Publications
Selected publications
- Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome. (Journal article - 2024)
- Gene essentiality evolves across a pangenome. (Journal article - 2022)
- Why prokaryotes have pangenomes. (Journal article - 2017)
- Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. (Journal article - 1998)
- Fatty acid biosynthesis in Mycobacterium tuberculosis: lateral gene transfer, adaptive evolution, and gene duplication. (Journal article - 2003)
- Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function. (Journal article - 2010)
- Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea. (Journal article - 2012)
- Metazoan opsin evolution reveals a simple route to animal vision. (Journal article - 2012)
- Evolutionary analyses of non-genealogical bonds produced by introgressive descent. (Journal article - 2012)
- Gene similarity networks provide tools for understanding eukaryote origins and evolution. (Journal article - 2013)
2024
Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome.
Beavan, A. J. S., Domingo-Sananes, M. R., & McInerney, J. O. (2024). Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome.. Proceedings of the National Academy of Sciences of the United States of America, 121(1), e2304934120. doi:10.1073/pnas.2304934120
2023
Bursts of novel composite gene families at major nodes in animal evolution
Fungal phylogeny reconstructed using heterogeneous models reveals new placement of Microsporidia
Contingency, Repeatability and Predictability in the Evolution of a Prokaryotic Pangenome
Prokaryotic Pangenomes Act as Evolving Ecosystems.
McInerney, J. O. (2023). Prokaryotic Pangenomes Act as Evolving Ecosystems.. Molecular biology and evolution, 40(1), msac232. doi:10.1093/molbev/msac232
2022
Distinct evolutionary trajectories in the <i>Escherichia coli</i> pangenome occur within sequence types.
Cummins, E. A., Hall, R. J., Connor, C., McInerney, J. O., & McNally, A. (2022). Distinct evolutionary trajectories in the <i>Escherichia coli</i> pangenome occur within sequence types.. Microbial genomics, 8(11). doi:10.1099/mgen.0.000903
Gene essentiality evolves across a pangenome.
Beavan, A. J. S., & McInerney, J. O. (2022). Gene essentiality evolves across a pangenome.. Nature microbiology, 7(10), 1510-1511. doi:10.1038/s41564-022-01231-8
High Frequency of Dynamic Rearrangements In Crispr loci
Prokaryote pangenomes are dynamic entities.
Cummins, E. A., Hall, R. J., McInerney, J. O., & McNally, A. (2022). Prokaryote pangenomes are dynamic entities.. Current opinion in microbiology, 66, 73-78. doi:10.1016/j.mib.2022.01.005
2021
Gene-gene relationships in an <i>Escherichia coli</i> accessory genome are linked to function and mobility.
Hall, R. J., Hall, R. J., Whelan, F. J., Cummins, E. A., Connor, C., McNally, A., & McInerney, J. O. (2021). Gene-gene relationships in an <i>Escherichia coli</i> accessory genome are linked to function and mobility.. Microbial genomics, 7(9). doi:10.1099/mgen.0.000650
Evidence for Selection in the Abundant Accessory Gene Content of a Prokaryote Pangenome.
Whelan, F. J., Hall, R. J., & McInerney, J. O. (2021). Evidence for Selection in the Abundant Accessory Gene Content of a Prokaryote Pangenome.. Molecular biology and evolution, 38(9), 3697-3708. doi:10.1093/molbev/msab139
Mechanisms That Shape Microbial Pangenomes.
Domingo-Sananes, M. R., & McInerney, J. O. (2021). Mechanisms That Shape Microbial Pangenomes.. Trends in microbiology, 29(6), 493-503. doi:10.1016/j.tim.2020.12.004
Gene-gene relationships in an <i>Escherichia coli</i> accessory genome are linked to function and mobility
2020
Evidence for selection in a prokaryote pangenome
Horizontal Gene Transfer as a Source of Conflict and Cooperation in Prokaryotes.
Hall, R. J., Whelan, F. J., McInerney, J. O., Ou, Y., & Domingo-Sananes, M. R. (2020). Horizontal Gene Transfer as a Source of Conflict and Cooperation in Prokaryotes.. Frontiers in microbiology, 11, 1569. doi:10.3389/fmicb.2020.01569
Pangenomes and Selection: The Public Goods Hypothesis
McInerney, J. O., Whelan, F. J., Domingo-Sananes, M. R., McNally, A., & O’Connell, M. J. (2020). Pangenomes and Selection: The Public Goods Hypothesis. In The Pangenome (pp. 151-167). Springer International Publishing. doi:10.1007/978-3-030-38281-0_7
Coinfinder: detecting significant associations and dissociations in pangenomes.
Whelan, F. J., Rusilowicz, M., & McInerney, J. O. (2020). Coinfinder: detecting significant associations and dissociations in pangenomes.. Microbial genomics, 6(3). doi:10.1099/mgen.0.000338
2019
Coinfinder: Detecting Significant Associations and Dissociations in Pangenomes
Selection-based model of prokaryote pangenomes
Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human.
McCartney, A. M., Hyland, E. M., Cormican, P., Moran, R. J., Webb, A. E., Lee, K. D., . . . O'Connell, M. J. (2019). Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human.. Genome biology and evolution, 11(9), 2678-2690. doi:10.1093/gbe/evz163
Eukaryote Genes Are More Likely than Prokaryote Genes to Be Composites.
