James Mcinerney

Overview

My research involves understanding how genes and genomes evolve. Evolution is the simple process of replicating biological entities, but with errors occasionally entering the system. These errors can be deleterious (not a good idea), neutral or advantageous. Natural selection is the process of making the decision about the benefit or otherwise of an evolutionary change. The types of changes that can occur varies from small changes such as nucleotides being replaced in a DNA strand, all the way up to mergers of distantly-related cells and the formation of entirely new kinds of life in the process. The implications for humanity in understanding evolutionary processes include better understandings of antibiotic resistance, better appreciation and understanding of the world around us and better understanding of what might happen in the future in our ever-changing world.

Biography

My BSc and PhD were awarded by University College Galway, where I studied from 1987 until 1994. Subsequently I 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 I 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, I took a sabbatical at the Center for Communicable Disease Dynamics at Harvard University, USA.  In 2015 I moved my research to The University of Manchester.

Research Focus:

The work in the lab is entirely computational molecular evolution.  We make software tools for carrying out new analyses, we analyse genomes and we contribute to theory.

Eukaryote Origins:

We have used "Omics" data in an effort to augment phylogenetic approaches for understanding the origin of eukaryotes.  There is a wealth of information from proteomics, transcriptomics and genomics and all these data contain useful information about organismal and genomic history.  We are investigating ways in which these data can be profitably used to answer questions on Eukaryotic Origins.

Horizontal Gene Transfer:

Genes create phenotypes and therefore, given what we know about inter-species gene transfer, it makes sense to try to understand phenotypes by understanding gene flow.  We are investigating how genes move from one organisms to another and trying to understand what the advantages of such moves might be and what effect they produced.

Genes-in-pieces:

Evolution is not linear and genes are quite often mosaic - being formed by the merging of DNA sequences with different histories.  We are investigating the extent of this process and we are gaining an understanding of how often it happens and why it happens.

N-Rooted Fusion Graphs:

Clearly, it is not possible to accurately display or analyse mosaic sequences using standard phylogenetic trees.  Therefore, we have invented N-Rooted Fusion Graphs for visualising these historical events.  N-Rooted Fusion Graphs differ from phylogenetic trees by having more than one root and having at least one node with an in-degree of 2 (this represents the merging of two unrelated or distantly related entities).  Current work involves the development of methods for constructing such graphs.

Software:

We have developed several software programs for evolutionary analyses.