1. Hyland EM*, Webb AE, Kennedy KF, Gerek N, Loscher CE, and O’Connell MJ* (2021) “Adaptive evolution in TIR domain-containing adapter inducing IFN-β (TRIF) leads to discordance between human and mouse TRIF-dependent innate immune signaling.” Genome Biology and Evolution 13 (12), https://doi.org/10.1093/gbe/evab268.
2. Taylor AS, Tinning H, Ovchinnikov V, Smith W, Pullinger AL, Sutton RA, Constantinides B, Wang D, Forde N, O’Connell MJ (2021) An ancestral burst of regulatory and protein innovation drives divergent implantation in eutherian mammals. bioRxiv https://www.biorxiv.org/content/10.1101/2021.07.22.453388v2
3. Douka K, Birds I, Wang D, Kosteletos A, Clayton S, Byford A, Vasconcelos EJR, O’Connell MJ, Deuchars J, Whitehouse A, Aspden JL. (2021) Cytoplasmic long noncoding RNAs are differentially regulated and translated during human neuronal differentiation. RNA. 27 (9), 1082-1101. https://rnajournal.cshlp.org/content/early/2021/06/30/rna.078782.121
4. Hopes T, Norris K, Agapiou M, McCarthy CGP, Lewis PA, O’Connell MJ, Fontana J, Julie L Aspden (2021) Ribosome heterogeneity in Drosophila melanogaster gonads through paralog-switching. Nucleic Acids Research, gkab606, https://doi.org/10.1093/nar/gkab606
5. Nikolopoulos G, Smith CEL, Poulter JA, Murillo G, Silva S, Brown CJ, Day PF, Soldani F, Al-Bahlani S, Harris SA, O’Connell MJ, Inglehearn CF, and Mighell AJ. (2021) Spectrum of pathogenic variants and founder effects in amelogenesis imperfecta associated with MMP20. Human Mutation. https://doi.org/10.1002/humu.24187 
6. Tinning H, Taylor A, Wang D,  Constantinides B, Sutton R, Oikonomu G, Velazquez MA, Thompson P, Treumann A, O’Connell MJ, Forde N. (2020). 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 J.  Aug;34(8):11015-11029. DOI: 10.1096/fj.202000882RR
7. Nikolopoulos G, Smith CEL, Brookes SJ, El‐Asrag ME, Brown CJ, Patel A, Murillo G, O’Connell MJ, Inglehearn CF, Mighell AJ. (2020) New missense variants in RELT causing hypomineralised amelogenesis imperfecta. Clinical Genetics https://doi.org/10.1111/cge.13721.
8. McInerney J.O., Whelan F.J., Domingo-Sananes M.R., McNally A., O’Connell M.J. (2020) Pangenomes and Selection: The Public Goods Hypothesis. In: Tettelin H., Medini D. (eds) The Pangenome. Springer, Cham. https://doi.org/10.1007/978-3-030-38281-0_7
9. Walker C, Siu-Ting K, Taylor A, O’Connell MJ, Bennett T. (2019) Strigolactone synthesis is ancestral in land plants, but canonical strigolactone signalling is a flowering plant innovation. BMC Biology 17:70 https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-019-0689-6
10. McCartney AM, Hyland EM, Cormican P, Moran RJ, Webb AE, Lee KD, Hernandez J, Prado-Martinez J, Creevey CJ, Aspden, JL, McInerney JO, Marques-Bonet T, and O’Connell MJ*. (2019) Gene Fusions derived by transcriptional readthrough are Driven by Segmental Duplication in Human. Genome Biology and Evolution. Sep 1;11(9):2678-2690 https://doi.org/10.1093/gbe/evz163
11. 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. (2019) 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. Aug 1;36(8):1746-1763. https://doi.org/10.1093/molbev/msz099
12. Siu-Ting K, Torres-Sánchez M, San Mauro D, Wilcockson D, Wilkinson M, Pisani D, O’Connell MJ, CreeveyCJ. (2019) Inadvertent paralog inclusion drives artefactual topologies and timetree estimates in phylogenomics. Molecular Biology and Evolution. Jun 1;36(6): 1344–1356 https://doi.org/10.1093/molbev/msz067
13. Tuteja R, McKeown PC*, Ryan P, Morgan CC, Donoghue MTA, Downing T, O’Connell MJ*, Spillane C*. (2019) Paternally expressed imprinted genes under positive Darwinian selection in Arabidopsis thaliana. Molecular Biology and Evolution. Jun 1;36(6):1239-1253 https://doi.org/10.1093/molbev/msz063
14. Cockburn JJB, Hesketh, SJ, Mulhair PJ, O’Connell MJ, and Way M. (2018) Insights into Kinesin-1 activation from the crystal structure of KLC2 bound to JIP3. Structure (Cell Press) Nov 6;26(11):1486-1498.e6 
15. Foley NM, Hughes GM, Huang Z, Clarke M, Jebb D, Whelan CV, Petit EJ, Touzalin F, Farcy O, Jones G, Ransome RD, Kacprzyk J, O’Connell MJ, Kerth G, Rebelo H, Rodrigues L, Puechmaille SJ, Teeling EC. (2018) Growing old, yet staying young: The role of telomeres in bats’ exceptional longevity. Science Advances 07 Feb 2018: Vol. 4(2).
