp. 110 - 126, http://dx.doi.org/10.3934/genet.2015.2.110

Waters PD, 2015, 'The loss of fragile Y chromosomes (comment on 10.1002/bies.201500040)', BioEssays, vol. 37, pp. 933 - 933, http://dx.doi.org/10.1002/bies.201500091

Cortez D; Marin R; Toledo-Flores D; Froidevaux L; Liechti A; Waters PD; Grützner F; Kaessmann H, 2014, 'Origins and functional evolution of y chromosomes across mammals', Nature, vol. 508, pp. 488 - 493, http://dx.doi.org/10.1038/nature13151

Rodríguez-Delgado CL; Waters SA; Waters DP, 2014, 'Paternal X inactivation does not correlate with X chromosome evolutionary strata in marsupials', BMC Evolutionary Biology, vol. 14, http://dx.doi.org/10.1186/s12862-014-0267-z

Livernois AM; Waters SA; Deakin JE; Marshall Graves JA; Waters PD, 2013, 'Independent Evolution of Transcriptional Inactivation on Sex Chromosomes in Birds and Mammals', PLoS Genetics, vol. 9, http://dx.doi.org/10.1371/journal.pgen.1003635

Gilbert C; Waters P; Feschotte C; Schaack S, 2013, 'Horizontal transfer of OC1 transposons in the Tasmanian devil', BMC Genomics, vol. 14, http://dx.doi.org/10.1186/1471-2164-14-134

Li G; Davis BW; Raudsepp T; Wilkerson AJP; Mason VC; Ferguson-Smith M; O'Brien PC; Waters PD; Murphy WJ, 2013, 'Comparative analysis of mammalian y chromosomes illuminates ancestral structure and lineage-specific evolution', Genome Research, vol. 23, pp. 1486 - 1495, http://dx.doi.org/10.1101/gr.154286.112

Livernois AM; Graves JAM; Waters PD, 2012, 'The origin and evolution of vertebrate sex chromosomes and dosage compensation', Heredity, vol. 108, pp. 50 - 58, http://dx.doi.org/10.1038/hdy.2011.106

Renfree MB; Papenfuss AT; Deakin JE; Lindsay J; Heider T; Belov K; Rens W; Waters PD; Pharo EA; Shaw G; Wong ESW; 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; Mohammadi A; Schneider NY; Hu Y; O'Hara W; Al Nadaf S; Wu C; Feng ZP; Cocks BG; Wang J; Flicek P; Searle SMJ; 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, 2011, 'Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development', Genome Biology, vol. 12, http://dx.doi.org/10.1186/gb-2011-12-8-r81

Chaumeil J; Waters PD; Koina E; Gilbert C; Robinson TJ; Graves JAM, 2011, 'Evolution from XIST-independent to XIST-controlled X-chromosome inactivation: Epigenetic modifications in distantly related mammals', PLoS ONE, vol. 6, pp. e19040, http://dx.doi.org/10.1371/journal.pone.0019040

Al Nadaf S; Deakin JE; Gilbert C; Robinson TJ; Graves JA; Waters PD, 2011, 'A cross-species comparison of escape from X inactivation in Eutheria: implications for evolution of X chromosome inactivation.', Chromosoma, vol. 121, pp. 71 - 78, http://dx.doi.org/10.1007/s00412-011-0343-8

Badenhorst D; Dobigny G; Adega F; Chaves R; O''Brien PCM; Ferguson-smith MA; Waters PD; Robinson TJ, 2011, 'Chromosomal evolution in Rattini (Muridae,Rodentia)', Chromosome Research, vol. 19, pp. 709 - 727, http://dx.doi.org/10.1007/s10577-011-9227-2

Murtagh V; 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, 2011, 'Evolutionary history of novel genes on the tammar wallaby Y chromosome: Implications for sex chromosome evolution', Genome Research, vol. 22, pp. 498 - 507, http://dx.doi.org/10.1101/gr.120790.111

Al Nadaf S; Waters PD; Koina E; Deakin JE; Jordan KS; Graves JAM, 2010, 'Activity map of the tammar X chromosome shows that marsupial X inactivation is incomplete and escape is stochastic', Genome Biology, vol. 11, http://dx.doi.org/10.1186/gb-2010-11-12-r122

Mohammadi A; Delbridge ML; Waters PD; Graves JA, 2009, 'Conservation of a chromosome arm in two distantly related marsupial species.', Cytogenetic and Genome Research, vol. 124, pp. 147 - 150, http://dx.doi.org/10.1159/000207522

Delbridge ML; Patel HR; Waters PD; Mcmillan DA; Graves JA, 2009, 'Does the human X contain a third evolutionary block? Origin of genes on human Xp11 and Xq28.', Genome Research, vol. 19, pp. 1350 - 1360, http://dx.doi.org/10.1101/gr.088625.108

