Faculty of Biological Sciences

Dr Mary O'Connell

BSc (Hons) PhD
University Academic Fellow in Biology
School of Biology

Background: My PhD (2005) addressed the role of positive selection in molecular evolution and assessed rate heterogeneity in protein coding regions of mammals - primarily the human and mouse genomes. Following on from this I took a position as an SFI postdoctoral fellow in University College Cork working primarily on the evolution of genomic imprinting in mammals and plants from an analytical and quantitative perspective. Six Months later (2006) and following open competition, I moved to my first fully tenured academic post at Dublin City University. There I established my own independent research team. I have continued to expand and develop my interests in both the analytical/empirical analyses of genomic data from a molecular evolutionary perspective and also in the more theoretical concepts around evolution of life on the planet. My research group (www.mol-evol.org) work on specific aspects of evolutionary genomics and we are primarily computational based with some wet bench collaborations/aspects to our work. We are currently 2 PhD students and 1 postdoctoral associate and have 2 further PhD positions available (see below).

Contact:  Miall 9.05, +44(0) 113 34 34890, email address for  

You can read more about Dr O'Connell's interests here:
www.mol-evol.org

Research Interests

Molecular Mechanisms of Evolution: Understanding the patterns and processes of evolution and the relationship between genotype, phenotype and fitness.

Current Projects

www.mol-evol.org

 

Faculty Research and Innovation



Studentship information

Undergraduate project topics:

  • None

Postgraduate studentship areas:

  • Currently recruiting 2 PhD students on the following projects:
  • "Genomic Innovation and the Emergence of Placentation in Mammals" http://www.findaphd.com/search/ProjectDetails.aspx?PJID=68382&LID=735
  • "Gene Fusion and the animal tree of life" - link to follow shortly.
  • Email me at m.oconnell@leeds.ac.uk for further details.

See also:

Modules taught

BLGY1124/1128 - The Diversity of Life/Living Planet
BLGY1303 - Tutorials for Biology and Genetics
BLGY2100 - Enhanced Study Skills for Biologists
BLGY3021 - Research Project
BLGY3243 - Advanced Topics in Zoology
BLGY3291 - Comparative Genomics
BLGY3340 - Biology Research Projects

Postgraduates

Peter Mulhair (Primary supervisor) 90% FTE
Ali Taylor (Primary supervisor) 70% FTE
Georgios Nikolopoulos (Co-supervisor) 33% FTE
David Orr (Co-supervisor) 50% FTE
Ioannis Tsagakis (Co-supervisor) 25% FTE

Morgan CC, Loughran NB, Walsh TA, Harrison AJ, O'Connell MJ Erratum to: Positive selection neighboring functionally essential sites and disease-implicated regions of mammalian reproductive proteins. BMC Evol Biol 17 170-, 2017
DOI:10.1186/s12862-017-1015-y

Lynch M, Walsh TA, Marszalowska I, Webb AE, Mac Aogáin M, Rogers TR, Windle H, Kelleher D, O’Connell MJ, Loscher CE Erratum to: Surface layer proteins from virulent Clostridium difficile ribotypes exhibit signatures of positive selection with consequences for innate immune response BMC Evolutionary Biology 17 -, 2017
DOI:10.1186/s12862-017-0990-3
View abstract

Webb AE, Walsh TA, O'Connell MJ VESPA: Very large-scale Evolutionary and Selective Pressure Analyses PeerJ Computer Science 3 -, 2017
DOI:10.7717/peerj-cs.118
View abstract

McInerney JO, McNally A, O'Connell MJ Why prokaryotes have pangenomes NATURE MICROBIOLOGY 2 -, 2017
DOI:10.1038/nmicrobiol.2017.40

Lynch M, Walsh TA, Marszalowska I, Webb AE, MacAogain M, Rogers TR, Windle H, Kelleher D, O'Connell MJ, Loscher CE Surface layer proteins from virulent Clostridium difficile ribotypes exhibit signatures of positive selection with consequences for innate immune response BMC EVOLUTIONARY BIOLOGY 17 -, 2017
DOI:10.1186/s12862-017-0937-8

