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Faculties & Departments
Department of Biology
Dr. James McInerney
Molecular Evolution and Bioinformatics Unit
- Dr. James McInerney;
- Tel: (353-1) 708 3860; Fax: (353-1) 708 3845
- e-mail: james.o.mcinerney@nuim.ie
- Virtual Institute of Bioinformatics Website
- Bioinformatics Laboratory Website
- Molecular Systematics and Evolution of Microorganisms Website
Head of Laboratory:
Dr. James McInerney, B.Sc., Ph.D. (NUI)
Research Interests:
Dr. McInerney’s research group is focused on understanding the evolution of genomes, proteomes and metabolomes and on understanding the influence of horizontal gene transfer, gene duplication and gene loss. The group has developed high throughput analysis software programs and algorithms for distributing large phylogeny reconstruction jobs. Dr. McInerney has organised or participated in numerous EMBO-funded courses and he was a founding director of ICHEC – the Irish Centre for High-End Computing.
The personnel right now are:
Postgraduate
- Fergal Martin
- Angela McCann
- Peter Clarke
- Carla Cummins
- Leanne Haggerty
- Aoife Doherty
- Sinead Hamilton
Computing Development Officer
- Brian Daly
Research Activities - Total overall funding €39,110,966.
Programme Grants Participation – Total € 35,900,000
2007 Programme for Research in Third Level Institutes Cycle IV (with seven other third level institutes). €9,500,000.
2006 Irish Centre for High End Computing Phase II funding (with NUIG, TCD, UCD, DCU, UCC, Tyndall Institute, DIAS). Request for €3,600,000.
2004 Irish Centre for High-End Computing: ICHEC (with NUIG, TCD, UCD, DIAS). Science Foundation Ireland (€ 3,400,000 awarded for Phase I). This grant was responsible for bringing high-performance computing to Ireland and we created Ireland’s first National High-End Computing facility.
2002 Programme for Alimentary Health (with UCC and UCD). Higher Education Authority Programme for Research in Third Level Institutes (PRTLI) Cycle III (€4,000,000). This grant facilitated the sequencing of two bacterial genomes and provided the support to interpret the data. My role was in developing bioinformatics methods to analyse lateral gene transfer (LGT).
2001 Institute of Biopharmaceutical sciences (with TCD, RCSI and UCC). Higher Education Authority Programme for Research in Third Level Institutes (PRTLI) Cycle II (€ 19,000,000). This grant provided the funding to set up a large multi-institutional centre for the integration of basic and clinical research.
Project Grants Awarded (2000-2009) - Total €2,528,666
2009 Science Foundation Ireland, Research Frontiers Programme. Title: Identification of the Modules in the Phylogenetic Network of Life. €209,366.
2007 Programme for Third Level Institutes Cycle IV. Title: Development of computational Sciences at NUI Maynooth. €250,000.
2007 Science Foundation Ireland UREKA Summer School 2008-2011. €188,000.
2007 Higher Education Authority equipment grant (with Dr. Rowan Fealy, Dr. Davide Pisani, Dr. Adam Winstanley). €210,000.
2007 Science Foundation Ireland, Research Frontiers Programme. Title: The shape of things to come: understanding the evolution of the shape of metabolic networks in Escherichia coli. €165,000.
2006 Science Foundation Ireland Equipment Grant. Title: High-end architecture computing cluster for bioinformatics. €50,000.
2006 Irish Research Council for Science, Engineering and Technology (IRCSET). Title: Prokaryote phylogenomics: lateral transfer, gene duplication and the evolution of bacterial genomes. €96,300. (Grant awarded by IRCSET to Dr. James Cotton to work in my lab).
2005 Science Foundation Ireland, Research Frontiers Programme. Title: Comparison of the nucleotide substitution versus the gene acquisition paradigms in microbes. -€163,000.
2004 Marie Curie post-doctoral fellowship (to Dr. Davide Pisani). Title: Inferring the Universal Tree, or network, of Life: Genomics, Supertrees, and Supernetworks– €166,000
2004 IRCSET post-doctoral fellowship (to Dr. Davide Pisani, declined).
2003 Enterprise Ireland Basic Research Grants Scheme. Title: Novel Heterogeneous Maximum Likelihood Methods For Detecting Adaptive Evolution – € 75,000
2003 NUI Maynooth Young Investigator Award. Title: Development of a Database of Neisseria meningitidis Homologs - € 5,000.
