Dr David Fitzpatrick

Biology

Lecturer
Lecturer and PI, Genome Evolution Lab

Callan
1.26
(01) 7086844

Biography

1996 - 2000: NUI Maynooth B.Sc. Biology (Hons).
2000 - 2004: NUI Maynooth PhD Bioinformatics.
2004 - 2005: N.U.I Maynooth. Postdoctoral Researcher.
2005 - 2007: University College Dublin. IRCSET Postdoctoral Fellow.
2007 - 2009: University College Dublin. HRB Postdoctoral Fellow.
2009 - Present: Maynooth University. Lecturer and PI of Genome Evolution Laboratory.


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. We are particularly interested in phytopathogens.


Contract Researchers

  Researcher Name Project Role Funding Body
2183543 Gene remodelling Postgraduate student National University of Ireland, Maynooth
2180853 Evolution of oomycete effectors Postgraduate student Irish Research Council (IRC)
2181498 Evolution of oomycetes Postgraduate student Irish Research Council (IRC)
2290414 Genomic, transcriptomic and proteomic analyses of A. bisporus strains resistant to mushroom virus X. Postgraduate student Teagasc

Peer Reviewed Journals

  Year Publication
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] [IR Link] [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] [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] [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] [IR Link] [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] [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] [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] [IR Link] [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] [IR Link] [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] [IR Link] [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] [IR Link] [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] [IR Link] [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] [IR Link] [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] [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] [IR Link] [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] [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] [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] [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] [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] [IR Link] [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] [IR Link] [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] [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] [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] [IR Link] [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] [IR Link] [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] [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] [IR Link] [Details]
2009 'What do we get when we make a tree of genomes?'
Haggerty L.S, Martin F.J, Fitzpatrick D.A and McInerney JO (2009) 'What do we get when we make a tree of genomes?'. PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON (BIOLOGY SERIES), [IR Link] [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] [IR Link] [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] [IR Link] [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] [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] [IR Link] [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] [IR Link] [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] [IR Link] [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] [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] [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] [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] [IR Link] [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] [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] [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] [IR Link] [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] [Details]

Book Chapters

  Year Publication
2014 'Comparative Genomics and Evolutionary Analyses of Human Fungal Pathogens'
David A Fitzpatrick (2014) 'Comparative Genomics and Evolutionary Analyses of Human Fungal Pathogens' In: Human Pathogenic Fungi: Molecular Biology and Pathogenic Mechanisms. [Details]
2011 'Fungal Genomics'
Fitzpatrick, D;Tovar, EMM (2011) 'Fungal Genomics' In: FUNGI: BIOLOGY AND APPLICATIONS, 2ND EDITION. OXFORD: BLACKWELL SCIENCE PUBL. [Details]
2011 'Fungal Genomics'
Fitzpatrick DA and Medina EM (2011) 'Fungal Genomics' In: Fungi: Biology and Applications. John Wiley and Sons. [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
2005 IRC Postdoctoral Fellowship Irish Research Council
2007 HRB Postdoctoral Research Fellow Health Research Board of Ireland

Education

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