Associate Professor Paul Waters

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Research Program

The lab focuses on better understanding the epigenetic regulation of transcription in diverse vertebrate representatives, specifically focussing on sex chromosomes. The ultimate goal is to understand how complex epigenetic silencing mechanisms evolved. We use eutherian, marsupial, monotreme and bird/reptile models. Representatives from these groups each have different (sometimes weird and wonderful) sex determining mechanisms and sex chromosome systems.

We examine X chromosome inactivation in wallabies and Tasmanian devils. We have particular interest in dosage compensation of the strange sex chromosomes of platypus, which have 5 X chromosomes and 5 Y chromosomes! We also study the Australian central bearded dragon, which are unusual in that they have both genetic and environmental sex determination. In more recent years we have been examining hibernation/brumation in dragon lizards.

Click for a��full list of��publications.��

Some cover highlights (click to link out):

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Teaching

Coordinator:

2^ndyear Genetics (BABS2204/2264)

Lecturer:

Molecules, Cells and Genes(BABS1201)
Human Molecular Genetics and Disease(BABS3151)
Genes, Genomes and Evolution(BABS3291)
Beginnings, Growth and Development A (MFAC1521)
Beginnings, Growth and Development B (MFAC1522)

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Supervision

PhD, MSc, Honours, and 3rd year Undergraduate projects in Epigenetics and Molecular Biology are available in the lab.

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Professional Experience

2019-current: Associate Professor, School of Biotechnology and Biomolecular Science
2014-2019: Senior Lecturer, School of Biotechnology and Biomolecular Science
2012-2014: ARC Fellow & Senior Lecturer, School of Biotechnology and Biomolecular Sciences
2009-2012: ARC Fellow, Evolution Ecology & Genetics, Research School of Biology, ANU
2007-2009: Research Fellow, Comparative Genomics Group, Research School of Biological Sciences, The Australian National University
2006-2007: Postdoctoral Fellow, ARC Centre for Kangaroo Genomics, Comparative Genomics Group, Research School of Biological Science, ANU
2003-2005: Postdoctoral Fellow, Evolutionary Genomics Group, Department of Zoology, Stellenbosch University, Private Bag X1, Matieland, South Africa

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Funding

APP1182667.��NHMRC Ideas Grant. 2020-2023 (AUD $562k). Clemens K & Waters PD. A role for long non-coding RNA in the persistence of drug seeking.
DP180100931. ARC Discovery Project. 2018-2020��(AUD $432k).��Waters PD & Morris KV.Silencing the X chromosome: Why and How.
DP170101147. ARC Discovery Project. 2017-2020��(AUD $1,007k).��Georges A, Deakin AE, Sarre S, Ezaz T, Waters PD, Schwanz L, Graves JAM & Holleley C. Sex determination in dragons – genetics, epigenetics and environment.��
DP1094868.��ARC Discovery Project. 2010-2013 (AUD $315k). Waters PD, DeakinJE & Graves JA.Epigenetic silencing in vertebrates – evolution and function from the bottom-up.��
DP0987091.��Australian Research Fellowship. 2009-2014 (AUD $560k). Waters PD. Origin and Evolution of Mammalian Dosage Compensation.

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Phone

+61-2 9065 1893

E-mail

p.waters@unsw.edu.au

Location

Office: Rm 3110, Level 3 Biosciences South (E26) Kensington Campus

Books | 2010

Deakin JE; Waters PD; Graves JAM, 2010, Marsupial genetics and genomics,

Books | 2010

Deakin JE; Waters PD; Graves JAM, 2010, Preface,

Books | 2010

Waters PD; Deakin JE, 2010, Part VIII: Marsupial genes and gene evolution,

Books | 2010

Waters PD, 2010, Part IV: Marsupial sex chromosomes,

Books | 2010

Waters PD, 2010, Part V: Marsupial epigenetics,
Book Chapters | 2021

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,

Book Chapters | 2018

McIntyre K; Waters S; Waters P, 2018, 'Sex Chromosomes', in Skinner MK (ed.), Encyclopedia of Reproduction, edn. 2, Academic Press, pp. 238 - 244,

