Dr David Fitzpatrick
Biography
2024 - Present: Leeds Beckett University. Visiting Professor.
2020 - Present: 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
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] |
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Teaching Interests
I currently teach or supervise students on the following modules
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 ProcessesBI101: From Cell to Organism