Biotechnology

Biographical Details:

Dr Mary J. O'Connell is the Principal Investigator of the Bioinformatics and Molecular Evolution Group. The group currently consists of six postgraduate research students and is funded by Science Foundation Ireland and IRCSET. Dr O'Connell graduated with her PhD in 2005 in Human Molecular Evolution. She was an SFI postdoctoral fellow in UCC before commencing her academic and group leader roles in DCU in 2006.

Research Interests:

Primarily our research is focussed on understanding mammalian evolution and disease from a molecular perspective. Our research involves comparative genomics, phylogenetics and evolutionary analysis of coding and non-coding DNA.

Selected Peer Reviewed Journals

• Noeleen B. Loughran1,2, Sara Hinde3, Sally McCormick-Hill3, Kevin G. Leidal3, Sarah Bloomberg3, Sinéad T. Loughran4, Brendan O¿Connor4, Ciarán Ó'Fágáin4, William M. Nauseef*,¿,3 and Mary J. O¿Connell*,¿,1,2. 2012. Functional Consequence of Positive Selection Revealed Through Rational Mutagenesis of Human Myeloperoxidase. Molecular Biology And Evolution,
• McInerney JO, Pisani D, Bapteste E, and MJ O'Connell. 2011. The public goods hypothesis for the evolution of life on Earth. Biology Direct, 6, 41
• Anthony Ryan, Mark Lynch, Sinead M. Smith, Sylvie Amu, Hendrik J. Nel, Claire E. McCoy, Jennifer K. Dowling, Eve Draper, Vincent O'Reilly, Ciara McCarthy, Julie O'Brien, Déirdre Ní Eidhin, Mary J. O'Connell, Brian Keogh, Charles O. Morton, Thomas R. Rogers, Padraic G. Fallon, Luke A. O'Neill, Dermot Kelleher, Christine E. Loscher1. 2011. A Role for TLR4 in Clostridium difficile infection and the Recognition of Surface Layer Proteins. Plos Pathogens, 7, 6
• 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. Evolution, doi: 10.1111/j.1558-5646.2010.01213.x,, ppdoi: 10.1111/j.1-doi: 10.1111/j.1.
• Mary J O'Connell. 2010. Selection and the cell cycle: Positive Darwinian Selection in a well-known DNA damage response pathway. Journal of Molecular Evolution. 71, 5-6, pp444-457.
• 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. Mammalian Genome. 21, 9-10, pp486-498.
• Claire C. Morgan, Noeleen B. Loughran, Thomas A. Walsh, Alan J. Harrison and Mary J.O'Connell. 2010. Positive selection neighboring functionally essential sites and disease-implicated regions of mammalian reproductive proteins. Bmc Evolutionary Biology, 10, 39
• Barry J. Ryan, Mary J O'Connell and Ciarán Ó'Fágáin. 2008. Consensus Mutagenesis Reveals that Non-Helical Regions Influence Thermal Stability of Horseradish Peroxidase. Biochimie, 90, 9, pp1389-1396.
• Loughran NB, O'Connor B, O'Fagain C, O'Connell MJ. 2008. The phylogeny of the Mammalian Heme Peroxidases and the evolution of their diverse functions. Bmc Evolutionary Biology, 8, 1, pp101-.
• Haun WJ, Laoueille-Duprat S, O'Connell M.J., Spillane C, Grossniklaus U, Phillips AR, Kaeppler SM, Springer NM. 2007. "Genomic imprinting, methylation and molecular evolution of maize Enhancer of zeste (Mez) homologs." Plant Journal. 49, 2, pp325-337.
• Mary J. O'Connell and James O. McInerney. 2005. "Adaptive evolution of the human fatty acid synthase gene: support for the cancer selection and fat utilization hypotheses?". Gene, 360, 2, pp151-159.
• Mary J. O'Connell and James O. McInerney. 2005. "Gamma chain receptor Interleukins: evidence for positive selection driving the evolution of cell-to-cell communicators in the mamalian immune system" Journal of Molecular Evolution. Journal of Molecular Evolution 61, 5, pp608-619.
• Simon A. Travers, Mary J. O'Connell, Grace P. McCormack, James O. McInerney. 2005. "Evidence for heterogeneous selective pressures in the evolution of the env gene in different HIV-1 subtypes". Journal Of Virology, 79, 3, pp1836-1841.
• Christopher J. Creevey David A. Fitzpatrick Gayle K. Philip Rhoda J. Kinsella Mary J. O'Connell Melissa M. Pentony Simon A. Travers Mark Wilkinson James O. McInerney. 2004. Does a tree-like phylogeny only exist at the tips in the eukaryotes?. Proceedings of the Royal Society of London B 271, 1557, pp2551-2558.

