Research outputs
Selected research outputs
- 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)
2026
Synteny-aware microbial pangenome graphs reveal blueprints of genomic variation
Constructive neutral evolution explains the emergence of specialised ribosomes in diverse eukaryotes
Prokaryotic Pangenomes Are Bet-Hedging Devices
Species-specific transformer models of bacterial gene order and content for genomic surveillance tasks
Genomic perplexity and the evolution of context-dependent function
Mcinerney, J. O. (2026). Genomic perplexity and the evolution of context-dependent function. MOLECULAR BIOLOGY AND EVOLUTION, 43(3), 15 pages. doi:10.1093/molbev/msag041
PanForest: predicting genes in genomes using random forests
Beavan, A. J. S., Domingo-Sananes, M. R., & McInerney, J. O. (2026). PanForest: predicting genes in genomes using random forests. BIOINFORMATICS, 42(1), 9 pages. doi:10.1093/bioinformatics/btag005
2025
Dissecting Phylogenetic Support: Unified Decay Indices, AU Tests, and Branch-Site Specific Visualizations
Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes
McInerney, J. O. (2025). Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes. MOLECULAR BIOLOGY AND EVOLUTION, 42(11), 7 pages. doi:10.1093/molbev/msaf279
Dynamic genomic constraints reveal fitness trade-offs underlying bacterial resistance evolution
Mammal placental phenotypes are predictable from microRNA repertoires
2024
Reconstructing the last common ancestor of all eukaryotes.
Richards, T. A., Eme, L., Archibald, J. M., Leonard, G., Coelho, S. M., de Mendoza, A., . . . Wideman, J. G. (2024). Reconstructing the last common ancestor of all eukaryotes.. PLoS biology, 22(11), e3002917. doi:10.1371/journal.pbio.3002917
Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome
Beavan, A., 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). doi:10.1073/pnas.2304934120
2023
Feasibility of large-scale systematic data collection in a quality improvement registry of deep brain stimulation in Parkinson’s disease
Jimenez-Shahed, J., York, M., Kirk, J., Berg, A., Schwalb, J., Siddiqui, M., & McInerney, J. (2023). Feasibility of large-scale systematic data collection in a quality improvement registry of deep brain stimulation in Parkinson’s disease. Parkinsonism & Related Disorders, 113. doi:10.1016/j.parkreldis.2023.105575
Bursts of novel composite gene families at major nodes in animal evolution
Fungal phylogeny reconstructed using heterogeneous models reveals new placement of Microsporidia
Data-driven phenotypic clustering of Parkinson’s disease patients seeking deep brain stimulation (P6-11.008)
Shahed, J. J., Berg, A., York, M., Schwalb, J., Kirk, J., Siddiqui, M., & McInerney, J. (2023). Data-driven phenotypic clustering of Parkinson’s disease patients seeking deep brain stimulation (P6-11.008). Neurology, 100(17_supplement_2). doi:10.1212/wnl.0000000000203914
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), 6 pages. doi:10.1093/molbev/msac232
Cerebrotendinous xanthomatosis tremor successfully controlled post-ventral intermediate nucleus-deep brain stimulation: a case report.
Rich, A. M., Karakoleva, E. V., McInerney, J., Farace, E., & De Jesus, S. (2023). Cerebrotendinous xanthomatosis tremor successfully controlled post-ventral intermediate nucleus-deep brain stimulation: a case report.. Frontiers in neurology, 14, 1243379. doi:10.3389/fneur.2023.1243379
2022
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
Subcortical Iron Accumulation Pattern May Predict Neuropsychological Outcomes After Subthalamic Nucleus Deep Brain Stimulation: A Pilot Study.
Brown, G., Du, G., Farace, E., Lewis, M. M., Eslinger, P. J., McInerney, J., . . . De Jesus, S. (2022). Subcortical Iron Accumulation Pattern May Predict Neuropsychological Outcomes After Subthalamic Nucleus Deep Brain Stimulation: A Pilot Study.. Journal of Parkinson's disease, 12(3), 851-863. doi:10.3233/jpd-212833
Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types
Cummins, E. A., Hall, R. J., Connor, C., McInerney, J. O., & McNally, A. (2022). Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types. Microbial Genomics, 8(11). doi:10.1099/mgen.0.000903
2021
North American survey on impact of the COVID-19 pandemic shutdown on DBS care.
