D. Fitzpatrick

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A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis

Jason E Stajich, David A Fitzpatrick, G. Butler, 2006, BMC Evolutionary Biology.

Genome phylogenies indicate a meaningful alpha-proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales.

David A Fitzpatrick, J. McInerney, C. Creevey, 2006, Molecular biology and evolution.

The Molecular Phylogeny of a Nematode-Specific Clade of Heterotrimeric G-Protein α-Subunit Genes

J. McInerney, G. McCormack, D. Fitzpatrick, 2006, Journal of Molecular Evolution.

Horizontal gene transfer in fungi.

D. Fitzpatrick, 2012, FEMS microbiology letters.

A Pluralistic Account of Homology: Adapting the Models to the Data

J. McInerney, W. Hanage, P. Lopez, 2013, Molecular biology and evolution.

Evolution of pathogenicity and sexual reproduction in eight Candida genomes

Manuel A. S. Santos, Martha B. Arnaud, Matthew D. Rasmussen, 2009, Nature.

Does a tree–like phylogeny only exist at the tips in the prokaryotes?

Simon A. A. Travers, J. McInerney, S. Travers, 2004, Proceedings of the Royal Society of London. Series B: Biological Sciences.

Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

Sean Doyle, István Nagy, Anna Lipzen, 2017, Nature Ecology & Evolution.

Pan-genome analyses of model fungal species

David A. Fitzpatrick, D. Fitzpatrick, Charley G. P. McCarthy, 2019, Microbial genomics.

Evolutionary, structural and functional analysis of the caleosin/peroxygenase gene family in the Fungi

A. Hanano, D. Fitzpatrick, D. Murphy, 2018, BMC Genomics.

Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer

Peer Bork, Jeroen Raes, Christopher J. Creevey, 2011, PloS one.

Reconstructing the Fungal Tree of Life Using Phylogenomics and a Preliminary Investigation of the Distribution of Yeast Prion-Like Proteins in the Fungal Kingdom

Gary W. Jones, E. Medina, D. Fitzpatrick, 2011, Journal of Molecular Evolution.

Phylogenomic Reconstruction of the Oomycete Phylogeny Derived from 37 Genomes

D. Fitzpatrick, Charley G. P. McCarthy, 2017, mSphere.

Systematic Search for Evidence of Interdomain Horizontal Gene Transfer from Prokaryotes to Oomycete Lineages

D. Fitzpatrick, Charley G. P. McCarthy, 2016, mSphere.

Evolutionary History of Prokaryotes : Tree or No Tree ?

J. McInerney, C. Creevey, D. Fitzpatrick, 2006 .

Evaluation of whether accelerated protein evolution in chordates has occurred before, after, or simultaneously with gene duplication.

Richard J. Edwards, C. O'Dushlaine, D. Shields, 2006, Molecular biology and evolution.

Control of Development, Secondary Metabolism and Light-Dependent Carotenoid Biosynthesis by the Velvet Complex of Neurospora crassa

E. Selker, S. Seiler, S. Doyle, 2019, Genetics.

Proteome and allergenome of the European house dust mite Dermatophagoides pteronyssinus

D. Fitzpatrick, Rose Waldron, Charley G. P. McCarthy, 2019, PloS one.

Investigating the Relationship between Topology and Evolution in a Dynamic Nematode Odor Genetic Network

D. Fitzpatrick, D. O’Halloran, 2012, International journal of evolutionary biology.

Comparative Analysis of Oomycete Genome Evolution Using the Oomycete Gene Order Browser (OGOB)

Kevin P. Byrne, D. Fitzpatrick, Jamie McGowan, 2018, Genome biology and evolution.

Genomic and Proteomic Dissection of the Ubiquitous Plant Pathogen, Armillaria mellea: Toward a New Infection Model System

Thomas M. Keane, D. Turner, T. Keane, 2013, Journal of proteome research.

Draft Genome Sequence of Dermatophagoides pteronyssinus, the European House Dust Mite

S. Doyle, D. Fitzpatrick, Rose Waldron, 2017, Genome Announcements.

Genome expansion and lineage-specific genetic innovations in the world’s largest organisms (Armillaria)

U. Güldener, M. Münsterkötter, K. Barry, 2017, bioRxiv.

Insights into the transcriptomic response of the plant engineering bacterium Ensifer adhaerens OV14 during transformation

E. Mullins, D. Fitzpatrick, F. Doohan, 2019, Scientific Reports.

Gene and genome trees conflict at many levels

Fergal J. Martin, J. McInerney, D. Fitzpatrick, 2009, Philosophical Transactions of the Royal Society B: Biological Sciences.

