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

Lister NC; Johnsson P; Waters PD; Morris KV, 2021, 'Pseudogenes: A Novel Source of Trans-Acting Antisense RNAs', in Pseudogenes: Functions and Protocols, pp. 219 - 236, http://dx.doi.org/10.1007/978-1-0716-1503-4_14

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

Waters PD; Robinson TJ, 2013, 'Evolution of the Mammalian X Chromosome', in , Wiley, http://dx.doi.org/10.1002/9780470015902.a0020739.pub2

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

Bond DM; Ortega-Recalde O; Laird MK; Hayakawa T; Richardson KS; Reese FCB; Kyle B; McIsaac-Williams BE; Robertson BC; van Heezik Y; Adams AL; Chang WS; Haase B; Mountcastle J; Driller M; Collins J; Howe K; Go Y; Thibaud-Nissen F; Lister NC; Waters PD; Fedrigo O; Jarvis ED; Gemmell NJ; Alexander A; Hore TA, 2023, 'The admixed brushtail possum genome reveals invasion history in New Zealand and novel imprinted genes', Nature Communications, 14, http://dx.doi.org/10.1038/s41467-023-41784-8

Smith J; Alfieri JM; Anthony N; Arensburger P; Athrey GN; Balacco J; Balic A; Bardou P; Barela P; Bigot Y; Blackmon H; Borodin PM; Carroll R; Casono MC; Charles M; Cheng H; Chiodi M; Cigan L; Coghill LM; Crooijmans R; Das N; Davey S; Davidian A; Degalez F; Dekkers JM; Derks M; Diack AB; Djikeng A; Drechsler Y; Dyomin A; Fedrigo O; Fiddaman SR; Formenti G; Frantz LAF; Fulton JE; Gaginskaya E; Galkina S; Gallardo RA; Geibel J; Gheyas AA; Godinez CJP; Goodell A; Graves JAM; Griffin DK; Haase B; Han JL; Hanotte O; Henderson LJ; Hou ZC; Howe K; Huynh L; Ilatsia E; Jarvis ED; Johnson SM; Kaufman J; Kelly T; Kemp S; Kern C; Keroack JH; Klopp C; Lagarrigue S; Lamont SJ; Lange M; Lanke A; Larkin DM; Larson G; Layos JKN; Lebrasseur O; Malinovskaya LP; Martin RJ; Cerezo MLM; Mason AS; McCarthy FM; McGrew MJ; Mountcastle J; Muhonja CK; Muir W; Muret K; Murphy TD; Ng'ang'a I; Nishibori M; O'Connor RE; Ogugo M; Okimoto R; Ouko O; Patel HR; Perini F; Pigozzi MI; Potter KC; Price PD; Reimer C; Rice ES; Rocos N; Rogers TF; Saelao P; Schauer J; Schnabel RD; Schneider VA; Simianer H; Smith A, 2023, 'Fourth Report on Chicken Genes and Chromosomes 2022', Cytogenetic and Genome Research, 162, pp. 405 - 528, http://dx.doi.org/10.1159/000529376

Waters PD; Graves JAM; Whiteley SL; Georges A; Ruiz-Herrera A, 2023, 'Three dimensions of thermolabile sex determination', BioEssays, 45, http://dx.doi.org/10.1002/bies.202200123

Valero-Regalón FJ; Solé M; López-Jiménez P; Valerio-de Arana M; Martín-Ruiz M; de la Fuente R; Marín-Gual L; Renfree MB; Shaw G; Berríos S; Fernández-Donoso R; Waters PD; Ruiz-Herrera A; Gómez R; Page J, 2023, 'Divergent patterns of meiotic double strand breaks and synapsis initiation dynamics suggest an evolutionary shift in the meiosis program between American and Australian marsupials', Frontiers in Cell and Developmental Biology, 11, http://dx.doi.org/10.3389/fcell.2023.1147610

Álvarez-González L; Arias-Sardá C; Montes-Espuña L; Marín-Gual L; Vara C; Lister NC; Cuartero Y; Garcia F; Deakin J; Renfree MB; Robinson TJ; Martí-Renom MA; Waters PD; Farré M; Ruiz-Herrera A, 2022, 'Principles of 3D chromosome folding and evolutionary genome reshuffling in mammals', Cell Reports, 41, http://dx.doi.org/10.1016/j.celrep.2022.111839

Hu L; Long J; Lin Y; Gu Z; Su H; Dong X; Lin Z; Xiao Q; Batbayar N; Bold B; Deutschová L; Ganusevich S; Sokolov V; Sokolov A; Patel HR; Waters PD; Graves JAM; Dixon A; Pan S; Zhan X, 2022, 'Arctic introgression and chromatin regulation facilitated rapid Qinghai-Tibet Plateau colonization by an avian predator', Nature Communications, 13, http://dx.doi.org/10.1038/s41467-022-34138-3

