Bioinformatics and Molecular Evolution Group Leader
Dr Mary J. O’Connell graduated with her BSc and PhD from the National University of Ireland Maynooth (NUIM). Her PhD work was on the topic of evolutionary rate heterogeneity in the coding regions of mammal genomes and her postdoctoral work at UCC was on genomic imprinting in mammal and plants. These projects spanned protein coding and non-coding aspects of mammal genomics and formed the foundation of her interest in functional comparative genomics and evolutionary medicine. In 2005 she became a fully tenured academic in the School of Biotechnology, Dublin City University where she established the Bioinformatics and Molecular Evolution research group. Her current research spans many areas of evolutionary biology, including phylogenetics and molecular adaptation, and integrates evolutionary predictions with molecular and biochemical analyses. She is focused on understanding the evolution of disease resistance by studying the molecular mechanisms of both protein and regulatory element evolution in the amniotes. Her research is funded by: Science Foundation Ireland (SFI), IRCSET, the Walsh and Pierse Trust fellowships, the DCU scholarship for academic excellence (O’Hare award), various research awards for early stage researchers and most recently she has been selected for a Fulbright scholar award.
My research group at DCU is interested in understanding the evolution of amniotes from the molecular perspective, and the application of this knowledge to evolutionary medicine. Specifically we are interested in mechanisms of generating evolutionary/phenotypic novelty such as molecular adaptation, the evolution of novel protein functions, and the emergence of novel regulatory elements. In order to carry these analyses out we design and implement a lot of our own code, this is often necessary when dealing with multiple large amniote genomes at once and it gives us huge flexibility in the types of analyses possible. We are interested in determining the molecular mechanisms underpinning: (i) the phenotypic variation in response to disease observed between different species, (ii) the emergence of novel tissue types in amniotes e.g. placenta, and (iii), the evolution of protein domain sharing networks. All of our research has at its core the directionality provided by phylogenetics and phylogenomics and these are central to our research. In summary our research encompasses: evolutionary biology, molecular comparative genomics, molecular comparative zoology, phylogenomics and bioinformatics.
The Bioinformatics and Molecular Evolution Research Group, Dublin City University.
Kabita Shakya, Mary J. O'Connell and Heather J. Ruskin (2012) The Landscape for Epigenetic/Epigenomic Biomedical Resources. Accepted for publication July 2012. Epigenetics.
Claire C. Morgan, Kabita Shakya, Andrew E. Webb, Thomas A. Walsh, Mark Lynch, Christine E. Loscher, Heather J. Ruskin and Mary J. O'Connell* (2012) Colon cancer associated genes exhibit signatures of positive selection at functionally significant positions. Accepted for publication June 2012. BMC Evolutionary Biology.
Mary J O'Connell*, Aisling M Doyle*, Thomas E Juenger, Channa Keshavaiah, Mark TA Donoghue, Reetu Tuteja and Charles Spillane (2012) In Arabidopsis thaliana codon volatility scores reflects GC3 composition rather than selective pressure. Accepted for publication June 2012. BMC Research Notes.
Loughran NB, McCormick-Hill S, Hinde S, Leidal KG, Bloomberg S, Loughran ST, O'Connor B, Fagan C, Nauseef WM*, and O'Connell MJ* (2012) Functional consequence of positive selection revealed through rational mutagenesis of human myeloperoxidase. doi:10.1093/molbev/mss073 Molecular Biology and Evolution. pdf
McInerney JO, Pisani D, Bapteste E, O'Connell MJ. (2011) The public goods hypothesis for the evolution of life on Earth. DOI:10.1186/1745-6150-6-41 Biology Direct. pdf
Ryan A, Lynch M, Smith SM, Amu S, Nel HJ, McCoy CE, Dowling JK, Draper E, O'Reilly E, McCarthy C, O'Brien J, Ni Eidhin D, O'Connell MJ, Keogh B, Morton CO, Rogers TR, Fallon PG, O'Neill LA, Kelleher D and Loscher CE. (2011) A role for TLR4 in Clostridium difficile infection and the recognition of surface layer proteins. DOI:10.1371/journal.ppat.1002076. PLoS Pathogens. pdf
McCole RB, Loughran NB, Chahal M, Fernandes LP, Roberts RG, Fraternali F, O'Connell MJ, Oakey RJ (2011) A Case-by-case evolutionary analysis of four Imprinted retrogenes. DOI: 10.1111/j.1558-5646.2010.01213.x Evolution. pdf
O'Connell, M.J.* (2010) Selection and the cell cycle: Positive Darwinian Selection in a well-known DNA damage response pathway. DOI: 10.1007/s00239-010-9399-y. Journal of Molecular Evolution. pdf
O'Connell, M.J.*, Loughran, N.B., Walsh, T.A., Donoghue, M.T.A., Schmid, K.J., Spillane, C. (2010) A phylogenetic approach to test for evidence of parental conflict or gene duplications associated with protein-encoding imprinted orthologous genes in placental mammals. DOI: 10.1007/s00335-010-9283-5. Mammalian Genome. pdf
Morgan, C.C., Loughran, N.B., Walsh, T.A., Harrison, A.J., and O'Connell, M.J.* (2010) Positive Selection neighboring functionally essential sites and disease-implicated regions of mammalian reproductive proteins BMC Evolutionary Biology. 10:39doi:10.1186/1471-2148-10-39. pdf
Loughran, N.B., O'Connor B., Fagan C., and O'Connell, M.J.* (2008) The Phylogeny of the Mammalian Heme Peroxidases and the evolution of their diverse functions BMC Evolutionary Biology. 8:101doi:10.1186/1471-2148-8-101. pdf
Ryan, B.J., O'Connell, M.J. and Fagan C.P. (2008) The consensus approach to protein stabilization is not a global solution: insights from extant and extinct peroxidases Biochimie. 90, (9), 1414-1421. pdf
Haun, W.J., Laoueille, S., O'Connell, M.J., Spillane, C., Grossniklaus, U., Phillips, A.R., Kaeppler, S.M. and Springer, N.M. (2007). Genomic imprinting, methylation and molecular evolution of maize Enhancer of Zeste (Mez) homologs Plant J. 49(2):325-337. pdf
O'Connell, M.J. and McInerney, J. O. (2007). Reconstructing the ancestral eukaryote - lessons from the past, future perspectives. In Reconstructing Ancient Proteins. Eds: David Liberles. Oxford University Press.
McInerney, J.O., Pisani, D., O'Connell, M.J., Fitzpatrick, D.A., Creevey, C.J. (2006). The evolutionary history of the prokaryotes: 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.
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 utilization hypotheses? Gene Nov 7;360(2):151-9.pdf
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. pdf
Travers, S.A., O'Connell, M.J., McCormack, G. and 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 Feb 79(3):1836-41. pdf
Creevey, C. J., Fitzpatrick, D. A., Philip, G. K., Kinsella, R. J., O'Connell, M.J., Pentony, M. M., Travers, S. 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 Dec 22;271(1557):2551-8. pdf