Dr David Fitzpatrick

    Biology, Human Health Institute

    Associate Professor

    Callan
    1.26
    (01) 708 6844

    Biography

    2024 - Present: Maynooth University. Professor and PI of Genome Evolution Laboratory.
    2024 - Present: Leeds Beckett University. Visiting Professor. 
    2020 - 2024: Maynooth University. Associate Professor and PI of Genome Evolution Laboratory.
    2009 - 2020: Maynooth University. Lecturer and PI of Genome Evolution Laboratory.
    2007 - 2009: University College Dublin. HRB Postdoctoral Fellow.
    2005 - 2007: University College Dublin. IRCSET Postdoctoral Fellow.
    2004 - 2005: N.U.I Maynooth. Postdoctoral Researcher.

    Education
    2015 - 2016 NUI Maynooth Postgraduate Diploma in Higher Education (PGDHE)
    2000 - 2004: NUI Maynooth PhD Bioinformatics.
    1996 - 2000: NUI Maynooth B.Sc. Biology (Hons).











    Research Interests

    The research of this laboratory focuses on the evolution of unicellular microorganisms paying special attention to fungal and oomycete species. We use genome sequencing, transcriptomics, proteomics, comparative genomics, phylogenomics, phylogenetics and synteny based tools to elucidate gene and genome evolution.


    Research Projects

    Title Role Description Start date End date Amount
    Biocontrol of Mushroom pathogens by Bacillus subtilis and genomic interactions between host, pathogen and biocontrol agent. PI (Joint with Prof. Kevin Kavanagh) 01/10/2020 01/10/2024 88000
    Analysis of introgression in prokaryotic genomes. PI 01/10/2015 30/09/2019 96000
    Teagasc Walsh fellowship application - Genomic, transcriptomic and proteomic analyses of A. bisporus strains resistant to mushroom virus X. PI 01/10/2015 30/09/2019 88000
    Utilising mushroom genomics to develop a molecular diagnostic for stable Agaricus bisporus inoculum and future strain development. PI 01/02/2015 31/07/2016 0
    nSilico Innovation Voucher PI 31/05/2013 30/09/2013 0
    Using the genome sequence of the emerging pathogen Candida krusei to identify virulence charateristics PI 01/01/2009 31/12/2011 0
    OMICs based investigation of a novel plant pathogen PI Phytophthora species include a broad range of devastating plant pathogens, which occur in both agricultural and natural settings. Phytophthora species have a significant impact on global agricultural resulting in multibillion-dollar losses and in many cases food shortages in developing countries. Phytophthora species cause significant ecological damage to forests and riparian areas. In particular, a new lethal disease of Alder trees has been observed in the last 25 years. Disease was shown to be caused by a new species called Phytophthora xalni. Phytophthora xalni is unique, as it has arisen from the hybridisation of two benign Phytophthora species (P. xmultiformis, P. uniformis). This illustrates the potential for the emergence of new plant pathogens through gene flow via hybridisation. The molecular mechanisms employed by P. xalni in terms of host range, infection and vegetative growth stages are unknown. To uncover these mechanisms this proposal proposes to sequence, annotate and compare the genomic sequences of P. xalni and its parents, followed by profiling mRNA and protein expression levels during its infection and benign growth stages to uncover key effector genes/proteins associated with infection. The forestry sector is worth approximately two billion euro to the Irish economy annually. Phytophthora xalni, is a significant issue to Alder trees. Alder improves soil fertility through its ability to fix nitrogen and also plays an important role in canal/river bank stability. This project sets out to uncover the mechanisms employed by P. xalni in initiating infection in healthy Alder trees. Understanding the molecular mechanisms of P. xalni will permit us to recommend controls against future infections. 01/10/2016 30/09/2020 96000

    Post Doctoral Fellows / Research Team

    Researcher Name Project Funding Body
    Joy Hanora Clarke Biocontrol of Mushroom pathogens by Bacillus subtilis and genomic interactions between host, pathogen and biocontrol agent.

