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Items: 41

1.

Evolutionary journey and characterisation of a novel pan-gene associated with beer strains of Saccharomyces cerevisiae.

Vakirlis N, Monerawela C, McManus G, Ribeiro O, McLysaght A, James T, Bond U.

Yeast. 2019 Jul;36(7):425-437. doi: 10.1002/yea.3391. Epub 2019 Jun 28.

PMID:
30963617
2.

Macrosynteny analysis shows the absence of ancient whole-genome duplication in lepidopteran insects.

Nakatani Y, McLysaght A.

Proc Natl Acad Sci U S A. 2019 Feb 5;116(6):1816-1818. doi: 10.1073/pnas.1817937116. Epub 2019 Jan 23. No abstract available.

3.

Computational Prediction of De Novo Emerged Protein-Coding Genes.

Vakirlis N, McLysaght A.

Methods Mol Biol. 2019;1851:63-81. doi: 10.1007/978-1-4939-8736-8_4.

PMID:
30298392
4.

Pseudogenes Provide Evolutionary Evidence for the Competitive Endogenous RNA Hypothesis.

Glenfield C, McLysaght A.

Mol Biol Evol. 2018 Dec 1;35(12):2886-2899. doi: 10.1093/molbev/msy183.

5.

A Family of Vertebrate-Specific Polycombs Encoded by the LCOR/LCORL Genes Balance PRC2 Subtype Activities.

Conway E, Jerman E, Healy E, Ito S, Holoch D, Oliviero G, Deevy O, Glancy E, Fitzpatrick DJ, Mucha M, Watson A, Rice AM, Chammas P, Huang C, Pratt-Kelly I, Koseki Y, Nakayama M, Ishikura T, Streubel G, Wynne K, Hokamp K, McLysaght A, Ciferri C, Di Croce L, Cagney G, Margueron R, Koseki H, Bracken AP.

Mol Cell. 2018 May 3;70(3):408-421.e8. doi: 10.1016/j.molcel.2018.03.005. Epub 2018 Apr 5.

6.

Faster Evolving Primate Genes Are More Likely to Duplicate.

O'Toole ÁN, Hurst LD, McLysaght A.

Mol Biol Evol. 2018 Jan 1;35(1):107-118. doi: 10.1093/molbev/msx270.

7.

Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes.

Nakatani Y, McLysaght A.

Bioinformatics. 2017 Jul 15;33(14):i369-i378. doi: 10.1093/bioinformatics/btx259.

8.

Dosage-sensitive genes in evolution and disease.

Rice AM, McLysaght A.

BMC Biol. 2017 Sep 1;15(1):78. doi: 10.1186/s12915-017-0418-y. Review.

9.

Dosage sensitivity is a major determinant of human copy number variant pathogenicity.

Rice AM, McLysaght A.

Nat Commun. 2017 Feb 8;8:14366. doi: 10.1038/ncomms14366.

10.

Open questions in the study of de novo genes: what, how and why.

McLysaght A, Hurst LD.

Nat Rev Genet. 2016 Sep;17(9):567-78. doi: 10.1038/nrg.2016.78. Epub 2016 Jul 25. Review.

PMID:
27452112
11.

Spatial Colocalization of Human Ohnolog Pairs Acts to Maintain Dosage-Balance.

Xie T, Yang QY, Wang XT, McLysaght A, Zhang HY.

Mol Biol Evol. 2016 Sep;33(9):2368-75. doi: 10.1093/molbev/msw108. Epub 2016 Jun 13.

12.

De Novo Genes Arise at a Slow but Steady Rate along the Primate Lineage and Have Been Subject to Incomplete Lineage Sorting.

Guerzoni D, McLysaght A.

Genome Biol Evol. 2016 Apr 25;8(4):1222-32. doi: 10.1093/gbe/evw074.

13.

A chromatin-independent role of Polycomb-like 1 to stabilize p53 and promote cellular quiescence.

Brien GL, Healy E, Jerman E, Conway E, Fadda E, O'Donovan D, Krivtsov AV, Rice AM, Kearney CJ, Flaus A, McDade SS, Martin SJ, McLysaght A, O'Connell DJ, Armstrong SA, Bracken AP.

Genes Dev. 2015 Nov 1;29(21):2231-43. doi: 10.1101/gad.267930.115. Epub 2015 Oct 22.

14.

New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation.

McLysaght A, Guerzoni D.

Philos Trans R Soc Lond B Biol Sci. 2015 Sep 26;370(1678):20140332. doi: 10.1098/rstb.2014.0332. Review.

15.

Ohnologs are overrepresented in pathogenic copy number mutations.

McLysaght A, Makino T, Grayton HM, Tropeano M, Mitchell KJ, Vassos E, Collier DA.

Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):361-6. doi: 10.1073/pnas.1309324111. Epub 2013 Dec 24.

16.

Genome-wide deserts for copy number variation in vertebrates.

Makino T, McLysaght A, Kawata M.

Nat Commun. 2013;4:2283. doi: 10.1038/ncomms3283.

PMID:
23917329
17.

Treasurer's report for financial year (FY) 2011.

McLysaght A.

Mol Biol Evol. 2013 May;30(5):1236. doi: 10.1093/molbev/mst049. Epub 2013 Apr 12. No abstract available.

PMID:
23584977
18.

Treasurer's report for financial year (FY) 2011.

McLysaght A.

Genome Biol Evol. 2013;5(4):680. doi: 10.1093/gbe/evt040. No abstract available.

19.

A survey of host range genes in poxvirus genomes.

