NonTreeThinking

Prof. James McInerney BSc PhD DSc

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James McInerney is the principal investigator of the group.

His BSc and PhD were awarded by University College Galway, where he studied from 1987 until 1994. Subsequently he worked as a post-doc at the National Diagnostics Centre in Galway and in the Department of Zoology at The Natural History Museum, London. In 1999 he set up the bioinformatics research group at NUI Maynooth and became the director of the Genetics and Bioinformatics degree course. For the academic year 2012-2013, he took a sabbatical at the Center for Communicable Disease Dynamics at Harvard University, USA.

In 2002, at the Pasteur Institute in Paris, Prof. McInerney was presented with a medal for his research at MEEGID VI and a year later he was recognized by NUI Maynooth for his research achievements when he was awarded the NUI Maynooth Young Investigator Award.  In 2009, he was a guest-editor, along with Prof James Lake and Prof. Mark Ragan of a special issue of Philosophical Transactions of the Royal Society of London (Biology Series), which is the world’s oldest continuously-published journal.  In 2011, he gave the “Ernst Mayr” Keynote lecture at the Mechanisms of Protein Evolution meeting in Denver Colorado.

He was one of the founding directors of the Irish Centre for High End Computing. He is an Associate Editor of Molecular Biology and Evolution, Biology Direct, Journal of Experimental Zoology and is currently serving as the secretary for the Society for Molecular Biology and Evolution.  He is also a regular commentator on scientific matters on TV, Radio and in the print media.

Work in the lab is focussed on gene and genome evolution, with the emphasis at the moment on horizontal gene transfer in prokaryotes and mobile genetic elements, the origin of the Eukaryotic cell and gene family evolution in eukaryotes.  In August 2011, Prof. McInerney and co-authors proposed that genes should be viewed as public goods and that this viewpoint is a better perspective on organismal and genome evolution than a Tree of Life viewpoint.  This viewpoint informs much of the work from the lab.

Prof. McInerney has supervised 23 PhD students, been awarded Marie Curie fellowships, been funded to the tune of more than €3.5 million in direct research funding and been involved in more than €39 Million in programme grants. In addition, he has published in Science, PNAS, Current Biology, TREE, Trends in Genetics, Proceedings of the Royal Society of London and so on. In total he has published more than 85 articles and been an invited speaker at more than 70 conferences.

Selected Publications


  • McInerney, J.O., O’Connell, M.J., and Pisani, D. (2014) The hybrid nature of the Eukaryota and a consilient view of life on Earth. Nature Reviews Microbiology 12(6):449-455. pdf
  • Liu S., Lorenzen E.D., Fumagalli M., Li B., Harris K., Xiong Z., Zhou L., Korneliussen T.S., Somel M., Babbitt C., Wray G., Li J., He W., Wang Z., Fu W., Xiang X., Morgan C.C., Doherty A., O’Connell M.J., McInerney J.O., Born E.W., Dalén L., Dietz R., Orlando L., Sonne C., Zhang G., Nielsen R., Willerslev E., Wang J. (2014) Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears. Cell, 157 (4):785–794.pdf
  • Alvarez-Ponce, D., Lopez, P., Bapteste, E. and McInerney, J.O. (2013). Gene similarity networks provide tools for understanding eukaryote origins and evolution.Proceedings of the National Academy of Sciences USA 110(17):E1594-1603. doi: 10.1073/pnas.1211371110.[pdf]
  • Nelson-Sathi, S., Dagan, T., Landan, G., Janssen, A., Steel, M., McInerney, J. O., Deppenmeier, U., and 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 USA 109 (50) 20537-20542, doi: 10.1073/pnas.1209119109.
  • Bapteste, E., Bouchard F., Baquero F., McInerney J.O., Lopez P. and Burian R.M. (2012). Evolutionary analyses of non-genealogical bonds produced by introgressive descent. Proceedings of the National Academy of Sciences USA 109:45 18266-18272, doi:10.1073/pnas.1206541109.
  • Feuda, R., Hamilton, S.C., McInerney, J.O. and Pisani, D. (2012) Metazoan opsin evolution reveals a simple route to animal vision. Proceedings of the National Academy of Sciences USA 109:46 18868-18872, doi: 10.1073/pnas.1204609109.
  • Cotton, J.A., and 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 USA 107:40 17252-17255. pdf
  • McInerney, J.O. and Pisani, D (2007) Genetics: Paradigm for Life. Science 318:1390-1391.
  • 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. pdf
  • McInerney, J.O. (1998). Replicational and Transcriptional Selection on Codon Usage in Borrelia burgdorferi. Proceedings of the National Academy of Sciences USA: 95 10698-10703.pdf

You can find more of our publications by clicking the publications tab at the top of this page.