    Peer Reviewed Journal

    Year Publication
    2024 Clarke, J.; Kosanovic, D.; Kavanagh, K.; Grogan, H.; Fitzpatrick, D.A. (2024) 'Draft genome sequence of the fungal biocontrol agent, Bacillus velezensis Kos'. Microbiology Resource Announcements, 13 . [Link] [DOI] [Full-Text]
    2024 Clarke, J.; McGuinness, B.; Fitzpatrick, D.; Kavanagh, K.; Grogan, H. (2024) 'Response of the mushroom pathogen Cladobotryum mycophilum to the fungicides prochloraz and metrafenone and two Bacillus-based biological control agents in mushroom crop trials'. Crop Protection, 177 . [Link] [DOI] [Full-Text]
    2024 Clarke, J.; Kavanagh, K.; Grogan, H.; Fitzpatrick, D.A. (2024) 'Population dynamics of mushroom casing over the course of Agaricus bisporus cultivation in the presence of Bacillus velezensis QST 713 and Bacillus velezensis Kos biocontrol agents'. Biological Control, 197 . [Link] [DOI] [Full-Text]
    2023 Petersen C; Sørensen T; Nielsen MR; Sondergaard TE; Sørensen JL; Fitzpatrick DA; Frisvad JC; Nielsen KL; (2023) 'Comparative genomic study of the Penicillium genus elucidates a diverse pangenome and 15 lateral gene transfer events'. Ima Fungus, 14 (1). [DOI] [Full-Text]
    2023 Shane G Downes, Rebecca A Owens, Kieran Walshe, David A Fitzpatrick, Amber Dorey, Gary W Jones, Sean Doyle (2023) 'Gliotoxin-mediated bacterial growth inhibition is caused by specific metal ion depletion'. Scientific Reports, 13 (1). [DOI] [Full-Text]
    2022 Doyle S.; Cuskelly D.D.; Conlon N.; Fitzpatrick D.A.; Gilmartin C.B.; Dix S.H.; Jones G.W. (2022) 'A Single Aspergillus fumigatus Gene Enables Ergothioneine Biosynthesis and Secretion by Saccharomyces cerevisiae'. International Journal of Molecular Sciences, 23 (18). [DOI] [Full-Text]
    2022 Dwyer, K; Bentley, IS; Fitzpatrick, DA; Saleh, AA; Tighe, E; McGleenan, E; Gaffney, D; Walsh, G (2022) 'Recombinant production, characterization and industrial application testing of a novel acidic exo/endo-chitinase from Rasamsonia emersonii'. Extremophiles : life under extreme conditions, 27 (2). [DOI] [Full-Text]
    2022 Daly P; Zhou D; Shen D; Chen Y; Xue T; Chen S; Zhang Q; Zhang J; McGowan J; Cai F; Pang G; Wang N; Sheikh TMM; Deng S; Li J; Soykam HO; Kara I; Fitzpatrick DA; Druzhinina IS; Bayram Akcapinar G; Wei L; (2022) 'Genome of Pythium myriotylum Uncovers an Extensive Arsenal of Virulence-Related Genes among the Broad-Host-Range Necrotrophic Pythium Plant Pathogens'. Microbiology Spectrum, . [DOI] [Full-Text]
    2022 Anna Rawlings, Eoin O'Connor, Suzy Moody, Ed Dudley, Lynne Boddy, Mike Fowler, David A. Fitzpatrick, Sean Doyle, Daniel Eastwood. (2022) 'Metabolic responses of two pioneer wood decay fungi to diurnally cycling temperature'. JOURNAL OF ECOLOGY, 110 (1):68-79. [Link] [DOI] [Full-Text]
    2022 Sarikaya Bayram Ö; Bayram Ö; Karahoda B; Meister C; Köhler AM; Thieme S; Elramli N; Frawley D; McGowan J; Fitzpatrick DA; Schmitt K; de Assis LJ; Valerius O; Goldman GH; Braus GH; (2022) 'F-box receptor mediated control of substrate stability and subcellular location organizes cellular development of Aspergillus nidulans'. PLoS Genetics, 18 (12). [DOI] [Full-Text]
    2022 Clarke J.; Grogan H.; Fitzpatrick D.; Kavanagh K. (2022) 'Characterising the proteomic response of mushroom pathogen Lecanicillium fungicola to Bacillus velezensis QST 713 and Kos biocontrol agents'. European Journal of Plant Pathology, . [DOI] [Full-Text]
    2021 Hanson S.J.; Cinnéide E.; Salzberg L.I.; Wolfe K.H.; McGowan J.; Fitzpatrick D.A.; Matlin K. (2021) 'Genomic diversity, chromosomal rearrangements, and interspecies hybridization in the Ogataea polymorpha species complex'. G3 (Bethesda, Md.), 11 (8). [DOI] [Full-Text]
    2021 Clarke J.; Grogan H.; Fitzpatrick D.; Kavanagh K. (2021) 'Analysis of the effect of Bacillus velezensis culture filtrate on the growth and proteome of Cladobotryum mycophilum'. Fungal Biology, . [DOI] [Full-Text]
