Publications by authors named "Paul D Waters"

44Publications

MicroRNA dynamics during hibernation of the Australian central bearded dragon (Pogona vitticeps).

Sci Rep 2020 10 20;10(1):17854. Epub 2020 Oct 20.

School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Sydney, Kensington, NSW, 2052, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-020-73706-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7576210PMC
October 2020

Meiotic Executioner Genes Protect the Y from Extinction.

Trends Genet 2020 10 6;36(10):728-738. Epub 2020 Aug 6.

Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08193, Spain; Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08193, Spain. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.tig.2020.06.008DOI Listing
October 2020

Do epigenetic changes drive corticosterone responses to alarm cues in larvae of an invasive amphibian?

Integr Comp Biol 2020 Jun 16. Epub 2020 Jun 16.

Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney NSW.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/icb/icaa082DOI Listing
June 2020

Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis.

Cell Rep 2019 07;28(2):352-367.e9

Departament de Biologia Cel.lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès 08193, Spain; Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès 08193, Spain. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.celrep.2019.06.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6635386PMC
July 2019

Waking the sleeping dragon: gene expression profiling reveals adaptive strategies of the hibernating reptile Pogona vitticeps.

BMC Genomics 2019 Jun 6;20(1):460. Epub 2019 Jun 6.

School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Sydney, Sydney, NSW, 2052, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5750-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6555745PMC
June 2019

Nonlinear sequence similarity between the and long noncoding RNAs suggests shared functions of tandem repeat domains.

RNA 2019 08 16;25(8):1004-1019. Epub 2019 May 16.

Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1261/rna.069815.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6633197PMC
August 2019

The Methylome of Vertebrate Sex Chromosomes.

Genes (Basel) 2018 May 1;9(5). Epub 2018 May 1.

School of Biotechnology & Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3390/genes9050230DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5977170PMC
May 2018

Landscape of DNA Methylation on the Marsupial X.

Mol Biol Evol 2018 02;35(2):431-439

School of Biotechnology & Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/molbev/msx297DOI Listing
February 2018

Fragile Y Chromosomes (retrospective on DOI 10.1002/bies.201500040).

Authors:
Paul D Waters

Bioessays 2017 11 15;39(11). Epub 2017 Sep 15.

School of Biotechnology & Biomolecular Sciences, UNSW Sydney NSW, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/bies.201700142DOI Listing
November 2017

Differential intron retention in chromatin modifier genes is implicated in reptile temperature-dependent sex determination.

Sci Adv 2017 06 14;3(6):e1700731. Epub 2017 Jun 14.

Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/sciadv.1700731DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5470834PMC
June 2017

The loss of fragile Y chromosomes (comment on 10.1002/bies.201500040).

Authors:
Paul D Waters

Bioessays 2015 Sep 10;37(9):933. Epub 2015 Aug 10.

Faculty of Science, School of Biotechnology and Biomolecular Sciences, UNSW Australia, Sydney, NSW, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/bies.201500091DOI Listing
September 2015

Long intervening non-coding RNA 00320 is human brain-specific and highly expressed in the cortical white matter.

Neurogenetics 2015 Jul 29;16(3):201-13. Epub 2015 Mar 29.

School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10048-015-0445-1DOI Listing
July 2015

Paternal X inactivation does not correlate with X chromosome evolutionary strata in marsupials.

BMC Evol Biol 2014 Dec 24;14:267. Epub 2014 Dec 24.

School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, 2052, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-014-0267-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4302592PMC
December 2014

Origins and functional evolution of Y chromosomes across mammals.

Nature 2014 Apr;508(7497):488-93

1] Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland [2] Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature13151DOI Listing
April 2014

Independent evolution of transcriptional inactivation on sex chromosomes in birds and mammals.

PLoS Genet 2013 18;9(7):e1003635. Epub 2013 Jul 18.

Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1003635DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715422PMC
January 2014

Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution.

Genome Res 2013 Sep 20;23(9):1486-95. Epub 2013 Jun 20.

Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.154286.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3759724PMC
September 2013

A cross-species comparison of escape from X inactivation in Eutheria: implications for evolution of X chromosome inactivation.

Chromosoma 2012 Feb 27;121(1):71-8. Epub 2011 Sep 27.

Evolution Ecology and Genetics, Research School of Biology, The Australian National University, ACT 2601, Canberra, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00412-011-0343-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3260438PMC
February 2012

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.