Selected Chapters

• O'Connell, M.J.* and McInerney, J.O. 2007. Reconstructing the ancestral eukaryote - lessons from the past. Ancestral Sequence reconstruction, pp103-113.
• McInerney, J.O., Pisani, D.E., O'Connell, M.J., Fitzpatrick, D.A., Creevey, C.J. 2007. Evolutionary History of Prokaryotes: Tree or no tree?. Reconstructing the Tree of Life, pp45-55.

• McInerney JO, Wolfe K, Teeling E and MJ O'Connell, , Society for Molecular Biology and Evolution Annual international conference, 23-JUN-12 - 26-JUN-12, Dublin, Ireland
• Morgan CC, Creevey CJ, Kilroy-Glynn P, and MJ O¿Connell., An issue of caution in the use of Mitochondrial data to infer the Mammalian Phylogeny., International Society for Computational Biology, 9th Annual Rocky Mountain Bioinformatics Conference, 08-DEC-11 - 10-DEC-11, Aspen/Snowmass, CO.
• Morgan CC, Foster PG, Webb AE, Pisani D, McInerney JO, and MJ O¿ Connell, Inferring the Mammalian Phylogeny using a Heterogeneous Approach, International Society for Computational Biology, 9th Annual Rocky Mountain Bioinformatics Conference, 08-DEC-11 - 10-DEC-11, Aspen/Snowmass, CO.
• Walsh TA, Holohan K, O¿Brien A, Carton R., Velasquez E, Morgan CC, Loughran NB, and MJ O¿Connell, Evolution of placenta specific genes and their regulatory elements., International Society for Computational Biology, 9th Annual Rocky Mountain Bioinformatics Conference, 08-DEC-11 - 10-DEC-11, Aspen/Snowmass, CO.
• Loughran NB, O¿Connor B, Ó Fágáin C, Nauseef W, and MJ O'Connell , Functional consequence of positive selection revealed through rational mutagenesis of human myeloperoxidase, 2011 SMBE satellite meeting on Mechanisms of Protein Evolution, 05-DEC-11 - 07-DEC-11, University of Colorado School of Medicine, Denver, CO, USA
• Walsh TA, Holohan K, O¿Brien A, Carton R., Velasquez E, Morgan CC, Loughran NB, and MJ O¿Connell, Evolution of placenta specific genes and their regulatory elements., 2011 SMBE satellite meeting on Mechanisms of Protein Evolution, 05-DEC-11 - 07-DEC-11, University of Colorado School of Medicine, Denver, CO, USA
• Morgan CC, Foster PG, Webb AE, Pisani D, McInerney JO, and MJ O¿ Connell., Inferring the Mammalian Phylogeny using a Heterogeneous Approach., 2011 SMBE satellite meeting on Mechanisms of Protein Evolution, 05-DEC-11 - 07-DEC-11, University of Colorado School of Medicine, Denver, CO, USA
• Morgan CC, Foster PG, Webb AE, Pisani D, McInerney JO, and MJ O¿ Connell., Inferring the Mammalian Phylogeny using a Heterogeneous Approach, Young systematists Forum 2011, 01-DEC-11 - 01-DEC-11, Natural History Museum, London
• Morgan CC, Foster PG, Webb AE, Pisani D, McInerney JO, and MJ O¿ Connell, Mammalian Phylogeny & Evolution: A Heterogeneous Modeling Approach, Evolution 2011, 17-JUN-11 - 21-JUN-11, Norman, Oklahoma, USA
• Walsh T.A., Holohan K.J., O¿Brien A.C., Velasquez E, and MJ O¿Connell., Evolution of placenta specific genes and their regulatory elements., Annual meeting of the Society for Molecular Biology and Evolution, SMBE 2010, 04-JUL-10 - 08-JUL-10, Lyon, France
• Walsh T.A., Holohan K.J., O¿Brien A.C., Velasquez E, and MJ O¿Connell., Evolution of Placenta specific genes and their regulatory networks, Evolution 2010, 25-JUN-10 - 29-JUN-10, Portland, Oregon
• O'Connell MJ, , Virtual institute of Bioinformatics in Eire annual research conference, 22-JAN-10 - 22-JAN-10, Dublin City University, Ireland
• Loughran N.B., O¿Connor B., Fagan C., and MJ O¿Connell., Functional effect of positively selected sites: rational mutagenesis of human myeloperoxidase, International Society for Computational Biology, 7th Annual Rocky Mountain Bioinformatics Conference, 10-DEC-09 - 13-DEC-09, Aspen/Snowmass, CO.
