Contact

• workRoom B62 Life Sciences
  University Park
  Nottingham
  NG7 2RD
  UK
• work0115 7487196
• Mary.O'Connell@nottingham.ac.uk
• www.mol-evol.org

Biography

I was a lecturer, then senior lecturer, then deputy head of department at the School of Biotechnology, Dublin City University from 2005 until 2015. In 2012, I spent a year as a Fulbright visiting professor at Harvard in the Department of Organismal and Evolutionary Biology and the Museum of Comparative Zoology, where I worked with Professor Scott Edwards and his group. In September 2015 I left DCU to take up my "250 Great Minds University Academic Fellowship" at the University of Leeds. At the University of Leeds, along with Dr. Niamh Forde and Dr. Julie Aspden, we established the Leedsomics research institute. In July 2018 I was appointed as an Associate Professor in the School of Life Sciences at the University of Nottingham, where I am currently based. I am a council member for the international Society for Molecular Biology and Evolution, and am an associate editor for both of the societies journals (GBE and MBE). I am an elected fellow of the Linnean Society and an invited research associated of the Natural History museum London for my work on comparative genomics.

I am passionate about promoting evolutionary biology and in 2012, I was a co-organiser of the annual SMBE meeting in Dublin, Ireland, which was attended by 1,300 delegates. I have organised and taught on EMBO advanced courses in Phylogenetics and phylogenomics in Maynooth, Ireland (2004), Medellin, Colombia (2009), Erice, Sicily (2013) and Iquitos, Peru (2016).

Expertise Summary

I am an evolutionary genomicist. My research group has four research areas of interest - Phylogenomics, Mechanisms of Protein evolution, Evolutionary Theory, and Adaptation.

Recent Publications

• MCCARTNEY, ANN M., HYLAND, EDEL M., CORMICAN, PAUL, MORAN, RAYMOND J., WEBB, ANDREW E., LEE, KATE D., HERNANDEZ-RODRIGUEZ, JESSICA, PRADO-MARTINEZ, JAVIER, CREEVEY, CHRISTOPHER J., ASPDEN, JULIE L., MCINERNEY, JAMES O., MARQUES-BONET, TOMAS and O'CONNELL, MARY J., 2019. Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human GENOME BIOLOGY AND EVOLUTION. 11(9), 2678-2690
• TOLLIS, MARC, ROBBINS, JOOKE, WEBB, ANDREW E., KUDERNA, LUKAS F. K., CAULIN, ALEAH F., GARCIA, JACINDA D., BERUBE, MARTINE, POURMAND, NADER, MARQUES-BONET, TOMAS, O'CONNELL, MARY J., PALSBOLL, PER J. and MALEY, CARLO C., 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. 36(8), 1746-1763
• COCKBURN, JOSEPH J. B., HESKETH, SOPHIE J., MULHAIR, PETER, THOMSEN, MAREN, O'CONNEL, MARY J. and WAY, MICHAEL, 2018. Insights into Kinesin-1 Activation from the Crystal Structure of KLC2 Bound to JIP3 STRUCTURE. 26(11), 1486-+
• MCINERNEY, J. O. and O'CONNELL, M. J., 2017. Microbiology: Mind the gaps in cellular evolution: Nature Nature. 541(7637), 297-299

