Dr David Fitzpatrick

Biology, Human Health Institute

Associate Professor

Callan
1.26
(01) 708 6844

Biography

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 Dip;oma 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

  Project Role Funding Body / Program Description Start Date End Date Award (€)
Biocontrol of Mushroom pathogens by Bacillus subtilis and genomic interactions between host, pathogen and biocontrol agent. PI (Joint with Prof. Kevin Kavanagh) Teagasc / Government State Bodies 01-OCT-20 01-OCT-24 88000
Analysis of introgression in prokaryotic genomes. PI Irish Research Council (IRC) / Government of Ireland Postgraduate Scholarship 01-OCT-15 30-SEP-19 96000
Teagasc Walsh fellowship application - Genomic, transcriptomic and proteomic analyses of A. bisporus strains resistant to mushroom virus X. PI Teagasc / Walsh Fellowships 01-OCT-15 30-SEP-19 88000
Utilising mushroom genomics to develop a molecular diagnostic for stable Agaricus bisporus inoculum and future strain development. PI Enterprise Ireland / Innovation Partnerships 01-FEB-15 31-JUL-16
nSilico Innovation Voucher PI Enterprise Ireland / Innovation Vouchers 31-MAY-13 30-SEP-13
Using the genome sequence of the emerging pathogen Candida krusei to identify virulence charateristics PI Health Research Board / HRB / Research Collaborative for Quality and Patient Safety (RCQPS) 01-JAN-09 31-DEC-11

Post Doctoral Fellows/Research Team

  Researcher Name Project Role Funding Body
Jamie Mc Gowan Evolution of oomycete effectors Postgraduate student Irish Research Council (IRC)