    2021 Daly P.; Chen S.; Xue T.; Li J.; Sheikh T.M.M.; Zhang Q.; Wang X.; Zhang J.; Fitzpatrick D.A.; McGowan J.; Shi X.; Deng S.; Jiu M.; Zhou D.; Druzhinina I.S.; Wei L. (2021) 'Dual-Transcriptomic, Microscopic, and Biocontrol Analyses of the Interaction Between the Bioeffector Pythium oligandrum and the Pythium Soft-Rot of Ginger Pathogen Pythium myriotylum'. Frontiers in Microbiology, 12 . [DOI] [Full-Text]
    2021 Funk T.; Pharris A.; Spiteri G.; Bundle N.; Melidou A.; Carr M.; Gonzalez G.; Garcia-Leon A.; Crispie F.; O’Connor L.; Murphy N.; Mossong J.; Vergison A.; Wienecke-Baldacchino A.K.; Abdelrahman T.; Riccardo F.; Stefanelli P.; Di Martino A.; Bella A.; Lo Presti A.; Casaca P.; Moreno J.; Borges V.; Isidro J.; Ferreira R.; Gomes J.P.; Dotsenko L.; Suija H.; Epstein J.; Sadikova O.; Sepp H.; Ikonen N.; Savolainen-Kopra C.; Blomqvist S.; Möttönen T.; Helve O.; Gomes-Dias J.; Adlhoch C.; Macori G.; Russell L.; Yandle Z.; Bennett C.; O'Byrne E.; Murphy A.; Tuite G.; Conroy A.; Duffy M.; Morley U.; Keoghan B.; Ford I.; Kennedy M.; McDonnell S.; Flynn A.; Clarke A.; Crowley A.; Martin C.; Kelly E.; Foxton J.; Hare D.; Dunford L.; Connell J.; Moran J.; Dean J.; Fanning S.; Rajan L.; De Gascun C.; Kenny J.; Cotter P.; Walsh C.; Lawton E.; Fitzpatrick A.; Mullins E.; Della Bartola M.; McCabe M.; Stapleton P.; Meaney C.; Fanning L.; Prentice M.; MacSharry J.; Dempsey C.; Mallon P.; Leon A.; Chaturvedi A.; Coughlan S.; McAndrew G.; Reddington K.; Walsh F.; Fitzpatrick D.; Smyth C.; O’Dwyer T.; Chambers T.; Clarke L.; Jebb D.; Klopp J.; Kavanagh D.; Haslam K.; Buckley P.; Lemass K.; Fitzpatrick F.; Burns K. (2021) 'Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021'. Eurosurveillance, 26 (16). [DOI] [Full-Text]
    2021 O'Connor E.; Doyle S.; Amini A.; Grogan H.; Fitzpatrick D.A. (2021) 'Transmission of mushroom virus X and the impact of virus infection on the transcriptomes and proteomes of different strains of Agaricus bisporus'. Fungal Biology, . [DOI] [Full-Text]
    2021 Moloney N.M.; Larkin A.; Xu L.; Fitzpatrick D.A.; Crean H.L.; Walshe K.; Haas H.; Decristoforo C.; Doyle S. (2021) 'Generation and characterisation of a semi-synthetic siderophore-immunogen conjugate and a derivative recombinant triacetylfusarinine C–specific monoclonal antibody with fungal diagnostic application'. Analytical Biochemistry, 632 . [DOI] [Full-Text]
    2021 Regeai S.O.; Fitzpatrick D.A.; Burnell A.M.; Kakouli T. (2021) 'Characterisation of the complete mitochondrial genome of the insect-parasitic nematode Heterorhabditis bacteriophora: An idiosyncratic gene order and the presence of multiple long non-coding regions'. Nematology, 24 (1):37-54. [DOI] [Full-Text]
    2020 McGowan J.; O’hanlon R.; Owens R.A.; Fitzpatrick D.A. (2020) 'Comparative genomic and proteomic analyses of three widespread phytophthora species: Phytophthora chlamydospora, phytophthora gonapodyides and phytophthora pseudosyringae'. Microorganisms, 8 (5). [DOI] [Full-Text]
    2020 O'Connor E.; Owens R.A.; Doyle S.; Amini A.; Grogan H.; Fitzpatrick D.A. (2020) 'Proteomic investigation of interhyphal interactions between strains of Agaricus bisporus'. Fungal Biology, 124 (6):579-591. [DOI] [Full-Text]
    2020 O'Connor E; Coates CJ; Eastwood DC; Fitzpatrick DA; Grogan H; (2020) 'FISHing in fungi: Visualisation of mushroom virus X in the mycelium of Agaricus bisporus by fluorescence in situ hybridisation'. Journal of Microbiological Methods, . [DOI] [Full-Text]
    2019 McCarthy CGP; Fitzpatrick DA; (2019) 'Pangloss: A Tool for Pan-Genome Analysis of Microbial Eukaryotes'. Genes, 10 (7). [DOI] [Full-Text]