Research themes:

– Horizontal Gene Transfer

– Eukaryote origins and early evolution

– Network analyses of evolution

– Synonymous Codon Usage

– Phylogenetics

– Phylogenetic Supertrees

– Adaptive Evolution

Research Interests

Prof. McInerney’s research group are interested in genomic evolution, particularly the influence of horizontal gene transfer on the evolution of genomes and gene duplications and losses in Vertebrates. We work on Eubacteria, Archaebacteria, Viruses, Eukaryotes.

 

Research Activities – Total overall funding €39,110,966.

Show Awarded Grant Information »

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, Medellín, 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.

Show Major Software Projects »

Major Software Projects:


2010  TIGER: Tree-Independent Generation of Evolutionary Rates.


2006  TOPD/FMTS: Software to Compare Phylogenetic Trees (Developed by Pere Puigbo, during his stay in the group).


2005  MultiPhyl: Phylogenetic Supercomputer.


2005  Modelgenerator: Selection of Amino Acid Substitution Matrices.


2004  DPRml: Distributed Phylogeny Reconstruction by Maximum Likelihood.


2004  CLANN: Investigating Phylogenetic Information Through Supertree Analysis.


2003  Crann: A Program for Detecting Adaptive Evolution in Protein-Coding DNA Sequences.


1998  GCUA: General Codon Usage Analysis.

Lab People

We are always looking for leading-edge post-docs and graduate students to join our team.  Feel free to email your CV to james[dot]o[dot]mcinerney[at]nuim[dot]ie.

Carla Cummins

Carla is working on a Science Foundation Ireland project that aims to understand the evolution of prokaryotic metabolism, in particular, the influence of horizontal gene transfer on metabolism. Carla is a graduate of the NUI Maynooth Genetics and Bioinformatics degree programme.

Leanne Haggerty

Leanne is funded by Science Foundation Ireland on a four-year PhD project to explore the species boundaries in bacteria. Leanne uses network mathematics in order to understand the homology linkages between different bacterial species.

Aoife Doherty

Aoife is funded by the Irish Research Council for Science Engineering and Technology to carry out a PhD on the timing of gene duplication and loss events among vertebrates. Aoife graduated from the NUI Maynooth biology programme in 2009.

Sinead Hamilton

Sinead is funded by the Irish Research Council for Science Engineering and Technology to carry out a PhD on the evolutionary trade-offs that occur during evolution. Sinead is a graduate of the BSc in biology programme of NUI Maynooth.

Anthony Doran

Anthony is funded by a Walsh Fellowship from Teagasc. He is jointly-supervised by Dr. Chris Creevey at Teagasc and is working on the development of methods for quickly identifying favourable traits in cattle.

Former Lab members 

Dr. David Alvarez-Ponce

David joined the group in 2010 following the completion of his PhD in Barcelona on the evolution of insulin networks in animals. David is funded on a Science Foundation Ireland Research Frontiers Project to investigate the evolution of prokaryote genomes.

Brian Daly

Brian worked on a Higher Education Authority (H.E.A.) Programme for Research in Third Level Institutes (PRTLI Cycle IV) project to integrate GRID technologies, high perfomance computing technologies and bioinformatics in Ireland.


Dr. Angela McCann

Angela McCann is a graduate of the Genetics and Bioinformatics degree course at NUI Maynooth. Angela worked at the Bioinformatics Core at the Royal College of Surgeons in Ireland in the summer of 2004. She graduated in 2005 and subsequently completed a PhD that examined the way in which genomes might fuse and to determine if these events have occurred in the past. Angela was funded by Science Foundation Ireland. Angela is currently working as a post-doc in the Environmental Research Institute in UCC.


Dr. Fergal Martin

Fergal Martin is a graduate of the NUI Maynooth Genetics and Bioinformatics degree programme. He has worked as a bioinformaticist during the summer holidays and was funded by The Wellcome Trust and The Health Research Board. Fergal was the recipient of an EMBARK scholarship and was funded by the Irish Research Council for Science, Engineering and Technology. Fergal worked on methods of identifying how biochemical pathways were put together. He is currently working as a post-doc in Trinity College Dublin


Dr. Victoria Svinti

Vicky worked on methods for the detection of reassortment and recombination. These included maximum likelihood and Bayesian inference approaches. Vicky is formerly a strudent of the NUI Maynooth BSc degree in Genetics and Bioinformatics and also spent a summer working at Cold Spring Harbor in New York.