2003 E.T.S. Walton, SFI Fellowship (to Prof A. Hughes). Title: New Approaches to Understanding Immune System Selection on Viral Proteins. – € 198,000.
2002 Marie Curie post-doctoral fellowship (to Dr. Joe Thorley – declined).
2002 Higher Education Authority, large piece of equipment grant. IBM Computing cluster. - €189,000.
2002 Higher Education Authority (HEA PRTLI III – Programme for Alimentary Health) €150,000.
2001 Enterprise Ireland (SC/01/474). Title: Sequence variation, lateral transfer and adaptive evolution in the meningococcal and gonococcal Neisseriae. – IR£ 77,000.
2000 Higher Education Authority (HEA PRTLI Cycle II – Institute for Biopharmaceutical Sciences) – IR£ 200,000.
2000 Health Research Board (HRB) (RP124/2000) Title: Detection of Adaptive evolution in Microbial and viral pathogenicity-associated genes. – IR£ 48,500.
Scholarship Grants: Total €480,000
2009 Walsh fellowship, Teagasc (co-supervised with Dr. Chris Creevey) - € 84,000
2009 Sinead Hamilton, IRCSET studentship - €72,000
2009 Aoife Doherty, IRCSET studentship - €72,000
2007 Slawomir Gruca, IRCSET Studentship (co-supervised with Dr. M. O’Connell)- €72,000.
2005 Fergal Martin, IRCSET Studentship - €60,000.
2003 Thomas Keane, IRCSET Studentship - €60,000.
2002 Gayle Philip, IRCSET Studentship - €60,000.
Undergraduate student grants: Total €20,500
2007 Leanne Haggerty, Science Foundation Ireland UREKA supplement Programme, €3,850.
2007 Carla Cummins, Science Foundation Ireland UREKA supplement Programme, €3,850.
2006 Carla Cummins, Science Foundation Ireland UREKA supplement Programme €3,850.
2005 Aisling Ní Ruairc, The Health Research Board €2,000
2004 Fergal Martin, The Society for General Microbiology STG £1,800
2004 Christina Toft, The Health Research Board €2,000.
2003 Fergal Martin, The Wellcome Trust €2,500
Course Grants: Total €181,800
2008 European Molecular Biology Organisation (EMBO) €22,800. “World Programme” Grant. Course on Gene and Genome Evolution, Medellin, Colombia.
2007 European Molecular Biology Organisation (EMBO) €25,000. “World Programme” Grant. Course on Phylogenetic and Phylogenomic Analysis, Jardim de Botanico, Rio de Janeiro, RJ, Brasil.
2006 European Molecular Biology Organisation (EMBO) € 25,000. “World Programme” Grant. Course on Comparative Genomics. FIOCRUZ, Avenida Brasil, Rio de Janeiro, RJ, Brasil.
2005 European Molecular Biology Organisation (EMBO) € 25,000. “World Programme” Grant. Course in high-throughput Phylogenetics, EMBRAPA, Rio de Janeiro, Brazil.
2004 European Molecular Biology Organisation (EMBO) € 16,000. “World Programme” Grant -. Course on High-Throughput Phylogenetics, Rio de Janeiro, Brazil.
2003 European Science Foundation (ESF), Bergen, Norway (with David Liberles, Norway). €14,000. Constructing a Tree of Life colloquium.
2003 European Molecular Biology Organisation (EMBO) - €25,000. Bioinformatics Summer School at NUI Maynooth.
2001 The Wellcome Trust Molecular Systematics and Evolution Course €7,000. Training Course, Sao Paulo, Brazil.
2000 European Molecular Biology Organisation (EMBO) – IR£18,500. Bioinformatics Summer School at NUI Maynooth.
1999-2001 British Association. Molecular Evolution Course, Rio de Janeiro, Brazil. Various funding tranches for travel and living expenses to teach bioinformatics courses in Brazil.
Publications (since 2002)
Lake, J.A., McInerney, J.O. And Ragan, M (2009) The network of life: genome beginnings and evolution. Philosophical Transactions of the Royal Society of London B: Biological Sciences 364, 2169-2175.
Haggerty, L.S, Martin, F.J., Fitzpatrick, D.A. and McInerney, J.O. (2009) Gene and Genome Trees Conflict at Many Levels. Philosophical Transactions of the Royal Society of London B: Biological Sciences 364, 2209-2219.
Hatadani, L.M., McInerney, J.O., de Medeiros, H.F., Martins Junqueira, A.C., de Azerdo-Espin, A.M. and Klaczko, L.B. (2009) Molecular Phylogeny of the Drosophila tripunctata and Closely Related Species Groups (Diptera: Drosophilidae). Molecular Phylogenetics and Evolution 51: 595–600.