    2019 Zuniga-Soto E; Fitzpatrick DA; Doohan FM; Mullins E; (2019) 'Insights into the transcriptomic response of the plant engineering bacterium Ensifer adhaerens OV14 during transformation'. Scientific Reports, 9 (1). [DOI] [Full-Text]
    2019 O'Connor E; McGowan J; McCarthy CGP; Amini A; Grogan H; Fitzpatrick DA; (2019) 'Whole Genome Sequence of the Commercially Relevant Mushroom Strain Agaricus bisporus var. bisporus ARP23'. G3 (Bethesda, Md.), . [DOI] [Full-Text]
    2019 Waldron R; McGowan J; Gordon N; McCarthy C; Mitchell EB; Fitzpatrick DA; (2019) 'Proteome and allergenome of the European house dust mite Dermatophagoides pteronyssinus'. PLoS ONE, 14 (5). [DOI] [Full-Text]
    2019 Bayram Ö.; Dettmann A.; Karahoda B.; Moloney N.; Ormsby T.; McGowan J.; Cea-Sánchez S.; Miralles-Durán A.; Brancini G.; Luque E.; Fitzpatrick D.; Cánovas D.; Corrochano L.; Doyle S.; Selker E.; Seiler S.; Bayram Ö. (2019) 'Control of development, secondary metabolism and light-dependent carotenoid biosynthesis by the velvet complex of Neurospora crassa'. Journal of Genetics, 212 (3):691-710. [DOI] [Full-Text]
    2019 Waldron R; McGowan J; Gordon N; Mitchell EB; Fitzpatrick DA; Doyle S; (2019) 'Characterisation of three novel β-1,3 glucanases from the medically important house dust mite Dermatophagoides pteronyssinus (airmid)'. Insect Biochemistry and Molecular Biology, 115 . [DOI] [Full-Text]
    2019 McCarthy CGP; Fitzpatrick DA; (2019) 'Pan-genome analyses of model fungal species'. Microbial Genomics, . [DOI] [Full-Text]
    2018 Rahman F; Hassan M; Hanano A; Fitzpatrick DA; McCarthy CGP; Murphy DJ; (2018) 'Evolutionary, structural and functional analysis of the caleosin/peroxygenase gene family in the Fungi'. BMC Genomics, 19 (1). [DOI] [Full-Text]
    2018 Namara LM; Griffin CT; Fitzpatrick D; Kavanagh K; Carolan JC; (2018) 'The effect of entomopathogenic fungal culture filtrate on the immune response and haemolymph proteome of the large pine weevil, Hylobius abietis'. Insect Biochemistry and Molecular Biology, . [DOI] [Full-Text]
    2018 O'Brien CE; McCarthy CGP; Walshe AE; Shaw DR; Sumski DA; Krassowski T; Fitzpatrick DA; Butler G; (2018) 'Genome analysis of the yeast Diutina catenulata, a member of the Debaryomycetaceae/Metschnikowiaceae (CTG-Ser) clade'. PLoS ONE, 13 (6). [DOI] [Full-Text]
    2018 McGowan J; Byrne KP; Fitzpatrick DA; (2018) 'Comparative Analysis of Oomycete Genome Evolution using the Oomycete Gene Order Browser (OGOB)'. Genome Biology and Evolution, . [DOI] [Full-Text]
    2018 Cullen L.; O’Connor A.; McCormack S.; Owens R.; Holt G.; Collins C.; Callaghan M.; Doyle S.; Smith D.; Schaffer K.; Fitzpatrick D.; McClean S. (2018) 'The involvement of the low-oxygen-activated locus of Burkholderia cenocepacia in adaptation during cystic fibrosis infection'. Scientific Reports, 8 (1). [DOI] [Full-Text]
    2017 McGowan J; Fitzpatrick DA; (2017) 'Genomic, Network, and Phylogenetic Analysis of the Oomycete Effector Arsenal'. Msphere, 2 (6). [DOI] [Full-Text]
    2017 McGill, LM; Fitzpatrick, DA; Pisani, D; Burnell, AM (2017) 'Estimation of phylogenetic divergence times in Panagrolaimidae and other nematodes using relaxed molecular clocks calibrated with insect and crustacean fossils'. Nematology, 19 . [DOI] [Full-Text]
    2017 McCarthy, CGP; Fitzpatrick, DA (2017) 'Phylogenomic Reconstruction of the Oomycete Phylogeny Derived from 37 Genomes'. Msphere, 2 . [DOI] [Full-Text]
    2017 McCarthy CGP; Fitzpatrick DA; (2017) 'Multiple Approaches to Phylogenomic Reconstruction of the Fungal Kingdom'. Advances in Genetics, 100 . [DOI] [Full-Text]
    2017 Mc Namara, L; Carolan, JC; Griffin, CT; Fitzpatrick, D; Kavanagh, K (2017) 'The effect of entomopathogenic fungal culture filtrate on the immune response of the greater wax moth, Galleria mellonella'. Journal of Insect Physiology, 100 :82-92. [DOI] [Full-Text]