Siddiqui, M. S., Jimenez-Shahed, J., Mari, Z., Walter, B. L., De Jesus, S., Panov, F., . . . Rosenow, J. M. (2021). North American survey on impact of the COVID-19 pandemic shutdown on DBS care.. Parkinsonism & related disorders, 92, 41-45. doi:10.1016/j.parkreldis.2021.10.011
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
Association of Handedness with Cognitive Outcomes in Essential Tremor Patients with Bilateral Deep Brain Stimulation: A Single-Center Retrospective Longitudinal Analysis (1510)
Malone, J., Geyer, N., Farace, E., McInerney, J., & De Jesus, S. (2021). Association of Handedness with Cognitive Outcomes in Essential Tremor Patients with Bilateral Deep Brain Stimulation: A Single-Center Retrospective Longitudinal Analysis (1510). Neurology, 96(15_supplement). doi:10.1212/wnl.96.15_supplement.1510
Patient reported baseline measures in RAD-PD reveal marked heterogeneity in a DBS cohort (2601)
Shahed, J. J., Berg, A., York, M., Siddiqui, M., Schwalb, J., & McInerney, J. (2021). Patient reported baseline measures in RAD-PD reveal marked heterogeneity in a DBS cohort (2601). Neurology, 96(15_supplement). doi:10.1212/wnl.96.15_supplement.2601
Practice Landscape of Lesional Procedures for Movement Disorders in North America (2341)
Siddiqui, M., McInerney, J., Schwalb, J., & Shahed, J. J. (2021). Practice Landscape of Lesional Procedures for Movement Disorders in North America (2341). Neurology, 96(15_supplement). doi:10.1212/wnl.96.15_supplement.2341
Gene-gene relationships in an <i>Escherichia coli</i> accessory genome are linked to function and mobility
Gene-gene relationships in an escherichia coli accessory genome are linked to function and mobility
Hall, R. J., Whelan, F. J., Cummins, E. A., Connor, C., McNally, A., & McInerney, J. O. (2021). Gene-gene relationships in an escherichia coli accessory genome are linked to function and mobility. Microbial Genomics, 7(9). doi:10.1099/MGEN.0.000650
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. doi:10.3389/fmicb.2020.01569
Evaluation of First-line Radiosurgery vs Whole-Brain Radiotherapy for Small Cell Lung Cancer Brain Metastases: The FIRE-SCLC Cohort Study.
Rusthoven, C. G., Yamamoto, M., Bernhardt, D., Smith, D. E., Gao, D., Serizawa, T., . . . Robin, T. P. (2020). Evaluation of First-line Radiosurgery vs Whole-Brain Radiotherapy for Small Cell Lung Cancer Brain Metastases: The FIRE-SCLC Cohort Study.. JAMA oncology, 6(7), 1028-1037. doi:10.1001/jamaoncol.2020.1271
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 Pangenome Diversity Dynamics and Evolution of Genomes (pp. 151-167). doi:10.1007/978-3-030-38281-0_7
Repeat Gamma-Knife Radiosurgery for Recurrent Glossopharyngeal Neuralgia: Case Report and Literature Review
Kaye, J., Daggubati, L., & McInerney, J. (2020). Repeat Gamma-Knife Radiosurgery for Recurrent Glossopharyngeal Neuralgia: Case Report and Literature Review. In Journal of Neurological Surgery Part B Skull Base Vol. 81 (pp. s1-s272). Thieme. doi:10.1055/s-0040-1702712
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
Repeat Gamma Knife Radiosurgery for Recurrent Glossopharyngeal Neuralgia: A Systematic Review and Our Initial Experience.
