Professor Aoife Mc Lysaght
Professor, Genetics
Publications and Further Research Outputs
Peer-Reviewed Publications
Vance Z, McLysaght A., Ohnologs and SSD Paralogs Differ in Genomic and Expression Features Related to Dosage Constraints., Genome biology and evolution, 15, (10), 2023, pevad174
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, (1), 2023, p2879
Redmond AK, McLysaght A., Horizontal transfer of vertebrate vision gene IRBP into the chordate ancestor., Proceedings of the National Academy of Sciences of the United States of America, 120, (34), 2023, pe2310390120
Redmond, A.K. and McLysaght, A., Reply to: Available data do not rule out Ctenophora as the sister group to all other Metazoa, Nature Communications, 14, (1), 2023
McLysaght, A., The deceptive simplicity of mendelian genetics, PLoS Biology, 20, (7), 2022
Vakirlis, N. and Vance, Z. and Duggan, K.M. and McLysaght, A., De novo birth of functional microproteins in the human lineage, Cell Reports, 41, (12), 2022
Vance Z, Niezabitowski L, Hurst LD, McLysaght A., Evidence from Drosophila Supports Higher Duplicability of Faster Evolving Genes., Genome biology and evolution, 14, (1), 2022
Redmond, A.K. and McLysaght, A., Author Correction: Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding (Nature Communications, (2021), 12, 1, (1783), 10.1038/s41467-021-22074-7), Nature Communications, 13, (1), 2022
Vakirlis, N. and Acar, O. and Hsu, B. and Coelho, N.C. and Van Oss, S.B. and Wacholder, A. and Medetgul-Ernar, K. and Bowman, R.W. and Hines, C.P. and Iannotta, J. and Parikh, S.B. and McLysaght, A. and Camacho, C.J. and Oâ Donnell, A.F. and Ideker, T. and Carvunis, A.-R., Author Correction: De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences (Nature Communications, (2020), 11, 1, (781), 10.1038/s41467-020-14500-z), Nature Communications, 12, (1), 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, (1), 2021, p4489
Nakatani, Y. and Shingate, P. and Ravi, V. and Pillai, N.E. and Prasad, A. and McLysaght, A. and Venkatesh, B., Publisher Correction: Reconstruction of proto-vertebrate, protocyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution (Nature Communications, (2021), 12, 1, (4489), 10.1038/s41467-021-24573-z), Nature Communications, 12, (1), 2021
Redmond, Anthony K., McLysaght, Aoife, Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding, Nature Communications, 12, (1), 2021
Vakirlis N, Carvunis AR, McLysaght A., Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes., eLife, 9, 2020
Nikolaos Vakirlis, Omer Acar, Brian Hsu, Nelson Castilho Coelho, S. Branden Van Oss, Aaron Wacholder, Kate Medetgul-Ernar, Ray W. Bowman II, Cameron P. Hines, John Iannotta, Saurin Bipin Parikh, Aoife McLysaght, Carlos J. Camacho, Allyson F. O'Donnell, Trey Ideker & Anne-Ruxandra Carvunis , De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences, Nature Communications, 11 , (781), 2020, p1-18
Vakirlis N, McLysaght A., Computational Prediction of De Novo Emerged Protein-Coding Genes., Methods in molecular biology (Clifton, N.J.), 1851, 2019, p63-81
Yoichiro Nakatani and Aoife McLysaght, Macrosynteny analysis shows the absence of ancient whole-genome duplication in lepidopteran insects., Proceedings of the National Academy of Sciences (USA), 2019, p1816-1818
Nikolaos Vakirlis, Anne-Ruxandra Carvunis, Aoife McLysaght, Synteny-based analyses indicate that sequence divergence is not the dominant source of orphan genes, 2019
Vakirlis, N. and Monerawela, C. and McManus, G. and Ribeiro, O. and McLysaght, A. and James, T. and Bond, U., Evolutionary journey and characterisation of a novel pan-gene associated with beer strains of Saccharomyces cerevisiae, Yeast, 36, (7), 2019, p425-437
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, Bracken AP., A Family of Vertebrate-Specific Polycombs Encoded by the LCOR/LCORL Genes Balance PRC2 Subtype Activities., Molecular Cell, 70, (3), 2018, p408-421
O'Toole, Ã .N. and Hurst, L.D. and McLysaght, A., Faster Evolving Primate Genes Are More Likely to Duplicate, Molecular Biology and Evolution, 35, (1), 2018, p107-118