Peer Reviewed Journals

  Year Publication
2020 'Proteomic investigation of interhyphal interactions between strains of Agaricus bisporus'
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] [Details]
2020 'Comparative genomic and proteomic analyses of three widespread phytophthora species: Phytophthora chlamydospora, phytophthora gonapodyides and phytophthora pseudosyringae'
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] [Details]
2020 'Recent advances in oomycete genomics'
McGowan J.;Fitzpatrick D.A. (2020) 'Recent advances in oomycete genomics'. Advances in Genetics, [DOI] [Details]
2020 'FISHing in fungi: Visualisation of mushroom virus X in the mycelium of Agaricus bisporus by fluorescence in situ hybridisation'
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] [Details]
2019 'Control of development, secondary metabolism and light-dependent carotenoid biosynthesis by the velvet complex of Neurospora crassa'
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] [Details]
2019 'Whole Genome Sequence of the Commercially Relevant Mushroom Strain Agaricus bisporus var. bisporus ARP23'
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] [Details]
2019 'Pangloss: A Tool for Pan-Genome Analysis of Microbial Eukaryotes'
McCarthy CGP;Fitzpatrick DA; (2019) 'Pangloss: A Tool for Pan-Genome Analysis of Microbial Eukaryotes'. Genes, 10 (7) [DOI] [full-text] [Details]
2019 'Characterisation of three novel β-1,3 glucanases from the medically important house dust mite Dermatophagoides pteronyssinus (airmid)'
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] [Details]
2019 'Proteome and allergenome of the European house dust mite Dermatophagoides pteronyssinus'
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] [Details]
2019 'Insights into the transcriptomic response of the plant engineering bacterium Ensifer adhaerens OV14 during transformation'
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] [Details]
2019 'Pan-genome analyses of model fungal species'
McCarthy CGP;Fitzpatrick DA; (2019) 'Pan-genome analyses of model fungal species'. Microbial Genomics, [DOI] [full-text] [Details]
2018 'The effect of entomopathogenic fungal culture filtrate on the immune response and haemolymph proteome of the large pine weevil, Hylobius abietis'
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] [Details]
2018 'The involvement of the low-oxygen-activated locus of Burkholderia cenocepacia in adaptation during cystic fibrosis infection'
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] [Details]
2018 'Evolutionary, structural and functional analysis of the caleosin/peroxygenase gene family in the Fungi'
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] [Details]
2018 'Comparative Analysis of Oomycete Genome Evolution using the Oomycete Gene Order Browser (OGOB)'
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] [Details]
2018 'Genome analysis of the yeast Diutina catenulata, a member of the Debaryomycetaceae/Metschnikowiaceae (CTG-Ser) clade'
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] [Details]
2017 'Proteomic Characterization of Armillaria mellea Reveals Oxidative Stress Response Mechanisms and Altered Secondary Metabolism Profiles'
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] [Details]
2017 'The effect of entomopathogenic fungal culture filtrate on the immune response of the greater wax moth, Galleria mellonella'
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] [Details]
2017 'Draft Genome Sequence of Dermatophagoides pteronyssinus, the European House Dust Mite'
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] [Details]
2017 'Genomic, Network, and Phylogenetic Analysis of the Oomycete Effector Arsenal'
McGowan J;Fitzpatrick DA; (2017) 'Genomic, Network, and Phylogenetic Analysis of the Oomycete Effector Arsenal'. Msphere, 2 (6) [DOI] [full-text] [Details]
2017 'Multiple Approaches to Phylogenomic Reconstruction of the Fungal Kingdom'
McCarthy CGP;Fitzpatrick DA; (2017) 'Multiple Approaches to Phylogenomic Reconstruction of the Fungal Kingdom'. Advances in Genetics, 100 [DOI] [full-text] [Details]
2017 'Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria'
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] [Details]
2017 'Phylogenomic Reconstruction of the Oomycete Phylogeny Derived from 37 Genomes'
McCarthy, CGP;Fitzpatrick, DA (2017) 'Phylogenomic Reconstruction of the Oomycete Phylogeny Derived from 37 Genomes'. Msphere, 2 [DOI] [full-text] [Details]
2017 'Estimation of phylogenetic divergence times in Panagrolaimidae and other nematodes using relaxed molecular clocks calibrated with insect and crustacean fossils'
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] [Details]
2016 'Antibiotic resistance genes across a wide variety of metagenomes'
Fitzpatrick D;Walsh F; (2016) 'Antibiotic resistance genes across a wide variety of metagenomes'. FEMS MICROBIOLOGY ECOLOGY, 92 (2) [DOI] [full-text] [Details]
2016 'Towards understanding the gliotoxin detoxification mechanism: in vivo thiomethylation protects yeast from gliotoxin cytotoxicity'
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] [Details]
2016 'Systematic Search for Evidence of Interdomain Horizontal Gene Transfer from Prokaryotes to Oomycete Lineages'
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] [Details]
2016 'Emergence and evolution of yeast prion and prion-like proteins'
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] [Details]
2015 'Interplay between Gliotoxin Resistance, Secretion, and the Methyl/Methionine Cycle in Aspergillus fumigatus'
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] [Details]
2015 'A role for the Parkinson's disease protein DJ-1 as a chaperone and antioxidant in the anhydrobiotic nematode Panagrolaimus superbus'
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] [Details]
2014 'RNA-seq reveals the pan-transcriptomic impact of attenuating the gliotoxin self-protection mechanism in Aspergillus fumigatus'
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] [Details]
2014 'A Pluralistic Account of Homology: Adapting the Models to the Data'
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] [Details]
2014 'The evolutionary history of the genes involved in the biosynthesis of the antioxidant ergothioneine'
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] [Details]
2014 'Different outcomes for the MYB floral symmetry genes DIVARICATA and RADIALIS during the evolution of derived actinomorphy in Plantago'
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] [Details]
2014 'Regulation of Nonribosomal Peptide Synthesis: bis-Thiomethylation Attenuates Gliotoxin Biosynthesis in Aspergillus fumigatus'
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] [Details]
2014 'Global transcript and phenotypic analysis of yeast cells expressing Ssa1, Ssa2, Ssa3 or Ssa4 as sole source of cytosolic Hsp70-Ssa chaperone activity'
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] [Details]
2013 'Genomic and Proteomic Dissection of the Ubiquitous Plant Pathogen, Armillaria mellea: Toward a New Infection Model System'
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] [Details]
2013 'A comparative study of the molecular evolution of signalling pathway members across olfactory, gustatory and photosensory modalities'
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] [Details]
2013 'Epidemiological and virological investigations of equine influenza outbreaks in Ireland (2010-2012)'
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] [Details]
2013 'Insight into the Family of Na+/Ca2+ Exchangers of Caenorhabditis elegans'
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] [Details]
2013 'Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling'
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] [Details]
2012 'Molecular characterization of an adaptive response to alkylating agents in the opportunistic pathogen Aspergillus fumigatus'
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] [Details]
2012 'Investigating the Relationship between Topology and Evolution in a Dynamic Nematode Odor Genetic Network'
Fitzpatrick DA, O'Halloran DM (2012) 'Investigating the Relationship between Topology and Evolution in a Dynamic Nematode Odor Genetic Network'. To be added, 2012 [DOI] [full-text] [Details]
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'
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] [Details]
2011 'Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer'
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] [Details]
2011 'Assessment of Inactivating Stop Codon Mutations in Forty Saccharomyces cerevisiae Strains: Implications for [PSI+] Prion-Mediated Phenotypes'
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] [Details]
2011 'The copper regulon of the human fungal pathogen Cryptococcus neoformans H99'
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] [Details]
2010 'Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser'
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] [Details]
2009 'Evolution of flower shape in Plantago lanceolata'
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] [Details]
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'
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] [Details]
2009 'Lines of Evidence for Horizontal Gene Transfer of a Phenazine Producing Operon into Multiple Bacterial Species'
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] [Details]
2009 'Gene and genome trees conflict at many levels'
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] [Details]
2009 'Evolution of pathogenicity and sexual reproduction in eight Candida genomes'
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] [Details]
2008 'Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis'
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] [Details]
2007 'Evaluation Of Whether Accelerated Protein Evolution In Chordates Has Occurred Before, After Or Simultaneously With Gene Duplication'
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] [Details]
2006 'Genome phylogenies indicate a meaningful α-proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales'
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] [Details]
2006 'Multiple lineage specific expansions within the guanylyl cyclase gene family'
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] [Details]
2006 'The molecular phylogeny of a nematode-specific clade of heterotrimeric G-protein alpha-subunit genes'
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] [Details]
2006 'A Fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis'
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] [Details]
2005 'Evidence of positive Darwinian selection in putative meningococcal vaccine antigens'
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] [Details]
2005 'The anhydrobiotic potential and molecular phylogenetics of species and strains of Panagrolaimus (Nematoda, Panagrolaimidae)'
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] [Details]
2005 'Evidence of positive Darwinian selection in Omp85, a highly conserved bacterial outer membrane protein essential for cell viability'
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] [Details]
2004 'Does a tree-like phytogeny only exist at the tips in the prokaryotes?'
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] [Details]
2003 'Fatty acid biosynthesis in Mycobacterium tuberculosis: Lateral gene transfer, adaptive evolution, and gene duplication'
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] [Details]