Kaye, J., Daggubati, L. C., Zeller, S., & McInerney, J. (2020). Repeat Gamma Knife Radiosurgery for Recurrent Glossopharyngeal Neuralgia: A Systematic Review and Our Initial Experience.. Stereotactic and functional neurosurgery, 98(5), 324-330. doi:10.1159/000508541
2019
Coinfinder: Detecting Significant Associations and Dissociations in Pangenomes
Selection-based model of prokaryote pangenomes
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). doi:10.3390/genes10090648
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., . . . Pisani, D. (2019). Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human. Genome Biology and Evolution, 11(9), 2676-2690. doi:10.1093/gbe/evz163
Using a quality improvement framework to examine deep brain stimulation in Parkinson’s disease: the RAD-PD initiative (P1.8-023)
Shahed, J. J., d’Haese, P. -F., Kirk, J., York, M., Berg, A., Shih, L., . . . McInerney, J. (2019). Using a quality improvement framework to examine deep brain stimulation in Parkinson’s disease: the RAD-PD initiative (P1.8-023). Neurology, 92(15_supplement). doi:10.1212/wnl.92.15_supplement.p1.8-023
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
Long-term Outcome of Globus Pallidus Internus Stimulation for Pisa Syndrome.
Anderson, B. L., Ziechmann, R., Huang, X., & McInerney, J. (2019). Long-term Outcome of Globus Pallidus Internus Stimulation for Pisa Syndrome.. Cureus, 11(1), e3838. doi:10.7759/cureus.3838
2018
Deep Brain Stimulation for Parkinson Disease Does not Worsen or Improve Postural Instability: A Prospective Cohort Trial.
Brandmeir, N. J., Brandmeir, C. L., Carr, D., Kuzma, K., & McInerney, J. (2018). Deep Brain Stimulation for Parkinson Disease Does not Worsen or Improve Postural Instability: A Prospective Cohort Trial.. Neurosurgery, 83(6), 1173-1182. doi:10.1093/neuros/nyx602
Systemic effects of deep brain stimulation on synergic control in Parkinson's disease.
Falaki, A., Jo, H. J., Lewis, M. M., O'Connell, B., De Jesus, S., McInerney, J., . . . Latash, M. L. (2018). Systemic effects of deep brain stimulation on synergic control in Parkinson's disease.. Clinical neurophysiology : official journal of the International Federation of Clinical Neurophysiology, 129(6), 1320-1332. doi:10.1016/j.clinph.2018.02.126
RAD-PD: Registry for the Advancement of DBS in Parkinson’s Disease (P4.064)
Jimenez-Shahed, J., Bressman, S., Burack, M., Farace, E., McInerney, J., Kirk, J., . . . York, M. (2018). RAD-PD: Registry for the Advancement of DBS in Parkinson’s Disease (P4.064). Neurology, 90(15_supplement). doi:10.1212/wnl.90.15_supplement.p4.064
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). 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. 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 OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 375(2109), 10 pages. 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, 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. doi:10.1038/nmicrobiol.2017.40
Response to Comment on: A Prospective Evaluation of an Outpatient Assessment of Postural Instability to Predict Risk of Falls in Patients with Parkinson's Disease Presenting for Deep Brain Stimulation.
Brandmeir, N. J., Brandmeir, C. L., Kuzma, K., & McInerney, J. (2017). Response to Comment on: A Prospective Evaluation of an Outpatient Assessment of Postural Instability to Predict Risk of Falls in Patients with Parkinson's Disease Presenting for Deep Brain Stimulation.. Movement disorders clinical practice, 4(2), 283-284. doi:10.1002/mdc3.12413
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
The use of custom 3D printed stereotactic frames for laser interstitial thermal ablation: technical note.
Brandmeir, N. J., McInerney, J., & Zacharia, B. E. (2016). The use of custom 3D printed stereotactic frames for laser interstitial thermal ablation: technical note.. Neurosurgical focus, 41(4), E3. doi:10.3171/2016.8.focus16219
An Analysis of Scalp Thickness and Other Novel Risk Factors for Deep Brain Stimulator Infections.
Brandmeir, N., Nehrbass, E., & McInerney, J. (2016). An Analysis of Scalp Thickness and Other Novel Risk Factors for Deep Brain Stimulator Infections.. Cureus, 8(9), e792. doi:10.7759/cureus.792
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). 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). 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
A Prospective Evaluation of an Outpatient Assessment of Postural Instability to Predict Risk of Falls in Patients with Parkinson's Disease Presenting for Deep Brain Stimulation.