Glenfield C, McLysaght A., Pseudogenes Provide Evolutionary Evidence for the Competitive Endogenous RNA Hypothesis., Molecular biology and evolution, 35, (12), 2018, p2886-2899
Rice A., McLysaght A., Dosage sensitivity is a major determinant of human copy number variant pathogenicity, Nature Communications, 8, 2017, p14366
Rice A.M, McLysaght A, Dosage-sensitive genes in evolution and disease, BMC Biology, 15, (1), 2017, p78-
Nakatani Y, McLysaght A, Genomes as documents of evolutionary history: A probabilistic macrosynteny model for the reconstruction of ancestral genomes, Bioinformatics, 33, (14), 2017, pi369 - i378
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, 8, (4), 2016, p1222-1232
McLysaght A, Hurst L.D, Open questions in the study of de novo genes: What, how and why, Nature Reviews Genetics, 17, (9), 2016, p567 - 578
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, 33, (9), 2016, p2368-2375
Guerzoni, D. and 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, 8, (4), 2016, p1222-1232
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, (1678), 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, Bracken AP, A chromatin-independent role of Polycomb-like 1 to stabilize p53 and promote cellular quiescence., Genes & Development, 29, (21), 2015, p2231-43
McLysaght, A., Treasurer' s report for financial year (FY) 2013, Molecular Biology and Evolution, 31, (12), 2014, p3375
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, (1), 2014, p361-6
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, 2013, p406-425
McLysaght, A., Treasurer's report for financial year (FY) 2012, Molecular Biology and Evolution, 30, (12), 2013, p2732
McLysaght, A., Treasurer's report for Financial Year (FY) 2011, Genome Biology and Evolution, 5, (4), 2013, p680
Makino T, McLysaght A, Kawata M, Genome-wide deserts for copy number variation in vertebrates., Nature communications, 4, 2013, p2283
McLysaght, A., Treasurer's report for financial year (FY) 2011, Molecular Biology and Evolution, 30, (5), 2013, p1236
Murphy DN, McLysaght A, De novo origin of protein-coding genes in murine rodents., PloS one, 7, (11), 2012, pe48650
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, (14), 2012, p5346-5351
Murphy, D.N. and McLysaght, A., De Novo Origin of Protein-Coding Genes in Murine Rodents, PLoS ONE, 7, (11), 2012
Makino T, McLysaght A, Positionally biased gene loss after whole genome duplication: evidence from human, yeast, and plant., Genome research, 22, (12), 2012, p2427-2435
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, (4), 2012, p305-316
Guerzoni, D. and McLysaght, A., De novo origins of human genes, PLoS Genetics, 7, (11), 2011
Daniele Guerzoni, Aoife McLysaght, De Novo Origins of Human Genes, PLoS Genetics, 7, (11, e1002381), 2011
Pérez-Bercoff Å, McLysaght A, Conant GC, Patterns of indirect protein interactions suggest a spatial organization to metabolism., Molecular bioSystems, 7, (11), 2011, p3056-3064
Pérez-Bercoff A, Makino T, McLysaght A, Duplicability of self-interacting human genes., BMC Evolutionary Biology, 10, (160), 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, (20), 2010, p9270-9274
The Evolution of Functional Gene Clusters In Eukaryote Genomes in, editor(s)Pierre Pontarotti , Evolutionary Biology: Concept, Modeling and Application, Springer, 2009, pp185 - 194, [Makino, T., and McLysaght, A.]
Evolutionary Analyses of Protein Interaction Networks in, editor(s)Xiao-Li Li, See-Kiong Ng , Biological Data Mining in Protein Interaction Networks, United States, IGI Global, 2009, [Makino, T. and McLysaght, A.]
Makino, T, Hokamp, K, McLysaght, A, The complex relationship of gene duplication and essentiality., Trends in genetics, 25, (4), 2009, p152 - 155
Knowles, DG, McLysaght, A, Recent de novo origin of human protein-coding genes., Genome Research, 19, (10), 2009, p1752-1759
Functional divergence of duplicated genes in, editor(s)Dittmar de la Cruz, K. and Liberles, D. , Evolution After Gene Duplication, Wiley, 2009, [Makino, T. Knowles D.G. and McLysaght, A.]