• View all publications

Please visit our lab website for more details: www.mol-evol.org

• MCCARTNEY, ANN M., HYLAND, EDEL M., CORMICAN, PAUL, MORAN, RAYMOND J., WEBB, ANDREW E., LEE, KATE D., HERNANDEZ-RODRIGUEZ, JESSICA, PRADO-MARTINEZ, JAVIER, CREEVEY, CHRISTOPHER J., ASPDEN, JULIE L., MCINERNEY, JAMES O., MARQUES-BONET, TOMAS and O'CONNELL, MARY J., 2019. Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human GENOME BIOLOGY AND EVOLUTION. 11(9), 2678-2690
• TOLLIS, MARC, ROBBINS, JOOKE, WEBB, ANDREW E., KUDERNA, LUKAS F. K., CAULIN, ALEAH F., GARCIA, JACINDA D., BERUBE, MARTINE, POURMAND, NADER, MARQUES-BONET, TOMAS, O'CONNELL, MARY J., PALSBOLL, PER J. and MALEY, CARLO C., 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. 36(8), 1746-1763
• COCKBURN, JOSEPH J. B., HESKETH, SOPHIE J., MULHAIR, PETER, THOMSEN, MAREN, O'CONNEL, MARY J. and WAY, MICHAEL, 2018. Insights into Kinesin-1 Activation from the Crystal Structure of KLC2 Bound to JIP3 STRUCTURE. 26(11), 1486-+
• MCINERNEY, J. O. and O'CONNELL, M. J., 2017. Microbiology: Mind the gaps in cellular evolution: Nature Nature. 541(7637), 297-299
• MCINERNEY, J. O., MCNALLY, A. and O'CONNELL, M. J., 2017. Why prokaryotes have pangenomes: Nat Microbiol Nat Microbiol. 2, 17040
• MCINERNEY, JAMES O., MCNALLY, ALAN and O'CONNELL, MARY J., 2017. Reply to 'The population genetics of pangenomes' NATURE MICROBIOLOGY. 2(12), 1575-1575
• WEBB, ANDREW E., WALSH, THOMAS A. and O'CONNELL, MARY J., 2017. VESPA: Very large-scale Evolutionary and Selective Pressure Analyses PEERJ COMPUTER SCIENCE.
• MORGAN, CLAIRE C., LOUGHRAN, NOELEEN B., WALSH, THOMAS A., HARRISON, ALAN J. and O'CONNELL, MARY J., 2017. Positive selection neighboring functionally essential sites and disease-implicated regions of mammalian reproductive proteins (vol 10, 39, 2010) BMC EVOLUTIONARY BIOLOGY. 17,
• LYNCH, MARK, WALSH, THOMAS A., MARSZALOWSKA, IZABELA, WEBB, ANDREW E., MACAOGAIN, MICHEAL, ROGERS, THOMAS R., WINDLE, HENRY, KELLEHER, DERMOT, O'CONNELL, MARY J. and LOSCHER, CHRISTINE E., 2017. Surface layer proteins from virulent Clostridium difficile ribotypes exhibit signatures of positive selection with consequences for innate immune response BMC EVOLUTIONARY BIOLOGY. 17,
• MCRAE, KATHRYN M., GOOD, BARBARA, HANRAHAN, JAMES P., MCCABE, MATTHEW S., CORMICAN, PAUL, SWEENEY, TORRES, O'CONNELL, MARY J. and KEANE, ORLA M., 2016. 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
• TARVER, JAMES E., DOS REIS, MARIO, MIRARAB, SIAVASH, MORAN, RAYMOND J., PARKER, SEAN, O'REILLY, JOSEPH E., KING, BENJAMIN L., O'CONNELL, MARY J., ASHER, ROBERT J., WARNOW, TANDY, PETERSON, KEVIN J., DONOGHUE, PHILIP C. J. and PISANI, DAVIDE, 2016. The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference GENOME BIOLOGY AND EVOLUTION. 8(2), 330-344
• GUNN, L., COLLINS, P. J., O'CONNELL, M. J. and O'SHEA, H., 2015. Phylogenetic investigation of enteric bovine coronavirus in Ireland reveals partitioning between European and global strains IRISH VETERINARY JOURNAL. 68,