Samantha Chui-Sang Lee

Sam worked on the 2009 Science Foundation Ireland-funded UREKA summer programme where she developed methods for assessing whether the position of a protein on a bacterial metabolic network influenced its expression pattern. Sam is a student at Dublin City University in the Genetics and Cell Biology BSc degree course.


Graham Hughes

Graham was funded by the Science Foundation Ireland UREKA programme. He worked on the development of methods to correctly identify orthologous genes in prokaryotic genomes using homology information and gene order data


Giorgio Corti

Giorgio was on a short visit from Italy and he worked on assessing the congruence of phylogenetic relationships inferred by different copies of ribosomal RNA genes in prokaryotes.


Dr. Davide Pisani

Davide Pisani obtained his PhD from the University of Bristol in the UK, working on theoretical phylogenetics as well as developing a genus-level phylogenetic supertree of all the dinosaurs. He subsequently worked as a post-doc at the NASA astrobiology Institute at Penn State university and then spent a short while working at The Natural History Museum, London before coming to Maynooth as a Marie Curie Fellow working on the origins of Eukaryotes. Davide is currently a member of staff at the Biology Department NUI Maynooth.


Dr. James Cotton

James Cotton graduated with a 1st class honours BA in Biological Sciences from The University of Oxford in 1997. He studied from 1999 to 2003 for his PhD at the University of Glasgow in the area of Vertebrate Phylogenomics and Gene Family Evolution. He then worked with Mark Wilkinson at The Natural History Museum in London, UK and at Maynooth on an SFI-funded post-doctoral project and later, James was awarded a post-doctoral fellowship by IRCSET, working on the origin of Eukaryotes. He is currently a researcher at The Sanger Institute.


Dr. Jennifer Commins

Jenny worked on the influence of random genetic drift and selection on the evolution of haploid organisms. This was investigated entirely using computational methods. Jenny developed a sequence evolution simulator and evaluated how different methods of analysing evolution would deal with different evolutionary scenarios. Jenny currently works in Trinity College Dublin as a post-doc


Dr. Gayle Philip

Gayle worked on the development of methods for the construction of phylogenetic supertrees from genomic data. In particular, she worked on the analysis of ancient relationships among the eukaryotes and on evaluating a variety of hypotheses relating to eukaryotic evolution. Gayle is currently working at the Victorian Life Sciences Comutation Initiative (VLSCI).


Caroline Finnerty

Caroline worked on the correlation between coding sequence evolution and the evolution of promoter sequences. In particular, she focussed on the mammals, working with completed genome sequences and predicted promoter sequences. Caroline is currently working in the high-flying area of proper business.


Dr. Thomas Keane

Thomas worked on the development of distributed computing methods in molecular phylogeny reconstruction. He developed the MultiPhyl software and the ModelGenerator software, both of whom are extensively used in phylogenetic laboratories worldwide. Thomas also worked on the evaluation of models of sequence evolution. Thomas is currently working as a staff member at The Sanger Centre in Cambridge, UK.


Dr. Rhoda Kinsella

Rhoda worked on the influence of horizontal gene transfer on the evolution of the Actinobacteria, focussing somewhat on the evolution of Mycobacterium tuberculosis, the bacterium that causes Tuberculosis. Rhoda found that this organism has obtained a number of its fatty acid synthesis genes from alpha-proteobacteria. Rhoda currently works at the Sanger Centre in Cambridge, UK.


Dr. Simon Travers

Simon worked on the evolution of HIV and focussed on an outbreak of subtype C in rural Malawi. He also worked on trying to understand the selective pressures acting on the virus globally. Simon is currently working in Galway as a post-doc.


Dr. Melissa Pentony

Melissa worked on the development of quartet-based methods for the construction of phylogenetic supertrees and on methods for evaluating the robustness of the hypotheses generated by these supertrees. Melissa is currently working as a post-doc in New York.


Dr. David Fitzpatrick

Dave worked on the origin of the mitochondrion and the phylogeny of the alpha proteobacteria as well as the evolution of a group of proteins that are essential for cell viability. Dave is currently working as a lecturer in NUI Maynooth.


Dr. Mary O’Connell

Mary worked on the evolution of the human and mouse genomes, in particular the selective pressures that have shaped their evolution over the past 100 million years or more. Mary is currently a lecturer at Dublin City University.


Dr. Chris Creevey

Chris worked in the lab first as a graduate student and subsequently as a post doc. He has developed the CLANN software as well as the CRANN software for inferring phylogenetic supertrees and for detecting selection respectively. Chris is currently a Reader in Rumen Systems Biology
 Stokes Lecturer at the Animal Bioscience Centre in Aberystwyth University.