Bratke, K.A. and McLysaght, A., Identification of multiple independent horizontal gene transfers into poxviruses using a comparative genomics approach, BMC Evolutionary Biology, 8, (67), 2008, p[1-13]
Makino, T, McLysaght, A, Interacting gene clusters and the evolution of the vertebrate immune system., Molecular Biology and Evolution, 25, (9), 2008, p1855 - 1862
Aoife McLysaght, Evolutionary steps of sex chromosomes are reflected in retrogenes, Trends in Genetics, 24, (10), 2008, p478 - 481
Artikis, A., O'Hare, G.M.P., Stathis, K., Vouros, G., Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 4995 LNAI, 2008
Makino, T. and McLysaght, A., Interacting gene clusters and the evolution of the vertebrate immune system (Molecular Biology and Evolution (2008) 25, 9 (1855-1862)), Molecular Biology and Evolution, 25, (12), 2008, p2771
Knowles D. G. and McLysaght A., High Rate of Recent Intron Gain and Loss in Simultaneously Duplicated Arabidopsis genes, Molecular Biology and Evolution, 23, (8), 2006, p1548 - 1557
Pollastri, G. and McLysaght, A., Porter: a new, accurate server for protein secondary structure prediction, Bioinformatics, 21, (8), 2005, p1719 - 1720
Aoife McLysaght, Daniel H. Huson (Eds.), Comparative Genomics- Lecture Notes in Bioinformatics 3678 (LNBI), Lecture Notes in Bioinformatic, Germany, Springer, 2005, 1 - 166pp
Trinh, P., McLysaght, A., Sankoff, D., Genomic Features in the Breakpoint Regions between Syntenic Blocks, Bioinformatics, 20 Suppl 1, 2004, pi318 - i325
McLysaght, A., Baldi, P.F., Gaut, B.S., Extensive gene gain associated with adaptive evolution of poxviruses, Proceedings of the National Academy of Sciences, USA, 100, (26), 2003, p15655 - 15660
Hampson, S., McLysaght, A., Gaut, B.S., Baldi, P.F., LineUp: Statistical Detection of Chromosomal Homology with Application to Plant Comparative Genomics, Genome Research, 13, (5), 2003, p999 - 1010
Hokamp, K., McLysaght, A. and Wolfe, K. H., The 2R hypothesis and the human genome sequence., Journal of Structural and Functional Genomics, 3, (1-4), 2003, p95 - 110
McLysaght, A., Hokamp K, and Wolfe, K.H., Extensive genomic duplication during early chordate evolution, Nature Genetics, 31, (2), 2002, p200 - 204
Aoife McLysaght, Evolution of Vertebrate Genome Organisation., University of Dublin, Trinity College, 2001
Lander, E.S.,.., McLysaght, A., et al., Initial sequencing and analysis of the human genome., Nature, 490, 2001, p860-921
McLysaght, A., Enright, A.J., Skrabanek, L. & Wolfe, K.H. , Estimation of synteny conservation and genome compaction between pufferfish (Fugu) and human., Yeast , 17, 2000, p22-36.
High frequency of inversions during eukaryote gene order evolution in, Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families, Dordrecht., Kluwer Academic Press, 2000, pp47 - 58, [McLysaght, A., Seoighe, C. and Wolfe, K.]
Non-Peer-Reviewed Publications
Aoife McLysaght, Departmental seminar, North Carolina State University (via online), 31 Jan 2022, 2022
Aoife McLysaght, Invited Lecture, Gordon Research Conference, Ecological and Evolutionary Genomics, Rhode Island, USA, July 2021, 2021
Aoife McLysaght, Departmental Seminar, Cambridge University, Zoology Department, January 2021, 2021
N. Vakirlis, KM Duggan, A McLysaght, De novo birth of functional, human-specific microproteins, bioRxiv, 2021
Aoife McLysaght, Seminar, Universitat Pompeu Fabra, Barcelona, Spain, October 2021, 2021
Aoife McLysaght, Departmental Seminar, Bristol University, UK, November 2020, 2020
Aoife McLysaght, Departmental Seminar, York University, UK, November 2020, 2020
Aoife McLysaght, Invited Departmental Seminar, Max Planck Institute for Molecular Genetics, Berlin, January 2020, 2020
Aoife McLysaght, Departmental Seminar, University of Edinburgh, 13 February 2019, 2019
Aoife Mclysaght, Invited Lecture, Cambridge Society for the Application of Research, Cambridge University, 4th March 2019, 2019
Aoife McLysaght, Nei Lectuire (Keynote), Society for Molecular Biology and Evolution, Manchester, UK, July 2019, 2019
Aoife McLysaght, Lord Phillips Memorial Lecture (named lecture), Cardiff Scientific Society, Cardiff, 2019
Aoife McLysaght, Darwin Day Lecture, Centre for Ecology and Evolution, UCL, London, 7th February 2018, 2018
Aoife McLysaght, Invited lecture, EMBO Workshop "Evolution in a Time of Genome Architecture", Naples, Italy, 13-15 Sept 2017 , 2017
Aoife McLysaght, Departmental Seminar, Cardiff University, 2017
Aoife McLysaght, Invited Lecture, Society for Molecular Biology and Evolution, Austin, Texas, USA, July 2017, 2017
Aoife McLysaght, Departmental Seminar, Vienna Graduate School of Population Genetics, Austria, Jan 19 2016 , 2016
Aoife McLysaght, Invited Keynote, Jacques Monod conference: , Roscoff, France, May 9-13, 2016 , 2016
Aoife McLysaght, Sir Julian Huxley Lecture (named lecture), Systematics Association, Linnean Society, London, 12 October 2016, 2016
Aoife McLysaght, Session Chair and Invited Talk, Genome Informatics, Cold Spring Harbor Laboratory, Long Island, USA, 28-31 October 2015 , 2015
Computational Tools and Resources in Plant Genome Informatics. in, editor(s)Paul Christou and Harry Klee , Handbook of Plant Biotechnology, Wiley, 2004, pp1 - 28, [Vision, T.J. and McLysaght, A.]