Waters PD; Graves JA, 2009, 'Monotreme sex chromosomes – implications for the evolution of amniote sex chromosomes', Reproduction Fertility and Development, vol. 21, pp. 943 - 951, http://dx.doi.org/10.1071/RD09250

Delgado CL; Waters PD; Gilbert C; Robinson TJ; Graves JA, 2009, 'Physical mapping of the elephant X chromosome: conservation of gene order over 105 million years.', Chromosome Research, vol. 17, pp. 917 - 926, http://dx.doi.org/10.1007/s10577-009-9079-1

Ezaz T; Moritz B; Waters PD; Graves JA; Georges A; Sarre SD, 2009, 'The ZW sex microchromosomes of an Australian dragon lizard share no homology with those of other reptiles or birds', Chromosome Research, vol. 17, pp. 965 - 973, http://dx.doi.org/10.1007/s10577-009-9102-6

Gilbert C; Pace JK; Waters PD, 2008, 'Target site analysis of RTE1_LA and its AfroSINE partner in the elephant genome', Gene, vol. 425, pp. 1 - 8, http://dx.doi.org/10.1016/j.gene.2008.08.013

Warren WC; Hillier LDW; 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; Ordó̃ez 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 AFA; Pask A; Temple-Smith P; Batzer MA; Walker JA; Konkel MK; Harris RS; Whittington CM; Wong ESW; 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, 2008, 'Genome analysis of the platypus reveals unique signatures of evolution (Nature (2008) 453, (175-183))', Nature, vol. 455, pp. 256, http://dx.doi.org/10.1038/nature07253

Waters PD; Marshall Graves JA; Thompson K; Sankovic N; Ezaz T, 2008, 'Identification of cryptic sex chromosomes and isolation of X- and Y-borne genes.', Methods in molecular biology (Clifton, N.J.), vol. 422, pp. 239 - 251, http://dx.doi.org/10.1007/978-1-59745-581-7_15

Waters PD; Dobigny G; Waddell PJ; Robinson TJ, 2008, 'LINE-1 elements: analysis by fluorescence in-situ hybridization and nucleotide sequences.', Methods in molecular biology (Clifton, N.J.), vol. 422, pp. 227 - 237, http://dx.doi.org/10.1007/978-1-59745-581-7_14

Veyrunes F; Waters PD; Miethke P; Rens W; McMillan D; Alsop AE; Grutzner F; Deakin J; Whittington CM; Schatzkamer K; Kremitzki CL; Graves T; Ferguson-smith MA; Warren W; Marshall Graves JA, 2008, 'Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes.', Genome Research, vol. 18, pp. 965 - 973, http://dx.doi.org/10.1101/gr.7101908

Deuve JL; Bennett NC; Ruiz-Herrera A; Waters PD; Britton-Davidian J; Robinson TJ, 2008, 'Dissection of a Y-autosome translocation in Cryptomys hottentotus (Rodentia, Bathyergidae) and implications for the evolution of a meiotic sex chromosome chain', Chromosoma, vol. 177, pp. 211 - 217, http://dx.doi.org/10.1007/s00412-007-0140-6

Warren WC; Hillier LW; Graves JAM; Birney E; Ponting CP; Grutzner F; Belov K; Miller W; Clarke L; Chinwalla AT; Yang SP; Heger A; Locke D; Miethke P; Waters PD; Veyrunes F; Fulton L; Fulton B; Graves T; Wallis J; Puente XS; Lopez-Otin C; Ordonez C; Eichler EE; Chen L; Cheng Z; Deakin J; Alsop A; Thompson K; Kirby P; Papenfuss AT; Wakefield MJ; Olender T; Lancet D; Huttley GA; Smit AFA; Pask A; Temple-Smith P; Batzer MA; Walker JA; Konkel MK; Harris RS; Whittington CM; Wong ESW; 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; Lefevre 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; Renfree M; Mardis ER; Wilson RK, 2008, 'Genome analysis of the platypus reveals unique signatures of evolution', Nature, vol. 453, pp. 175 - 184, http://dx.doi.org/10.1038/nature06936

Deakin J; Koina E; Waters PD; Doherty R; Patel VS; Delbridge ML; Dobson B; Fong J; Hu Y; Hurk C; Pask AJ; Shaw G; Smith C; Thompson K; Wakefield MJ; Yu H; Renfree M; Graves JA, 2008, 'Physical map of two tammar wallaby chromosomes: a strategy for mapping in non-model mammals', Chromosome Research, vol. 16, pp. 1159 - 1175, http://dx.doi.org/10.1007/s10577-008-1266-y

Wallis MC; Waters PD; Graves JA, 2008, 'Sex determination in mammals-before and after the evolution of SRY', CMLS - Cellular and Molecular Life Sciences, vol. 65, pp. 3182 - 3195, http://dx.doi.org/10.1007/s00018-008-8109-z


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