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Aoife McLysaght, PhD - Publications

Affiliations: 
Smurfit Institute of Genetics University of Dublin, Trinity College 
Website:
http://www.gen.tcd.ie/molevol/
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51 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Vance Z, McLysaght A. Ohnologs and SSD Paralogs Differ in Genomic and Expression Features Related to Dosage Constraints. Genome Biology and Evolution. 15. PMID 37776514 DOI: 10.1093/gbe/evad174  0.471
2023 Redmond AK, Casey D, Gundappa MK, Macqueen DJ, McLysaght A. Independent rediploidization masks shared whole genome duplication in the sturgeon-paddlefish ancestor. Nature Communications. 14: 2879. PMID 37208359 DOI: 10.1038/s41467-023-38714-z  0.503
2022 Vakirlis N, Vance Z, Duggan KM, McLysaght A. De novo birth of functional microproteins in the human lineage. Cell Reports. 41: 111808. PMID 36543139 DOI: 10.1016/j.celrep.2022.111808  0.376
2022 Vance Z, Niezabitowski L, Hurst LD, McLysaght A. Evidence from Drosophila Supports Higher Duplicability of Faster Evolving Genes. Genome Biology and Evolution. 14. PMID 35018456 DOI: 10.1093/gbe/evac003  0.389
2021 Nakatani Y, Shingate P, Ravi V, Pillai NE, Prasad A, McLysaght A, Venkatesh B. Publisher Correction: Reconstruction of proto-vertebrate, protocyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution. Nature Communications. 12: 4704. PMID 34326346 DOI: 10.1038/s41467-021-25110-8  0.328
2021 Nakatani Y, Shingate P, Ravi V, Pillai NE, Prasad A, McLysaght A, Venkatesh B. Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution. Nature Communications. 12: 4489. PMID 34301952 DOI: 10.1038/s41467-021-24573-z  0.415
2021 Vakirlis N, Acar O, Hsu B, Coelho NC, Van Oss SB, Wacholder A, Medetgul-Ernar K, Bowman RW, Hines CP, Iannotta J, Parikh SB, McLysaght A, Camacho CJ, O'Donnell AF, Ideker T, et al. Author Correction: De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. Nature Communications. 12: 200. PMID 33398071 DOI: 10.1038/s41467-020-20609-y  0.341
2020 Vakirlis N, Carvunis AR, McLysaght A. Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes. Elife. 9. PMID 32066524 DOI: 10.7554/Elife.53500  0.559
2020 Vakirlis N, Acar O, Hsu B, Castilho Coelho N, Van Oss SB, Wacholder A, Medetgul-Ernar K, Bowman RW, Hines CP, Iannotta J, Parikh SB, McLysaght A, Camacho CJ, O'Donnell AF, Ideker T, et al. De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. Nature Communications. 11: 781. PMID 32034123 DOI: 10.1038/S41467-020-14500-Z  0.459
2020 Vakirlis N, Carvunis A, McLysaght A. Author response: Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes Elife. DOI: 10.7554/Elife.53500.Sa2  0.43
2019 Vakirlis N, Monerawela C, McManus G, Ribeiro O, McLysaght A, James T, Bond U. Evolutionary Journey and Characterisation of a Novel Pan-Gene Associated with Beer Strains of S. cerevisiae. Yeast (Chichester, England). PMID 30963617 DOI: 10.1002/Yea.3391  0.48
2019 Nakatani Y, McLysaght A. Macrosynteny analysis shows the absence of ancient whole-genome duplication in lepidopteran insects. Proceedings of the National Academy of Sciences of the United States of America. PMID 30674659 DOI: 10.1073/Pnas.1817937116  0.448
2019 Vakirlis N, McLysaght A. Computational Prediction of De Novo Emerged Protein-Coding Genes. Methods in Molecular Biology (Clifton, N.J.). 1851: 63-81. PMID 30298392 DOI: 10.1007/978-1-4939-8736-8_4  0.573
2018 Glenfield C, McLysaght A. Pseudogenes provide evolutionary evidence for the competitive endogenous RNA hypothesis. Molecular Biology and Evolution. PMID 30252115 DOI: 10.1093/Molbev/Msy183  0.419
2018 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, ... ... McLysaght A, et al. A Family of Vertebrate-Specific Polycombs Encoded by the LCOR/LCORL Genes Balance PRC2 Subtype Activities. Molecular Cell. PMID 29628311 DOI: 10.1016/J.Molcel.2018.03.005  0.354