Book Chapters | 2013

Waters PD; Robinson TJ, 2013, 'Evolution of the Mammalian X Chromosome', in , Wiley,

Book Chapters | 2010

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,

Book Chapters | 2010

Murtagh VJ; Waters PD; Marshall Graves JA, 2010, 'Compact but complex - The marsupial Y chromosome', in Marsupial Genetics and Genomics, pp. 207 - 228,
Journal articles | 2024

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,

Journal articles | 2024

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,

Journal articles | 2024

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,

Journal articles | 2024

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,

Journal articles | 2024

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,

Journal articles | 2024

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,

Journal articles | 2024

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,

Journal articles | 2023

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,

Journal articles | 2023

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,

Journal articles | 2023

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,

Journal articles | 2023

Waters PD; Graves JAM; Whiteley SL; Georges A; Ruiz-Herrera A, 2023, 'Three dimensions of thermolabile sex determination', BioEssays, 45,

Journal articles | 2022

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,

Journal articles | 2022

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,

Journal articles | 2022

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,

Journal articles | 2022

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,

Journal articles | 2022

Ruiz-Herrera A; Waters PD, 2022, 'Fragile, unfaithful and persistent Ys—on how meiosis can shape sex chromosome evolution', Heredity, 129, pp. 22 - 30,

Journal articles | 2022

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,

Journal articles | 2022

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,

Journal articles | 2021

Harding EF; Russo AG; Yan GJH; Waters PD; White PA, 2021, 'Ancient viral integrations in marsupials: A potential antiviral defence', Virus Evolution, 7,

Journal articles | 2021

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,

Journal articles | 2021

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', ,

Journal articles | 2021

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,

Journal articles | 2020

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,

Journal articles | 2020

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,

Journal articles | 2020

Waters PD; Ruiz-Herrera A, 2020, 'Meiotic Executioner Genes Protect the Y from Extinction', Trends in Genetics, 36, pp. 728 - 738,

Journal articles | 2019

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,

Journal articles | 2019

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,

Journal articles | 2019

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,

Journal articles | 2018

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,

Journal articles | 2018

Waters SA; Capraro A; McIntyre KL; Graves JAM; Waters PD, 2018, 'The methylome of vertebrate sex chromosomes', Genes, 9, pp. 230,

Journal articles | 2018

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,

Journal articles | 2017

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,

Journal articles | 2017

Waters PD, 2017, 'Fragile Y Chromosomes (retrospective on DOI 10.1002/bies.201500040)', BioEssays, 39,

Journal articles | 2015

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,

Journal articles | 2015

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,

Journal articles | 2015

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,

Journal articles | 2015

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,

Journal articles | 2015

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

Journal articles | 2015

Waters SA; Waters PD, 2015, 'Imprinted X chromosome inactivation: evolution of mechanisms in distantly related mammals', AIMS GENETICS, 2, pp. 110 - 126,

Journal articles | 2014

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,

Journal articles | 2014

Rodríguez-Delgado CL; Waters SA; Waters DP; Waters P, 2014, 'Paternal X inactivation does not correlate with X chromosome evolutionary strata in marsupials', BMC Evolutionary Biology, 14, pp. 267,

Journal articles | 2013

Gilbert C; Waters P; Feschotte C; Schaack S, 2013, 'Horizontal transfer of OC1 transposons in the Tasmanian devil', BMC Genomics, 14,

Journal articles | 2013

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,

Journal articles | 2013

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, pp. e1003635,

Journal articles | 2012

Livernois AM; Graves JAM; Waters PD, 2012, 'The origin and evolution of vertebrate sex chromosomes and dosage compensation', Heredity, 108, pp. 50 - 58,

