Mary J. O'Connell, PhD - Publications

2002-2005 Biology National University of Ireland, Maynooth 
 2005-2006 University College Cork, Cork, County Cork, Ireland 
 2006- Bioinformatics Dublin City University, Dublin, County Dublin, Ireland 
Molecular evolution, adaptive evolution, vertebrates, phylogenetics

40 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Siu-Ting K, Torres-Sánchez M, San Mauro D, Wilcockson D, Wilkinson M, Pisani D, O'Connell MJ, Creevey CJ. Inadvertent paralog inclusion drives artefactual topologies and timetree estimates in phylogenomics. Molecular Biology and Evolution. PMID 30903171 DOI: 10.1093/Molbev/Msz067  1
2017 McInerney JO, McNally A, O'Connell MJ. Reply to 'The population genetics of pangenomes'. Nature Microbiology. 2: 1575. PMID 29176701 DOI: 10.1038/S41564-017-0068-4  1
2017 McInerney JO, McNally A, O'Connell MJ. Why prokaryotes have pangenomes. Nature Microbiology. 2: 17040. PMID 28350002 DOI: 10.1038/Nmicrobiol.2017.40  1
2017 McInerney JO, O'Connell MJ. Microbiology: Mind the gaps in cellular evolution. Nature. 541: 297-299. PMID 28102241 DOI: 10.1038/Nature21113  1
2016 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 PC, Pisani D. The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference. Genome Biology and Evolution. PMID 26733575 DOI: 10.1093/Gbe/Evv261  1
2015 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 of London. Series B, Biological Sciences. 370. PMID 26323755 DOI: 10.1098/Rstb.2014.0323  1
2015 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. PMID 25980602 DOI: 10.1016/J.Febslet.2015.05.017  1
2015 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: 1717-29. PMID 25758009 DOI: 10.1093/Molbev/Msv051  1
2014 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: 200-7. PMID 25468019 DOI: 10.1016/j.vetpar.2014.10.023  1
2014 McInerney JO, O'Connell MJ. Evolutionary developmental biology: Ghost locus appears. Nature. 514: 570-1. PMID 25355355 DOI: 10.1038/514570A  1
2014 Morgan CC, Creevey CJ, O'Connell MJ. Mitochondrial data are not suitable for resolving placental mammal phylogeny. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 25: 636-47. PMID 25239304 DOI: 10.1007/S00335-014-9544-9  0.84
2014 Baldwin MW, Toda Y, Nakagita T, O'Connell MJ, Klasing KC, Misaka T, Edwards SV, Liberles SD. Sensory biology. Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor. Science (New York, N.Y.). 345: 929-33. PMID 25146290 DOI: 10.1126/Science.1255097  1
2014 Loughran NB, O'Connell MJ, O'Connor B, O'Fágáin C. Stability properties of an ancient plant peroxidase. Biochimie. 104: 156-9. PMID 24919139 DOI: 10.1016/J.Biochi.2014.05.012  1
2014 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: 449-55. PMID 24814066 DOI: 10.1038/Nrmicro3271  1
2014 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, et al. Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears. Cell. 157: 785-94. PMID 24813606 DOI: 10.1016/J.Cell.2014.03.054  1
2014 Collins LE, Lynch M, Marszalowska I, Kristek M, Rochfort K, O'Connell M, Windle H, Kelleher D, Loscher CE. Surface layer proteins isolated from Clostridium difficile induce clearance responses in macrophages. Microbes and Infection / Institut Pasteur. 16: 391-400. PMID 24560642 DOI: 10.1016/J.Micinf.2014.02.001  1
2014 Haggerty LS, Jachiet PA, 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: 501-16. PMID 24273322 DOI: 10.1093/Molbev/Mst228  1
2013 Morgan CC, Mc Cartney AM, Donoghue MT, Loughran NB, Spillane C, Teeling EC, O'Connell MJ. Molecular adaptation of telomere associated genes in mammals. Bmc Evolutionary Biology. 13: 251. PMID 24237966 DOI: 10.1186/1471-2148-13-251  1
2013 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: 2145-56. PMID 23813979 DOI: 10.1093/Molbev/Mst117  1
2013 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: 265. PMID 23597168 DOI: 10.1186/1471-2164-14-265  1