• KILCREASE, JAMES, RODRIGUEZ-URIBE, LAURA, RICHINS, RICHARD D., ARCOS, JUAN MANUEL GARCIA, VICTORINO, JESUS and O'CONNELL, MARY A., 2015. Correlations of carotenoid content and transcript abundances for fibrillin and carotenogenic enzymes in Capsicum annum fruit pericarp PLANT SCIENCE. 232, 57-66
• MORAN, RAYMOND J., MORGAN, CLAIRE C. and O'CONNELL, MARY J., 2015. A Guide to Phylogenetic Reconstruction Using Heterogeneous Models-A Case Study from the Root of the Placental Mammal Tree COMPUTATION. 3(2), 177-196
• WEBB, ANDREW E., GEREK, Z. NEVIN, MORGAN, CLAIRE C., WALSH, THOMAS A., LOSCHER, CHRISTINE E., EDWARDS, SCOTT V. and O'CONNELL, MARY J., 2015. Adaptive Evolution as a Predictor of Species-Specific Innate Immune Response MOLECULAR BIOLOGY AND EVOLUTION. 32(7), 1717-1729
• KEANE, MICHAEL, SEMEIKS, JEREMY, WEBB, ANDREW E., LI, YANG I., QUESADA, VICTOR, CRAIG, THOMAS, MADSEN, LONE BRUHN, VAN DAM, SIPKO, BRAWAND, DAVID, MARQUES, PATRICIA I., MICHALAK, PAWEL, KANG, LIN, BHAK, JONG, YIM, HYUNG-SOON, GRISHIN, NICK V., NIELSEN, NYNNE HJORT, HEIDE-JORGENSEN, MADS PETER, OZIOLOR, ELIAS M., MATSON, COLE W., CHURCH, GEORGE M., STUART, GARY W., PATTON, JOHN C., GEORGE, J. CRAIG, SUYDAM, ROBERT, LARSEN, KNUD, LOPEZ-OTIN, CARLOS, O'CONNELL, MARY J., BICKHAM, JOHN W., THOMSEN, BO and DE MAGALHAES, JOAO PEDRO, 2015. Insights into the Evolution of Longevity from the Bowhead Whale Genome CELL REPORTS. 10(1), 112-122
• HUGHES, L, CARTON, R, MINGUZZI, S, MCENTEE, G, DEINUM, E.E, O'CONNELL, M,A 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. 589(15), 37173
• MCINERNEY, J. O. and O'CONNELL, M. J., 2014. Evolutionary developmental biology: Ghost locus appears: Nature Nature. 514(7524), 570-1
• LIU, S., LORENZEN, E. D., FUMAGALLI, M., LI, B., HARRIS, K., XIONG, Z., ZHOU, L., KORNELIUSSEN, T. S., SOMEL, M., BABBITT, C., WRAY, G., LI, J., HE, W., WANG, Z., FU, W., XIANG, X., MORGAN, C. C., DOHERTY, A., O'CONNELL, M. J., MCINERNEY, J. O., BORN, E. W., DALEN, 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 Cell. 157(4), 785-94
• MCINERNEY, J. O., O'CONNELL, M. J. and PISANI, D., 2014. The hybrid nature of the Eukaryota and a consilient view of life on Earth: Nat Rev Microbiol Nat Rev Microbiol. 12(6), 449-55
• HAGGERTY, L. S., JACHIET, P. A., HANAGE, W. P., FITZPATRICK, D. A., LOPEZ, P., O'CONNELL, M. J., PISANI, D., WILKINSON, M., BAPTESTE, E. and MCINERNEY, J. O., 2014. A pluralistic account of homology: adapting the models to the data: Mol Biol Evol Mol Biol Evol. 31(3), 501-16
• BALDWIN, MAUDE W., TODA, YASUKA, NAKAGITA, TOMOYA, O'CONNELL, MARY J., KLASING, KIRK C., MISAKA, TAKUMI, EDWARDS, SCOTT V. and LIBERLES, STEPHEN D., 2014. Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor SCIENCE. 345(6199), 929-933
• BALDWIN, MAUDE W, TODA, YASUKA, NAKAGITA, TOMOYA, O'CONNELL, MARY J, KLASING, KIRK C, MISAKA, TAKUMI, EDWARDS, SCOTT V and LIBERLES, STEPHEN D, 2014. Data from: Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor Dryad.
• LOUGHRAN, N. B., O'CONNELL, M. J., O'CONNOR, B. and O'FAGAIN, C., 2014. Stability properties of an ancient plant peroxidase BIOCHIMIE. 104, 156-159