Journal articles | 2011

Al Nadaf S; Deakin JE; Gilbert C; Robinson TJ; Graves JA; Waters PD; Waters P, 2011, 'A cross-species comparison of escape from X inactivation in Eutheria: implications for evolution of X chromosome inactivation.', Chromosoma, 121, pp. 71 - 78,

Journal articles | 2011

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, 19, pp. 709 - 727

Journal articles | 2011

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, 6,

Journal articles | 2011

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, 22, pp. 498 - 507

Journal articles | 2011

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, pp. 414,

Journal articles | 2010

Al Nadaf S; Waters PD; Koina E; Deakin JE; Jordan KS; Graves JAM; Waters P, 2010, 'Activity map of the tammar X chromosome shows that marsupial X inactivation is incomplete and escape is stochastic', Genome Biology, 11, pp. r122,

Journal articles | 2009

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, 19, pp. 1350 - 1360

Journal articles | 2009

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, 17, pp. 917 - 926

Journal articles | 2009

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, 17, pp. 965 - 973

Journal articles | 2009

Mohammadi A; Delbridge ML; Waters PD; Graves JA, 2009, 'Conservation of a chromosome arm in two distantly related marsupial species.', Cytogenetic and Genome Research, 124, pp. 147 - 150

Journal articles | 2009

Waters PD; Graves JA, 2009, 'Monotreme sex chromosomes – implications for the evolution of amniote sex chromosomes', Reproduction Fertility and Development, 21, pp. 943 - 951,

Journal articles | 2008

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, 16, pp. 1159 - 1175

Journal articles | 2008

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, 177, pp. 211 - 217,

Journal articles | 2008

Gilbert C; Pace JK; Waters PD, 2008, 'Target site analysis of RTE1_LA and its AfroSINE partner in the elephant genome', Gene, 425, pp. 1 - 8

Journal articles | 2008

Gilbert C; Pace JK; Waters PD, 2008, 'Target site analysis of RTE1_LA and its AfroSINE partner in the elephant genome', Gene, 425, pp. 1 - 8,

Journal articles | 2008

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, 18, pp. 965 - 973

Journal articles | 2008

Wallis MC; Waters PD; Graves JA, 2008, 'Sex determination in mammals-before and after the evolution of SRY', CMLS - Cellular and Molecular Life Sciences, 65, pp. 3182 - 3195

Journal articles | 2008

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, 455, pp. 256,

Journal articles | 2008

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, 453, pp. 175 - 184

Journal articles | 2008

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.), 422, pp. 227 - 237,

Journal articles | 2008

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.), 422, pp. 239 - 251,

Journal articles | 2008

Waters PD; Robinson TJ, 2008, 'Evolution of the MammalianXChromosome', ,

Journal articles | 2007

Kirby PJ; Greaves IK; Koina E; Waters PD; Marshall Graves JA, 2007, 'CORE-SINE blocks comprise a large fraction of monotreme genomes; implications for vertebrate chromosome evolution.', Chromosome Research, 15, pp. 975 - 984,

Journal articles | 2007

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 J; 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; Graves JA; Ponting CP; Breen M; Samollow PB; Lander ES; Lindblad-Toh K, 2007, 'Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences.', Nature, 447, pp. 167 - 177

Journal articles | 2007

Wallis MC; Waters PD; Delbridge ML; Kirby PJ; Pask A; Grutzner F; Rens W; Ferguson-smith MA; Graves JA, 2007, 'Sex determination in platypus and echidna: autosomal location of SOX3 confirms the absence of SRY from monotremes.', Chromosome Research, 15, pp. 949 - 959

Journal articles | 2007

Waters PD; Dobigny G; Waddell PJ; Robinson TJ, 2007, 'Evolutionary history of LINE-1 in the major clades of placental mammals', PLoS ONE, 2, pp. e158

Journal articles | 2007

Waters PD; Ruiz-Herrera A; Dobigny G; Garcia Caldes M; Robinson TJ, 2007, 'Sex chromosomes of basal placental mammals', Chromosoma, 116, pp. 511 - 518