The evolutionary history of the genes involved in the biosynthesis of the antioxidant ergothioneine.

S. Doyle, D. Fitzpatrick, Gary W. Jones, 2014, Gene.

Molecular characterization of an adaptive response to alkylating agents in the opportunistic pathogen Aspergillus fumigatus

Gary W. Jones, G. Margison, S. Doyle, 2012, Nucleic acids research.

Recent advances in oomycete genomics.

D. Fitzpatrick, Jamie McGowan, 2020, Advances in genetics.

The effect of entomopathogenic fungal culture filtrate on the immune response and haemolymph proteome of the large pine weevil, Hylobius abietis.

J. Carolan, D. Fitzpatrick, K. Kavanagh, 2018, Insect biochemistry and molecular biology.

Genome of Pythium myriotylum Uncovers an Extensive Arsenal of Virulence-Related Genes among the Broad-Host-Range Necrotrophic Pythium Plant Pathogens

Nan Wang, Yifan Chen, D. Shen, 2022, Microbiology spectrum.

Metabolic responses of two pioneer wood decay fungi to diurnally cycling temperature

Mike S. Fowler, L. Boddy, D. Eastwood, 2020, Journal of Ecology.

The involvement of the low-oxygen-activated locus of Burkholderia cenocepacia in adaptation during cystic fibrosis infection

Darren L. Smith, S. McClean, S. Doyle, 2018, Scientific Reports.

A Single Aspergillus fumigatus Gene Enables Ergothioneine Biosynthesis and Secretion by Saccharomyces cerevisiae

S. Doyle, D. Fitzpatrick, N. Conlon, 2022, International journal of molecular sciences.

Characterising the proteomic response of mushroom pathogen Lecanicillium fungicola to Bacillus velezensis QST 713 and Kos biocontrol agents

D. Fitzpatrick, K. Kavanagh, H. Grogan, 2022, European journal of plant pathology.

RNA-seq reveals the pan-transcriptomic impact of attenuating the gliotoxin self-protection mechanism in Aspergillus fumigatus

T. Keane, Gary W. Jones, S. Doyle, 2014, BMC Genomics.

A comparative study of the molecular evolution of signalling pathway members across olfactory, gustatory and photosensory modalities

D. Fitzpatrick, D. O’Halloran, Chao He, 2013, Journal of Genetics.

The anhydrobiotic potential and molecular phylogenetics of species and strains of Panagrolaimus (Nematoda, Panagrolaimidae)

D. Fitzpatrick, J. Browne, A. Burnell, 2005, Journal of Experimental Biology.

Characterisation of three Novel β-1,3 glucanases from the Medically Important House Dust Mite Dermatophagoides pteronyssinus (airmid).

S. Doyle, D. Fitzpatrick, Rose Waldron, 2019, Insect biochemistry and molecular biology.

Dual-Transcriptomic, Microscopic, and Biocontrol Analyses of the Interaction Between the Bioeffector Pythium oligandrum and the Pythium Soft-Rot of Ginger Pathogen Pythium myriotylum

Lihui Wei, D. Fitzpatrick, Irina S Druzhinina, 2021, Frontiers in Microbiology.

Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling

Klaus O. Kopec, P. Hegemann, A. Bateman, 2013, Genome Biology.

Genomic, Network, and Phylogenetic Analysis of the Oomycete Effector Arsenal

D. Fitzpatrick, Jamie McGowan, 2017, mSphere.

Comparative genomic study of the Penicillium genus elucidates a diverse pangenome and 15 lateral gene transfer events

J. Frisvad, K. Nielsen, D. Fitzpatrick, 2023, IMA Fungus.

Antibiotic resistance genes across a wide variety of metagenomes.

D. Fitzpatrick, F. Walsh, David Fitzpatrick, 2016, FEMS microbiology ecology.

FISHing in fungi: Visualisation of mushroom virus X in the mycelium of Agaricus bisporus by fluorescence in situ hybridisation.