McInerney JO, O'Connell MJ Microbiology: Mind the gaps in cellular evolution Nature 541 297-299, 2017
DOI:10.1038/nature21113
View abstract

Williams JM, Bezak T, Das M, Ning Z, Lucking EF, Kelly VP, Harrison P, Young P, O'Connell MJ, Dockery P, O'Halloran KD, Moore T Psg22 null mouse embryos develop normally under normoxic and hypoxic conditions of pregnancy Science Matters -, 2016
DOI:10.19185/matters.201611000023
View abstract

McRae KM, Good B, Hanrahan JP, McCabe MS, Cormican P, Sweeney T, O'Connell MJ, Keane OM Transcriptional profiling of the ovine abomasal lymph node reveals a role for timing of the immune response in gastrointestinal nematode resistance. Veterinary parasitology 224 96-108, 2016
DOI:10.1016/j.vetpar.2016.05.014
View abstract

Tarver JE, dos Reis M, Mirarab S, Moran RJ, Parker S, O'Reilly JE, King BL, O'Connell MJ, Asher RJ, Warnow T, Peterson KJ, Donoghue PCJ, Pisani D The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference Genome Biology and Evolution 8 330-344, 2016
DOI:10.1093/gbe/evv261
View abstract

Gunn L, Collins PJ, O'Connell MJ, O'shea H Phylogenetic investigation of enteric bovine coronavirus in Ireland reveals partitioning between European and global strains Irish Veterinary Journal 68 -, 2015
DOI:10.1186/s13620-015-0060-3
View abstract

McInerney J, Pisani D, O Connell MJ The ring of life hypothesis for eukaryote origins is supported by multiple kinds of data Philosophical Transactions of the Royal Society B: Biological Sciences 370 -, 2015
DOI:10.1098/rstb.2014.0322
View abstract

Hughes L, Carton R, Minguzzi S, McEntee G, Deinum EE, O'Connell MJ, Parle-McDermott A An active second dihydrofolate reductase enzyme is not a feature of rat and mouse, but they do have activity in their mitochondria FEBS Letters 589 1855-1862, 2015
DOI:10.1016/j.febslet.2015.05.017
View abstract

Webb AE, Gerek ZN, Morgan CC, Walsh TA, Loscher CE, Edwards SV, O'Connell MJ Adaptive Evolution as a Predictor of Species-Specific Innate Immune Response Molecular Biology and Evolution 32 1717-1729, 2015
DOI:10.1093/molbev/msv051
View abstract

Keane M, Semeiks J, Webb AE, Li YI, Quesada V, Craig T, Madsen LB, Van Dam S, Brawand D, Marques PI, Michalak P, Kang L, Bhak J, Yim H-S, Grishin NV, Nielsen NH, Heide-Jørgensen MP, Oziolor EM, Matson CW, Church GM, Stuart GW, Patton JC, George JC, Suydam R, Larsen K, López-Otín C, O'Connell MJ, Bickham JW, Thomsen B, De Magalhães JP Insights into the evolution of longevity from the bowhead whale genome Cell Reports 10 112-122, 2015
DOI:10.1016/j.celrep.2014.12.008
View abstract

O'Connell MJ, Moran RJ, Morgan CC A guide to phylogenetic reconstruction using heterogeneous models– a case study from the root of the placental mammal tree Computation 177-196, 2015

McInerney JO, O'Connell MJ Evolutionary developmental biology: Ghost locus appears Nature 514 570-571, 2014
DOI:10.1038/514570a

Baldwin MW, Toda Y, Nakagita T, O'Connell MJ, Klasing KC, Misaka T, Edwards SV, Liberles SD Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor Science 345 929-933, 2014
DOI:10.1126/science.1255097
View abstract