Journal articles | 2007

Waters PD; Wallis MC; Marshall Graves JA, 2007, 'Mammalian sex – origin and evolution of the Y chromosome and SRY', Seminars in Cell and Developmental Biology, 18, pp. 389 - 400

Journal articles | 2006

Dobigny G; Waters PD; Robinson TJ, 2006, 'Absence of hypomethylation and LINE-1 amplification in a white x black rhinoceros hybrid', Genetica, 127, pp. 81 - 86,

Journal articles | 2005

Waters PD; Delbridge ML; Deakin JE; El-Mogharbel N; Kirby PJ; Carvalho-Silva DR; Marshall Graves JA, 2005, 'Autosomal location of genes from the conserved mammalian X in the platypus (Ornithorhynchus anatinus): Implications for mammalian sex chromosome evolution', Chromosome Research, 13, pp. 401 - 410,

Journal articles | 2004

Carvalho-Silva DR; O'Neill RJW; Brown JD; Huynh K; Waters PD; Pask AJ; Delbridge ML; Marshall Graves JA, 2004, 'Molecular characterization and evolution of X and Y-borne ATRX homologues in American marsupials', Chromosome Research, 12, pp. 795 - 804,

Journal articles | 2004

Dobigny G; Ozouf-Costaz C; Waters PD; Bonillo C; Coutanceau JP; Volobouev V, 2004, 'LINE-1 amplification accompanies explosive genome repatterning in rodents', Chromosome Research, 12, pp. 787 - 793,

Journal articles | 2004

Waters PD; Dobigny G; Pardini AT; Robinson TJ, 2004, 'LINE-1 distribution in Afrotheria and Xenarthra: Implications for understanding the evolution of LINE-1 in eutherian genomes', Chromosoma, 113, pp. 137 - 144,

Journal articles | 2003

Waters PD; Sankovic N; Kirby PJ; Delbridge ML; Graves JA, 2003, 'Assignment of the thymosin beta 4 X/Y chromosome (TMSB4X/Y) gene to tammar wallaby chromosome 5p by fluorescence in situ hybridisation', Cytogenetic and Genome Research, 103,

Journal articles | 2002

Kirby PJ; Waters PD; Delbridge M; Svartman M; Stewart AN; Nagai K; Graves JAM, 2002, 'Cloning and mapping of platypus SOX2 and SOX14: Insights into SOX group B evolution', Cytogenetic and Genome Research, 98, pp. 96 - 100,

Journal articles | 2002

Waters PD; Kirby PJ; Graves JAM, 2002, 'Assignment of the protocadherin 20 (PCDH20) gene to tammar wallaby chromosome 6q by fluorescence in situ hybridisation', Cytogenetic and Genome Research, 98,

Journal articles | 2001

Waters PD; Duffy B; Frost CJ; Delbridge ML; Graves JAM, 2001, 'The human Y chromosome derives largely from a single autosomal region added to the sex chromosomes 80-130 million years ago', Cytogenetics and Cell Genetics, 92, pp. 74 - 79,

Journal articles | 2001

Waters PD; Kirby PJ; Graves JAM, 2001, 'Assignment¹ of the SMARCF1 gene to tammar wallaby chromosome 5q by fluorescence in situ hybridisation', Cytogenetics and Cell Genetics, 93, pp. 315 - 316
Working Papers | 2019

Youngson NA; Castino MR; Stuart A; Kershaw KA; Holmes NM; Waters PD; Morris KV; Clemens KJ, 2019, A natural antisense to brain-derived neurotrophic factor impairs extinction of drug seeking, Cold Spring Harbor Laboratory,
Preprints | 2024

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, 2024, A genome assembly and annotation for the Australian alpine skinkBassiana duperreyiusing long-read technologies,