D. Eastwood, D. Fitzpatrick, C. Coates, 2020, Journal of microbiological methods.

Whole Genome Sequence of the Commercially Relevant Mushroom Strain Agaricus bisporus var. bisporus ARP23

D. Fitzpatrick, E. O’Connor, Charley G. P. McCarthy, 2019, G3: Genes, Genomes, Genetics.

Different outcomes for the MYB floral symmetry genes DIVARICATA and RADIALIS during the evolution of derived actinomorphy in Plantago.

K. Wolff, D. Fitzpatrick, J. M. Nugent, 2014, The New phytologist.

Proteomic investigation of interhyphal interactions between strains of Agaricus bisporus.

S. Doyle, D. Fitzpatrick, E. O’Connor, 2020, Fungal biology.

The copper regulon of the human fungal pathogen Cryptococcus neoformans H99

D. Higgins, D. Thiele, D. Fitzpatrick, 2011, Molecular microbiology.

The Cu regulon of the human fungal pathogen Cryptococcus neoformans H99: Cuf1 activates distinct genes in response to both Cu excess and deficiency

D. Higgins, D. Thiele, D. Fitzpatrick, 2011 .

Comparative Genomic Analysis of Pathogenic Yeasts and the Evolution of Virulence

G. Butler, D. Fitzpatrick, 2010 .

Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser

Kevin P. Byrne, David A Fitzpatrick, G. Butler, 2010, BMC Genomics.

Pangloss: A Tool for Pan-Genome Analysis of Microbial Eukaryotes

Charley G P McCarthy, David A Fitzpatrick, D. Fitzpatrick, 2019, Genes.

Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis

G. Butler, D. Fitzpatrick, M. E. Logue, 2008, BMC Evolutionary Biology.

Proteomic Characterization of Armillaria mellea Reveals Oxidative Stress Response Mechanisms and Altered Secondary Metabolism Profiles

Thomas M. Keane, T. Keane, D. Fitzpatrick, 2017, Microorganisms.

Multiple lineage specific expansions within the guanylyl cyclase gene family

D. Fitzpatrick, D. O’Halloran, A. Burnell, 2006, BMC Evolutionary Biology.

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

D. Fitzpatrick, A. Burnell, T. Kakouli-Duarte, 2021, Nematology.

Assessment of Inactivating Stop Codon Mutations in Forty Saccharomyces cerevisiae Strains: Implications for [PSI +] Prion- Mediated Phenotypes

D. Morris, E. Kenny, P. Cormican, 2011, PloS one.

A role for the Parkinson’s disease protein DJ-1 as a chaperone and antioxidant in the anhydrobiotic nematode Panagrolaimus superbus

G. Kinsella, S. Doyle, D. Fitzpatrick, 2014, Cell Stress and Chaperones.

Multiple Approaches to Phylogenomic Reconstruction of the Fungal Kingdom.

D. Fitzpatrick, Charley G. P. McCarthy, 2017, Advances in genetics.

Genomic diversity, chromosomal rearrangements, and interspecies hybridization in the Ogataea polymorpha species complex

K. H. Wolfe, D. Fitzpatrick, S. Hanson, 2021, G3.

Emergence and evolution of yeast prion and prion-like proteins

P. Harrison, D. Fitzpatrick, Lu An, 2016, BMC Evolutionary Biology.

Estimation of phylogenetic divergence times in Panagrolaimidae and other nematodes using relaxed molecular clocks calibrated with insect and crustacean fossils

D. Fitzpatrick, D. Pisani, A. Burnell, 2017 .

Novel primers for the amplification of nuclear DNA introns in the entomopathogenic nematode Heterorhabditis bacteriophora and their cross‐amplification in seven other Heterorhabditis species

D. Fitzpatrick, J. T. Jones, J. Browne, 2009, Molecular ecology resources.

Comparative Genomic and Proteomic Analyses of Three Widespread Phytophthora Species: Phytophthora chlamydospora, Phytophthora gonapodyides and Phytophthora pseudosyringae

D. Fitzpatrick, R. O’Hanlon, R. Owens, 2020, Microorganisms.

Global transcript and phenotypic analysis of yeast cells expressing Ssa1, Ssa2, Ssa3 or Ssa4 as sole source of cytosolic Hsp70-Ssa chaperone activity

D. Fitzpatrick, S. Ali, N. Hasin, 2014, BMC Genomics.

Evidence of Positive Darwinian Selection in Putative Meningococcal Vaccine Antigens

J. McInerney, C. Creevey, D. Fitzpatrick, 2005, Journal of Molecular Evolution.

Evidence of Positive Darwinian Selection in Omp85, a Highly ConservedBacterial Outer Membrane Protein Essential for Cell Viability

James O. McInerney, David A. Fitzpatrick, J. McInerney, 2005, Journal of Molecular Evolution.