• Loughran, N. B., O¿Connor, B., Ó Fágáin, C., and MJ O¿Connell, The phylogeny of mammalian heme peroxidases: insights into their functional specificity from comparative genomic analyses., Iowa Inflammation Program Seminar Series, 22-MAY-09 - 22-MAY-09, Carver College of Medicine, University of Iowa, Iowa, USA
• Loughran N.B., O¿Connor B., Fagan C., and MJ O¿Connell, The Phylogeny of the Mammalian Heme Peroxidases and the evolution of their diverse functions, 6th International Human Peroxidase Meeting, 19-APR-09 - 22-APR-09, Chapel Hill, North Carolina, NC
• O¿Connell, M.J.*, Loughran N., Donoghue M., Schmid K. and Spillane C., The mammalian imprintome ¿ testing the theories, International Society for Computational Biology, 6th Annual Rocky Mountain Bioinformatics Conference, 03-DEC-08 - 07-DEC-08, Aspen/Snowmass, CO.
• McGettigan, P and O'Connell M.J.*, Cancer Selection Hypothesis: darwinian evolution of a well known DNA damage response pathway., SMBE, Society for Molecular Biology and Evolution Annual international conference, 22-JUN-07 - 29-JUN-07, Hallifax University, Nova Scotia, CA
• O'Connell, M.J., Foster, P.G. and McInerney, J.O., "Estimating the number of amino acid fixations in the human lineage since divergence from mouse", Genomes, Evolution and Bioinformatics 2006, 24-MAY-06 - 30-MAY-06, Arizona State University
• O'Connell MJ, , Virtual institute of Bioinformatics in Eire annual research conference, 12-APR-06 - 12-APR-06, Dublin City University, Ireland
• O'Connell, M.J., "Towards an understanding of the role of Positive Selection in Protein Moleculr Evolution", Evolution 2005, 10-JUN-05 - 15-JUN-05, University of Fairbanks, Alaska
• O'Connell, M.J., *, Using Ancestral Sequence reconstruction to understand protein function, 29-MAR-05 - 31-MAR-05, Kristineberg, Sweden
• O'Connell, M.J. and McInerney, J.O., Gamma chain receptor interleukins: evidence for positive selection driving the evolution of cell-to-cell communicators in the mammalian immune system., The 12th international conference on intelligent systems for molecular biology and the 3rd European conference on computational biology., 31-JUL-04 - 04-AUG-04, Glasgow, Scotland
• O'Connell, M.J., Adaptive evolution of the gamma chain dependent cytokines across the mammalia: implications for disease modeling., VIBE Biannual research meeting, 06-MAY-04 - 06-MAY-04, National University of Ireland Maynooth.
• O'Connell, M.J., The making of Man: large scale bioinformatic approaches for comparative genomic analysis of the human and mouse proteomes., School of Biotechnology seminar series, DCU., 02-MAR-03 - 02-MAR-03, Dublin City University
• O'Connell, M.J. and McInerney J.O., Extensive lineage specific rate heterogeneity between the human and mouse proteomes., Higher Education Authority Annual Meeting, 08-JAN-03 - 08-JAN-03, Royal College of Surgeons Ireland
• O'Connell, M.J. and McInerney, J.O., Rate Heterogeneity in Human and Mouse proteomes, an example of positive selection at work., VIBE Biannual research meeting., 25-NOV-02 - 25-NOV-02, Royal College of Surgeons Ireland
• O'Connell, M.J., McInerney, J.O. and Perriere G., Lineage Specific rate heterogeneity in the human and mouse proteomes., Molecular Evolution (Evolution, Genomics, bioinformatics) annual meeting. Jointly organised by the International Society for Molecular Evolution (ISME) and the Society for Molecular Biology and Evolut, 13-JUN-02 - 16-JUN-02, Sorrento (Naples), Italy
• O'Connell, M.J. and McInerney J.O., Human evolution and the Y chromosome, The 7th annual meeting of PhD students in Evolutionary Biology, 21-MAR-01 - 24-MAR-01, Munich, Germany