Liu S, Lorenzen ED, Fumagalli M, Li B, Harris K, Xiong Z, Zhou L, Korneliussen TS, Somel M, Babbitt C, Wray G, Li J, He W, Wang Z, Fu W, Xiang X, Morgan CC, Doherty A, O'Connell MJ, McInerney JO, Born EW, Dalén L, Dietz R, Orlando L, Sonne C, Zhang G, Nielsen R, Willerslev E, Wang J Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears Cell 157 785-794, 2014
DOI:10.1016/j.cell.2014.03.054
View abstract

Haggerty LS, Jachiet P-A, Hanage WP, Fitzpatrick DA, Lopez P, O'Connell MJ, Pisani D, Wilkinson M, Bapteste E, McInerney JO A pluralistic account of homology: Adapting the models to the data Molecular Biology and Evolution 31 501-516, 2014
DOI:10.1093/molbev/mst228
View abstract

McInerney JO, O'Connell MJ, Pisani D The hybrid nature of the Eukaryota and a consilient view of life on Earth Nature Reviews Microbiology 12 449-455, 2014
DOI:10.1038/nrmicro3271
View abstract

Loughran NB, O'Connell MJ, O'Connor B,Ó'Fágáin C Stability properties of an ancient plant peroxidase Biochimie 104 156-159, 2014
DOI:10.1016/j.biochi.2014.05.012
View abstract

McRae KM, Good B, Hanrahan JP, Glynn A, O'Connell MJ, Keane OM Response to Teladorsagia circumcincta infection in Scottish Blackface lambs with divergent phenotypes for nematode resistance Veterinary Parasitology 206 200-207, 2014
DOI:10.1016/j.vetpar.2014.10.023
View abstract

Morgan CC, Creevey CJ, O Connell MJ Mitochondrial data are not suitable for resolving placental mammal phylogeny Mammalian Genome 25 636-647, 2014
DOI:10.1007/s00335-014-9544-9
View abstract

Collins LE, Lynch M, Marszalowska I, Kristek M, Rochfort K, O'Connell MJ, Windle H, Kelleher D, Loscher CE Surface Layer Proteins isolated from Clostridium difficile induce clearance responses in Macrophages Microbes and Infection -, 2014

Morgan CC, Mc Cartney AM, Donoghue MTA, Loughran NB, Spillane C, Teeling EC, O'Connell MJ Molecular adaptation of telomere associated genes in mammals BMC Evolutionary Biology 13 -, 2013
DOI:10.1186/1471-2148-13-251
View abstract

Morgan CC, Foster PG, Webb AE, Pisani D, McInerney JO, O'Connell MJ Heterogeneous models place the root of the placental mammal phylogeny Molecular Biology and Evolution 30 2145-2156, 2013
DOI:10.1093/molbev/mst117
View abstract

Dmitriev P, Barat A, Polesskaya A, O'Connell MJ, Robert T, Dessen P, Walsh TA, Lazar V, Turki A, Carnac G, Laoudj-Chenivesse D, Lipinski M, Vassetzky YS Simultaneous miRNA and mRNA transcriptome profiling of human myoblasts reveals a novel set of myogenic differentiation-associated miRNAs and their target genes BMC Genomics 14 -, 2013
DOI:10.1186/1471-2164-14-265
View abstract

Loughran NB, Hinde S, McCormick-Hill S, Leidal KG, Bloomberg S, Loughran ST, O'Connor B,Ó'Fágáin C, Nauseef WM, O'Connell MJ Functional consequence of positive selection revealed through rational mutagenesis of human myeloperoxidase Molecular Biology and Evolution 29 2039-2046, 2012
DOI:10.1093/molbev/mss073
View abstract

O'Connell MJ, Doyle AM, Juenger TE, Donoghue MTA, Keshavaiah C, Tuteja R, Spillane C In Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure BMC Research Notes 5 -, 2012
DOI:10.1186/1756-0500-5-359
View abstract

Shakya K, O'Connell MJ, Ruskin HJ The landscape for epigenetic/epigenomic biomedical resources Epigenetics 7 982-986, 2012
DOI:10.4161/epi.21493
View abstract

Morgan CC, Shakya K, Webb A, Walsh TA, Lynch M, Loscher CE, Ruskin HJ, O'Connell MJ Colon cancer associated genes exhibit signatures of positive selection at functionally significant positions. BMC evolutionary biology 12 114-, 2012
DOI:10.1186/1471-2148-12-114
View abstract

