Research Topics
| James O McInerneySummaryAffiliation: National University of Ireland Country: Ireland Publications
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Detail Information
Publications
Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justifiedThomas M Keane
Department of Biology, National University of Ireland, Maynooth, Co Kildare, Ireland
BMC Evol Biol 6:29. 2006..These matrices are normally used as surrogates, rather than deriving the maximum likelihood model from the dataset being examined. With few exceptions, selection between alternative matrices has been carried out in an ad hoc manner...- The Public Goods Hypothesis for the evolution of life on EarthJames O McInerney
Molecular Evolution and Bioinformatics Unit, Department of Biology, National University of Ireland Maynooth, County Kildare, Ireland
Biol Direct 6:41. 2011..We argue for this change using an axiomatic approach that shows that the Public Goods hypothesis is a better accommodation of the observed data than the Tree of Life hypothesis... - The causes of protein evolutionary rate variationJames O McInerney
Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland
Trends Ecol Evol 21:230-2. 2006..It will be interesting to see whether this is shown to be a universal rule for all biological systems... - Planctomycetes and eukaryotes: a case of analogy not homologyJames O McInerney
Department of Biology, National University of Ireland Maynooth, Maynooth, Co Kildare, Ireland
Bioessays 33:810-7. 2011.... - Genetics. Paradigm for lifeJames O McInerney
Department of Biology, National University of Ireland Maynooth, Maynooth, County Kildare, Ireland
Science 318:1390-1. 2007 - The prokaryotic tree of life: past, present... and future?James O McInerney
Department of Biology, National University of Ireland Maynooth, Maynooth, County Kildare, Ireland
Trends Ecol Evol 23:276-81. 2008..Horizontal gene transfer is now known to be a significant influence on genome evolution. The next decade is likely to resolve whether or not we retain the centuries-old metaphor of the tree for all of life... - The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methodsAngela McCann
Bioinformatics Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, CO, Kildare, Ireland
BMC Evol Biol 8:312. 2008..In particular, we focus on Conditioned Reconstruction as it is a method that is designed to work well even if HGT is present... - Gene and genome trees conflict at many levelsLeanne S Haggerty
Department of Biology, The National University of Ireland, Maynooth, County Kildare, Ireland
Philos Trans R Soc Lond B Biol Sci 364:2209-19. 2009..We examine 27 closely related genomes from the YESS group of gamma proteobacteria and a variety of four-taxon datasets from a diverse range of prokaryotes in order to explore the kinds of effects HGT has had on these organisms... - Supertrees disentangle the chimerical origin of eukaryotic genomesDavide Pisani
Department of Biology, The National University of Ireland, Maynooth, Maynooth, County Kildare, Ireland, UK
Mol Biol Evol 24:1752-60. 2007..The results reject all but two of the current hypotheses for the origin of eukaryotes: those assuming a sulfur-dependent or hydrogen-dependent syntrophy for the origin of mitochondria... - Evidence of positive Darwinian selection in putative meningococcal vaccine antigensDavid A Fitzpatrick
Department of Biology, National University of Ireland, Maynooth, Co. Kildare, Ireland
J Mol Evol 61:90-8. 2005.... - Genome phylogenies indicate a meaningful alpha-proteobacterial phylogeny and support a grouping of the mitochondria with the RickettsialesDavid A Fitzpatrick
Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland
Mol Biol Evol 23:74-85. 2006..This alignment infers that the sister group of the mitochondria, for the taxa that have been sampled, is the order Rickettsiales... - Recurring cluster and operon assembly for Phenylacetate degradation genesFergal J Martin
Department of Biology, National University of Ireland Maynooth, Maynooth, Co Kildare, Ireland
BMC Evol Biol 9:36. 2009..In this work we test the hypothesis that cluster formation is most likely due to a selective pressure to gradually co-localise protein products and that operon formation is not an inevitable conclusion of the process... - Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of functionJames A Cotton
Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland
Proc Natl Acad Sci U S A 107:17252-5. 2010..This importance reflects these genes' origin as the ancestral nuclear component of the eukaryotic genome... - Evidence for heterogeneous selective pressures in the evolution of the env gene in different human immunodeficiency virus type 1 subtypesSimon A A Travers
Biology Department, National University of Ireland, Maynooth, County Kildare, Ireland
J Virol 79:1836-41. 2005..The presence of such sites indicates heterogeneity of selective pressures within HIV-1 group M subtype evolution that may account for the various levels of fitness of the subtypes... - Does a tree-like phylogeny only exist at the tips in the prokaryotes?Christopher J Creevey
Bioinformatics and Pharmacogenomics Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland
Proc Biol Sci 271:2551-8. 2004..This approach will help decide the extent to which we can say that there is a prokaryotic phylogeny and where in the phylogeny a cohesive genomic signal exists... - Fatty acid biosynthesis in Mycobacterium tuberculosis: lateral gene transfer, adaptive evolution, and gene duplicationRhoda J Kinsella
Bioinformatics and Pharmacogenomics Laboratory, Biology Department, National University of Ireland, Maynooth, County Kildare, Ireland
Proc Natl Acad Sci U S A 100:10320-5. 2003..Additionally, adaptive evolution and gene duplication have been an influence in the evolution of the pathway. This study provides a key insight into how M. tuberculosis has developed its unique fatty acid synthetic abilities... - Evidence of positive Darwinian selection in Omp85, a highly conserved bacterial outer membrane protein essential for cell viabilityDavid A Fitzpatrick
Department of Biology, National University of Ireland, Maynooth, Country Kildare, Ireland
J Mol Evol 60:268-73. 2005..Alternatively amino acids within membrane-spanning regions of the protein are found to be under purifying selection most likely as a result of structural constraints... - The molecular phylogeny of a nematode-specific clade of heterotrimeric G-protein alpha-subunit genesDavid A Fitzpatrick