Ou, Y., & McInerney, J. O. (2019). Eukaryote Genes Are More Likely than Prokaryote Genes to Be Composites.. Genes, 10(9), E648. doi:10.3390/genes10090648
The co-occurrence and co-exclusion of evolving objects in prokaryotes
Whelan, F. J., Rusilowicz, M., & McInerney, J. O. (2019). The co-occurrence and co-exclusion of evolving objects in prokaryotes. Access Microbiology, 1(1A). doi:10.1099/acmi.ac2019.po0380
Reconstructing and Analysing The Genome of The Last Eukaryote Common Ancestor to Better Understand the Transition from FECA to LECA
2018
Bipartite Network Analysis of Gene Sharings in the Microbial World.
Corel, E., Méheust, R., Watson, A. K., McInerney, J. O., Lopez, P., & Bapteste, E. (2018). Bipartite Network Analysis of Gene Sharings in the Microbial World.. Molecular biology and evolution, 35(4), 899-913. doi:10.1093/molbev/msy001
Formation of chimeric genes with essential functions at the origin of eukaryotes.
Méheust, R., Bhattacharya, D., Pathmanathan, J. S., McInerney, J. O., Lopez, P., & Bapteste, E. (2018). Formation of chimeric genes with essential functions at the origin of eukaryotes.. BMC biology, 16(1), 30. doi:10.1186/s12915-018-0500-0
Function-related replacement of bacterial siderophore pathways.
Bruns, H., Crüsemann, M., Letzel, A. -C., Alanjary, M., McInerney, J. O., Jensen, P. R., . . . Ziemert, N. (2018). Function-related replacement of bacterial siderophore pathways.. The ISME journal, 12(2), 320-329. doi:10.1038/ismej.2017.137
2017
The role of public goods in planetary evolution.
McInerney, J. O., & Erwin, D. H. (2017). The role of public goods in planetary evolution.. Philosophical transactions. Series A, Mathematical, physical, and engineering sciences, 375(2109), 20160359. doi:10.1098/rsta.2016.0359
Reply to 'The population genetics of pangenomes'.
McInerney, J. O., McNally, A., & O'Connell, M. J. (2017). Reply to 'The population genetics of pangenomes'.. Nature microbiology, 2(12), 1575. doi:10.1038/s41564-017-0068-4
Horizontal gene transfer is less frequent in eukaryotes than prokaryotes but can be important (retrospective on DOI 10.1002/bies.201300095).
McInerney, J. O. (2017). Horizontal gene transfer is less frequent in eukaryotes than prokaryotes but can be important (retrospective on DOI 10.1002/bies.201300095).. BioEssays : news and reviews in molecular, cellular and developmental biology, 39(6). doi:10.1002/bies.201700002
Why prokaryotes have pangenomes.
McInerney, J. O., McNally, A., & O'Connell, M. J. (2017). Why prokaryotes have pangenomes.. Nature microbiology, 2, 17040. doi:10.1038/nmicrobiol.2017.40
Microbiology: Mind the gaps in cellular evolution.
McInerney, J. O., & O'Connell, M. J. (2017). Microbiology: Mind the gaps in cellular evolution.. Nature, 541(7637), 297-299. doi:10.1038/nature21113
Society for Molecular Biology and Evolution, Council and Business Meetings, 2016, Gold Coast Australia.
McInerney, J. O. (2017). Society for Molecular Biology and Evolution, Council and Business Meetings, 2016, Gold Coast Australia.. Molecular biology and evolution, 34(1), 243-244. doi:10.1093/molbev/msw276
2016
Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations.
McNally, A., Oren, Y., Kelly, D., Pascoe, B., Dunn, S., Sreecharan, T., . . . Corander, J. (2016). Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations.. PLoS genetics, 12(9), e1006280. doi:10.1371/journal.pgen.1006280
Evolution: A four billion year old metabolism.
McInerney, J. O. (2016). Evolution: A four billion year old metabolism.. Nature microbiology, 1(9), 16139. doi:10.1038/nmicrobiol.2016.139
"Every Gene Is Everywhere but the Environment Selects": Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis.
Fondi, M., Karkman, A., Tamminen, M. V., Bosi, E., Virta, M., Fani, R., . . . McInerney, J. O. (2016). "Every Gene Is Everywhere but the Environment Selects": Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis.. Genome biology and evolution, 8(5), 1388-1400. doi:10.1093/gbe/evw077
Society for<i>Molecular Biology and Evolution</i>, Council and Business Meetings, 2015, Vienna Austria
McInerney, J. O. (2016). Society for<i>Molecular Biology and Evolution</i>, Council and Business Meetings, 2015, Vienna Austria. Molecular Biology and Evolution, 33(1), 299-300. doi:10.1093/molbev/msv275
2015
Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis.
Akanni, W. A., Siu-Ting, K., Creevey, C. J., McInerney, J. O., Wilkinson, M., Foster, P. G., & Pisani, D. (2015). Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis.. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 370(1678), 20140337. doi:10.1098/rstb.2014.0337
The ring of life hypothesis for eukaryote origins is supported by multiple kinds of data.
McInerney, J., Pisani, D., & O'Connell, M. J. (2015). The ring of life hypothesis for eukaryote origins is supported by multiple kinds of data.. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 370(1678), 20140323. doi:10.1098/rstb.2014.0323
Endosymbiotic origin and differential loss of eukaryotic genes.