    2017 Collins C; Hurley R; Almutlaqah N; O'Keeffe G; Keane TM; Fitzpatrick DA; Owens RA; (2017) 'Proteomic Characterization of Armillaria mellea Reveals Oxidative Stress Response Mechanisms and Altered Secondary Metabolism Profiles'. Microorganisms, 5 (3). [DOI] [Full-Text]
    2017 Waldron R; McGowan J; Gordon N; McCarthy C; Mitchell EB; Doyle S; Fitzpatrick DA; (2017) 'Draft Genome Sequence of Dermatophagoides pteronyssinus, the European House Dust Mite'. Genome Announcements, 5 (32). [DOI] [Full-Text]
    2017 Sipos G; Prasanna AN; Walter MC; O'Connor E; Bálint B; Krizsán K; Kiss B; Hess J; Varga T; Slot J; Riley R; Bóka B; Rigling D; Barry K; Lee J; Mihaltcheva S; LaButti K; Lipzen A; Waldron R; Moloney NM; Sperisen C; Kredics L; Vágvölgyi C; Patrignani A; Fitzpatrick D; Nagy I; Doyle S; Anderson JB; Grigoriev IV; Güldener U; Münsterkötter M; Nagy LG; (2017) 'Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria'. Nature Ecology & Evolution, . [DOI] [Full-Text]
    2016 Fitzpatrick D; Walsh F; (2016) 'Antibiotic resistance genes across a wide variety of metagenomes'. FEMS MICROBIOLOGY ECOLOGY, 92 (2). [DOI] [Full-Text]
    2016 McCarthy CG; Fitzpatrick DA; (2016) 'Systematic Search for Evidence of Interdomain Horizontal Gene Transfer from Prokaryotes to Oomycete Lineages'. Msphere, 1 (5). [DOI] [Full-Text]
    2016 An L.; Fitzpatrick D.; Harrison P. (2016) 'Emergence and evolution of yeast prion and prion-like proteins'. BMC Evolutionary Biology, 16 (1). [DOI] [Full-Text]
    2016 Smith EB; Dolan SK; Fitzpatrick DA; Doyle S; Jones GW; (2016) 'Towards understanding the gliotoxin detoxification mechanism: in vivo thiomethylation protects yeast from gliotoxin cytotoxicity'. Microbial Cell (Graz, Austria), 3 (3). [DOI] [Full-Text]
    2015 Culleton, BA; Lall, P; Kinsella, GK; Doyle, S; McCaffrey, J; Fitzpatrick, DA; Burnell, AM (2015) 'A role for the Parkinson's disease protein DJ-1 as a chaperone and antioxidant in the anhydrobiotic nematode Panagrolaimus superbus'. Cell Stress and Chaperones, 20 :121-137. [DOI] [Full-Text]
    2015 Owens, RA; O'Keeffe, G; Smith, EB; Dolan, SK; Hammel, S; Sheridan, KJ; Fitzpatrick, DA; Keane, TM; Jones, GW; Doyle, S (2015) 'Interplay between Gliotoxin Resistance, Secretion, and the Methyl/Methionine Cycle in Aspergillus fumigatus'. Eukaryotic Cell, 14 :941-957. [DOI] [Full-Text]
    2014 Reardon, W; Gallagher, P; Nolan, KM; Wright, H; Cardenosa-Rubio, MC; Bragalini, C; Lee, CS; Fitzpatrick, DA; Corcoran, K; Wolff, K; Nugent, JM (2014) 'Different outcomes for the MYB floral symmetry genes DIVARICATA and RADIALIS during the evolution of derived actinomorphy in Plantago'. New Phytologist, 202 :716-725. [DOI] [Full-Text]
    2014 Dolan, SK; Owens, RA; O'Keeffe, G; Hammel, S; Fitzpatrick, DA; Jones, GW; Doyle, S (2014) 'Regulation of Nonribosomal Peptide Synthesis: bis-Thiomethylation Attenuates Gliotoxin Biosynthesis in Aspergillus fumigatus'. Chemistry and Biology, 21 :999-1012. [DOI] [Full-Text]
    2014 Hasin, N; Cusack, SA; Ali, SS; Fitzpatrick, DA; Jones, GW (2014) 'Global transcript and phenotypic analysis of yeast cells expressing Ssa1, Ssa2, Ssa3 or Ssa4 as sole source of cytosolic Hsp70-Ssa chaperone activity'. BMC Genomics, 15 . [DOI] [Full-Text]
    2014 Haggerty, LS; Jachiet, PA; Hanage, WP; Fitzpatrick, DA; Lopez, P; O'Connell, MJ; Pisani, D; Wilkinson, M; Bapteste, E; McInerney, JO (2014) 'A Pluralistic Account of Homology: Adapting the Models to the Data'. Molecular Biology and Evolution, 31 :501-516. [DOI] [Full-Text]
    2014 Jones, GW; Doyle, S; Fitzpatrick, DA (2014) 'The evolutionary history of the genes involved in the biosynthesis of the antioxidant ergothioneine'. Gene, 549 :161-170. [DOI] [Full-Text]
    2014 O'Keeffe, G; Hammel, S; Owens, RA; Keane, TM; Fitzpatrick, DA; Jones, GW; Doyle, S (2014) 'RNA-seq reveals the pan-transcriptomic impact of attenuating the gliotoxin self-protection mechanism in Aspergillus fumigatus'. BMC Genomics, 15 . [DOI] [Full-Text]