16. Webb AE, Walsh TA, O’Connell MJ*. (2017) VESPA: Very large-scale Evolutionary and Selective Pressure Analyses. PeerJ Computer Science
17. Lynch M, Walsh TA, Marszalowska I, Webb AE, MacAogáin M, Rogers TR, Windle H, Kelleher D, O’Connell MJ*, Loscher CE (2017). Surface Layer Proteins from virulent Clostridium difficile ribotypes exhibit signatures of positive selection with consequences for innate immune response. BMC Evolutionary Biology. 
18. McInerney JO, McNally A, and O’Connell MJ (2017). Why Prokaryotes have pangenomes. Nature Microbiology. 
19. McInerney JO and O’Connell MJ (2017). Mind the Gaps in Cellular Evolution. Nature. 
20. Williams JM, Bezak T, Das M, Ning Z, Lucking EF, Kelly VP, Harrison P, Young P, O’Connell MJ, Dockery P, O’Halloran KD, and Moore T* (2016). Psg22 null mouse embryos develop normally under normoxic and hypoxic conditions of pregnancy. Science Matters. 
21. McRae KM, Good B, Hanrahan JP, McCabe MS, Cormican P, Sweeney T, O’Connell MJ, Keane OM* (2016). Transcriptional profiling of the ovine abomasal lymph node reveals a role for timing of the immune response in gastrointestinal nematode resistance. Veterinary Parasitology.
22. Tarver JE*, dos Reis M, Mirarab S, Moran RJ, Parker S, King BL, O’Connell MJ, Asher RJ, Warnow T, Peterson KJ, Donoghue PCJ and Pisani D* (2016). The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference. Genome Biology and Evolution. 
23. McInerney JO, Pisani D and O’Connell MJ (2015). The Ring Of Life Hypothesis For Eukaryote Origins Is Supported By Multiple Kinds Of Data. Philosophical Transactions of the Royal Society of London, B Series .
24. Hughes L, Carton R, Minguzzia S, McEntee, Deinumd EE, O’Connell MJ, and Parle-McDermott A* (2015) An active second dihydrofolate reductase enzyme is not a feature of rat and mouse, but they do have activity in their mitochondria. FEBs Letters..
25. Webb AE, Gerek ZN, Morgan CC, Walsh AT, Loscher CE, Edwards SV, O’Connell MJ* (2015) Adaptive Evolution as a predictor of species-specific innate immune response. Molecular Biology and Evolution. .
26. Moran RJ, Morgan CC, O’Connell MJ* (2015) A guide to phylogenetic reconstruction using heterogeneous models – a case study from the root of the placental mammal tree. Computation. .
27. Keane M*, Semeiks J*, Webb AE*, Li YI, Quesada V, Craig T, Bruhn Madsen L, van Dam S, Brawand D, Marques PI, Michalak P, Kang L, Bhak J, Yim HS, 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 (2015) Insights into the evolution of longevity from the bowhead whale genome. (*here indicates first authors) Cell Reports. .
28. McInerney JO and O’Connell MJ (2014) Evolutionary Developmental Biology: Ghost Locus Appears. Nature  .
29. McRae KM, Good B, Hanrahan JP, Glynn A, O’Connell MJ, Keane OM (2014) Response to Teladorsagia circumcincta infection in Scottish Blackface lambs with divergent phenotypes for nematode resistance. Veterinary Parasitology .
30. Morgan CC, Creevey CJ, and O’Connell MJ (2014) Mitochondrial data are not suitable for resolving Placental mammal phylogeny. Mammalian Genome .
31. Baldwin MW,  Toda Y, Nakagita T, O’Connell MJ, Klasing KC , Misaka T, Edwards SV and Liberles SD (2014) Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor. Science  
32. Loughran NB, O’Connell MJ, O’Connor B, O’Fagain C (2014). Stability properties of an ancient plant peroxidase. Biochimie
33. McInerney JO, O’Connell MJ and Pisani D (2014) The hybrid nature of the Eukaryota and a consilient view of life on Earth. Nature Reviews Microbiology .
34. 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 and Wang J (2014) Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears. Cell Volume 157, Issue 4, p785–794, 8 May..
35. Collins LE, Lynch M, Marszalowska I, Kristek M, Rochfort K, O’Connell MJ, Windle H, Kelleher D and Loscher CE (2014) Surface Layer Proteins Isolated from Clostridium difficile Induce Clearance Responses in Macrophages. Microbes and Infection. http://dx.doi.org/10.1016/j.micinf.2014.02.001 .
36. Haggerty LS, Jachiet PA, Hanage WP, Fitzpatrick D, Lopez P, O’Connell MJ, Pisani D, Wilkinson M, Bapteste E and McInerney JO* (2014) A pluralistic account of homology: adapting the models to the data. Molecular Biology and Evolution. doi: 10.1093/molbev/mst228 .