Fatty acid biosynthesis in Mycobacterium tuberculosis: Lateral gene transfer, adaptive evolution, and gene duplication

J. McInerney, R. Kinsella, C. Creevey, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Lines of Evidence for Horizontal Gene Transfer of a Phenazine Producing Operon into Multiple Bacterial Species

D. Fitzpatrick, 2009, Journal of Molecular Evolution.

The chemosensory system of Caenorhabditis elegans and other nematodes

D. Fitzpatrick, D. O’Halloran, A. Burnell, 2006 .

The effect of entomopathogenic fungal culture filtrate on the immune response of the greater wax moth, Galleria mellonella.

J. Carolan, D. Fitzpatrick, K. Kavanagh, 2017, Journal of insect physiology.

Epidemiological and virological investigations of equine influenza outbreaks in Ireland (2010–2012)

D. Fitzpatrick, A. Cullinane, S. Gildea, 2013, Influenza and other respiratory viruses.

Insight into the Family of Na+/Ca2+ Exchangers of Caenorhabditis elegans

Damien M. O’Halloran, D. Fitzpatrick, Daniel E. Martin-Herranz, 2013, Genetics.

Genome analysis of the yeast Diutina catenulata, a member of the Debaryomycetaceae/Metschnikowiaceae (CTG-Ser) clade

G. Butler, D. Fitzpatrick, Annie E Walshe, 2018, PloS one.

Evolution of flower shape in Plantago lanceolata

M. Fares, D. Fitzpatrick, J. M. Nugent, 2009, Plant Molecular Biology.

Regulation of nonribosomal peptide synthesis: bis-thiomethylation attenuates gliotoxin biosynthesis in Aspergillus fumigatus.

S. Doyle, D. Fitzpatrick, R. Owens, 2014, Chemistry & biology.

Transmission of mushroom virus X and the impact of virus infection on the transcriptomes and proteomes of different strains of Agaricus bisporus.

S. Doyle, D. Fitzpatrick, E. O’Connor, 2021, Fungal biology.

Insights into the transcriptomic response of the plant engineering bacterium Ensifer adhaerens OV14 during transformation

E. Mullins, D. Fitzpatrick, F. Doohan, 2019, Scientific Reports.

F-box receptor mediated control of substrate stability and subcellular location organizes cellular development of Aspergillus nidulans

G. Braus, D. Fitzpatrick, Kerstin Schmitt, 2022, PLoS genetics.

Towards understanding the gliotoxin detoxification mechanism: in vivo thiomethylation protects yeast from gliotoxin cytotoxicity

S. Doyle, D. Fitzpatrick, S. Dolan, 2016, Microbial cell.

Interplay between Gliotoxin Resistance, Secretion, and the Methyl/Methionine Cycle in Aspergillus fumigatus

T. Keane, S. Doyle, D. Fitzpatrick, 2015, Eukaryotic Cell.

Interplay between Gliotoxin Resistance, Secretion and the

T. Keane, S. Doyle, D. Fitzpatrick, 2015 .

Generation and characterisation of a semi-synthetic siderophore-immunogen conjugate and a derivative recombinant triacetylfusarinine C-specific monoclonal antibody with fungal diagnostic application.

C. Decristoforo, S. Doyle, D. Fitzpatrick, 2021, Analytical biochemistry.

Author Correction: Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

U. Güldener, M. Münsterkötter, K. Barry, 2018, Nature Ecology & Evolution.

A Two Pronged Approach to the Detection of Cimex Lectularius (common bed bug) Using Novel Bed Bug Proteins

S. Doyle, D. Fitzpatrick, N. Gordon, 2016 .

4 Evolutionary History of Prokaryotes: Tree or No Tree?