McInerney JO, Pisani D, Bapteste E, O'Connell MJ The public goods hypothesis for the evolution of life on Earth Biology Direct 6 -, 2011
DOI:10.1186/1745-6150-6-41
View abstract

Ryan A, Lynch M, Smith SM, Amu S, Nel HJ, McCoy CE, Dowling JK, Draper E, O'Reilly V, McCarthy C, O'Brien J, Eidhin D, O'Connell MJ, Keogh B, Morton CO, Rogers TR, Fallon PG, O'Neill LA, Kelleher D, Loscher CE A role for TLR4 in clostridium difficile infection and the recognition of surface layer proteins PLoS Pathogens 7 -, 2011
DOI:10.1371/journal.ppat.1002076
View abstract

Mccole RB, Loughran NB, Chahal M, Fernandes LP, Roberts RG, Fraternali F, O'Connell MJ, Oakey RJ A Case-By-Case Evolutionary Analysis Of Four Imprinted Retrogenes Evolution 65 1413-1427, 2011
DOI:10.1111/j.1558-5646.2010.01213.x
View abstract

O'Connell MJ Selection and the cell cycle: Positive darwinian selection in a well-Known DNA damage response pathway Journal of Molecular Evolution 71 444-457, 2010
DOI:10.1007/s00239-010-9399-y
View abstract

O'Connell MJ, Loughran NB, Walsh TA, Donoghue MTA, Schmid KJ, Spillane C 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 21 486-498, 2010
DOI:10.1007/s00335-010-9283-5
View abstract

Morgan CC, Loughran NB, Walsh TA, Harrison AJ, O'Connell MJ Positive selection neighboring functionally essential sites and disease-implicated regions of mammalian reproductive proteins BMC Evolutionary Biology 10 -, 2010
DOI:10.1186/1471-2148-10-39
View abstract

Ryan BJ, O'Connell MJ,Ó'Fágáin C Consensus mutagenesis reveals that non-helical regions influence thermal stability of horseradish peroxidase Biochimie 90 1389-1396, 2008
DOI:10.1016/j.biochi.2008.04.009
View abstract

O'Connell MJ, McInerney JO Reconstructing the ancestral eukaryote: lessons from the past In Ancestral Sequence Reconstruction , 2008
DOI:10.1093/acprof:oso/9780199299188.003.0010
View abstract

Loughran NB, O'Connor B,Ó'Fágáin C, O'Connell MJ The phylogeny of the mammalian heme peroxidases and the evolution of their diverse functions BMC Evolutionary Biology 8 -, 2008
DOI:10.1186/1471-2148-8-101
View abstract

Haun WJ, Laoueillé-Duprat S, O'Connell MJ, Spillane C, Grossniklaus U, Phillips AR, Kaeppler SM, Springer NM Genomic imprinting, methylation and molecular evolution of maize Enhancer of zeste (Mez) homologs Plant Journal 49 325-337, 2007
DOI:10.1111/j.1365-313X.2006.02965.x
View abstract

O'Connell MJ, McInerney JO Adaptive evolution of the human fatty acid synthase gene: Support for the cancer selection and fat utilization hypotheses? Gene 360 151-159, 2005
DOI:10.1016/j.gene.2005.06.020
View abstract

O'Connell MJ, McInerney JO 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 61 608-619, 2005
DOI:10.1007/s00239-004-0313-3
View abstract

Travers SA, O'Connell MJ, McCormack G, McInerney JO Evidence for heterogeneous selective pressures in the evolution of the env gene in different human immunodeficiency virus type 1 subtypes Journal of Virology -, 2005

Creevey CJ, Fitzpatrick DA, Philip GK, Kinsella RJ, O'Connell MJ, Pentony MM, Travers SA, Wilkinson M, McInerney JO A tree-like phylogeny only exists at the tips in the prokaryotes Proceedings of the Royal Society of London Biology -, 2004