Authors:
Marilyn B Renfree Anthony T Papenfuss Janine E Deakin James Lindsay Thomas Heider Katherine Belov Willem Rens Paul D Waters Elizabeth A Pharo Geoff Shaw Emily S W Wong Christophe M Lefèvre Kevin R Nicholas Yoko Kuroki Matthew J Wakefield Kyall R Zenger Chenwei Wang Malcolm Ferguson-Smith Frank W Nicholas Danielle Hickford Hongshi Yu Kirsty R Short Hannah V Siddle Stephen R Frankenberg Keng Yih Chew Brandon R Menzies Jessica M Stringer Shunsuke Suzuki Timothy A Hore Margaret L Delbridge Hardip R Patel Amir Mohammadi Nanette Y Schneider Yanqiu Hu William O'Hara Shafagh Al Nadaf Chen Wu Zhi-Ping Feng Benjamin G Cocks Jianghui Wang Paul Flicek Stephen M J Searle Susan Fairley Kathryn Beal Javier Herrero Dawn M Carone Yutaka Suzuki Sumio Sugano Atsushi Toyoda Yoshiyuki Sakaki Shinji Kondo Yuichiro Nishida Shoji Tatsumoto Ion Mandiou Arthur Hsu Kaighin A McColl Benjamin Lansdell George Weinstock Elizabeth Kuczek Annette McGrath Peter Wilson Artem Men Mehlika Hazar-Rethinam Allison Hall John Davis David Wood Sarah Williams Yogi Sundaravadanam Donna M Muzny Shalini N Jhangiani Lora R Lewis Margaret B Morgan Geoffrey O Okwuonu San Juana Ruiz Jireh Santibanez Lynne Nazareth Andrew Cree Gerald Fowler Christie L Kovar Huyen H Dinh Vandita Joshi Chyn Jing Fremiet Lara Rebecca Thornton Lei Chen Jixin Deng Yue Liu Joshua Y Shen Xing-Zhi Song Janette Edson Carmen Troon Daniel Thomas Amber Stephens Lankesha Yapa Tanya Levchenko Richard A Gibbs Desmond W Cooper Terence P Speed Asao Fujiyama Jennifer A M Graves Rachel J O'Neill Andrew J Pask Susan M Forrest Kim C Worley

Genome Biol 2011 Aug 29;12(8):R81. Epub 2011 Aug 29.

The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/gb-2011-12-8-r81DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3277949PMC
August 2011

Chromosomal evolution in Rattini (Muridae, Rodentia).

Chromosome Res 2011 Aug 18;19(6):709-27. Epub 2011 Aug 18.

Evolutionary Genomics Group, Botany and Zoology Department, University of Stellenbosch, Private Bag X1, 7604 Matieland, South Africa.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10577-011-9227-2DOI Listing
August 2011

Evolution from XIST-independent to XIST-controlled X-chromosome inactivation: epigenetic modifications in distantly related mammals.

PLoS One 2011 Apr 25;6(4):e19040. Epub 2011 Apr 25.

Comparative Genomics Group, Evolution Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019040PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3081832PMC
April 2011

Activity map of the tammar X chromosome shows that marsupial X inactivation is incomplete and escape is stochastic.

Genome Biol 2010 23;11(12):R122. Epub 2010 Dec 23.

Research School of Biology, The Australian National University, Biology Place, Canberra 0200, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/gb-2010-11-12-r122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3046482PMC
June 2011

Monotreme sex chromosomes--implications for the evolution of amniote sex chromosomes.

Reprod Fertil Dev 2009 ;21(8):943-51

Comparative Genomics Group, Research School of Biological Sciences, School of Biology, The Australian National University, GPO Box 475, Canberra, ACT 2601, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1071/RD09250DOI Listing
February 2010

Physical mapping of the elephant X chromosome: conservation of gene order over 105 million years.

Chromosome Res 2009 30;17(7):917-26. Epub 2009 Sep 30.

Comparative Genomics Group, Research School of Biology, The Australian National University, GPO Box 475, ACT 2601, Canberra, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10577-009-9079-1DOI Listing
March 2010

Does the human X contain a third evolutionary block? Origin of genes on human Xp11 and Xq28.

Genome Res 2009 Aug 13;19(8):1350-60. Epub 2009 May 13.

The ARC Centre of Excellence for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, ACT Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.088625.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720175PMC
August 2009

Physical map of two tammar wallaby chromosomes: a strategy for mapping in non-model mammals.

Chromosome Res 2008 8;16(8):1159-75. Epub 2008 Nov 8.

ARC Centre of Excellence for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 0200, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10577-008-1266-yDOI Listing
March 2009

Target site analysis of RTE1_LA and its AfroSINE partner in the elephant genome.

Gene 2008 Dec 28;425(1-2):1-8. Epub 2008 Aug 28.

Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.gene.2008.08.013DOI Listing
December 2008

Identification of cryptic sex chromosomes and isolation of X- and Y-borne genes.

Methods Mol Biol 2008 ;422:239-51

Research School of Biological Sciences, The Australian National University, Canberra, Australia.

View Article

Download full-text PDF

Source
http://www.piku.org.au/reprints/2008_Waters_Ezaz%20et%20al_%
Web Search
http://link.springer.com/10.1007/978-1-59745-581-7_15
Publisher Site
http://dx.doi.org/10.1007/978-1-59745-581-7_15DOI Listing
August 2008

LINE-1 elements: analysis by fluorescence in-situ hybridization and nucleotide sequences.

Methods Mol Biol 2008 ;422:227-37

Research School of Biological Sciences, The Australian National University, Canberra, Australia.

View Article

Download full-text PDF

Source
http://link.springer.com/10.1007/978-1-59745-581-7_14
Publisher Site
http://dx.doi.org/10.1007/978-1-59745-581-7_14DOI Listing
August 2008

Genome analysis of the platypus reveals unique signatures of evolution.