Brandmeir, N. J., Brandmeir, C. L., Kuzma, K., & McInerney, J. (2016). A Prospective Evaluation of an Outpatient Assessment of Postural Instability to Predict Risk of Falls in Patients with Parkinson's Disease Presenting for Deep Brain Stimulation.. Movement disorders clinical practice, 3(2), 151-155. doi:10.1002/mdc3.12257
Society for molecular biology and evolution, council and business meetings, 2015, vienna Austria
Mcinerney, J. O. (2016). Society for molecular biology and evolution, council and business meetings, 2015, vienna Austria. Molecular Biology and Evolution, 33(1), 299-300. doi:10.1093/molbev/msv275
2015
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 B Biological Sciences, 370(1678). doi:10.1098/rstb.2014.0323
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 B Biological Sciences, 370(1678). doi:10.1098/rstb.2014.0337
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
Volumetric brain analysis in neurosurgery: Part 3. Volumetric CT analysis as a predictor of seizure outcome following temporal lobectomy.
Mandell, J. G., Hill, K. L., Nguyen, D. T. D., Moser, K. W., Harbaugh, R. E., McInerney, J., . . . Schiff, S. J. (2015). Volumetric brain analysis in neurosurgery: Part 3. Volumetric CT analysis as a predictor of seizure outcome following temporal lobectomy.. Journal of neurosurgery. Pediatrics, 15(2), 133-143. doi:10.3171/2014.9.peds12428
Evolution by pervasive gene fusion in antibiotic resistance and antibiotic synthesizing genes
Coleman, O., Hogan, R., McGoldrick, N., Rudden, N., & McInerney, J. O. (2015). 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). doi:10.1038/514570a
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
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), 2207-2209. doi:10.1093/gbe/evu173
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
Nonoperative management of odontoid fractures: a review of 59 cases.
Rizk, E., Kelleher, J. P., Zalatimo, O., Reiter, T., Harbaugh, R., McInerney, J., & Sheehan, J. (2013). Nonoperative management of odontoid fractures: a review of 59 cases.. Clinical neurology and neurosurgery, 115(9), 1653-1656. doi:10.1016/j.clineuro.2013.02.017
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 (Vol. 29, Iss. 8, pp. 439-441). 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(1). doi:10.1186/1471-2148-13-146
Erratum: Metazoan opsin evolution reveals a simple route to animal vision (Proceedings of the National Academy of Sciences of the United States of America (2012) 109 (18868-18872) DOI: 10.1073/pnas.1204609109)
Feuda, R., Hamilton, S. C., McInerney, J. O., & Pisani, D. (2013). Erratum: Metazoan opsin evolution reveals a simple route to animal vision (Proceedings of the National Academy of Sciences of the United States of America (2012) 109 (18868-18872) DOI: 10.1073/pnas.1204609109). Proceedings of the National Academy of Sciences of the United States of America, 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
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
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 and Evolution (Vol. 28, Iss. 11, pp. 624-625). doi:10.1016/j.tree.2013.09.002
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., & Buriane, 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
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(1), 782-790. doi:10.1093/gbe/evr073
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, 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. doi:10.1186/1745-6150-6-41
2010
Changes in Prognostic Factors for Glioblastoma Between 1998 and 2006 in the SEER Database
Flickinger, J. C., Lunsford, L. D., Kondziolka, D., Lieberman, F. S., Wagner, H., McInerney, J., . . . Varlotto, J. M. (2010). Changes in Prognostic Factors for Glioblastoma Between 1998 and 2006 in the SEER Database. International Journal of Radiation Oncology • Biology • Physics, 78(3), s265. doi:10.1016/j.ijrobp.2010.07.631
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, 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 B Biological Sciences, 364(1527), 2209-2219. doi:10.1098/rstb.2009.0042
The network of life: Genome beginnings and evolution
Ragan, M. A., Mclnerney, J. O., & Lake, J. A. (2009). The network of life: Genome beginnings and evolution. Philosophical Transactions of the Royal Society 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., Medeiros, H. F. D., Junqueira, A. C. M., Azeredo-Espin, A. M. D., & 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(1). 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(1). doi:10.1186/1471-2148-8-312
Reconstructing the ancestral eukaryote: lessons from the past
O'Connell, M. J., & McInerney, J. O. (2008). Reconstructing the ancestral eukaryote: lessons from the past. In Ancestral Sequence Reconstruction. doi:10.1093/acprof:oso/9780199299188.003.0010
Cognitive Improvement after Deep Brain Stimulator Placement for Treatment of Movement Disorders