Biology Department, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland
J Mol Evol 63:87-94. 2006..This neuronal gene expansion most likely occurred in nematodes to enable them to compensate for the small number of chemosensory cells and the limited emphasis on cephalization during nematode evolution... - The Opisthokonta and the Ecdysozoa may not be clades: stronger support for the grouping of plant and animal than for animal and fungi and stronger support for the Coelomata than EcdysozoaGayle K Philip
Department of Biology, National University of Ireland Maynooth, Co. Kildare, Ireland
Mol Biol Evol 22:1175-84. 2005..In the light of this new tree, we re-analyze the evolution of intron gain and loss in the rpL14 gene and find that it is much more compatible with the hypothesis presented here than with the Opisthokonta hypothesis... - MultiPhyl: a high-throughput phylogenomics webserver using distributed computingThomas M Keane
Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Hinxton, UK
Nucleic Acids Res 35:W33-7. 2007..A MultiPhyl webserver is available for public use at: http://www.cs.nuim.ie/distributed/multiphyl.php... - The human genome retains relics of its prokaryotic ancestry: human genes of archaebacterial and eubacterial origin exhibit remarkable differencesDavid Alvarez-Ponce
Department of Biology, National University of Ireland Maynooth, Maynooth, Co Kildare, Ireland
Genome Biol Evol 3:782-90. 2011..Taken together, these results show that more than 2 billion years after eukaryogenesis, the human genome retains at least two somewhat distinct communities of genes... - A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biasesCarla A Cummins
Molecular Evolution and Bioinformatics Unit, Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland
Syst Biol 60:833-44. 2011..We feel this method can be useful for phylogeny reconstruction, understanding evolutionary rate variation, and for understanding selection variation on different characters... - Detecting adaptive molecular evolution: additional tools for the parasitologistJames O McInerney
Bioinformatics and Pharmacogenomics Laboratory, Department of Biology, National University of Ireland, Maynooth, Co. Kildare, Ireland
Adv Parasitol 54:359-79. 2003..Studies of the interaction of these proteins with the antigen-presenting cells of the immune system should lead to a better understanding of malarial infection... - Gene evolution and drug discoveryJames O McInerney
Bioinformatics and Pharmacogenomics Laboratory, National University of Ireland, Maynooth, County Kildare
Methods Mol Biol 316:87-109. 2006..In this chapter, we review the most interesting approaches for inferring the evolutionary history of DNA and protein sequences and indicate how these analyses can be useful in the drug discovery process... - Timing and reconstruction of the most recent common ancestor of the subtype C clade of human immunodeficiency virus type 1Simon A A Travers
Biology Department, National University of Ireland, Maynooth, Maynooth, Co. Kildare, Ireland
J Virol 78:10501-6. 2004..Here we suggest that the most recent common ancestor of subtype C appeared in the mid- to late 1960s. Sensitivity analyses, by which possible biases due to oversampling from one district were explored, gave very similar estimates... - An algorithm for detecting directional and non-directional positive selection, neutrality and negative selection in protein coding DNA sequencesChristopher J Creevey
Bioinformatics and Pharmacogenomics Laboratory, Department of Biology, National University of Ireland, Co. Kildare, Maynooth, Ireland
Gene 300:43-51. 2002..The method is fast and accurate, easy to implement, sensitive to short-lived selection events and robust with respect to sampling density and proportion of sites under the influence of positive selection... - Eukaryotic genes in Mycobacterium tuberculosis? Possible alternative explanationsRhoda J Kinsella
Trends Genet 19:687-9. 2003 - Gene prediction using the Self-Organizing Map: automatic generation of multiple gene modelsShaun Mahony
National Centre for Biomedical Engineering Science, NUI, Galway, Galway, Ireland
BMC Bioinformatics 5:23. 2004..It is likely that future improvements in gene finding will involve the development of methods that can adequately deal with intra-genomic compositional variation... - TOPD/FMTS: a new software to compare phylogenetic treesPere Puigbò
Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Rovira i Virgili University, Tarragona, Spain
Bioinformatics 23:1556-8. 2007..AVAILABILITY: The Perl source code of TOPD/FMTS is available at http://genomes.urv.es/topd... - The shape of supertrees to come: tree shape related properties of fourteen supertree methodsMark Wilkinson
Department of Zoology, The Natural History Museum, London SW7 5BD, United Kingdom
Syst Biol 54:419-31. 2005..Use of multiple methods and/or weighting schemes may allow practical assessment of the extent to which inferences from real data depend upon methodological biases with respect to input tree shape or size... - Gamma chain receptor interleukins: evidence for positive selection driving the evolution of cell-to-cell communicators in the mammalian immune systemJames O McInerney
Bioinformatics and Molecular Evolution Laboratory, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
J Mol Evol 61:608-19. 2005..These findings highlight the importance of adaptive evolutionary events in the evolution of this central network in the immune system and suggest underlying causes for differences in defense responses in the mammalia... - On the desirability of models for inferring genome phylogeniesJames O McInerney
Trends Microbiol 14:1-2. 2006 - Molecular evidence for dim-light vision in the last common ancestor of the vertebratesDavide Pisani
Curr Biol 16:R318-9; author reply R320. 2006 - Of clades and clans: terms for phylogenetic relationships in unrooted treesMark Wilkinson
Trends Ecol Evol 22:114-5. 2007 - Adaptive evolution of the human fatty acid synthase gene: support for the cancer selection and fat utilization hypotheses?James O McInerney
Bioinformatics and Molecular Evolution Laboratory, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
Gene 360:151-9. 2005..We speculate that the role played by FAS either in cancer development or in human brain development has created this selective pressure, although we cannot rule out the various other functions of FAS...