Waters, Paul - University of New South Wales - School of Biotechnology and Biomolecular Science

个人简介

2013-current: Senior Lecturer, School of BABS, UNSW 2009-2012: ARC Fellow, Evolution Ecology & Genetics, Research School of Biology, The Australian National University 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, The Australian National University 2003-2005: Postdoctoral Fellow, Evolutionary Genomics Group, Department of Zoology, Stellenbosch University, Private Bag X1, Matieland, South Africa

研究领域

My research centres on better understanding epigenetic regulation of transcription in diverse vertebrate representatives, specifically focussing on sex chromosomes dosage compensation. The ultimate goal is to understand how complex epigenetic silencing mechanisms evolved. During my PhD I focused on the gene content and evolution of marsupial Y chromosomes, and throughout my first postdoc in South Africa I focused on the genomics of Afrotheria (basal eutherian mammals; which include elephant, aardvarks, etc.). I was awarded an ARC discovery project to further explore the epigenetics of vertebrate dosage compensation. The next stage of vertebrate genomics and epigenetics for my group involves much use of short read sequencing technologies. I am currently using the Tasmanian devil to develop a technique for sequencing a whole mammal Y chromosome. For a study of dosage compensation in phylogenetically important vertebrate taxa, I have sequenced the transcriptomes from a male and female elephant, along with a male and female opossum. I use ChIP-Seq to examine the chromatin modifications associated with vertebrate dosage compensation. I have ChIP samples being sequenced from the same opossum cell lines that the transcriptomes were sequenced, which will allow me to directly correlate transcription levels with chromatin modifications on a genome wide scale, avoiding problems associated with variation between individuals and tissue type.

近期论文

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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, pp. 45, http://dx.doi.org/10.1186/s13742-015-0085-2 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, no. 9, 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, vol. 37, no. 9, 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, vol. 16, no. 3, 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 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, no. 1, http://dx.doi.org/10.1186/s12862-014-0267-z 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, no. 7497, pp. 488 - 493, http://dx.doi.org/10.1038/nature13151 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, no. 9, pp. 1486 - 1495, http://dx.doi.org/10.1101/gr.154286.112 Gilbert C; Waters P; Feschotte C; Schaack S, 2013, 'Horizontal transfer of OC1 transposons in the Tasmanian devil', BMC Genomics, vol. 14, no. 1, http://dx.doi.org/10.1186/1471-2164-14-134 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, no. 7, http://dx.doi.org/10.1371/journal.pgen.1003635 Al Nadaf S; Deakin JE; Gilbert C; Robinson TJ; Graves JA; Waters PD, 2012, 'A cross-species comparison of escape from X inactivation in Eutheria: implications for evolution of X chromosome inactivation.', Chromosoma: biology of the nucleus, vol. 121, no. 1, pp. 71 - 78, http://dx.doi.org/10.1007/s00412-011-0343-8 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, 2012, 'Evolutionary history of novel genes on the tammar wallaby Y chromosome: Implications for sex chromosome evolution.', Genome Research, vol. 22, no. 3, pp. 498 - 507, http://dx.doi.org/10.1101/gr.120790.111 Livernois AM; Graves JAM; Waters PD, 2012, 'The origin and evolution of vertebrate sex chromosomes and dosage compensation', Heredity, vol. 108, no. 1, pp. 50 - 58, http://dx.doi.org/10.1038/hdy.2011.106 Chaumeil J; Waters PD; Koina E; Gilbert C; Robinson TJ; Graves JA, 2011, 'Evolution from XIST-independent to XIST-controlled X-chromosome inactivation: epigenetic modifications in distantly related mammals.', PLoS One, vol. 6, no. 4, pp. e19040, http://dx.doi.org/10.1371/journal.pone.0019040 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: the international journal for all aspects of chromosome and nuclear biology, vol. 19, no. 6, pp. 709 - 727, http://dx.doi.org/10.1007/s10577-011-9227-2 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, 2011, 'Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development', Genome Biology: biology for the post-genomic era, vol. 12, no. 8, http://dx.doi.org/10.1186/gb-2011-12-8-r81 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: biology for the post-genomic era, vol. 11, no. 12, http://dx.doi.org/10.1186/gb-2010-11-12-r122 Mohammadi A; Delbridge ML; Waters PD; Marshall Graves JA, 2009, 'Conservation of a chromosome arm in two distantly related marsupial species', Cytogenetic and Genome Research, vol. 124, no. 2, pp. 147 - 150, http://dx.doi.org/10.1159/000207522 Delbridge ML; Patel HR; Waters PD; McMillan DA; Marshall Graves JA, 2009, 'Does the human X contain a third evolutionary block? Origin of genes on human Xp11 and Xq28', Genome Research, vol. 19, no. 8, pp. 1350 - 1360, http://dx.doi.org/10.1101/gr.088625.108 Rodríguez Delgado CL; Waters PD; Gilbert C; Robinson TJ; Graves JAM, 2009, 'Physical mapping of the elephant X chromosome: Conservation of gene order over 105 million years', Chromosome Research: the international journal for all aspects of chromosome and nuclear biology, vol. 17, no. 7, pp. 917 - 926, http://dx.doi.org/10.1007/s10577-009-9079-1