Creevey, C.J. and McInerney, J.O. (2009). Trees from Trees: Construction of Phylogenetic Supertrees using CLANN. In DNA Sequence Analysis. Ed.: David Posada. 537:139-61.
Martin, F.J. and 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.
McCann, A., Cotton, J.A. and McInerney, J.O. (2008) The Tree of Genomes: A Comparison of Genome Phylogeny Reconstruction Methods. BMC Evolutionary Biology 8:312 doi:10.1186/1471-2148-8-312.
McInerney, J.O., Cotton, J.A. and Pisani, D. (2008). The Prokaryotic Tree of Life: Past, Present...and Future? Trends in Ecology and Evolution 23(5):276-81.
McInerney, J.O. and Pisani, D. (2007). Paradigm for Life. Science 318: 1390-1391.
Pisani, D., Cotton, J.A. and McInerney, J.O. (2007) Supertrees Disentangle The Chimerical Origin Of Eukaryotic Genomes. Molecular Biology and Evolution 24(8):1752-1760.
Puigbò, P., Garcia-Vallvé, S., and McInerney, J.O. (2007). TOPD/FMTS: a New Software Program to Compare Phylogenetic Trees. Bioinformatics 23(12):1556-1558.
Keane, T.M., Goode, M., Naughton, T.J., and McInerney, J.O. (2007). MultiPhyl: a High-throughput Phylogenetics Supercomputer, Nucleic Acids Research 35: W33-W37.
Wilkinson, M., McInerney, J.O., Hirt, R.P., Foster, P.G., and Embley, T.M. (2007). Of Clades and Clans: Terms for Phylogenetic Relationships in Unrooted Trees. Trends in Ecology and Evolution, 22(3) 114-115.
O’Connell, M.J. and McInerney, J.O. (2007). Reconstructing the ancestral eukaryote: Lessons from the past. In: Ancestral Sequence Reconstruction. Ed: David Liberles. Oxford University Press. 103-116.
O’Halloran, D.M., Fitzpatrick, D.A., McCormack, G.P., McInerney, J.O. and Burnell, A.M. (2006). The Molecular Phylogeny and Functional Significance of a Nematode Specific Clade of Heterotrimeric G-protein α-Subunit Genes. Journal of Molecular Evolution, 63: 87-94.
McInerney, J.O. (2006). The Causes of Protein Evolutionary Rate Variation. Trends in Ecology and Evolution. 21(5) 230-232.
Pisani, D. Mohun, S.M., Harris, S.R., McInerney, J.O. and Wilkinson, M. (2006). Molecular evidence for dim-light vision in the last common ancestor of the Vertebrates. Current Biology 16(9): 381-319.
McInerney, J.O., Pisani, D., O’Connell, M.J., Fitzpatrick, D.A. and Creevey, C.J. (2006). A Prokaryotic Phylogenetic Tree: Yes or No? In Towards the Tree of Life: taxonomy and systematics of large and species rich taxa. Eds: Trevor Hodkinson, John Parnell and Steve Waldren. CRC Press.
Keane, T.M., Creevey, C.J, Pentony, M.M. and 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 6:29.
Keane, T.M., Page, A., Naughton, T.M., Travers, S.A.A., McInerney, J.O. (2006). Building Large Phylogenetic Trees on Coarse-Grained Parallel Machines. Algorithmica DOI:Â 10.1007/s00453-006-1215-0.
McInerney, J.O. (2006). On the Desirability of Models for Inference of Genome Phylogenies. Trends in Microbiology 14(1):1-2.
Fitzpatrick, D.A. and 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 74-85.
O’Connell, M.J. and McInerney, J.O. (2005). Adaptive Evolution of the Human Fatty Acid Synthase Gene: Support for the Cancer Selection and Fat Utilisation Hypotheses? Gene 360(2): 151-159.
Keane, T.M, Page, A.J. McInerney, J.O. and Naughton, T.J. (2005). A high-throughput bioinformatics distributed computing platform. Proceedings - IEEE Symposium on Computer-Based Medical Systems. p. 377-382.
O’Connell, M.J. and 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.
Wilkinson, M., Cotton, J., Creevey, C.J., Eulenstein O., Harris, S.R., Lapointe, F-J. McInerney, J.O., Pisani, D and J. Thorley (2005). The Shape of Supertrees to Come: Input Tree Shape Biases and Some Axiomatic Properties of Fourteen Supertree Methods. Systematic Biology 54(3):419-31.