Ku, C., Nelson-Sathi, S., Roettger, M., Sousa, F. L., Lockhart, P. J., Bryant, D., . . . Martin, W. F. (2015). Endosymbiotic origin and differential loss of eukaryotic genes.. Nature, 524(7566), 427-432. doi:10.1038/nature14963
Evolution by Pervasive Gene Fusion in Antibiotic Resistance and Antibiotic Synthesizing Genes
Coleman, O., Hogan, R., McGoldrick, N., Rudden, N., & McInerney, J. (n.d.). Evolution by Pervasive Gene Fusion in Antibiotic Resistance and Antibiotic Synthesizing Genes. Computation, 3(2), 114-127. doi:10.3390/computation3020114
Origins of major archaeal clades correspond to gene acquisitions from bacteria.
Nelson-Sathi, S., Sousa, F. L., Roettger, M., Lozada-Chávez, N., Thiergart, T., Janssen, A., . . . Martin, W. F. (2015). Origins of major archaeal clades correspond to gene acquisitions from bacteria.. Nature, 517(7532), 77-80. doi:10.1038/nature13805
2014
Society for Molecular Biology and Evolution, Council and Business Meetings, 2013, Chicago, IL
McInerney, J. O. (2014). Society for Molecular Biology and Evolution, Council and Business Meetings, 2013, Chicago, IL. Molecular Biology and Evolution, 31(12), 3376-3378. doi:10.1093/molbev/msu273
Evolutionary developmental biology: Ghost locus appears.
McInerney, J. O., & O'Connell, M. J. (2014). Evolutionary developmental biology: Ghost locus appears.. In Nature (Vol. 514, Iss. 7524, pp. 570-571). [Print]. doi:10.1038/514570a
SMBE Satellite meeting on reticulated microbial evolution 2014--meeting report.
Dagan, T., Bapteste, E., McInerney, J. O., & Martin, W. F. (2014). SMBE Satellite meeting on reticulated microbial evolution 2014--meeting report.. Genome biology and evolution, 6(9), 2206-2209. doi:10.1093/gbe/evu173
Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears.
Liu, S., Lorenzen, E. D., Fumagalli, M., Li, B., Harris, K., Xiong, Z., . . . Wang, J. (2014). Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears.. Cell, 157(4), 785-794. doi:10.1016/j.cell.2014.03.054
Integration of two ancestral chaperone systems into one: the evolution of eukaryotic molecular chaperones in light of eukaryogenesis.
Bogumil, D., Alvarez-Ponce, D., Landan, G., McInerney, J. O., & Dagan, T. (2014). Integration of two ancestral chaperone systems into one: the evolution of eukaryotic molecular chaperones in light of eukaryogenesis.. Molecular biology and evolution, 31(2), 410-418. doi:10.1093/molbev/mst212
A pluralistic account of homology: adapting the models to the data.
Haggerty, L. S., Jachiet, P. -A., Hanage, W. P., Fitzpatrick, D. A., Lopez, P., O'Connell, M. J., . . . McInerney, J. O. (2014). A pluralistic account of homology: adapting the models to the data.. Molecular biology and evolution, 31(3), 501-516. doi:10.1093/molbev/mst228
The hybrid nature of the Eukaryota and a consilient view of life on Earth.
McInerney, J. O., O'Connell, M. J., & Pisani, D. (2014). The hybrid nature of the Eukaryota and a consilient view of life on Earth.. Nature reviews. Microbiology, 12(6), 449-455. doi:10.1038/nrmicro3271
2013
Society for Molecular Biology and Evolution, Council and Business Meetings, 2013, Chicago, IL
McInerney, J. O. (2013). Society for Molecular Biology and Evolution, Council and Business Meetings, 2013, Chicago, IL. Molecular Biology and Evolution, 30(12), 2733-2734. doi:10.1093/molbev/mst202
Society for Molecular Biology and Evolution, Council and Business Meetings, 2013, Chicago, IL
McInerney, J. O. (2013). Society for Molecular Biology and Evolution, Council and Business Meetings, 2013, Chicago, IL. Genome Biology and Evolution, 5(11), 2094-2095. doi:10.1093/gbe/evt166
Translational selection frequently overcomes genetic drift in shaping synonymous codon usage patterns in vertebrates.
Doherty, A., & McInerney, J. O. (2013). Translational selection frequently overcomes genetic drift in shaping synonymous codon usage patterns in vertebrates.. Molecular biology and evolution, 30(10), 2263-2267. doi:10.1093/molbev/mst128
Heterogeneous models place the root of the placental mammal phylogeny.
Morgan, C. C., Foster, P. G., Webb, A. E., Pisani, D., McInerney, J. O., & O'Connell, M. J. (2013). Heterogeneous models place the root of the placental mammal phylogeny.. Molecular biology and evolution, 30(9), 2145-2156. doi:10.1093/molbev/mst117
Networks: expanding evolutionary thinking.
Bapteste, E., van Iersel, L., Janke, A., Kelchner, S., Kelk, S., McInerney, J. O., . . . Whitfield, J. (2013). Networks: expanding evolutionary thinking.. In Trends in genetics : TIG (Vol. 29, Iss. 8, pp. 439-441). [Print-Electronic]. doi:10.1016/j.tig.2013.05.007
EGN: a wizard for construction of gene and genome similarity networks.