McInerney, J., Ranasinghe, M., Jennings, T., & Farace, E. (2008). Cognitive Improvement after Deep Brain Stimulator Placement for Treatment of Movement Disorders. Neurosurgery, 62(6), 1422. doi:10.1227/01.neu.0000333521.08915.8f
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 and 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, 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(SUPPL.2), 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, 23(12), 1556-1558. doi:10.1093/bioinformatics/btm135
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 and 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 New York, 45(3), 285-300. doi:10.1007/s00453-006-1215-0
The molecular phylogeny of a nematode-specific clade of heterotrimeric G-protein α-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 α-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, 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 and 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., & McInerney, 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. 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 α-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 α-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 [1]
McInerney, J. O. (2006). On the desirability of models for inferring genome phylogenies [1]. Trends in Microbiology, 14(1), 1-2. doi:10.1016/j.tim.2005.10.006
2005
A high-throughput bioinformatics distributed computing platform
Keane, T. M., Page, A. J., McInerney, J. O., & Naughton, T. J. (2005). A high-throughput bioinformatics distributed computing platform. In Proceedings IEEE Symposium on Computer Based Medical Systems (pp. 377-382).
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, 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, 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 and Evolution (Vol. 20, Iss. 3, pp. 105-107). doi:10.1016/j.tree.2005.01.007
2004
Does a tree-like phytogeny 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 phytogeny only exist at the tips in the prokaryotes?. Proceedings of the Royal Society B 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 Gene Structure and Expression, 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. 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 Phylogenetic Supertrees (Vol. 4, pp. 227-246). Springer Nature. 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, 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. E., 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(2), 435-441. doi:10.1099/ijs.0.02344-0
A new approach to gene prediction using the self-organizing map
Mahony, S., Smith, T. J., McInerney, J. O., & Golden, A. (2003). A new approach to gene prediction using the self-organizing map. In Proceedings of the 2003 IEEE Bioinformatics Conference Csb 2003 (pp. 444-445). doi:10.1109/CSB.2003.1227365
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. Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics, 2604, 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, 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. Pharmacogenomics Journal, 2(4), 207-208. doi:10.1038/sj.tpj.6500111
Stereotactic radiosurgery providing long-term tumor control of cavernous sinus meningiomas.
Lee, J. Y. K., Niranjan, A., McInerney, J., Kondziolka, D., Flickinger, J. C., & Lunsford, L. D. (2002). Stereotactic radiosurgery providing long-term tumor control of cavernous sinus meningiomas.. Journal of neurosurgery, 97(1), 65-72. doi:10.3171/jns.2002.97.1.0065
Long-term results after stereotactic radiosurgery for patients with cavernous malformations.
Hasegawa, T., McInerney, J., Kondziolka, D., Lee, J. Y. K., Flickinger, J. C., & Lunsford, L. D. (2002). Long-term results after stereotactic radiosurgery for patients with cavernous malformations.. Neurosurgery, 50(6), 1190-1197. doi:10.1097/00006123-200206000-00003
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
2001
740 Cost Effectiveness of Routine Intraoperative Angiography during Aneurysm Surgery
Tang, G., McInerney, J., Cawley, M., Harbaugh, R. E., Dion, J. E., & Barrow, D. L. (2001). 740 Cost Effectiveness of Routine Intraoperative Angiography during Aneurysm Surgery. Neurosurgery, 49(2), 518. doi:10.1097/00006123-200108000-00104
740 Cost Effectiveness of Routine Intraoperative Angiography during Aneurysm Surgery
Tang, G., McInerney, J., Cawley, M., Harbaugh, R. E., Dion, J. E., & Barrow, D. L. (2001). 740 Cost Effectiveness of Routine Intraoperative Angiography during Aneurysm Surgery. Neurosurgery, 49(2), 518. doi:10.1227/00006123-200108000-00104
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, 14(4), 372-373. doi:10.1093/bioinformatics/14.4.372
1997
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
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., & Powell, 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 B Biological Sciences, 264(1388), 1663-1669. doi:10.1098/rspb.1997.0231
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 and 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