    2013 Gildea, S; Fitzpatrick, DA; Cullinane, A (2013) 'Epidemiological and virological investigations of equine influenza outbreaks in Ireland (2010-2012)'. Influenza and other Respiratory Viruses, 7 :61-72. [DOI] [Full-Text]
    2013 He, C; Fitzpatrick, DA; O'Halloran, DM (2013) 'A comparative study of the molecular evolution of signalling pathway members across olfactory, gustatory and photosensory modalities'. Journal of Genetics, 92 :327-334. [DOI] [Full-Text]
    2013 Sharma, V; He, C; Sacca-Schaeffer, J; Brzozowski, E; Martin-Herranz, DE; Mendelowitz, Z; Fitzpatrick, DA; O'Halloran, DM (2013) 'Insight into the Family of Na+/Ca2+ Exchangers of Caenorhabditis elegans'. Journal of Genetics, 195 . [DOI] [Full-Text]
    2013 Collins, C; Keane, TM; Turner, DJ; O'Keeffe, G; Fitzpatrick, DA; Doyle, S (2013) 'Genomic and Proteomic Dissection of the Ubiquitous Plant Pathogen, Armillaria mellea: Toward a New Infection Model System'. Journal of Proteome Research, 12 :2552-2570. [DOI] [Full-Text]
    2013 Clarke, M; Lohan, AJ; Liu, B; Lagkouvardos, I; Roy, S; Zafar, N; Bertelli, C; Schilde, C; Kianianmomeni, A; Burglin, TR; Frech, C; Turcotte, B; Kopec, KO; Synnott, JM; Choo, C; Paponov, I; Finkler, A; Tan, CSH; Hutchins, AP; Weinmeier, T; Rattei, T; Chu, JS; Gimenez, G; Irimia, M; Rigden, DJ; Fitzpatrick, DA; Lorenzo-Morales, J; Bateman, A; Chiu, CH; Tang, P; Hegemann, P; Fromm, H; Raoult, D; Greub, G; Miranda-Saavedra, D; Chen, N; Nash, P; Ginger, ML; Horn, M; Schaap, P; Caler, L; Loftus, BJ (2013) 'Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling'. Genome Biology, 14 . [DOI] [Full-Text]
    2012 Fitzpatrick DA, O'Halloran DM (2012) 'Investigating the Relationship between Topology and Evolution in a Dynamic Nematode Odor Genetic Network'. International journal of evolutionary biology, 2012 . [DOI] [Full-Text]
    2012 O'Hanlon, KA; Margison, GP; Hatch, A; Fitzpatrick, DA; Owens, RA; Doyle, S; Jones, GW (2012) 'Molecular characterization of an adaptive response to alkylating agents in the opportunistic pathogen Aspergillus fumigatus'. Nucleic Acids Research, 40 :7806-7820. [DOI] [Full-Text]
    2011 Medina, EM; Jones, GW; Fitzpatrick, DA (2011) 'Reconstructing the Fungal Tree of Life Using Phylogenomics and a Preliminary Investigation of the Distribution of Yeast Prion-Like Proteins in the Fungal Kingdom'. Journal of Molecular Evolution, 73 :116-133. [DOI] [Full-Text]
    2011 Ding, C; Yin, J; Tovar, EMM; Fitzpatrick, DA; Higgins, DG; Thiele, DJ (2011) 'The copper regulon of the human fungal pathogen Cryptococcus neoformans H99'. Molecular Microbiology, 81 :1560-1576. [DOI] [Full-Text]
    2011 Creevey, CJ; Doerks, T; Fitzpatrick, DA; Raes, J; Bork, P (2011) 'Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer'. PLoS ONE, 6 . [DOI] [Full-Text]
    2011 Fitzpatrick, DA; O'Brien, J; Moran, C; Hasin, N; Kenny, E; Cormican, P; Gates, A; Morris, DW; Jones, GW (2011) 'Assessment of Inactivating Stop Codon Mutations in Forty Saccharomyces cerevisiae Strains: Implications for [PSI+] Prion-Mediated Phenotypes'. PLoS ONE, 6 . [DOI] [Full-Text]
    2010 Fitzpatrick, DA; O'Gaora, P; Byrne, KP; Butler, G (2010) 'Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser'. BMC Genomics, 11 . [DOI] [Full-Text]
    2009 Regeai, SO; Dolan, KM; Fitzpatrick, DA; Browne, JA; Jones, JT; Burnell, AM (2009) 'Novel primers for the amplification of nuclear DNA introns in the entomopathogenic nematode Heterorhabditis bacteriophora and their cross-amplification in seven other Heterorhabditis species'. Molecular Ecology Resources, 9 :421-424. [DOI] [Full-Text]
    2009 Haggerty, LS; Martin, FJ; Fitzpatrick, DA; McInerney, JO (2009) 'Gene and genome trees conflict at many levels'. Philosophical Transactions of the Royal Society B: Biological Sciences, 364 :2209-2219. [DOI] [Full-Text]