Halary, S., McInerney, J. O., Lopez, P., & Bapteste, E. (2013). EGN: a wizard for construction of gene and genome similarity networks.. BMC evolutionary biology, 13, 146. doi:10.1186/1471-2148-13-146
Correction for Feuda et al., Metazoan opsin evolution reveals a simple route to animal vision
Correction for Feuda et al., Metazoan opsin evolution reveals a simple route to animal vision (2013). Proceedings of the National Academy of Sciences, 110(17), 7097. doi:10.1073/pnas.1304910110
Gene similarity networks provide tools for understanding eukaryote origins and evolution.
Alvarez-Ponce, D., Lopez, P., Bapteste, E., & McInerney, J. O. (2013). Gene similarity networks provide tools for understanding eukaryote origins and evolution.. Proceedings of the National Academy of Sciences of the United States of America, 110(17), E1594-E1603. doi:10.1073/pnas.1211371110
More than tree dimensions: inter-lineage evolution's ecological importance.
McInerney, J. O. (2013). More than tree dimensions: inter-lineage evolution's ecological importance.. In Trends in ecology & evolution (Vol. 28, Iss. 11, pp. 624-625). [Print-Electronic]. doi:10.1016/j.tree.2013.09.002
New approaches for unravelling reassortment pathways.
Svinti, V., Cotton, J. A., & McInerney, J. O. (2013). New approaches for unravelling reassortment pathways.. BMC evolutionary biology, 13, 1. doi:10.1186/1471-2148-13-1
2012
Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea.
Nelson-Sathi, S., Dagan, T., Landan, G., Janssen, A., Steel, M., McInerney, J. O., . . . Martin, W. F. (2012). Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea.. Proceedings of the National Academy of Sciences of the United States of America, 109(50), 20537-20542. doi:10.1073/pnas.1209119109
Metazoan opsin evolution reveals a simple route to animal vision.
Feuda, R., Hamilton, S. C., McInerney, J. O., & Pisani, D. (2012). Metazoan opsin evolution reveals a simple route to animal vision.. Proceedings of the National Academy of Sciences of the United States of America, 109(46), 18868-18872. doi:10.1073/pnas.1204609109
Evolutionary analyses of non-genealogical bonds produced by introgressive descent.
Bapteste, E., Lopez, P., Bouchard, F., Baquero, F., McInerney, J. O., & Burian, R. M. (2012). Evolutionary analyses of non-genealogical bonds produced by introgressive descent.. Proceedings of the National Academy of Sciences of the United States of America, 109(45), 18266-18272. doi:10.1073/pnas.1206541109
Increased genome sampling reveals a dynamic relationship between gene duplicability and the structure of the primate protein-protein interaction network.
Doherty, A., Alvarez-Ponce, D., & McInerney, J. O. (2012). Increased genome sampling reveals a dynamic relationship between gene duplicability and the structure of the primate protein-protein interaction network.. Molecular biology and evolution, 29(11), 3563-3573. doi:10.1093/molbev/mss165
2011
A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases.
Cummins, C. A., & McInerney, J. O. (2011). A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases.. Systematic biology, 60(6), 833-844. doi:10.1093/sysbio/syr064
Goods-thinking vs. tree-thinking: Finding a place for mobile genetic elements.
McInerney, J., Cummins, C., & Haggerty, L. (2011). Goods-thinking vs. tree-thinking: Finding a place for mobile genetic elements.. Mobile genetic elements, 1(4), 304-308. doi:10.4161/mge.19153
Planctomycetes and eukaryotes: a case of analogy not homology.
McInerney, J. O., Martin, W. F., Koonin, E. V., Allen, J. F., Galperin, M. Y., Lane, N., . . . Embley, T. M. (2011). Planctomycetes and eukaryotes: a case of analogy not homology.. BioEssays : news and reviews in molecular, cellular and developmental biology, 33(11), 810-817. doi:10.1002/bies.201100045
The Public Goods Hypothesis for the evolution of life on Earth.
McInerney, J. O., Pisani, D., Bapteste, E., & O'Connell, M. J. (2011). The Public Goods Hypothesis for the evolution of life on Earth.. Biology direct, 6, 41. doi:10.1186/1745-6150-6-41
The human genome retains relics of its prokaryotic ancestry: human genes of archaebacterial and eubacterial origin exhibit remarkable differences.
Alvarez-Ponce, D., & McInerney, J. O. (2011). The human genome retains relics of its prokaryotic ancestry: human genes of archaebacterial and eubacterial origin exhibit remarkable differences.. Genome biology and evolution, 3, 782-790. doi:10.1093/gbe/evr073
2010
Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function.
Cotton, J. A., & McInerney, J. O. (2010). Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function.. Proceedings of the National Academy of Sciences of the United States of America, 107(40), 17252-17255. doi:10.1073/pnas.1000265107
2009
Trees from trees: construction of phylogenetic supertrees using clann.
Creevey, C. J., & McInerney, J. O. (2009). Trees from trees: construction of phylogenetic supertrees using clann.. Methods in molecular biology (Clifton, N.J.), 537, 139-161. doi:10.1007/978-1-59745-251-9_7
Gene and genome trees conflict at many levels.