2017 O'Toole ÁN, Hurst LD, McLysaght A. Faster Evolving Primate Genes are More Likely to Duplicate. Molecular Biology and Evolution. PMID 29126243 DOI: 10.1093/Molbev/Msx270  0.465
2017 Nakatani Y, McLysaght A. Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes. Bioinformatics (Oxford, England). 33: i369-i378. PMID 28881993 DOI: 10.1093/Bioinformatics/Btx259  0.521
2017 Rice AM, McLysaght A. Dosage-sensitive genes in evolution and disease. Bmc Biology. 15: 78. PMID 28863777 DOI: 10.1186/S12915-017-0418-Y  0.467
2017 Rice AM, McLysaght A. Dosage sensitivity is a major determinant of human copy number variant pathogenicity. Nature Communications. 8: 14366. PMID 28176757 DOI: 10.1038/Ncomms14366  0.517
2016 McLysaght A, Hurst LD. Open questions in the study of de novo genes: what, how and why. Nature Reviews. Genetics. PMID 27452112 DOI: 10.1038/Nrg.2016.78  0.533
2016 Xie T, Yang QY, Wang XT, McLysaght A, Zhang HY. Spatial Colocalization of Human Ohnolog Pairs Acts to Maintain Dosage-Balance. Molecular Biology and Evolution. PMID 27297469 DOI: 10.1093/Molbev/Msw108  0.493
2016 Guerzoni D, McLysaght A. De novo genes arise at a slow but steady rate along the primate lineage and have been subject to incomplete lineage sorting. Genome Biology and Evolution. PMID 27056411 DOI: 10.1093/Gbe/Evw074  0.551
2015 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, et al. A chromatin-independent role of Polycomb-like 1 to stabilize p53 and promote cellular quiescence. Genes & Development. PMID 26494712 DOI: 10.1101/Gad.267930.115  0.315
2015 McLysaght A, Guerzoni D. New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370: 20140332. PMID 26323763 DOI: 10.1098/Rstb.2014.0332  0.528
2014 McLysaght A, Makino T, Grayton HM, Tropeano M, Mitchell KJ, Vassos E, Collier DA. Ohnologs are overrepresented in pathogenic copy number mutations. Proceedings of the National Academy of Sciences of the United States of America. 111: 361-6. PMID 24368850 DOI: 10.1073/Pnas.1309324111  0.521
2013 Makino T, McLysaght A, Kawata M. Genome-wide deserts for copy number variation in vertebrates. Nature Communications. 4: 2283. PMID 23917329 DOI: 10.1038/Ncomms3283  0.482
2013 Bratke KA, McLysaght A, Rothenburg S. A survey of host range genes in poxvirus genomes. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 14: 406-25. PMID 23268114 DOI: 10.1016/J.Meegid.2012.12.002  0.396
2012 Murphy DN, McLysaght A. De novo origin of protein-coding genes in murine rodents. Plos One. 7: e48650. PMID 23185269 DOI: 10.1371/Journal.Pone.0048650  0.476
2012 Makino T, McLysaght A. Positionally biased gene loss after whole genome duplication: evidence from human, yeast, and plant. Genome Research. 22: 2427-35. PMID 22835904 DOI: 10.1101/Gr.131953.111  0.559
2012 Satake M, Kawata M, McLysaght A, Makino T. Evolution of vertebrate tissues driven by differential modes of gene duplication. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. 19: 305-16. PMID 22490996 DOI: 10.1093/Dnares/Dss012  0.434
2012 Pessia E, Makino T, Bailly-Bechet M, McLysaght A, Marais GA. Mammalian X chromosome inactivation evolved as a dosage-compensation mechanism for dosage-sensitive genes on the X chromosome. Proceedings of the National Academy of Sciences of the United States of America. 109: 5346-51. PMID 22392987 DOI: 10.1073/Pnas.1116763109  0.384
2011 Guerzoni D, McLysaght A. De novo origins of human genes. Plos Genetics. 7: e1002381. PMID 22102832 DOI: 10.1371/Journal.Pgen.1002381  0.552
2011 Pérez-Bercoff Å, McLysaght A, Conant GC. Patterns of indirect protein interactions suggest a spatial organization to metabolism. Molecular Biosystems. 7: 3056-64. PMID 21881679 DOI: 10.1039/C1Mb05168G  0.547
