Aoife Mc Lysaght
Professor, Genetics

Publications and Further Research Outputs

Peer-Reviewed Publications

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 Journal Article, 2017 DOI URL

Rice A., McLysaght A., Dosage sensitivity is a major determinant of human copy number variant pathogenicity, Nature Communications, 8, 2017, p14366 Journal Article, 2017 DOI TARA - Full Text

Rice A.M, McLysaght A, Dosage-sensitive genes in evolution and disease, BMC Biology, 15, (1), 2017, p78- Journal Article, 2017 URL DOI TARA - Full Text

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 Journal Article, 2016 DOI

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 Journal Article, 2016 DOI

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 Journal Article, 2016 URL DOI

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 Journal Article, 2015 TARA - Full Text DOI

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 Journal Article, 2015 DOI

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 Journal Article, 2014

McLysaght A, Treasurer' s report for financial year (FY) 2013, Molecular Biology and Evolution, 31, (12), 2014, p3375- Journal Article, 2014 DOI URL

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 Journal Article, 2013 DOI TARA - Full Text

Makino T, McLysaght A, Kawata M, Genome-wide deserts for copy number variation in vertebrates., Nature communications, 4, 2013, p2283 Journal Article, 2013

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 Journal Article, 2012 DOI TARA - Full Text

Murphy DN, McLysaght A, De novo origin of protein-coding genes in murine rodents., PloS one, 7, (11), 2012, pe48650 Journal Article, 2012 TARA - Full Text DOI

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 Journal Article, 2012 DOI TARA - Full Text

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 Journal Article, 2012 TARA - Full Text DOI

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 Journal Article, 2011 DOI

Daniele Guerzoni, Aoife McLysaght, De Novo Origins of Human Genes, PLoS Genetics, 7, (11, e1002381), 2011 Journal Article, 2011 TARA - Full Text

Pérez-Bercoff A, Makino T, McLysaght A, Duplicability of self-interacting human genes., BMC Evolutionary Biology, 10, (160), 2010 Journal Article, 2010 TARA - Full Text DOI

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 Journal Article, 2010 TARA - Full Text

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.] Book Chapter, 2009

Knowles, DG, McLysaght, A, Recent de novo origin of human protein-coding genes., Genome Research, 19, (10), 2009, p1752-1759 Journal Article, 2009 TARA - Full Text DOI

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.] Book Chapter, 2009

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.] Book Chapter, 2009

Makino, T, Hokamp, K, McLysaght, A, The complex relationship of gene duplication and essentiality., Trends in genetics, 25, (4), 2009, p152 - 155 Journal Article, 2009 TARA - Full Text DOI

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] Journal Article, 2008 URL TARA - Full Text DOI

Aoife McLysaght, Evolutionary steps of sex chromosomes are reflected in retrogenes, Trends in Genetics, 24, (10), 2008, p478 - 481 Journal Article, 2008 TARA - Full Text

Makino, T, McLysaght, A, Interacting gene clusters and the evolution of the vertebrate immune system., Molecular Biology and Evolution, 25, (9), 2008, p1855 - 1862 Journal Article, 2008 DOI TARA - Full Text URL

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 Journal Article, 2006 TARA - Full Text DOI URL

Pollastri, G. and McLysaght, A., Porter: a new, accurate server for protein secondary structure prediction, Bioinformatics, 21, (8), 2005, p1719 - 1720 Journal Article, 2005 DOI URL TARA - Full Text

Molecular Biology and Evolution, Oxford University Press, [eds.], 2005 Editorial Board, 2005

Aoife McLysaght, Daniel H. Huson (Eds.), Comparative Genomics, Germany, Springer, 2005, 1 - 166pp Book, 2005 URL

Trinh, P., McLysaght, A., Sankoff, D., Genomic Features in the Breakpoint Regions between Syntenic Blocks, Bioinformatics, 20 Suppl 1, 2004, pi318 - i325 Journal Article, 2004 URL DOI TARA - Full Text

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 Journal Article, 2003 URL DOI TARA - Full Text

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 Journal Article, 2003 URL DOI

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 Journal Article, 2003 DOI URL TARA - Full Text

McLysaght, A., Hokamp K, and Wolfe, K.H., Extensive genomic duplication during early chordate evolution, Nature Genetics, 31, (2), 2002, p200 - 204 Journal Article, 2002 DOI URL

Lander, E.S., McLysaght, A., et al., Initial sequencing and analysis of the human genome., Nature, 490, 2001, p860-921 Journal Article, 2001 URL