Haggerty, L. S., Martin, F. J., Fitzpatrick, D. A., & McInerney, J. O. (2009). Gene and genome trees conflict at many levels.. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 364(1527), 2209-2219. doi:10.1098/rstb.2009.0042
The network of life: genome beginnings and evolution. Introduction.
Ragan, M. A., McInerney, J. O., & Lake, J. A. (2009). The network of life: genome beginnings and evolution. Introduction.. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 364(1527), 2169-2175. doi:10.1098/rstb.2009.0046
Molecular phylogeny of the Drosophila tripunctata and closely related species groups (Diptera: Drosophilidae).
Hatadani, L. M., McInerney, J. O., de Medeiros, H. F., Junqueira, A. C. M., de Azeredo-Espin, A. M., & Klaczko, L. B. (2009). Molecular phylogeny of the Drosophila tripunctata and closely related species groups (Diptera: Drosophilidae).. Molecular phylogenetics and evolution, 51(3), 595-600. doi:10.1016/j.ympev.2009.02.022
Recurring cluster and operon assembly for Phenylacetate degradation genes.
Martin, F. J., & McInerney, J. O. (2009). Recurring cluster and operon assembly for Phenylacetate degradation genes.. BMC evolutionary biology, 9, 36. doi:10.1186/1471-2148-9-36
2008
The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods.
McCann, A., Cotton, J. A., & McInerney, J. O. (2008). The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods.. BMC evolutionary biology, 8, 312. doi:10.1186/1471-2148-8-312
The prokaryotic tree of life: past, present... and future?
McInerney, J. O., Cotton, J. A., & Pisani, D. (2008). The prokaryotic tree of life: past, present... and future?. Trends in ecology & evolution, 23(5), 276-281. doi:10.1016/j.tree.2008.01.008
2007
Genetics. Paradigm for life.
McInerney, J. O., & Pisani, D. (2007). Genetics. Paradigm for life.. Science (New York, N.Y.), 318(5855), 1390-1391. doi:10.1126/science.1151657
Supertrees disentangle the chimerical origin of eukaryotic genomes.
Pisani, D., Cotton, J. A., & McInerney, J. O. (2007). Supertrees disentangle the chimerical origin of eukaryotic genomes.. Molecular biology and evolution, 24(8), 1752-1760. doi:10.1093/molbev/msm095
MultiPhyl: a high-throughput phylogenomics webserver using distributed computing.
Keane, T. M., Naughton, T. J., & McInerney, J. O. (2007). MultiPhyl: a high-throughput phylogenomics webserver using distributed computing.. Nucleic acids research, 35(Web Server issue), W33-W37. doi:10.1093/nar/gkm359
TOPD/FMTS: a new software to compare phylogenetic trees.
Puigbò, P., Garcia-Vallvé, S., & McInerney, J. O. (2007). TOPD/FMTS: a new software to compare phylogenetic trees.. Bioinformatics (Oxford, England), 23(12), 1556-1558. doi:10.1093/bioinformatics/btm135
Reconstructing the ancestral eukaryote: lessons from the past
O'Connell, M. J., & McInerney, J. O. (2007). Reconstructing the ancestral eukaryote: lessons from the past. In Ancestral Sequence Reconstruction (pp. 103-114). Oxford University PressOxford. doi:10.1093/acprof:oso/9780199299188.003.0010
Of clades and clans: terms for phylogenetic relationships in unrooted trees.
Wilkinson, M., McInerney, J. O., Hirt, R. P., Foster, P. G., & Embley, T. M. (2007). Of clades and clans: terms for phylogenetic relationships in unrooted trees.. Trends in ecology & evolution, 22(3), 114-115. doi:10.1016/j.tree.2007.01.002
2006
Building Large Phylogenetic Trees on Coarse-Grained Parallel Machines
Keane, T. M., Page, A. J., Naughton, T. J., Travers, S. A. A., & McInerney, J. O. (2006). Building Large Phylogenetic Trees on Coarse-Grained Parallel Machines. Algorithmica, 45(3), 285-300. doi:10.1007/s00453-006-1215-0
The molecular phylogeny of a nematode-specific clade of heterotrimeric G-protein alpha-subunit genes.
O'Halloran, D. M., Fitzpatrick, D. A., McCormack, G. P., McInerney, J. O., & Burnell, A. M. (2006). The molecular phylogeny of a nematode-specific clade of heterotrimeric G-protein alpha-subunit genes.. Journal of molecular evolution, 63(1), 87-94. doi:10.1007/s00239-005-0215-z
Molecular evidence for dim-light vision in the last common ancestor of the vertebrates.
Pisani, D., Mohun, S. M., Harris, S. R., McInerney, J. O., & Wilkinson, M. (2006). Molecular evidence for dim-light vision in the last common ancestor of the vertebrates.. Current biology : CB, 16(9), R318-R319. doi:10.1016/j.cub.2006.03.090
The causes of protein evolutionary rate variation.
McInerney, J. O. (2006). The causes of protein evolutionary rate variation.. Trends in ecology & evolution, 21(5), 230-232. doi:10.1016/j.tree.2006.03.008
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 justified.