37. Morgan CC, McCartney AM, Donoghue MTA, Loughran NB, Spillane C, Teeling EC and O’Connell MJ* (2013) Molecular adaptation of telomere associated genes in mammals. BMC Evolutionary Biology. 13:251. doiL10.1186/1471-2148-13-251 .
38. Morgan CC, Foster PG, Webb AE, Pisani D, McInerney JO and O’Connell MJ* (2013) Heterogeneous models place the root of the placental mammal phylogeny. Molecular Biology and Evolution. doi: 10.1093/molbev/mst11 .
39. Dmitriev P, Barat A, Polesskaya A, O’Connell MJ, Robert T, Dessen T, Walsh TA, Lazar V, Turki A, Carnac G, Laoudj-Chenivesse D, Lipinski M and Vassetzky YS. (2013) 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. doi:10.1186/1471-2164-14-265   .
40. Shakya K, O’Connell MJ and Ruskin HJ (2012) The Landscape for Epigenetic/Epigenomic Biomedical Resources. Epigenetics 7(9):982-6 .
41. Morgan CC, Shakya K, Webb AE, Walsh TA, Lynch M, Loscher CE, Ruskin HJ and O’Connell MJ* (2012) Colon cancer associated genes exhibit signatures of positive selection at functionally significant positions. BMC Evolutionary Biology 12:114 doi:10.1186/1471-2148-12-114 .
42. O’Connell MJ*, Doyle AM*, Juenger TE, Keshavaiah C, Donoghue MTA, Tuteja R and Spillane C (2012) In Arabidopsis thaliana codon volatility scores reflects GC3 composition rather than selective pressure. BMC Research Notes 5:359. doi: 10.1186/1756-0500-5-359. .
43. 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. Molecular Biology and Evolution 29 (8): 2039-2046 .
44. McInerney JO, Pisani D, Bapteste E, and O’Connell MJ (2011) The public goods hypothesis for the evolution of life on Earth. DOI:10.1186/1745-6150-6-41 Biology Direct  .
45. 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 .
46. McCole RB, Loughran NB, Chahal M, Fernandes LP, Roberts RG, Fraternali F, O’Connell MJ and Oakey RJ (2011) A Case-by-case evolutionary analysis of four Imprinted retrogenes. DOI: 10.1111/j.1558-5646.2010.01213.x Evolution .
47. O’Connell MJ* (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 .
48. O’Connell MJ*, Loughran NB, Walsh TA, Donoghue MTA, Schmid KJ, and 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 .
49. Morgan CC, Loughran NB, Walsh TA, Harrison AJ, and O’Connell MJ* (2010) Positive Selection neighboring functionally essential sites and disease-implicated regions of mammalian reproductive proteins. 10:39doi:10.1186/1471-2148-10-39 BMC Evolutionary Biology .
50. Loughran NB, O’Connor B, Fagan C and O’Connell MJ* (2008) The Phylogeny of the Mammalian Heme Peroxidases and the evolution of their diverse functions. 8:101doi:10.1186/1471-2148-8-101 BMC Evolutionary Biology .
51. Ryan BJ, O’Connell MJ and Fagan CP (2008) The consensus approach to protein stabilization is not a global solution: insights from extant and extinct peroxidases.  90, (9), 1414-1421 Biochimie .
52. Haun WJ, Laoueille S, O’Connell MJ, Spillane C, Grossniklaus U, Phillips AR, Kaeppler SM and Springer NM (2007). Genomic imprinting, methylation and molecular evolution of maize Enhancer of Zeste (Mez) homologs. 49(2):325-337 Plant J.  
53. O’Connell MJ and McInerney JO (2007). Reconstructing the ancestral eukaryote – lessons from the past, future perspectives. In Reconstructing Ancient Proteins. Eds: David Liberles. Oxford University Press.
54. McInerney JO, Pisani D, O’Connell MJ, Fitzpatrick DA, Creevey CJ (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.
55. O’Connell MJ and McInerney JO (2005). Adaptive evolution of the human fatty acid synthase gene: Support for the cancer selection and fat utilization hypotheses? Nov 7;360(2):151-159 Gene .
56. O’Connell MJ and McInerney JO (2005). Gamma chain receptor Interleukins: evidence for positive selection driving the evolution of cell-to-cell communicators in the mammalian immune system. 61(5):608-619 Journal of Molecular Evolution .
57. Travers SA, O’Connell MJ, McCormack G and McInerney JO (2005). Evidence for heterogeneous selective pressures in the evolution of the env gene in different human immunodeficiency virus type 1 subtypes. Feb 79(3):1836-1841 Journal of Virology .
58. Creevey CJ, Fitzpatrick DA, Philip GK, Kinsella RJ, O’Connell MJ, Pentony MM, Travers SA, Wilkinson M and McInerney JO (2004). Does a tree-like phylogeny only exist at the tips in the prokaryotes?  Dec 22;271(1557):2551-2558 Proceedings of the Royal Society of London Biology .