2012 Shakya K, O'Connell MJ, Ruskin HJ. The landscape for epigenetic/epigenomic biomedical resources. Epigenetics : Official Journal of the Dna Methylation Society. 7: 982-6. PMID 22874136 DOI: 10.4161/Epi.21493  1
2012 O'Connell MJ, Doyle AM, Juenger TE, Donoghue MT, Keshavaiah C, Tuteja R, Spillane C. In Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure. Bmc Research Notes. 5: 359. PMID 22805311 DOI: 10.1186/1756-0500-5-359  1
2012 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. PMID 22788692 DOI: 10.1186/1471-2148-12-114  1
2012 Loughran NB, Hinde S, McCormick-Hill S, Leidal KG, Bloomberg S, Loughran ST, O'Connor B, O'Fágáin C, Nauseef WM, O'Connell MJ. Functional consequence of positive selection revealed through rational mutagenesis of human myeloperoxidase. Molecular Biology and Evolution. 29: 2039-46. PMID 22355012 DOI: 10.1093/Molbev/Mss073  1
2011 McInerney JO, Pisani D, Bapteste E, O'Connell MJ. The Public Goods Hypothesis for the evolution of life on Earth. Biology Direct. 6: 41. PMID 21861918 DOI: 10.1186/1745-6150-6-41  1
2011 Ryan A, Lynch M, Smith SM, Amu S, Nel HJ, McCoy CE, Dowling JK, Draper E, O'Reilly V, McCarthy C, O'Brien J, Ní Eidhin D, O'Connell MJ, Keogh B, Morton CO, et al. A role for TLR4 in Clostridium difficile infection and the recognition of surface layer proteins. Plos Pathogens. 7: e1002076. PMID 21738466 DOI: 10.1371/Journal.Ppat.1002076  1
2011 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; International Journal of Organic Evolution. 65: 1413-27. PMID 21166792 DOI: 10.1111/j.1558-5646.2010.01213.x  1
2010 O'Connell MJ. Selection and the cell cycle: positive Darwinian selection in a well-known DNA damage response pathway. Journal of Molecular Evolution. 71: 444-57. PMID 21057781 DOI: 10.1007/s00239-010-9399-y  1
2010 O'Connell MJ, Loughran NB, Walsh TA, Donoghue MT, 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 : Official Journal of the International Mammalian Genome Society. 21: 486-98. PMID 20931201 DOI: 10.1007/S00335-010-9283-5  1
2010 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: 39. PMID 20149245 DOI: 10.1186/1471-2148-10-39  1
2008 Ryan BJ, O'Connell MJ, O'Fágáin C. Consensus mutagenesis reveals that non-helical regions influence thermal stability of horseradish peroxidase. Biochimie. 90: 1389-96. PMID 18486625 DOI: 10.1016/J.Biochi.2008.04.009  1
2008 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. PMID 18371223 DOI: 10.1186/1471-2148-8-101  1
2008 O'Connell MJ, McInerney JO. Reconstructing the ancestral eukaryote: lessons from the past Ancestral Sequence Reconstruction. DOI: 10.1093/acprof:oso/9780199299188.003.0010  1
2007 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. The Plant Journal : For Cell and Molecular Biology. 49: 325-37. PMID 17181776 DOI: 10.1111/J.1365-313X.2006.02965.X  1
2005 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. PMID 16205981 DOI: 10.1007/S00239-004-0313-3  1
2005 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. PMID 16154299 DOI: 10.1016/J.Gene.2005.06.020  1
2005 Travers SAA, O'Connell MJ, McCormack GP, 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. 79: 1836-1841. PMID 15650207 DOI: 10.1128/Jvi.79.3.1836-1841.2005  1
2004 Creevey CJ, Fitzpatrick DA, Philip GK, Kinsella RJ, O'Connell MJ, Pentony MM, Travers SA, Wilkinson M, McInerney JO. Does a tree-like phylogeny only exist at the tips in the prokaryotes? Proceedings. Biological Sciences / the Royal Society. 271: 2551-8. PMID 15615680 DOI: 10.1098/Rspb.2004.2864  1
1997 Cozzi E, Tucker AW, Langford GA, Pino-Chavez G, Wright L, O'Connell MJ, Young VJ, Lancaster R, McLaughlin M, Hunt K, Bordin MC, White DJ. Characterization of pigs transgenic for human decay-accelerating factor. Transplantation. 64: 1383-92. PMID 9392299  1
1996 O'Connell MJ, Chua R, Hoyos B, Buck J, Chen Y, Derguini F, Hämmerling U. Retro-retinoids in regulated cell growth and death. The Journal of Experimental Medicine. 184: 549-55. PMID 8760808 DOI: 10.1084/Jem.184.2.549  1
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