Keane, T. M., Creevey, C. J., Pentony, M. M., Naughton, T. J., & Mclnerney, J. O. (2006). 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 justified.. BMC evolutionary biology, 6, 29. doi:10.1186/1471-2148-6-29
Evolutionary history of prokaryotes: Tree or no tree?
McInerney, J. O., Pisani, D. E., O’Connell, M. J., Fitzpatrick, D. A., & Creevey, C. J. (2006). Evolutionary history of prokaryotes: Tree or no tree?. In Reconstructing the Tree of Life: Taxonomy and Systematics of Species Rich Taxa (pp. 49-59). doi:10.1201/9781420009538
Gene evolution and drug discovery.
McInerney, J. O., Finnerty, C. S., Commins, J. M., & Philip, G. K. (2006). Gene evolution and drug discovery.. Methods in molecular biology (Clifton, N.J.), 316, 87-109. doi:10.1385/1-59259-964-8:87
Genome phylogenies indicate a meaningful alpha-proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales.
Fitzpatrick, D. A., Creevey, C. J., & McInerney, J. O. (2006). Genome phylogenies indicate a meaningful alpha-proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales.. Molecular biology and evolution, 23(1), 74-85. doi:10.1093/molbev/msj009
On the desirability of models for inferring genome phylogenies.
McInerney, J. O. (2006). On the desirability of models for inferring genome phylogenies.. Trends in microbiology, 14(1), 1-2. doi:10.1016/j.tim.2005.10.006
2005
Adaptive evolution of the human fatty acid synthase gene: support for the cancer selection and fat utilization hypotheses?
O'Connell, M. J., & McInerney, J. O. (2005). Adaptive evolution of the human fatty acid synthase gene: support for the cancer selection and fat utilization hypotheses?. Gene, 360(2), 151-159. doi:10.1016/j.gene.2005.06.020
Gamma chain receptor interleukins: evidence for positive selection driving the evolution of cell-to-cell communicators in the mammalian immune system.
O'Connell, M. J., & McInerney, J. O. (2005). Gamma chain receptor interleukins: evidence for positive selection driving the evolution of cell-to-cell communicators in the mammalian immune system.. Journal of molecular evolution, 61(5), 608-619. doi:10.1007/s00239-004-0313-3
Evidence of positive Darwinian selection in putative meningococcal vaccine antigens.
Fitzpatrick, D. A., Creevey, C. J., & McInerney, J. O. (2005). Evidence of positive Darwinian selection in putative meningococcal vaccine antigens.. Journal of molecular evolution, 61(1), 90-98. doi:10.1007/s00239-004-0290-6
The shape of supertrees to come: tree shape related properties of fourteen supertree methods.
Wilkinson, M., Cotton, J. A., Creevey, C., Eulenstein, O., Harris, S. R., Lapointe, F. -J., . . . Thorley, J. L. (2005). The shape of supertrees to come: tree shape related properties of fourteen supertree methods.. Systematic biology, 54(3), 419-431. doi:10.1080/10635150590949832
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 Ecdysozoa.
Philip, G. K., Creevey, C. J., & McInerney, J. O. (2005). 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 Ecdysozoa.. Molecular biology and evolution, 22(5), 1175-1184. doi:10.1093/molbev/msi102
DPRml: distributed phylogeny reconstruction by maximum likelihood.
Keane, T. M., Naughton, T. J., Travers, S. A. A., McInerney, J. O., & McCormack, G. P. (2005). DPRml: distributed phylogeny reconstruction by maximum likelihood.. Bioinformatics (Oxford, England), 21(7), 969-974. doi:10.1093/bioinformatics/bti100
Clann: investigating phylogenetic information through supertree analyses.
Creevey, C. J., & McInerney, J. O. (2005). Clann: investigating phylogenetic information through supertree analyses.. Bioinformatics (Oxford, England), 21(3), 390-392. doi:10.1093/bioinformatics/bti020
Evidence for heterogeneous selective pressures in the evolution of the env gene in different human immunodeficiency virus type 1 subtypes.
Travers, S. A. A., O'Connell, M. J., McCormack, G. P., & McInerney, J. O. (2005). Evidence for heterogeneous selective pressures in the evolution of the env gene in different human immunodeficiency virus type 1 subtypes.. Journal of virology, 79(3), 1836-1841. doi:10.1128/jvi.79.3.1836-1841.2005
Evidence of positive Darwinian selection in Omp85, a highly conserved bacterial outer membrane protein essential for cell viability.
Fitzpatrick, D. A., & McInerney, J. O. (2005). Evidence of positive Darwinian selection in Omp85, a highly conserved bacterial outer membrane protein essential for cell viability.. Journal of molecular evolution, 60(2), 268-273. doi:10.1007/s00239-004-0194-5
New methods ring changes for the tree of life.
McInerney, J. O., & Wilkinson, M. (2005). New methods ring changes for the tree of life.. In Trends in ecology & evolution (Vol. 20, Iss. 3, pp. 105-107). [Print]. doi:10.1016/j.tree.2005.01.007
2004
Does a tree-like phylogeny only exist at the tips in the prokaryotes?
Creevey, C. J., Fitzpatrick, D. A., Philip, G. K., Kinsella, R. J., O'Connell, M. J., Pentony, M. M., . . . McInerney, J. O. (2004). Does a tree-like phylogeny only exist at the tips in the prokaryotes?. Proceedings. Biological sciences, 271(1557), 2551-2558. doi:10.1098/rspb.2004.2864
Timing and reconstruction of the most recent common ancestor of the subtype C clade of human immunodeficiency virus type 1.