2011 Makino T, Knowles DG, McLysaght A. Functional Divergence of Duplicated Genes Evolution After Gene Duplication. 23-30. DOI: 10.1002/9780470619902.ch2  0.329
2010 Pérez-Bercoff A, Makino T, McLysaght A. Duplicability of self-interacting human genes. Bmc Evolutionary Biology. 10: 160. PMID 20509897 DOI: 10.1186/1471-2148-10-160  0.459
2010 Makino T, McLysaght A. Ohnologs in the human genome are dosage balanced and frequently associated with disease. Proceedings of the National Academy of Sciences of the United States of America. 107: 9270-4. PMID 20439718 DOI: 10.1073/Pnas.0914697107  0.563
2009 Knowles DG, McLysaght A. Recent de novo origin of human protein-coding genes. Genome Research. 19: 1752-9. PMID 19726446 DOI: 10.1101/Gr.095026.109  0.553
2009 Makino T, Hokamp K, McLysaght A. The complex relationship of gene duplication and essentiality. Trends in Genetics : Tig. 25: 152-5. PMID 19285746 DOI: 10.1016/J.Tig.2009.03.001  0.527
2008 McLysaght A. Evolutionary steps of sex chromosomes are reflected in retrogenes. Trends in Genetics : Tig. 24: 478-81. PMID 18774619 DOI: 10.1016/J.Tig.2008.07.006  0.33
2008 Makino T, McLysaght A. Interacting gene clusters and the evolution of the vertebrate immune system. Molecular Biology and Evolution. 25: 1855-62. PMID 18573844 DOI: 10.1093/Molbev/Msn137  0.521
2008 Bratke KA, McLysaght A. Identification of multiple independent horizontal gene transfers into poxviruses using a comparative genomics approach. Bmc Evolutionary Biology. 8: 67. PMID 18304319 DOI: 10.1186/1471-2148-8-67  0.531
2006 Knowles DG, McLysaght A. High rate of recent intron gain and loss in simultaneously duplicated Arabidopsis genes. Molecular Biology and Evolution. 23: 1548-57. PMID 16720694 DOI: 10.1093/Molbev/Msl017  0.451
2004 Trinh P, McLysaght A, Sankoff D. Genomic features in the breakpoint regions between syntenic blocks. Bioinformatics (Oxford, England). 20: i318-25. PMID 15262815 DOI: 10.1093/bioinformatics/bth934  0.364
2003 McLysaght A, Baldi PF, Gaut BS. Extensive gene gain associated with adaptive evolution of poxviruses. Proceedings of the National Academy of Sciences of the United States of America. 100: 15655-60. PMID 14660798 DOI: 10.1073/Pnas.2136653100  0.57
2003 Hokamp K, McLysaght A, Wolfe KH. The 2R hypothesis and the human genome sequence. Journal of Structural and Functional Genomics. 3: 95-110. PMID 12836689 DOI: 10.1023/A:1022661917301  0.642
2003 Hampson S, McLysaght A, Gaut B, Baldi P. LineUp: statistical detection of chromosomal homology with application to plant comparative genomics. Genome Research. 13: 999-1010. PMID 12695327 DOI: 10.1101/Gr.814403  0.387
2002 McLysaght A, Hokamp K, Wolfe KH. Extensive genomic duplication during early chordate evolution. Nature Genetics. 31: 200-4. PMID 12032567 DOI: 10.1038/Ng884  0.7
2001 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, ... ... McLysaght A, et al. Initial sequencing and analysis of the human genome. Nature. 409: 860-921. PMID 11237011 DOI: 10.1038/35057062  0.644
2001 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, ... ... McLysaght A, et al. Erratum: Initial sequencing and analysis of the human genome: International Human Genome Sequencing Consortium (Nature (2001) 409 (860-921)) Nature. 412: 565-566. DOI: 10.1038/35087627  0.645
2000 McLysaght A, Enright AJ, Skrabanek L, Wolfe KH. Estimation of synteny conservation and genome compaction between pufferfish (Fugu) and human. Yeast (Chichester, England). 17: 22-36. PMID 10797599 DOI: 10.1002/(Sici)1097-0061(200004)17:1<22::Aid-Yea5>3.0.Co;2-S  0.675
2000 McLysaght A, Enright AJ, Skrabanek L, Wolfe KH. Estimation of synteny conservation and genome compaction between pufferfish (Fugu) and human Yeast. 17: 22-36.  0.586
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