Fitzpatrick, D.A., Creevey, C.J. and McInerney, J.O. (2005) Evidence of Positive Darwinian Selection in Putative Meningococcal Vaccine Antigens. Journal of Molecular Evolution 61(1), 90-98.
Philip, G.K., Creevey, C.J. and 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, 1175-1184.
Keane, T.M., Naughton, T.J., Travers, S.A.A, McInerney, J.O. and McCormack, G.P. (2005). DPRml: Distributed Phylogeny Reconstruction by Maximum Likelihood. Bioinformatics 21: 969-974.
McInerney, J.O. and Wilkinson, M. (2005). New Methods Ring Changes for The Tree of Life. Trends in Ecology and Evolution 20 (3) 105-107.
Fitzpatrick, D.A. and 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.
Creevey, C.J. and McInerney, J.O. (2005). CLANN: Investigating Phylogenetic Information Through Supertree Analysis. Bioinformatics 21 (3) 390-392.
McInerney, J.O., Finnerty, C., Commins, J. and Philip, G.K. (2005). Gene evolution and drug discovery. In Bioinformatics and Drug Discovery. Humana Press DOI: 10.1226/1588293467.
Travers, S.A.A., O’Connell, M.J., McCormack, G.P. and McInerney, J.O. (2005). Evidence for heterogeneous selective pressures in the evolution of the env gene in different HIV-1 subtypes. Journal of Virology 79 (3) 1836-1841.
Creevey, C.J., Fitzpatrick, D.A., Philip, G.K., Kinsella, R.J., O’Connell, M.J., Pentony, M.M., Travers, S.A.A., Wilkinson, M., and McInerney, J.O. (2004). Does a Tree-like Phylogeny Only Exist at the Tips in the Prokaryotes? Proceedings of The Royal Society of London, Biology Series 271(1557):2551-8.
Travers, S.A.A., Clewley, J.P., Glynn, J.R., Fine, P.E.M., Crampin, A.C., Sibande, F., Mulawa, D., McInerney, J.O., and 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.
Casey, O.M., Fitzpatrick, R., McInerney, J. O., Morris, D., Powell, R., and Sreenan, J.M. (2004). Analysis of gene expression in the bovine corpus luteum through generation and characterisation of 960 ESTs. Biochim Biophys Acta. 1679(1):10-17.
Wilkinson, M., Thorley, J.L., Pisani, D.E., Lapointe, F-J and McInerney, J.O. (2004) Some Desiderata for Meta-Analytical Supertrees. In Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life. Kluwer Academic Publishers, Dordrecht. ISBN 1-4020-2329-4. 564 pp.
Mahony, S., McInerney, J.O, Smith, T. and Golden, A (2004) Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models. BMC Bioinformatics 5(1): 23.
Kinsella, R.J. and McInerney J.O. (2003). Eukaryotic genes in Mycobacterium tuberculosis? Possible alternative explanations. Trends in Genetics, 19, issue 12 687-689.
McInerney, J.O., Littlewood, D.T.J. and Creevey, C.J. (2003). Detecting Adaptive Molecular Evolution: Additional Tools for the Parasitologist. Advances in Parasitology 54, 360-379.
Kinsella, R.J., Fitzpatrick, D.A., Creevey, C.J. and 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 USA, 100, 10320-10325.
Creevey, C.J. and McInerney J.O. (2003). CRANN: A Program for Detecting Adaptive Evolution in Protein-Coding DNA Sequences. Bioinformatics. 19, issue 13, 1726.
Enright M.R., McInerney J.O. and Griffin CT. (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. 53 435-441.
Creevey, C.J. and McInerney, J.O. (2002) An algorithm for detecting directional and non-directional positive selection, neutrality and negative selection in protein coding DNA sequences. Gene: 300 (1-2) 43-51.
Keane, T., Allen, R., Naughton, T.J., McInerney, J.O. and J. Waldron (2002). Distributed computing for DNA analysis. in Principles and Practice of Programming in Java. James F. Power and John T. Waldron, Eds., pp. 65-70.
McInerney, J.O., Wernecke, M., Mullarkey, M. and Powell, R. (2002) Bacteria and Archaea: Molecular techniques reveal astonishing novel diversity. Biodiversity 3:3-10.
McInerney, J. O. (2002) Bioinformatics in a Post-Genomic Era – The need for an Integrative Approach. The Pharmacogenomics Journal. 2:207-208.