Publications List

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Nakatani, Y., and McLysaght, A. (2017). Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes Bioinformatics (ISMB issue), in press
Rice, A., and McLysaght, A. (2017). Dosage sensitivity is a major determinant of human copy number variant pathogenicity. Nature Communications 8:14366
McLysaght, A. and Hurst, L.D. (2017). Open questions in th study of de novo genes: what, how and why. Nature Reviews Genetics 17(9):567-578
Xie T, Yang QY, Wang XT, McLysaght* A, and Zhang* HY.(2016) [*corresponding author] Spatial Colocalization of Human Ohnolog Pairs Acts to Maintain Dosage-Balance Mol Biol Evol 33(9):2368-2375
Guerzoni, D., and McLysaght, A. (2016). 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):1222-1232
Brien, G.L., Healy, E., Jerman, E., Conway, E., Fadda, E., O'Donovan, D., Krivtsov, A.V., Rice, A.M., Kearney, C.J., Flaus, A., McDade, S.S., Martin, S.J., McLysaght, A., O'Connell, D.J., Armstrong, S.A., Bracken, A.P. (2015). A chromatin-independent role of Polycomb-like 1 to stabilize p%£ and promote cellular quiescence. Genes Dev 29(21):2231-43
McLysaght, A., and Guerzoni, D. (2015). New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation. Philos Trans R Soc Lond B 370(1678):20140332
McLysaght, A., Makino, T., Grayton, H.M., Tropeano, M., Mitchell, K.J., Vassos, E., Collier, D.A., (2014). Ohnologs are overrepresented in pathogenic copy number mutations. Proc. Natl. Acad. Sci., USA 111:361-366
Makino, T., McLysaght, A., and Kawata, M. (2013). Genome-wide deserts for copy number variation in vertebrates Nature Communications 4:2283
Bratke, K., McLysaght, A., and Rothenburg, S. (2013). A survey of host range genes in poxvirus genomes Infection, Genetics and Evolution 14:406-425
Makino, T. and McLysaght, A. (2012). Positionally-biased gene loss after whole genome duplication: Evidence from human, yeast and plant. Genome Research 22:2427
Murphy, D.N. and McLysaght, A. (2012).De Novo Origin of Protein-Coding Genes in Murine Rodents PLoS One 7(11):e48650
Satake, M., Kawata, M., McLysaght, A., and Makino, T. (2012). Evolution of Vertebrate Tissues Driven by Differential Modes of Gene Duplication. DNA Research 19:305
Pessia, E., Makino, T., Bailly-Bechet, M., McLysaght, A., and Marais, G.A.B. (2012). Mammalian X Chromosome Inactivation evolved as a dosage compensation mechanism for dosage-sensitive genes on the X chromosome PNAS 109(14):5346-51 Commentary
Guerzoni, D. and McLysaght, A. (2011). De novo origins of human genes. PLoS Genetics 7(11): e1002381.
Perez-Bercoff, A., McLysaght, and Conant, G.C. (2011). Patterns of indirect protein interactions suggest a spatial organization to metabolism. Molecular BioSystems 7:3056
Makino, T., and McLysaght, A. (2010). Ohnologs in the human genome are dosage balanced and frequently associated with disease P.N.A.S. 19(10):1752-9 Research Highlights in Nature Reviews Genetics
Perez-Bercoff, A., Makino, T., and McLysaght, A. (2010). Duplicability of self-interacting human genes BMC Evolutionary Biology 10:160
Knowles, D.G., and McLysaght, A. (2009). Recent de novo origin of human protein-coding genes Genome Research 19(10):1752-9 Commentary
Makino, T., Hokamp, K. and McLysaght, A. (2009). The complex relationship of gene duplication and essentiality. Trends in Genetics 25(4) 152-155.
Makino, T. Knowles D.G. and McLysaght, A. (2009). Functional divergence of duplicated genes In Evolution After Gene Duplication (Dittmar de la Cruz, K. and Liberles, D. eds.), Wiley
Makino, T. and McLysaght, A. (2009). 185-194 The Evolution of Functional Gene Clusters in Eukaryote Genomes In Evolutionary Biology: Concept, Modeling and Application (Pierre Pontarotti, editor) Springer
Makino, T. and McLysaght, A. (2009). Evolutionary Analyses of Protein Interaction Networks. In Biological Data Mining in Protein Interaction Networks (Xiao-Li Li, See-Kiong Ng eds.), United States, IGI Global
McLysaght, A. (2008). Evolutionary steps of sex chromosomes are reflected in retrogenes. Trends in Genetics 24(10):478-481
Makino, T. and McLysaght, A. (2008). Interacting Gene Clusters and the Evolution of the Vertebrate Immune System. Molecular Biology and Evolution 25(9):1855-1862 In the news ...
Bratke, K. A. and McLysaght, A. (2008). Identification of multiple independent horizontal gene transfers into poxviruses using a comparative genomics approach. BMC Evolutionary Biology 8:67
Knowles, D. G. and McLysaght, A. (2006). High Rate of Recent Intron Gain and Loss in Simultaneously Duplicated Arabidopsis Genes. Molecular Biology and Evolution 23(8):1548-1557
McLysaght, A. and Huson, D.H. (Eds.) (2005). Comparative Genomics Lecture Notes in Bioinformatics LNBI 3678, Springer, Germany.
Pollastri, G. and McLysaght, A. (2005). Porter: a new, accurate server for protein secondary structure prediction Bioinformatics 21(8):1719-1720
Trinh, P., McLysaght, A., Sankoff, D., (2004). Genomic Features in the Breakpoint Regions between Syntenic Blocks Bioinformatics 20(Suppl 1):i318-i325
McLysaght, A., Baldi, P.F., Gaut, B.S., (2003). Extensive gene gain associated with adaptive evolution of poxviruses Proc. Natl. Acad. Sci. 100(26):15655-15660
Hampson, S., McLysaght, A., Gaut, B.S., Baldi, P.F. (2003). LineUp: Statistical Detection of Chromosomal Homology with Application to Plant Comparative Genomics. Genome Research 13:999-1010
Vision, T.J. and McLysaght, A. (2004). Computational Tools and Resources in Plant Genome Informatics. In Handbook of Plant Biotechnology (Paul Christou and Harry Klee eds.) Wiley
Hokamp, K., McLysaght, A. and Wolfe, K. H. (2003). The 2R hypothesis and the human genome sequence. Journal of Structural and Functional Genomics. 3:95-110.
McLysaght, A., Hokamp K, and Wolfe, K.H. (2002). Extensive genomic duplication during early chordate evolution. Nature Genetics 31(2):200-204.
McLysaght, A. (October, 2001). Evolution of Vertebrate Genome Organisation. Ph.D. Thesis University of Dublin, Trinity College
Lander, E.S. et al. (2001) Initial sequencing and analysis of the human genome. Nature 409:860-921.
  McLysaght, A., Seoighe, C. and Wolfe, K. (2000). 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 (Sankoff, D. & Nadeau, J. H., eds.), pp. 47-58. Kluwer Academic Press, Dordrecht.
McLysaght, A., Enright, A.J., Skrabanek, L. & Wolfe, K.H. (2000) Estimation of synteny conservation and genome compaction between pufferfish (Fugu) and human. Yeast 17:22-36.