    2009 Fitzpatrick, DA (2009) 'Lines of Evidence for Horizontal Gene Transfer of a Phenazine Producing Operon into Multiple Bacterial Species'. Journal of Molecular Evolution, 68 :171-185. [DOI] [Full-Text]
    2009 Reardon, W; Fitzpatrick, DA; Fares, MA; Nugent, JM (2009) 'Evolution of flower shape in Plantago lanceolata'. Plant Molecular Biology, 71 :241-250. [DOI] [Full-Text]
    2009 Butler G, Rasmussen MD, Lin MF, Santos MA, Sakthikumar S, Munro CA, Rheinbay E, Grabherr M, Forche A, Reedy JL, Agrafioti I, Arnaud MB, Bates S, Brown AJ, Brunke S, Costanzo MC, Fitzpatrick DA, de Groot PW, Harris D, Hoyer LL, Hube B, Klis FM, Kodira C, Lennard N, Logue ME, Martin R, Neiman AM, Nikolaou E, Quail MA, Quinn J, Santos MC, Schmitzberger FF, Sherlock G, Shah P, Silverstein KA, Skrzypek MS, Soll D, Staggs R, Stansfield I, Stumpf MP, Sudbery PE, Srikantha T, Zeng Q, Berman J, Berriman M, Heitman J, Gow NA, Lorenz MC, Birren BW, Kellis M, Cuomo CA (2009) 'Evolution of pathogenicity and sexual reproduction in eight Candida genomes'. Nature, 459 :657-662. [DOI] [Full-Text]
    2008 Fitzpatrick DA, Logue ME, Butler G. (2008) 'Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis'. BMC Evolutionary Biology, 24 . [DOI] [Full-Text]
    2007 Johnston CR, O'Dushlaine C, Fitzpatrick D.A., Edwards RJ, Shields DC (2007) 'Evaluation Of Whether Accelerated Protein Evolution In Chordates Has Occurred Before, After Or Simultaneously With Gene Duplication'. Molecular Biology and Evolution, 24 :315-323. [DOI] [Full-Text]
    2006 O'Halloran, DM; Fitzpatrick, DA; McCormack, GP; McInerney, JO; Burnell, AM (2006) 'The molecular phylogeny of a nematode-specific clade of heterotrimeric G-protein alpha-subunit genes'. Journal of Molecular Evolution, 63 :87-94. [DOI] [Full-Text]
    2006 Fitzpatrick, DA; O'Halloran, DM; Burnell, AM (2006) 'Multiple lineage specific expansions within the guanylyl cyclase gene family'. BMC Evolutionary Biology, 6 . [DOI] [Full-Text]
    2006 Fitzpatrick D.; Creevey C.; McInerney J. (2006) 'Genome phylogenies indicate a meaningful α-proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales'. Molecular Biology and Evolution, 23 (1):74-85. [DOI] [Full-Text]
    2006 Fitzpatrick D.A, Logue ME, Stajich JE, Butler G. (2006) 'A Fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis'. BMC Evolutionary Biology, 6 . [DOI] [Full-Text]
    2005 Fitzpatrick, DA; McInerney, JO (2005) 'Evidence of positive Darwinian selection in Omp85, a highly conserved bacterial outer membrane protein essential for cell viability'. Journal of Molecular Evolution, 60 :268-273. [DOI] [Full-Text]
    2005 Shannon, AJ; Browne, JA; Boyd, J; Fitzpatrick, DA; Burnell, AM (2005) 'The anhydrobiotic potential and molecular phylogenetics of species and strains of Panagrolaimus (Nematoda, Panagrolaimidae)'. Journal of Experimental Biology, 208 :2433-2445. [DOI] [Full-Text]
    2005 Fitzpatrick, DA; Creevey, CJ; McInerney, JO (2005) 'Evidence of positive Darwinian selection in putative meningococcal vaccine antigens'. Journal of Molecular Evolution, 61 :90-98. [DOI] [Full-Text]
    2004 Creevey C.; Fitzpatrick D.; Philip G.; Kinsella R.; O'Connell M.; Pentony M.; Travers S.; Wilkinson M.; McInerney J. (2004) 'Does a tree-like phytogeny only exist at the tips in the prokaryotes?'. Proceedings of the Royal Society B: Biological Sciences, 271 (1557):2551-2558. [DOI] [Full-Text]
    2003 Kinsella, RJ; Fitzpatrick, DA; Creevey, CJ; McInerney, JO (2003) 'Fatty acid biosynthesis in Mycobacterium tuberculosis: Lateral gene transfer, adaptive evolution, and gene duplication'. Proceedings of the National Academy of Sciences of the United States of America, 100 :10320-10325. [DOI] [Full-Text]