Travers, S. A. A., Clewley, J. P., Glynn, J. R., Fine, P. E. M., Crampin, A. C., Sibande, F., . . . McCormack, G. P. (2004). Timing and reconstruction of the most recent common ancestor of the subtype C clade of human immunodeficiency virus type 1.. Journal of virology, 78(19), 10501-10506. doi:10.1128/jvi.78.19.10501-10506.2004
Analysis of gene expression in the bovine corpus luteum through generation and characterisation of 960 ESTs.
Casey, O. M., Fitzpatrick, R., McInerney, J. O., Morris, D. G., Powell, R., & Sreenan, J. M. (2004). Analysis of gene expression in the bovine corpus luteum through generation and characterisation of 960 ESTs.. Biochimica et biophysica acta, 1679(1), 10-17. doi:10.1016/j.bbaexp.2004.03.011
Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models.
Mahony, S., McInerney, J. O., Smith, T. J., & Golden, A. (2004). Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models.. BMC bioinformatics, 5, 23. doi:10.1186/1471-2105-5-23
Some Desiderata for Liberal Supertrees
Wilkinson, M., Thorley, J. L., Pisani, D., Lapointe, F. -J., & McInerney, J. O. (2004). Some Desiderata for Liberal Supertrees. In Computational Biology (pp. 227-246). Springer Netherlands. doi:10.1007/978-1-4020-2330-9_11
2003
Fatty acid biosynthesis in Mycobacterium tuberculosis: lateral gene transfer, adaptive evolution, and gene duplication.
Kinsella, R. J., Fitzpatrick, D. A., Creevey, C. J., & McInerney, J. O. (2003). Fatty acid biosynthesis in Mycobacterium tuberculosis: lateral gene transfer, adaptive evolution, and gene duplication.. Proceedings of the National Academy of Sciences of the United States of America, 100(18), 10320-10325. doi:10.1073/pnas.1737230100
CRANN: detecting adaptive evolution in protein-coding DNA sequences.
Creevey, C. J., & McInerney, J. O. (2003). CRANN: detecting adaptive evolution in protein-coding DNA sequences.. Bioinformatics (Oxford, England), 19(13), 1726. doi:10.1093/bioinformatics/btg225
Characterization of endospore-forming bacteria associated with entomopathogenic nematodes, Heterorhabditis spp., and description of Paenibacillus nematophilus sp. nov.
Enright, M. R., McInerney, J. O., & Griffin, C. T. (2003). Characterization of endospore-forming bacteria associated with entomopathogenic nematodes, Heterorhabditis spp., and description of Paenibacillus nematophilus sp. nov.. International journal of systematic and evolutionary microbiology, 53(Pt 2), 435-441. doi:10.1099/ijs.0.02344-0
Detecting adaptive molecular evolution: additional tools for the parasitologist.
McInerney, J. O., Littlewood, D. T. J., & Creevey, C. J. (2003). Detecting adaptive molecular evolution: additional tools for the parasitologist.. Advances in parasitology, 54, 359-379. doi:10.1016/s0065-308x(03)54009-x
Distributed Java Platform with Programmable MIMD Capabilities
Keane, T., Allen, R., Naughton, T. J., McInerney, J., & Waldron, J. (2003). Distributed Java Platform with Programmable MIMD Capabilities. Unknown Journal, 122-131. doi:10.1007/3-540-36520-6_11
Eukaryotic genes in Mycobacterium tuberculosis? Possible alternative explanations.
Kinsella, R. J., & McInerney, J. O. (2003). Eukaryotic genes in Mycobacterium tuberculosis? Possible alternative explanations.. Trends in genetics : TIG, 19(12), 687-689. doi:10.1016/j.tig.2003.10.001
2002
An algorithm for detecting directional and non-directional positive selection, neutrality and negative selection in protein coding DNA sequences.
Creevey, C. J., & McInerney, J. O. (2002). An algorithm for detecting directional and non-directional positive selection, neutrality and negative selection in protein coding DNA sequences.. In Gene Vol. 300 (pp. 43-51). doi:10.1016/s0378-1119(02)01039-9
Bioinformatics in a post-genomics world--the need for an inclusive approach.
McInerney, J. O. (2002). Bioinformatics in a post-genomics world--the need for an inclusive approach.. The pharmacogenomics journal, 2(4), 207-208. doi:10.1038/sj.tpj.6500111
Bacteria and Archaea: Molecular techniques reveal astonishing diversity
McInerney, J. O., Mullarkey, M., Wernecke, M. E., & Powell, R. (2002). Bacteria and Archaea: Molecular techniques reveal astonishing diversity. Biodiversity, 3(2), 3-10. doi:10.1080/14888386.2002.9712571
2000
Molecular cloning of an Atlantic salmon nucleoside diphosphate kinase cDNA and its pattern of expression during embryogenesis.
Murphy, M., Harte, T., McInerney, J., & Smith, T. J. (2000). Molecular cloning of an Atlantic salmon nucleoside diphosphate kinase cDNA and its pattern of expression during embryogenesis.. Gene, 257(1), 139-148. doi:10.1016/s0378-1119(00)00374-7
Re: Spectral analysis of echinoderm small subunit ribosomal RNA gene sequence data.