Book Chapters

  Year Publication
2017 'Applications of Genomics to Fungi'
Fitzpatrick D.A (2017) 'Applications of Genomics to Fungi' In: Kevin Kavanagh (eds). Biology and Applications. United Kingdom: Wiley Blackwell. [Details]
2017 'Multiple Approaches to Phylogenomic Reconstruction of the Fungal Kingdom'
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] [Details]
2014 'Comparative Genomics and Evolutionary Analyses of Human Fungal Pathogens'
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. [Details]
2011 'Fungal Genomics'
Fitzpatrick, D;Tovar, EMM (2011) 'Fungal Genomics' In: FUNGI: BIOLOGY AND APPLICATIONS, 2ND EDITION. OXFORD: BLACKWELL SCIENCE PUBL. [Details]
2010 'Comparative genomic analysis of pathogenic yeasts and the evolution of virulence'
Fitzpatrick, David A. and Geraldine Butler (2010) 'Comparative genomic analysis of pathogenic yeasts and the evolution of virulence' In: The Yeast Handbook: Pathogenic Yeasts. Berlin: Springer. [Details]
2006 'Chemoreception and Chemoreceptor Genes in Nematodes'
O’Halloran, DM. Fitzpatrick, DA and Burnell, AM. (2006) 'Chemoreception and Chemoreceptor Genes in Nematodes' In: Chemical Communication: from Genes to Ecosystems. Frontis Publishing. [Details]
2006 'A Prokaryotic Phylogenetic Tree: Yes or No?'
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: Towards the Tree of Life: taxonomy and systematics of large and species rich taxa (Systematic Association special volume). CRC Press. [Details]

Thesis

  Year Publication
2004 A study of selection and recombination in microorganisms and a place for the mitochondrion among the alpha-proteobacteria.
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 [Details]

Honours and Awards

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

Professional Associations

  Association Function From / To
Irish Fungal Society (IFS) Treasurer 01-JAN-14 / 02-JAN-17
Irish Fungal Society (IFS) Member 01-JAN-08 /
American Society For Microbiology Member 01-JAN-16 /
Microbiology Society Member 01-JAN-18 /

Committees

  Committee Function From / To
Academic Council Member 2019 /
Academic Council Research Committee Member 2019 /
FSE outreach committee Member 2009 /
Departmental Research Committee Member 2019 /
Departmental Outreach Committee Chair 2019 /

Employment

  Employer Position From / To
Maynooth University Lecturer 01-JAN-09 /
University College Dublin Postdoctoral Fellow 01-JAN-07 / 31-DEC-09
University College Dublin Postdoctoral Fellow 01-SEP-05 / 31-DEC-07
Maynooth University Postdoctoral Researcher 01-SEP-04 / 31-AUG-05

Education

  Year Institution Qualification Subject
2005 N.U.I Maynooth Ph.D Evolutionary Biology and Bioinformatics
2016 Maynooth University PGDHE Education
2000 N.U.I Maynooth B. Sc. (Hons) Biology

Outreach Activities

  Description

Link

Reviews

  Journal Role
Plos Genetics Reviewer
Plos One Associate Editor
Nature Communications Reviewer
Fungal Genetics And Biology Reviewer
Fungal Biology Reviewer
Molecular Biology And Evolution Reviewer
Genome Biology And Evolution Reviewer
Journal Of Molecular Evolution Reviewer
Scientific Reports Reviewer

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 Postgraduates

  Graduation Student Name University Degree Thesis
2020 Eoin O'Connor Maynooth University PhD Characterising the molecular response of Agaricus bisporus to mushroom virus X infection
2020 Charley McCarthy Maynooth University PhD A tale of two clades: genome evolution of oomycetes and fungi
2020 Rose Waldron Maynooth University PhD Genomic and Proteomic Characterisation of the European House Dust Mite, Dermatophagoides pteronyssinus
2020 Robert Leigh Maynooth University PhD Studies on The Modular Evolution of Genes
2017 Robert Carton Maynooth University PhD Next Generation Sequencing Technology and Phylogenomics Enhance the Resolution of Deep Node Phylogenies: A Study of the Protostomia
2013 Cassandra Collins Maynooth University PhD A Genomic and Proteomic Investigation of the Plant Pathogen Armillaria mellea: Buried Treasure or Hidden Threat?