    Reviews

    Year Publication
    2012 Fitzpatrick, DA (2012) Horizontal gene transfer in fungi. MALDEN: [Reviews] [DOI]

    Book Chapter

    Year Publication
    2020 McGowan, J; Fitzpatrick, DA (2020) 'Recent advances in oomycete genomics' In: ADVANCES IN GENETICS, VOL 105. LONDON : ACADEMIC PRESS LTD-ELSEVIER SCIENCE LTD. [DOI]
    2017 Fitzpatrick D.A (2017) 'Applications of Genomics to Fungi' In: Biology and Applications. United Kingdom : Wiley Blackwell. [Link]
    2017 McCarthy, CGP; Fitzpatrick, DA (2017) 'Multiple Approaches to Phylogenomic Reconstruction of the Fungal Kingdom' In: FUNGAL PHYLOGENETICS AND PHYLOGENOMICS. SAN DIEGO : ELSEVIER ACADEMIC PRESS INC. [DOI]
    2014 Fitzpatrick, DA (2014) 'Comparative Genomics and Evolutionary Analyses of Human Fungal Pathogens' In: HUMAN PATHOGENIC FUNGI: MOLECULAR BIOLOGY AND PATHOGENIC MECHANISMS. WYMONDHAM : CAISTER ACADEMIC PRESS.
    2011 Fitzpatrick, D; Tovar, EMM (2011) 'Fungal Genomics' In: FUNGI: BIOLOGY AND APPLICATIONS, 2ND EDITION. OXFORD : BLACKWELL SCIENCE PUBL.
    2010 Fitzpatrick, David A. and Geraldine Butler (2010) 'Comparative genomic analysis of pathogenic yeasts and the evolution of virulence' In: H. Ruth Asbee and Elanine M. Bignell(Eds.). The Yeast Handbook: Pathogenic Yeasts. Berlin : Springer.
    2006 O’Halloran, DM. Fitzpatrick, DA and Burnell, AM. (2006) 'Chemoreception and Chemoreceptor Genes in Nematodes' In: Marcel Dicke and Willem Takken(Eds.). Chemical Communication: from Genes to Ecosystems. : Frontis Publishing.
    2006 McInerney, J.O., Pisani, D., O’Connell, M.J., Fitzpatrick, D.A. and Creevey,C.J. (2006) 'A Prokaryotic Phylogenetic Tree: Yes or No?' In: Trevor Hodkinson, John Parnell and Steve Waldren(Eds.). Towards the Tree of Life: taxonomy and systematics of large and species rich taxa (Systematic Association special volume). : CRC Press.

    Thesis

    Year Publication
    2004 David A Fitzpatrick (2004) A study of selection and recombination in microorganisms and a place for the mitochondrion among the alpha-proteobacteria. NUI Maynooth: [Thesis] [Full-Text]
    Certain data included herein are derived from the © Web of Science (2024) of Clarivate. All rights reserved.

    Outreach Activities

    Organisation Type Description
    SFI Science Week Civic Society [Link]

    Professional Associations

    Description Function From / To
    Irish Fungal Society (IFS) Treasurer 01/01/2014 - 02/01/2017
    Irish Fungal Society (IFS) Member 01/01/2008 -
    American Society For Microbiology Member 01/01/2016 -
    Microbiology Society Member 01/01/2018 -

    Honors and Awards

    Date Title Awarding Body
    01/01/2005 Doctoral Student Prize of. Achievement in Science and Engine Maynooth University
    01/10/2005 IRC Postdoctoral Fellowship Irish Research Council
    01/10/2007 HRB Postdoctoral Research Fellow Health Research Board of Ireland

    Committees

    Committee Function From / To
    Academic Council Member 01/06/2019 -
    Academic Council Research Committee Member 01/10/2019 -
    FSE outreach committee Member 01/11/2009 -
    Departmental Research Committee Member 02/09/2019 -
    Departmental Outreach Committee Chair 02/09/2019 -

    Employment

    Employer Position From / To
    Maynooth University Lecturer 01/01/2009 -
    University College Dublin Postdoctoral Fellow 01/01/2007 - 31/12/2009
    Maynooth University Associate Professor 20/10/2020 -
    Maynooth University Postdoctoral Researcher 01/09/2004 - 31/08/2005
    University College Dublin Postdoctoral Fellow 01/09/2005 - 31/12/2007

    Education

    Start date Institution Qualification Subject
    N.U.I Maynooth Ph.D Evolutionary Biology and Bioinformatics
    Maynooth University PGDHE Education
    N.U.I Maynooth B. Sc. (Hons) Biology

    Teaching Interests

    I currently teach or supervise students on the following modules

    BI606: Introduction to Bioinformatics
    BI430: Biotechnology Placements
    BI423: Literature project 1
    BI424: Literature project 2
    BI427: Laboratory research project
    BI425: Advanced practicals
    BI315: Introduction to Bioinformatics
    BI308: Proteomics
    BI305: Dissertation)
    BI205: Biotechnology Processes
    BI101: From Cell to Organism




    Recent Students

    Graduation date Name Degree
    2020 Dr Eoin O'Connor PhD
    2020 Dr Charley McCarthy PhD
    2020 Dr Rose Waldron PhD
    2020 Dr Robert Leigh PhD
    2017 Dr Robert Carton PhD
    2013 Dr Cassandra Collins PhD
    2021 Dr Jamie McGowan PhD