Bratke KA, McLysaght A, Rothenburg S.

Infect Genet Evol. 2013 Mar;14:406-25. doi: 10.1016/j.meegid.2012.12.002. Epub 2012 Dec 23.

20.

De novo origin of protein-coding genes in murine rodents.

Murphy DN, McLysaght A.

PLoS One. 2012;7(11):e48650. doi: 10.1371/journal.pone.0048650. Epub 2012 Nov 21.

21.

Positionally biased gene loss after whole genome duplication: evidence from human, yeast, and plant.

Makino T, McLysaght A.

Genome Res. 2012 Dec;22(12):2427-35. doi: 10.1101/gr.131953.111. Epub 2012 Jul 26.

22.

Evolution of vertebrate tissues driven by differential modes of gene duplication.

Satake M, Kawata M, McLysaght A, Makino T.

DNA Res. 2012;19(4):305-16. doi: 10.1093/dnares/dss012. Epub 2012 Apr 5.

23.

Mammalian X chromosome inactivation evolved as a dosage-compensation mechanism for dosage-sensitive genes on the X chromosome.

Pessia E, Makino T, Bailly-Bechet M, McLysaght A, Marais GA.

Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5346-51. doi: 10.1073/pnas.1116763109. Epub 2012 Mar 5.

24.

De novo origins of human genes.

Guerzoni D, McLysaght A.

PLoS Genet. 2011 Nov;7(11):e1002381. doi: 10.1371/journal.pgen.1002381. Epub 2011 Nov 10. No abstract available.

25.

Patterns of indirect protein interactions suggest a spatial organization to metabolism.

Pérez-Bercoff Å, McLysaght A, Conant GC.

Mol Biosyst. 2011 Nov;7(11):3056-64. doi: 10.1039/c1mb05168g. Epub 2011 Aug 31.

PMID:
21881679
26.

Duplicability of self-interacting human genes.

Pérez-Bercoff A, Makino T, McLysaght A.

BMC Evol Biol. 2010 May 28;10:160. doi: 10.1186/1471-2148-10-160.

27.

Ohnologs in the human genome are dosage balanced and frequently associated with disease.

Makino T, McLysaght A.

Proc Natl Acad Sci U S A. 2010 May 18;107(20):9270-4. doi: 10.1073/pnas.0914697107. Epub 2010 May 3.

28.

Recent de novo origin of human protein-coding genes.

Knowles DG, McLysaght A.

Genome Res. 2009 Oct;19(10):1752-9. doi: 10.1101/gr.095026.109. Epub 2009 Sep 2.

29.

The complex relationship of gene duplication and essentiality.

Makino T, Hokamp K, McLysaght A.

Trends Genet. 2009 Apr;25(4):152-5. doi: 10.1016/j.tig.2009.03.001. Epub 2009 Mar 13.

PMID:
19285746
30.

Evolutionary steps of sex chromosomes are reflected in retrogenes.

McLysaght A.

Trends Genet. 2008 Oct;24(10):478-81. doi: 10.1016/j.tig.2008.07.006. Epub 2008 Sep 5.

PMID:
18774619
31.

Interacting gene clusters and the evolution of the vertebrate immune system.

Makino T, McLysaght A.

Mol Biol Evol. 2008 Sep;25(9):1855-62. doi: 10.1093/molbev/msn137. Epub 2008 Jun 23. Erratum in: Mol Biol Evol. 2008 Dec;25(12). doi: 10.1093/molbev/msn241.

PMID:
18573844
32.
33.

High rate of recent intron gain and loss in simultaneously duplicated Arabidopsis genes.

Knowles DG, McLysaght A.

Mol Biol Evol. 2006 Aug;23(8):1548-57. Epub 2006 May 23.

PMID:
16720694
34.

Porter: a new, accurate server for protein secondary structure prediction.

Pollastri G, McLysaght A.

Bioinformatics. 2005 Apr 15;21(8):1719-20. Epub 2004 Dec 7.

PMID:
15585524
35.

Genomic features in the breakpoint regions between syntenic blocks.

Trinh P, McLysaght A, Sankoff D.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i318-25.

PMID:
15262815
36.

Extensive gene gain associated with adaptive evolution of poxviruses.

McLysaght A, Baldi PF, Gaut BS.

Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15655-60. Epub 2003 Dec 5.

37.

The 2R hypothesis and the human genome sequence.

Hokamp K, McLysaght A, Wolfe KH.

J Struct Funct Genomics. 2003;3(1-4):95-110. Review.

PMID:
12836689
38.

LineUp: statistical detection of chromosomal homology with application to plant comparative genomics.

Hampson S, McLysaght A, Gaut B, Baldi P.

Genome Res. 2003 May;13(5):999-1010. Epub 2003 Apr 14.

39.

Extensive genomic duplication during early chordate evolution.

McLysaght A, Hokamp K, Wolfe KH.

Nat Genet. 2002 Jun;31(2):200-4. Epub 2002 May 28.

PMID:
12032567
40.

Initial sequencing and analysis of the human genome.

Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J; International Human Genome Sequencing Consortium.

Nature. 2001 Feb 15;409(6822):860-921. Erratum in: Nature 2001 Aug 2;412(6846):565. Nature 2001 Jun 7;411(6838):720. Szustakowki, J [corrected to Szustakowski, J].

41.

Estimation of synteny conservation and genome compaction between pufferfish (Fugu) and human.

McLysaght A, Enright AJ, Skrabanek L, Wolfe KH.

Yeast. 2000 Apr;17(1):22-36.

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