Chauve, L., Bazzani, E.*, Verdier, C.*, Butler, L., Atimise, M.E., McGarry, A., and McLysaght, A. (2025).
Evidence for increased stress resistance due to polyploidy from synthetic autotetraploid Caenorhabditis elegans.
bioRxiv, 06. 28.546823
* Equal second author contribution
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Rice, A.M., Li, Y., Donnelly, P., and McLysaght, A. (2024).
Evolution of dosage-sensitive genes by tissue-restricted expression changes.
bioRxiv, 10.17.618887
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Vargas-Chavez, C., Benitez-Alvarez, L., Martinez-Redondo, G.I., Alvarez-Gonzalez, L., Salces-Ortiz, J., Eleftheriadi, K., Escudero, N., Guiglielmoni, N., Flot, J.F., Novo, M., Ruiz-Herrera, A., McLysaght, A., Fernandez, R. (2024).
A punctuated burst of massive genomic rearrangements and the origin of non-marine annelids.
bioRxiv, 05.16.594344
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Redmond, A.K., Mohanty, D.S., McLysaght, A., and Macqueen, D.J. (2023).
Phylogenetic origins of the complement system in the ancestor of animals.
Developmental & Comparative Immunology, 148:104997
|
Redmond, A.K., and McLysaght, A. (2023).
Horizontal transfer of vertebrate vision gene IRBP into the chordate ancestor.
Proceedings of the National Academy of Sciences, 120(34):e2310390120
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Vance, Z., and McLysaght, A. (2023).
Ohnologs and SSD Paralogs Differ in Genomic and Expression Features Related to Dosage Constraints.
Genome Biology and Evolution, 15(10):evad174
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Redmond, A., Casey, D., Gundappa, M.K., Macqueen, D.J., and McLysaght, A. (2023).
Independent rediploidization masks shared whole genome duplication in the sturgeon-paddlefish ancestor.
Nature Communications, 14(1):2879
|
Redmond, A., and McLysaght, A. (2023).
Reply to: Available data do not rule out Ctenophora as the sister group to all other Metazoa.
Nature Communications, 14(1):710
|
McLysaght, A. (2022).
The deceptive simplicity of mendelian genetics.
PLoS Biology, 20(7):e3001691
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Vakirlis, N., Vance, Z., Duggan, K.M., and McLysaght, A. (2022).
De novo birth of functional microproteins in the human lineage.
Cell Reports, 41(12):111808
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Vance, Z., Niezabitowski, L., Hurst, L.D., and McLysaght, A. (2022).
Evidence from Drosophila Supports Higher Duplicability of Faster Evolving Genes.
Genome biology and evolution, 14(1):evac003
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Nakatani, Y., Shingate, P., Ravi, V., Pillai, N.E., Prasad, A., McLysaght, A., and Venkatesh, B. (2021).
Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution.
Nature communications, 12(1):4489
|
Redmond, A., and McLysaght, A. (2021).
Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding.
Nature Communications, 12(1):1783
|
Vakirlis, N., Carvunis, A.R., McLysaght, A. (2020).
Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes.
eLife, 9:e53500
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Vakirlis, N., Acar, O., Hsu, B., Coelho, N.C., Oss, S.B.V., Wacholder, A., Medetgul-Ernar, K., Bowman II, R.W., Hines, C.P., Iannotta, J., Parikh, S.B., McLysaght, A., Camacho, C.J., O'Donnell, A.F., Ideker, T., and Carvunis, A.R. (2020).
De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences.
Nature Communications, 11:781
|
Vakirlis, N., and McLysaght, A. (2019).
Computational Prediction of De Novo Emerged Protein-Coding Genes.
Methods in molecular biology (Clifton, N.J.), 1851:63-81
|
Nakatani, Y., and McLysaght, A. (2019).
Macrosynteny analysis shows the absence of ancient whole-genome duplication in lepidopteran insects.
Proceedings of the National Academy of Sciences (USA), 116(6):1816–1818
|
Vakirlis, N., Monerawela, C., McManus, G., Ribeiro, O., McLysaght, A., James, T., and Bond, U. (2019).
Evolutionary journey and characterisation of a novel pan‐geneassociated with beer strains of Saccharomyces cerevisiae.
Yeast, 36(7):425–437
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Conway, E., Jerman, E., Healy, E., Ito, S., Holoch, D., Oliviero, G., Deevy, O., Glancy, E., Fitzpatrick, D.J., Mucha, M., Watson, A., Rice, A.M., 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., and Bracken, A.P. (2018).
A Family of Vertebrate-Specific Polycombs Encoded by the LCOR/LCORL Genes Balance PRC2 Subtype Activities.
Molecular Cell, 70(3):408-421.e8
|
O'Toole,, Á.N., Hurst, L.D., and McLysaght, A. (2018).
Faster Evolving Primate Genes Are More Likely to Duplicate.
Mol. Biol. Evol, 35(1):107–118
|
Glenfield, C., and McLysaght, A. (2018).
Pseudogenes Provide Evolutionary Evidence for the Competitive Endogenous RNA Hypothesis.
Mol. Biol. Evol., 35(12):2886–2899
|
Rice, A.M., and McLysaght, A. (2017).
Dosage-sensitive genes in evolution and disease.
BMC Biology, 15(1):78
|
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), 33(14):i369-i378
|
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. (2016).
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 p53 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
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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
|
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
|
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
|
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
|
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. |