• MCRAE, KATHRYN M., GOOD, BARBARA, HANRAHAN, JAMES P., GLYNN, ASSUMPTA, O'CONNELL, MARY J. and KEANE, ORLA M., 2014. Response to Teladorsagia circumcincta infection in Scottish Blackface lambs with divergent phenotypes for nematode resistance VETERINARY PARASITOLOGY. 206(3-4), 200-207
• COLLINS, LAURA E., LYNCH, MARK, MARSZALOWSKA, IZABELA, KRISTEK, MAJA, ROCHFORT, KEITH, O'CONNELL, MARY, WIND, HENRY, KELLEHER, DERMOT and LOSCHER, CHRISTINE E., 2014. Surface layer proteins isolated from Clostridium difficile induce clearance responses in macrophages MICROBES AND INFECTION. 16(5), 391-400
• MORGAN, CLAIRE C., FOSTER, PETER G., WEBB, ANDREW E., PISANI, DAVIDE, MCINERNEY, JAMES O. and O'CONNELL, MARY J., 2013. Heterogeneous Models Place the Root of the Placental Mammal Phylogeny MOLECULAR BIOLOGY AND EVOLUTION. 30(9), 2145-2156
• MORGAN, CLAIRE C., MC CARTNEY, ANN M., DONOGHUE, MARK T.A., LOUGHRAN, NOELEEN B., SPILLANE, CHARLES, TEELING, EMMA C. and O'CONNELL, MARY J., 2013. Molecular adaptation of telomere associated genes in mammals. BMC Evolutionary Biology. 13, Article251, 1-13
• DMITRIEV, PETR, BARAT, ANA, POLESSKAYA, ANNA, O'CONNELL, MARY J., ROBERT, THOMAS, DESSEN, PHILIPPE, WALSH, THOMAS A., LAZAR, VLADIMIR, TURKI, AHMED, CARNAC, GILLES, LAOUDJ-CHENIVESSE, DALILA, LIPINSKI, MARC and VASSETZKY, YEGOR S., 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,
• O'CONNELL, MARY J, DOYLE, AISLING M, JUENGER, THOMAS E, DONOGHUE, MARK T A, KESHAVAIAH, CHANNA, TUTEJA, REETU and SPILLANE, CHARLES, 2012. In Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure. BMC research notes. 5, 359
• LOUGHRAN, NOELEEN B., HINDE, SARA, MCCORMICK-HILL, SALLY, LEIDAL, KEVIN G., BLOOMBERG, SARAH, LOUGHRAN, SINEAD T., O'CONNOR, BRENDAN, O'FAGAIN, CIARAN, NAUSEEF, WILLIAM M. and O'CONNELL, MARY J., 2012. Functional Consequence of Positive Selection Revealed through Rational Mutagenesis of Human Myeloperoxidase MOLECULAR BIOLOGY AND EVOLUTION. 29(8), 2039-2046
• SHAKYA, KABITA, O'CONNELL, MARY J. and RUSKIN, HEATHER J., 2012. The landscape for epigenetic/epigenomic biomedical resources EPIGENETICS. 7(9), 982-986
• RODRIGUEZ-URIBE, LAURA, GUZMAN, IVETTE, RAJAPAKSE, WATHSALA, RICHINS, RICHARD D. and O'CONNELL, MARY A., 2012. Carotenoid accumulation in orange-pigmented Capsicum annuum fruit, regulated at multiple levels JOURNAL OF EXPERIMENTAL BOTANY. 63(1), 517-526
• MORGAN, CLAIRE C., SHAKYA, KABITA, WEBB, ANDREW, WALSH, THOMAS A., LYNCH, MARK, LOSCHER, CHRISTINE E., RUSKIN, HEATHER J. and O'CONNELL, MARY J., 2012. Colon cancer associated genes exhibit signatures of positive selection at functionally significant positions BMC EVOLUTIONARY BIOLOGY. 12,
• MCINERNEY, J. O., PISANI, D., BAPTESTE, E. and O'CONNELL, M. J., 2011. The Public Goods Hypothesis for the evolution of life on Earth: Biol Direct Biol Direct. 6, 41
• RYAN, ANTHONY, LYNCH, MARK, SMITH, SINEAD M., AMU, SYLVIE, NEL, HENDRIK J., MCCOY, CLAIRE E., DOWLING, JENNIFER K., DRAPER, EVE, O'REILLY, VINCENT, MCCARTHY, CIARA, O'BRIEN, JULIE, EIDHIN, DEIRDRE NI, O'CONNELL, MARY J., KEOGH, BRIAN, MORTON, CHARLES O., ROGERS, THOMAS R., FALLON, PADRAIC G., O'NEILL, LUKE A., KELLEHER, DERMOT and LOSCHER, CHRISTINE E., 2011. A Role for TLR4 in Clostridium difficile Infection and the Recognition of Surface Layer Proteins PLOS PATHOGENS. 7(6),
