Article

Clarke, Joy, Kosanovic, Dejana, Kavanagh, Kevin, Grogan, Helen, Fitzpatrick, David A. and Geddes-McAlister, Jennifer (2024) Draft genome sequence of the fungal biocontrol agent, Bacillus velezensis Kos. Microbiology Resource Announcements, 13 (8). ISSN 2576-098X

Clarke, Joy, Kavanagh, Kevin, Grogan, Helen and Fitzpatrick, David 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. p. 105600. ISSN 1049-9644

Petersen, Celine, Sørensen, Trine, Nielsen, Mikkel R., Sondergaard, Teis E., Sørensen, Jens L., Fitzpatrick, David A., Frisvad, Jens C. and Nielsen, Kåre L. (2023) Comparative genomic study of the Penicillium genus elucidates a diverse pangenome and 15 lateral gene transfer events. IMA Fungus, 14 (3). pp. 1-17. ISSN 2210-6359

Downes, Shane G., Owens, Rebecca A., Walshe, Kieran, Fitzpatrick, David A., Dorey, Amber, Jones, Gary W. and Doyle, Sean (2023) Gliotoxin-mediated bacterial growth inhibition is caused by specific metal ion depletion. Scientific Reports, 13 (1). ISSN 2045-2322

Dwyer, Kelly, Bentley, Ian S., Fitzpatrick, David A., Saleh, Aliabbas A., Tighe, Emma, McGleenan, Eibhilin, Gaffney, Darragh and Walsh, Gary (2023) Recombinant production, characterization and industrial application testing of a novel acidic exo/endo-chitinase from Rasamsonia emersonii. Extremophiles, 27 (10). pp. 1-17. ISSN 1431-0651

Clarke, Joy, Grogan, Helen, Fitzpatrick, David A. and Kavanagh, Kevin (2022) Analysis of the effect of Bacillus velezensis culture filtrate on the growth and proteome of Cladobotryum mycophilum. Fungal Biology, 126 (1). pp. 11-19. ISSN 1878-6146

Clarke, Joy, Grogan, Helen, Fitzpatrick, David A. and Kavanagh, Kevin (2022) Characterising the proteomic response of mushroom pathogen Lecanicillium fungicola to Bacillus velezensis QST 713 and Kos biocontrol agent. European Journal of Plant Pathology, 163. pp. 369-379. ISSN 1573-8469

Freitag, Michael, Sarikaya Bayram, Özlem, Bayram, Ozgur, Karahoda, Betim, Meister, Cindy, Köhler, Anna M., Thieme, Sabine, Elramli, Nadia, Frawley, Dean, McGowan, Jamie, Fitzpatrick, David A., Schmitt, Kerstin, de Assis, Leandro Jose, Valerius, Oliver, Goldman, Gustavo H. and Braus, Gerhard H. (2022) F-box receptor mediated control of substrate stability and subcellular location organizes cellular development of Aspergillus nidulans. PLOS Genetics, 18 (12). e1010502. ISSN 1553-7404

Freitag, Michael, Sarikaya Bayram, Özlem, Bayram, Ozgur, Karahoda, Betim, Meister, Cindy, Köhler, Anna M., Thieme, Sabine, Elramli, Nadia, Frawley, Dean, McGowan, Jamie, Fitzpatrick, David A., Schmitt, Kerstin, de Assis, Leandro Jose, Valerius, Oliver, Goldman, Gustavo H. and Braus, Gerhard H. (2022) F-box receptor mediated control of substrate stability and subcellular location organizes cellular development of Aspergillus nidulans. PLOS Genetics, 18 (12). e1010502. ISSN 1553-7404

Daly, Paul, Zhou, Dongmei, Shen, Danyu, Chen, Yifan, Xue, Taiqiang, Chen, Siqiao, Zhang, Qimeng, Zhang, Jinfeng, McGowan, Jamie, Cai, Feng, Pang, Guan, Wang, Nan, Sheikh, Taha Majid Mahmood, Deng, Sheng, Li, Jingjing, Soykam, Hüseyin Okan, Kara, Irem, Fitzpatrick, David A., Druzhinina, Irina S., Bayram Akcapinar, Günseli, Wei, Lihui, Burbank, Lindsey Price and Matson, Michael (2022) Genome of Pythium myriotylum Uncovers an Extensive Arsenal of Virulence-Related Genes among the Broad-Host-Range Necrotrophic Pythium Plant Pathogens. Microbiology Spectrum, 10 (4). ISSN 2165-0497

Rawlings, Anna, O'Connor, Eoin, Moody, Suzy C., Dudley, Ed, Boddy, Lynne, Fowler, Mike S., Fitzpatrick, David A., Doyle, Sean and Eastwood, Dan C. (2022) Metabolic responses of two pioneer wood decay fungi to diurnally cycling temperature. Journal of Ecology, 110 (1). pp. 68-79. ISSN 0022-0477

Doyle, Sean, Cuskelly, Daragh D., Conlon, Niall, Fitzpatrick, David A., Gilmartin, Ciara B., Dix, Sophia H. and Jones, Gary W. (2022) A Single Aspergillus fumigatus Gene Enables Ergothioneine Biosynthesis and Secretion by Saccharomyces cerevisiae. International Journal of Molecular Sciences, 23 (18). p. 10832. ISSN 1422-0067

Regeai, Sassia Omar, Fitzpatrick, David A., Burnell, Ann M. and Kakouli-Duarte, Thomais (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). pp. 37-54. ISSN 1388-5545

Daly, Paul, Chen, Siqiao, Xue, Taiqiang, