By Associate Professor Paul Waters

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

McIntyre KL; Waters SA; Waters PD, 2018, 'Sex Chromosomes', in Encyclopedia of Reproduction Volume 1 6 Second Edition, 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

Hanrahan BJ; Alreja K; Reis ALM; Chang JK; Dissanayake DSB; Edwards RJ; Bertozzi T; Hammond JM; O'Meally D; Deveson IW; Georges A; Waters P; Patel HR, 2025, 'A genome assembly and annotation for the Australian alpine skink Bassiana duperreyi using long-read technologies.', G3 (Bethesda), 15, http://dx.doi.org/10.1093/g3journal/jkaf046

Marín-Gual L; Hogg CJ; Chang JK; Pask AJ; Renfree MB; Waters PD; Ruiz-Herrera A, 2025, 'Meiotic dynamics in a unique Australian marsupial provide new insights into the evolution of neo-sex chromosomes in the early stages of differentiation', Frontiers in Cell and Developmental Biology, 13, http://dx.doi.org/10.3389/fcell.2025.1562403

McIntyre KL; Waters SA; Zhong L; Hart-Smith G; Raftery M; Chew ZA; Patel HR; Graves JAM; Waters PD, 2024, 'Identification of the RSX interactome in a marsupial shows functional coherence with the Xist interactome during X inactivation', Genome Biology, 25, http://dx.doi.org/10.1186/s13059-024-03280-0

Milton AM; Marín-Gual L; Lister NC; McIntyre KL; Grady PGS; Laird MK; Bond DM; Hore TA; O’Neill RJ; Pask AJ; Renfree MB; Ruiz-Herrera A; Waters PD, 2024, 'Imprinted X chromosome inactivation in marsupials: The paternal X arrives at the egg with a silent DNA methylation profile', Proceedings of the National Academy of Sciences of the United States of America, 121, http://dx.doi.org/10.1073/pnas.2412185121

Hogg CJ; Edwards RJ; Farquharson KA; Silver LW; Brandies P; Peel E; Escalona M; Jaya FR; Thavornkanlapachai R; Batley K; Bradford TM; Chang JK; Chen Z; Deshpande N; Dziminski M; Ewart KM; Griffith OW; Marin Gual L; Moon KL; Travouillon KJ; Waters P; Whittington CM; Wilkins MR; Helgen KM; Lo N; Ho SYW; Ruiz Herrera A; Paltridge R; Marshall Graves JA; Renfree M; Shapiro B; Ottewell K; Belov K, 2024, 'Erratum: Author Correction: Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial (Nature ecology & evolution (2024) 8 7 DOI: 10.1038/s41559-024-02436-2)', Nature Ecology Evolution, 8, pp. 1776, http://dx.doi.org/10.1038/s41559-024-02519-0

MacDonald E; Whibley A; Waters PD; Patel H; Edwards RJ; Ganley ARD, 2024, 'Origin and maintenance of large ribosomal RNA gene repeat size in mammals', Genetics, 228, http://dx.doi.org/10.1093/genetics/iyae121

Lister NC; Milton AM; Patel HR; Waters SA; Hanrahan BJ; McIntyre KL; Livernois AM; Horspool WB; Wee LK; Ringel AR; Mundlos S; Robson MI; Shearwin-Whyatt L; Grützner F; Marshall Graves JA; Ruiz-Herrera A; Waters PD, 2024, 'Incomplete transcriptional dosage compensation of chicken and platypus sex chromosomes is balanced by post-transcriptional compensation', Proceedings of the National Academy of Sciences of the United States of America, 121, http://dx.doi.org/10.1073/pnas.2322360121

Harding EF; Mercer LK; Yan GJH; Waters PD; White PA, 2024, 'Invasion and Amplification of Endogenous Retroviruses in Dasyuridae Marsupial Genomes', Molecular Biology and Evolution, 41, http://dx.doi.org/10.1093/molbev/msae160

Hogg CJ; Edwards RJ; Farquharson KA; Silver LW; Brandies P; Peel E; Escalona M; Jaya FR; Thavornkanlapachai R; Batley K; Bradford TM; Chang JK; Chen Z; Deshpande N; Dziminski M; Ewart KM; Griffith OW; Marin Gual L; Moon KL; Travouillon KJ; Waters P; Whittington CM; Wilkins MR; Helgen KM; Lo N; Ho SYW; Ruiz Herrera A; Paltridge R; Marshall Graves JA; Renfree M; Shapiro B; Ottewell K; Belov K; Gibson C; Maxwell R; Spencer Z; Napangati Y; Butler M; West J; West J; James M; Napangati N; Gibson L; West P; Gibson A; West S; West K; Japaltjari W; Blackwood E, 2024, 'Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial', Nature Ecology and Evolution, 8, pp. 1311 - 1326, http://dx.doi.org/10.1038/s41559-024-02436-2

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, pp. 17854, 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, 20, pp. 460, 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, pp. 230, 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, pp. e1700731, 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

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