Preprints | 2023

Hanrahan B; Chang K; Lister N; Dissanayake DSB; Hammond J; Reis ALM; Deveson I; Ruiz-Herrera A; Patel H; Marshall Graves J; Georges A; Waters P, 2023, Both phenotypic and genotypic sex influence sex chromosome dosage compensation in a sex reversing lizard,

Preprints | 2023

Hogg C; Edwards R; Farquharson K; Silver L; Brandies P; Peel E; Escalona M; Jaya F; Sun R; Batley K; Bradford T; Chang K; Chen Z; Deshpande N; Dziminski M; Ewart K; Griffith O; Marin-Gual L; Moon K; Travouillon K; Waters P; Whittington C; Wilkins M; Helgen K; Lo N; Ho S; Ruiz-Herrera A; Paltridge R; Graves J; Renfree M; Shapiro B; Ottewell K; Rangers KC; Belov K, 2023, Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial,

Preprints | 2023

Lister N; Milton A; Patel H; Waters S; Hanrahan B; McIntyre K; Livernois A; Wee LK; Ringel A; Mundlos S; Robson M; Shearwin-Whyatt L; Grützner F; Marshall Graves J; Ruiz-Herrera A; Waters P, 2023, Incomplete transcriptional dosage compensation of vertebrate sex chromosomes is balanced by post-transcriptional compensation,

Preprints | 2023

McIntyre K; Waters S; Zhong L; Hart-Smith G; Raftery M; Graves JM; Waters P, 2023, Functional coherence of theXistandRSXprotein interactomes: X chromosome inactivation in marsupials,

Preprints | 2023

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, ,

Conference Papers | 2022

Waters PD; Ruiz-Herrera A, 2022, 'The persistent Y hypothesis', in HUMAN REPRODUCTION, OXFORD UNIV PRESS,

Conference Abstracts | 2020

Eyck HJF; Sarma RR; Crino OL; Waters PD; Crossland M; Shine R; Rollins LA, 2020, 'Corticosterone response to experimental manipulation of methylation in invasive amphibian larvae', in INTEGRATIVE AND COMPARATIVE BIOLOGY, OXFORD UNIV PRESS INC, TX, Austin, Vol. 60, pp. E66 - E66, presented at Annual Meeting of the Society-for-Integrative-and-Comparative-Biology (SICB), TX, Austin, 03 January 2020 - 07 January 2020,

Preprints | 2019

Sprague D; Waters SA; Kirk JM; Wang JR; Samollow PB; Waters PD; Calabrese JM, 2019, Non-linear sequence similarity between the Xist and Rsx long noncoding RNAs suggests shared functions of tandem repeat domains,

Conference Papers | 2007

Robinson T; Waters P; Ruiz-Herrera A; Dobigny G; Garcia M, 2007, 'Sex chromosomes of basal placental mammals', in CHROMOSOME RESEARCH, SPRINGER, NETHERLANDS, Amsterdam, pp. 75 - 75, presented at 16th International Chromosome Conference (ICC 16), NETHERLANDS, Amsterdam, 25 August 2007 - 29 August 2007,

Conference Papers | 2007

Veyrunes F; Rens W; Waters P; Miethke P; Alsop A; Grutzner F; Deakin J; Ferguson-Smith M; Graves J, 2007, 'Does the platypus sex chromosome system derive from an ancestral bird ZW system?', in CHROMOSOME RESEARCH, SPRINGER, NETHERLANDS, Amsterdam, pp. 72 - 73, presented at 16th International Chromosome Conference (ICC 16), NETHERLANDS, Amsterdam, 25 August 2007 - 29 August 2007,

Conference Papers | 2001

Graves JAM; Waters PD, 2001, 'Mammalian sex chromosome evolution - The rise and fall of the Y chromosome', in Schmid M (ed.), CHROMOSOMES TODAY, VOL 14, SPRINGER, GERMANY, Wurzburg, pp. 3 - 14, presented at 14th International Chromosomes Conference, GERMANY, Wurzburg, 04 September 2001 - 08 September 2001,

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