• MCCOLE, RUTH B., LOUGHRAN, NOELEEN B., CHAHAL, MANDEEP, FERNANDES, LUIS P., ROBERTS, ROLAND G., FRATERNALI, FRANCA, O'CONNELL, MARY J. and OAKEY, REBECCA J., 2011. A CASE-BY-CASE EVOLUTIONARY ANALYSIS OF FOUR IMPRINTED RETROGENES EVOLUTION. 65(5), 1413-1427
• O'CONNELL, MARY J., 2010. Selection and the Cell Cycle: Positive Darwinian Selection in a Well-Known DNA Damage Response Pathway JOURNAL OF MOLECULAR EVOLUTION. 71(5-6), 444-457
• O'CONNELL, MARY J., LOUGHRAN, NOELEEN B., WALSH, THOMAS A., DONOGHUE, MARK T. A., SCHMID, KARL J. and SPILLANE, CHARLES, 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), 486-498
• RICHINS, RICHARD D., MICHELETTO, SANDRA and O'CONNELL, MARY A., 2010. Gene expression profiles unique to chile (Capsicum annuum L.) resistant to Phytophthora root rot PLANT SCIENCE. 178(2), 192-201
• MORGAN, CLAIRE C., LOUGHRAN, NOELEEN B., WALSH, THOMAS A., HARRISON, ALAN J. and O'CONNELL, MARY J., 2010. Positive selection neighboring functionally essential sites and disease-implicated regions of mammalian reproductive proteins BMC EVOLUTIONARY BIOLOGY. 10,
• RYAN, BARRY J., O'CONNELL, MARY J. and O'FAGAIN, CIARAN, 2008. Consensus mutagenesis reveals that non-helical regions influence thermal stability of horseradish peroxidase BIOCHIMIE. 90(9), 1389-1396
• LOUGHRAN, NOELEEN B., O'CONNOR, BRENDAN, O'FAGAIN, CIARAN and O'CONNELL, MARY J., 2008. The phylogeny of the mammalian heme peroxidases and the evolution of their diverse functions BMC EVOLUTIONARY BIOLOGY. 8,
• O'CONNELL, M.J. and MCINERNEY, J.O., 2007. Reconstructing the ancestral eukaryote: lessons from the past: Ancestral sequence reconstruction Ancestral sequence reconstruction. 103
• HAUN, WILLIAM J., LAOUEILLE-DUPRAT, SYLVIA, O'CONNELL, MARY J., SPILLANE, CHARLES, GROSSNIKLAUS, UELI, PHILLIPS, ALLISON R., KAEPPLER, SHAWN M. and SPRINGER, NATHAN M., 2007. Genomic imprinting, methylation and molecular evolution of maize Enhancer of zeste (Mez) homologs PLANT JOURNAL. 49(2), 325-337
• TRAVERS, S. A., O'CONNELL, M. J., MCCORMACK, G. P. and MCINERNEY, J. O., 2005. Evidence for heterogeneous selective pressures in the evolution of the env gene in different human immunodeficiency virus type 1 subtypes: J Virol J Virol. 79(3), 1836-41
• O'CONNELL, M. J. and MCINERNEY, J. O., 2005. Gamma chain receptor interleukins: evidence for positive selection driving the evolution of cell-to-cell communicators in the mammalian immune system: J Mol Evol J Mol Evol. 61(5), 608-19
• O'CONNELL, M. J. and MCINERNEY, J. O., 2005. Adaptive evolution of the human fatty acid synthase gene: support for the cancer selection and fat utilization hypotheses?: Gene Gene. 360(2), 151-9
• CREEVEY, C.J, FITZPATRICK, D.A, PHILIP, G.K, KINSELLA, R.J, O'CONNELL, M,A, PENTONY, M.M, TRAVERS, S.A, WIKINSON, M and MCINERNEY, J.O, 2004. Does a tree-like phytogeny only exist at the tips in the prokaryotes? Proceedings of the Royal Society B: Biological Sciences. 271(557), 2551-2558