LANDER, ES, INITIAL SEQUENCING AND ANALYSIS OF THE HUMAN GENOME, by LINTON, LM , NATURE, 409, 2001 Review, 2001

Aoife McLysaght, Evolution of Vertebrate Genome Organisation., University of Dublin, Trinity College, 2001 Thesis, 2001 URL

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. Journal Article, 2000 URL TARA - Full Text DOI

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.] Book Chapter, 2000

Aoife McLysaght, Anton J. Enright, Lucy Skrabanek, Kenneth H. Wolfe , Estimation of synteny conservation and genome compaction between pufferfish (Fugu) and human, Yeast, 17, (1), 2000, p22 - 36 Journal Article, 2000 DOI

Non-Peer-Reviewed Publications

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.] Book Chapter, 2004

Research Expertise

Description

In this lab we conduct molecular evolution research through bioinformatics methods. The current focus of our research is on the origin and evolution of new genes and gene loss. We are examining these phenomena in two widely different groups of organisms: vertebrates and poxviruses. Organisms innovate, differentiate and adapt through the gain, loss and relocation of genes in their genome. Analysis of the recently sequenced chicken genome revealed many differences in the gene content of vertebrate genomes. Gene gain during vertebrate evolution has been associated with the evolution of the ape brain (the GLUD2 gene involved in neurotransmitter flux was acquired about 23 million years ago), the development of adaptive immunity (the RAG1/2 genes that increase the coding capacity of the MHC were acquired by horizontal gene transfer from bacteria), and disease (the apolipoprotein(a) gene was acquired by mammals and is associated with cholesterol build-up on artery walls). Gene loss has been associated with disease (e.g., the absence of the urate oxidase gene in humans and great apes results in a susceptibility to kidney stones), and is also a mode of genomic differentiation. It has also been postulated that in some cases new genes may exist in close physical clusters (in terms of their position on the chromosome) which may have a role in their function, for example by facilitating concerted regulation of expression or grouping genes involved in the same metabolic pathway. We are studying genomic sequence available from many vertebrates in order to examine the phylogenetic distribution of genes present in each vertebrate lineage and to examine the molecular evolution of genes that have been gained recently in the vertebrate lineage. Poxviruses have simple genomes amenable to analysis and are therefore a useful system to study. Many different members of the poxvirus group are important infectious agents in humans and other vertebrates (this group includes smallpox and myxomatosis) and so a greater understanding of their evolution may also be useful for understanding their pathogenicity and host specificity. The properties of the origin and evolution of new genes in poxviruses are expected to be different from the properties in vertebrate genomes both because of the comparative simplicity of poxvirus genomes, and also because of the differences in their life cycle (for example, the fact that the viruses are intracellular parasites is likely to make horizontal gene transfer, or gene capture from the host, a more frequent occurrence that in vertebrates).

Projects

  • Title
    • Dosage-sensitive genes in evolution and disease
  • Funding Agency
    • European Research Council
  • Date From
    • Jan 2013
  • Date To
    • Dec 3017
  • 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
    • The Origin of New Genes in Poxviruses
  • Funding Agency
    • IRCSET
  • Date From
    • October 2005
  • Date To
    • September 2008

Keywords

ACCELERATED SEQUENCE EVOLUTION; ANCIENT; Biocomputing; BIOINFORMATICS; COEVOLUTION; COMPARATIVE GENOMICS; COMPLETE NUCLEOTIDE-SEQUENCE; CONCERTED EVOLUTION; Evolution; EVOLUTION RATE; Evolutionary Biology; EVOLUTIONARY CHANGES; EVOLUTIONARY RELATIONSHIPS; EVOLUTIONARY SIGNIFICANCE; GENES; Genetics; Genomes, Genomics; Genomics; HIGH-FREQUENCY RETROTRANSPOSITION; Human Evolution; HYPOTHESIS; LINKAGE; Molecular evolution; Molecular Genetics; MONOAMINE-OXIDASE-A; PATTERN; POLYPLOIDS; RECEPTOR; SEQUENCE; VERTEBRATE EVOLUTION

Recognition

Awards and Honours

European Research Council (ERC) Starting Researcher Award 2013-2018

President of Ireland Young Researcher's Award (Science Foundation Ireland) 2005

Dawson Prize in Genetics 1997

Memberships

Associate Editor - Molecular Biology and Evolution 2005

Editorial Board, Cell Reports 2012

Society for Molecular Biology and Evolution (SMBE) 2005 – present

Member - Genetics Society (UK) 1999 – present