Research Expertise
Projects
- Title
- Gene expression level as a keystone to understanding gene duplication: evolutionary constraints, opportunities, and disease
- Funding Agency
- ERC
- Date From
- 01/01/2019
- Date To
- 30/12/2023
- Title
- SFI ERC Supplement
- Funding Agency
- Science Foundation Ireland
- Date From
- 01/01/2019
- Date To
- 30/12/2023
- Title
- Dosage-sensitive genes in evolution and disease
- Funding Agency
- European Research Council
- Date From
- Jan 2013
- Date To
- Dec 2018
- Title
- SFI ERC Supplement
- Funding Agency
- Science Foundation Ireland
- Date From
- 1 Jan 2013
- Date To
- 31 Dec 2018
- Title
- Origin and Evolution of Vertebrate de novo Genes
- Funding Agency
- Science Foundation Ireland
- Date From
- 2010
- Date To
- 2014
- Title
- Gene Gains, Losses and Relocations during Vertebrate Evolution
- Funding Agency
- Science Foundation Ireland
- Date From
- October 2005
- Date To
- September 2010
- Title
- Supplement to Gene Gains, Losses and Relocations in Vertebrate Evolution
- Summary
- Additional funding provided after midway review of SFI PIYRA grant as the grant was exceeding expectations and producing excellent results.
- Funding Agency
- Science Foundation Ireland
- Title
- The Origin of New Genes in Poxviruses
- Funding Agency
- IRCSET
- Date From
- October 2005
- Date To
- September 2008
- Title
- Systematic search of RegulAtory elements coNtrOlling autosomal Monoallelic expression (RANDOM)
- Funding Agency
- Marie Skłodowska Curie Actions
- Title
- INTEGRATE
- Summary
- Additional funding for Genomics Data Science CRT
- Funding Agency
- Marie Skłodowska Curie Actions
- Title
- Genomics Data Science CRT
- Summary
- Centre for Research Training (CRT) for Genomics Data Science PhD. Value to TCD is an estimate and depends on numbers of PhD students who take up their projects here.
- Funding Agency
- Science Foundation Ireland
- Date From
- 2019
- Date To
- 2026
Recognition
Representations
Academic Editor for PLoS Biology journal
President, Society for Molecular Biology and Evolution (SMBE)
External Advisory Board for the Milner Centre for Evolution, Bath University
Senior Editor of Molecular Biology and Evolution Journal
Associate Editor of Molecular Biology and Evolution
Associate Editor of Genome Biology and Evolution Journal
Editorial Board Member of Cell Reports
Elected as Treasurer of the Society for Molecular Biology and Evolution (three year term)
External Examiner, Bioinformatics and Genetics Degree, NUI Maynooth
Awards and Honours
European Research Council (ERC) Consolidator Award
JBS Haldane Prize Lectures (Genetics Society UK)
Selected for portrait in RIA as part of Women on Walls project: https://www.ria.ie/women-walls-0
European Research Council (ERC) Starting Researcher Award
President of Ireland Young Researcher's Award (Science Foundation Ireland)
Memberships
President, Society for Molecular Biology and Evolution
Treasurer, Society for Molecular Biology and Evolution
Member - Society for Molecular Biology and Evolution (SMBE)
Member - Genetics Society (UK)