Authors:
Wesley C Warren LaDeana W Hillier Jennifer A Marshall Graves Ewan Birney Chris P Ponting Frank Grützner Katherine Belov Webb Miller Laura Clarke Asif T Chinwalla Shiaw-Pyng Yang Andreas Heger Devin P Locke Pat Miethke Paul D Waters Frédéric Veyrunes Lucinda Fulton Bob Fulton Tina Graves John Wallis Xose S Puente Carlos López-Otín Gonzalo R Ordóñez Evan E Eichler Lin Chen Ze Cheng Janine E Deakin Amber Alsop Katherine Thompson Patrick Kirby Anthony T Papenfuss Matthew J Wakefield Tsviya Olender Doron Lancet Gavin A Huttley Arian F A Smit Andrew Pask Peter Temple-Smith Mark A Batzer Jerilyn A Walker Miriam K Konkel Robert S Harris Camilla M Whittington Emily S W Wong Neil J Gemmell Emmanuel Buschiazzo Iris M Vargas Jentzsch Angelika Merkel Juergen Schmitz Anja Zemann Gennady Churakov Jan Ole Kriegs Juergen Brosius Elizabeth P Murchison Ravi Sachidanandam Carly Smith Gregory J Hannon Enkhjargal Tsend-Ayush Daniel McMillan Rosalind Attenborough Willem Rens Malcolm Ferguson-Smith Christophe M Lefèvre Julie A Sharp Kevin R Nicholas David A Ray Michael Kube Richard Reinhardt Thomas H Pringle James Taylor Russell C Jones Brett Nixon Jean-Louis Dacheux Hitoshi Niwa Yoko Sekita Xiaoqiu Huang Alexander Stark Pouya Kheradpour Manolis Kellis Paul Flicek Yuan Chen Caleb Webber Ross Hardison Joanne Nelson Kym Hallsworth-Pepin Kim Delehaunty Chris Markovic Pat Minx Yucheng Feng Colin Kremitzki Makedonka Mitreva Jarret Glasscock Todd Wylie Patricia Wohldmann Prathapan Thiru Michael N Nhan Craig S Pohl Scott M Smith Shunfeng Hou Mikhail Nefedov Pieter J de Jong Marilyn B Renfree Elaine R Mardis Richard K Wilson

Nature 2008 May;453(7192):175-83

Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature06936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803040PMC
May 2008

Core-SINE blocks comprise a large fraction of monotreme genomes; implications for vertebrate chromosome evolution.

Chromosome Res 2007 9;15(8):975-84. Epub 2008 Jan 9.

Comparative Genomics Group, Research School of Biological Science, The Australian National University, Canberra, ACT 2601, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10577-007-1187-1DOI Listing
April 2008

Sex chromosomes of basal placental mammals.

Chromosoma 2007 Dec 30;116(6):511-8. Epub 2007 Jun 30.

Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00412-007-0116-6DOI Listing
December 2007

Mammalian sex--Origin and evolution of the Y chromosome and SRY.

Semin Cell Dev Biol 2007 Jun 24;18(3):389-400. Epub 2007 Feb 24.

Comparative Genomics Group, Research School of Biological Sciences, The Australian National University, GPO Box 475, ACT 2601, Canberra, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.semcdb.2007.02.007DOI Listing
June 2007

Evolutionary history of LINE-1 in the major clades of placental mammals.

PLoS One 2007 Jan 17;2(1):e158. Epub 2007 Jan 17.

Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Matieland, South Africa.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000158PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1764860PMC
January 2007

Absence of hypomethylation and LINE-1 amplification in a white x black rhinoceros hybrid.

Genetica 2006 May;127(1-3):81-6

Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10709-005-2483-3DOI Listing
May 2006

Autosomal location of genes from the conserved mammalian X in the platypus (Ornithorhynchus anatinus): implications for mammalian sex chromosome evolution.

Chromosome Res 2005 ;13(4):401-10

Comparative Genomics Group, Research Group of Biological Science, The Australian National University, Canberra, ACT, 2601, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10577-005-0978-5DOI Listing
September 2005

Molecular characterization and evolution of X and Y-borne ATRX homologues in American marsupials.

Chromosome Res 2004 ;12(8):795-804

Research School of Biological Science, Australian National University, ACT 0200, Canberra, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10577-005-5376-5DOI Listing
May 2005

LINE-1 amplification accompanies explosive genome repatterning in rodents.

Chromosome Res 2004 ;12(8):787-93

Laboratoire Origine, Structure et Evolution de la Biodiversité, Muséum National d'Histoire Naturelle, 55, rue Buffon, F75005, Paris, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10577-005-5265-yDOI Listing
May 2005

LINE-1 distribution in Afrotheria and Xenarthra: implications for understanding the evolution of LINE-1 in eutherian genomes.

Chromosoma 2004 Sep 29;113(3):137-44. Epub 2004 Jul 29.

Evolutionary Genomics Group, Department of Zoology, University of Stellenbosch, Private Bag X1, 7602, Matieland, South Africa.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00412-004-0301-9DOI Listing
September 2004