Hu L; Long J; Lin Y; Gu Z; Su H; Dong X; Lin Z; Xiao Q; Batbayar N; Bold B; Deutschová L; Ganusevich S; Sokolov V; Sokolov A; Patel HR; Waters PD; Graves JAM; Dixon A; Pan S; Zhan X, 2022, 'Author Correction: Arctic introgression and chromatin regulation facilitated rapid Qinghai-Tibet Plateau colonization by an avian predator (Nature Communications, (2022), 13, 1, (6413), 10.1038/s41467-022-34138-3)', Nature Communications, 13, http://dx.doi.org/10.1038/s41467-022-35205-5

Marín-Gual L; González-Rodelas L; M. Garcias M; Kratochvíl L; Valenzuela N; Georges A; Waters PD; Ruiz-Herrera A, 2022, 'Meiotic chromosome dynamics and double strand break formation in reptiles', Frontiers in Cell and Developmental Biology, 10, http://dx.doi.org/10.3389/fcell.2022.1009776

Ruiz-Herrera A; Waters PD, 2022, 'Fragile, unfaithful and persistent Ys—on how meiosis can shape sex chromosome evolution', Heredity, 129, pp. 22 - 30, http://dx.doi.org/10.1038/s41437-022-00532-2

Waters PD; Ruiz-Herrera A, 2022, 'O-095 The persistent Y hypothesis', Human Reproduction, 37, http://dx.doi.org/10.1093/humrep/deac104.114

Youngson NA; Castino MR; Stuart A; Kershaw KA; Holmes NM; Heffernan EC; Waters PD; Morris KV; Clemens KJ, 2022, 'A role for a novel natural antisense-BDNF in the maintenance of nicotine-seeking', Addiction Neuroscience, 2, http://dx.doi.org/10.1016/j.addicn.2022.100010

Marín-Gual L; González-Rodelas L; Pujol G; Vara C; Martín-Ruiz M; Berríos S; Fernández-Donoso R; Pask A; Renfree MB; Page J; Waters PD; Ruiz-Herrera A, 2022, 'Strategies for meiotic sex chromosome dynamics and telomeric elongation in Marsupials', PLoS Genetics, 18, http://dx.doi.org/10.1371/journal.pgen.1010040

Lister NC; Milton AM; Hanrahan BJ; Waters PD, 2021, 'Between the devil and the deep blue sea: Non-coding rnas associated with transmissible cancers in tasmanian devil, domestic dog and bivalves', Non-coding RNA, 7, http://dx.doi.org/10.3390/ncrna7040072

Waters PD; Patel HR; Ruiz-Herrera A; Alvarez-Gonzalez L; Lister NC; Simakov O; Ezaz T; Kaur P; Frere C; Grutzner F; Georges A; Marshall Graves JA, 2021, 'Microchromosomes are building blocks of bird, reptile, and mammal chromosomes', Proceedings of the National Academy of Sciences of the United States of America, 118, http://dx.doi.org/10.1073/pnas.2112494118

Harding EF; Russo AG; Yan GJH; Waters PD; White PA, 2021, 'Ancient viral integrations in marsupials: A potential antiviral defence', Virus Evolution, 7, http://dx.doi.org/10.1093/ve/veab076

Waters P; Patel H; Ruiz-Herrera A; Álvarez-González L; Lister N; Simakov O; Ezaz T; Kaur P; Frere C; Grützner F; Georges A; Graves JM, 2021, 'Microchromosomes are building blocks of bird, reptile and mammal chromosomes', , http://dx.doi.org/10.1101/2021.07.06.451394

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?', Integrative and Comparative Biology, 60, pp. 1481 - 1494, http://dx.doi.org/10.1093/icb/icaa082

Capraro A; O‘Meally D; Waters SA; Patel HR; Georges A; Waters PD, 2020, 'MicroRNA dynamics during hibernation of the Australian central bearded dragon (Pogona vitticeps)', Scientific Reports, 10, http://dx.doi.org/10.1038/s41598-020-73706-9

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

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, 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, 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, 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, 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, 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, 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, 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, 10, http://dx.doi.org/10.1371/journal.pone.0137893

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

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, 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, 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, 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, 2, pp. 110 - 126, http://dx.doi.org/10.3934/genet.2015.2.110

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, 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, 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, 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, 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, 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, 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, 12, http://dx.doi.org/10.1186/gb-2011-12-8-r81


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