McCormack, G. P., Keegan, B. F., McInerney, J. O., & Powell, R. (2000). Re: Spectral analysis of echinoderm small subunit ribosomal RNA gene sequence data.. Molecular phylogenetics and evolution, 15(2), 327-329. doi:10.1006/mpev.1999.0747
1999
Indications of relationships between poriferan classes using full-length 18S rRNA gene sequences
Adams, C. L., McInerney, J. O., & Kelly, M. (1999). Indications of relationships between poriferan classes using full-length 18S rRNA gene sequences. Memoirs of the Queensland Museum, 44(1-2), 33-43.
Phylogenetic resolution potential of 18S and 28S rRNA genes within the lithistid astrophorida
McInerney, J. O., Adams, C. L., Kelly, M., & Borges, K. D. (1999). Phylogenetic resolution potential of 18S and 28S rRNA genes within the lithistid astrophorida. Memoirs of the Queensland Museum, 44(1-2), 343-351.
1998
Replicational and transcriptional selection on codon usage in Borrelia burgdorferi.
McInerney, J. O. (1998). Replicational and transcriptional selection on codon usage in Borrelia burgdorferi.. Proceedings of the National Academy of Sciences of the United States of America, 95(18), 10698-10703. doi:10.1073/pnas.95.18.10698
Book Reviews
Plomin, R., Manning, J., Holloway, J., Douglas, A., & Mcinerney, J. O. (1998). Book Reviews. Heredity, 81(1), 120-124. doi:10.1046/j.1365-2540.1998.00420.x
GCUA: general codon usage analysis.
McInerney, J. O. (1998). GCUA: general codon usage analysis.. Bioinformatics (Oxford, England), 14(4), 372-373. doi:10.1093/bioinformatics/14.4.372
1997
Phylogenetic analysis of Group I marine archaeal rRNA sequences emphasizes the hidden diversity within the primary group Archaea
McInerney, J. O., Mullarkey, M., Wernecke, M. E., & Powel, R. (1997). Phylogenetic analysis of Group I marine archaeal rRNA sequences emphasizes the hidden diversity within the primary group Archaea. Proceedings of the Royal Society of London. Series B: Biological Sciences, 264(1388), 1663-1669. doi:10.1098/rspb.1997.0231
Codon usage patterns in Trichomonas vaginalis
McInerney, J. O. (1997). Codon usage patterns in Trichomonas vaginalis. European Journal of Protistology, 33(3), 266-273. doi:10.1016/s0932-4739(97)80004-1
Prokaryotic Genome Evolution as Assessed by Multivariate Analysis of Codon Usage Patterns
McINERNEY, J. O. (1997). Prokaryotic Genome Evolution as Assessed by Multivariate Analysis of Codon Usage Patterns. Microbial & Comparative Genomics, 2(1), 89-97. doi:10.1089/omi.1.1997.2.89
1996
Codon usage patterns in the Atlantic salmon Salmo salar L
McInerney, J. O. (1996). Codon usage patterns in the Atlantic salmon Salmo salar L. Molecular Marine Biology and Biotechnology, 5(4), 344-351.
1995
Sequence of the gene encoding the 16S rRNA of the beer spoilage organism Megasphaera cerevisiae.
Doyle, L. M., McInerney, J. O., Mooney, J., Powell, R., Haikara, A., & Moran, A. P. (1995). Sequence of the gene encoding the 16S rRNA of the beer spoilage organism Megasphaera cerevisiae.. Journal of industrial microbiology, 15(2), 67-70. doi:10.1007/bf01569801
Sequence analysis and evolutionary aspects of piscine alpha-1-microglobulin/bikunin mRNA transcripts.
Hanley, S., McInerney, J. O., & Powell, R. (1995). Sequence analysis and evolutionary aspects of piscine alpha-1-microglobulin/bikunin mRNA transcripts.. Molecular marine biology and biotechnology, 4(2), 105-109.
Detection of micro-organisms in the environment.
Powell, R., Mullarkey, M., O'Brien, D., & McInerney, J. O. (1995). Detection of micro-organisms in the environment.. In Biochemical Society transactions Vol. 23 (pp. 435-437). doi:10.1042/bst0230435
Extraction of Prokaryotic Genomic DNA from Marine Microbial Communities Suitable for Amplification Using the Polymerase Chain Reaction
McInerney, J. O., Paskins, L., Eardly, D., Patching, J. W., & Powell, R. (1995). Extraction of Prokaryotic Genomic DNA from Marine Microbial Communities Suitable for Amplification Using the Polymerase Chain Reaction. Internationale Revue der gesamten Hydrobiologie und Hydrographie, 80(2), 351-360. doi:10.1002/iroh.19950800222
Recovery and phylogenetic analysis of novel archaeal rRNA sequences from a deep-sea deposit feeder.
McInerney, J. O., Wilkinson, M., Patching, J. W., Embley, T. M., & Powell, R. (1995). Recovery and phylogenetic analysis of novel archaeal rRNA sequences from a deep-sea deposit feeder.. Applied and environmental microbiology, 61(4), 1646-1648. doi:10.1128/aem.61.4.1646-1648.1995