Research Interests
We are interested in genomic evolution, particularly the influence of horizontal gene transfer on the evolution of genomes and the influence of this process on the evolution of metabolism. We work on bacteria, Archaea, Viruses, Eukaryotes.
Group Leader: James McInerney
Dr. McInerney is the principal investigator of the group. His primary degree 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. Following his return to Ireland
in 1999, he set up the bioinformatics research group and became the director of the Genetics and Bioinformatics degree
course. He was one of the founding directors of the Irish Centre for High End Computing. He is currently working as a Senior Lecturer and is an Associate Editor of Molecular Biology and Evolution and The Open Evolution Journal.
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 has begun a project to examine the way in which genomes might
fuse and to determine if these events have occurred in the past. Angela is funded by Science Foundation Ireland.
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 is the recipient of an EMBARK scholarship and is currently
funded by the Irish Research Council for Science, Engineering and Technology. Fergal is working on
methods of identifying how biochemical pathways were put together.
Victoria Svinti
Vicky is working on methods for the detection of reassortment and recombination.
These include maximum likelihood and Bayesian inference approaches.
Vicky is formerly a strudent of the NUI Maynooth BSc degree in Genetics and
Bioinformatics and has spent a summer working at Cold Spring Harbor in New York.
Peter Clarke
Peter is working on a Science Foundation Ireland project to investigate
how metabolic networks evolve, the substructure in these networks and how horizontal gene
transfer influences the shape of these networks. Peter has previously worked at CalTech
in California as well as Hatfield University in the UK and The Natural History Museum
in London.
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.
Brian Daly
Brian is working on a Higher Education Authority (H.E.A.) Protramme for Research in Third Level Institutes (PRTLI Cycle IV)
project to integrate GRID technologies, high perfomance computing technologies and bioinformatics in Ireland.
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 lecturer at Queen Mary University, London
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 University of
Hawaii as a post-doc.
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 at UCL.
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 post-doc in University College Dublin.
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
working at the European Molecular Biology Laboratory in Heidelberg, Germany.