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Mary J. O'Connell, PhD - Publications

Affiliations: 
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 
Area:
Molecular evolution, adaptive evolution, vertebrates, phylogenetics
Website:
http://mol-evol.org/
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49 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
2023 Ovchinnikov V, Uliano-Silva M, Wilkinson M, Wood J, Smith M, Oliver K, Sims Y, Torrance J, Suh A, McCarthy SA, Durbin R, O'Connell MJ. Caecilian genomes reveal the molecular basis of adaptation, and convergent evolution of limblessness in snakes and caecilians. Molecular Biology and Evolution. 40. PMID 37194566 DOI: 10.1093/molbev/msad102  0.446
2023 McCarthy CGP, Mulhair PO, Siu-Ting K, Creevey CJ, O'Connell MJ. Improving Orthologous Signal and Model Fit in Datasets Addressing the Root of the Animal Phylogeny. Molecular Biology and Evolution. 40. PMID 36649189 DOI: 10.1093/molbev/msac276  0.724
2022 Mulhair PO, McCarthy CGP, Siu-Ting K, Creevey CJ, O'Connell MJ. Filtering artifactual signal increases support for Xenacoelomorpha and Ambulacraria sister relationship in the animal tree of life. Current Biology : Cb. PMID 36356574 DOI: 10.1016/j.cub.2022.10.036  0.744
2021 Hyland EM, Webb AE, Kennedy KF, Gerek Ince ZN, Loscher CE, O'Connell MJ. Adaptive Evolution in TRIF Leads to Discordance between Human and Mouse Innate Immune Signaling. Genome Biology and Evolution. 13. PMID 34893845 DOI: 10.1093/gbe/evab268  0.733
2020 Tinning H, Taylor A, Wang D, Constantinides B, Sutton R, Oikonomou G, Velazquez MA, Thompson P, Treumann A, O'Connell MJ, Forde N. The role of CAPG in molecular communication between the embryo and the uterine endometrium: Is its function conserved in species with different implantation strategies? Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. PMID 32619075 DOI: 10.1096/Fj.202000882Rr  0.312
2019 Walker CH, Siu-Ting K, Taylor A, O'Connell MJ, Bennett T. Strigolactone synthesis is ancestral in land plants, but canonical strigolactone signalling is a flowering plant innovation. Bmc Biology. 17: 70. PMID 31488154 DOI: 10.1186/S12915-019-0689-6  0.676
2019 Tollis M, Robbins J, Webb AE, Kuderna LFK, Caulin AF, Garcia JD, Bèrubè M, Pourmand N, Marques-Bonet T, O'Connell MJ, Palsbøll PJ, Maley CC. Return to the sea, get huge, beat cancer: an analysis of cetacean genomes including an assembly for the humpback whale (Megaptera novaeangliae). Molecular Biology and Evolution. PMID 31070747 DOI: 10.1093/Molbev/Msz099  0.576
2019 Tuteja R, McKeown PC, Ryan P, Morgan CC, Donoghue MTA, Downing T, O'Connell MJ, Spillane C. Paternally expressed imprinted genes under positive Darwinian selection in Arabidopsis thaliana. Molecular Biology and Evolution. PMID 30913563 DOI: 10.1093/Molbev/Msz063  0.62
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  0.794
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  0.467
2017 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 Evolutionary Biology. 17: 170. PMID 28732464 DOI: 10.1186/s12862-017-1015-y  0.768
2017 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: 135. PMID 28606132 DOI: 10.1186/s12862-017-0990-3  0.719
2017 McInerney JO, McNally A, O'Connell MJ. Why prokaryotes have pangenomes. Nature Microbiology. 2: 17040. PMID 28350002 DOI: 10.1038/Nmicrobiol.2017.40  0.623
2017 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: 90. PMID 28335725 DOI: 10.1186/S12862-017-0937-8  0.717
2017 McInerney JO, O'Connell MJ. Microbiology: Mind the gaps in cellular evolution. Nature. 541: 297-299. PMID 28102241 DOI: 10.1038/Nature21113  0.594
2016 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. PMID 27270397 DOI: 10.1016/J.Vetpar.2016.05.014  0.759
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  0.673
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  0.678
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  0.785
2015 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 HS, Grishin NV, et al. Insights into the evolution of longevity from the bowhead whale genome. Cell Reports. 10: 112-22. PMID 25565328 DOI: 10.1016/J.Celrep.2014.12.008  0.591
2015 Moran R, Morgan C, O'Connell M. A Guide to Phylogenetic Reconstruction Using Heterogeneous Models—A Case Study from the Root of the Placental Mammal Tree Computation. 3: 177-196. DOI: 10.3390/computation3020177  0.499
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  0.737
2014 McInerney JO, O'Connell MJ. Evolutionary developmental biology: Ghost locus appears. Nature. 514: 570-1. PMID 25355355 DOI: 10.1038/514570A  0.645
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  0.719
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  0.715
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  0.673
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  0.768
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  0.524
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  0.793
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  0.779
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  0.78
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  0.476
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  0.407
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  0.816
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  0.743
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  0.709
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  0.512
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  0.752
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  0.815
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  0.796
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  0.765
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  0.494
2007 Stewart C, Mazourek M, Stellari GM, O'Connell M, Jahn M. Genetic control of pungency in C. chinense via the Pun1 locus. Journal of Experimental Botany. 58: 979-91. PMID 17339653 DOI: 10.1093/Jxb/Erl243  0.329
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  0.355
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  0.559
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  0.647
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  0.609
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  0.758
1994 Wolters A, Jacobsen E, O'Connell M, Bonnema G, Ramulu KS, Jong Hd, Schoenmakers H, Wijbrandi J, Koornneef M. Somatic hybridization as a tool for tomato breeding. Euphytica. 79: 265-277. DOI: 10.1007/Bf00022527  0.322
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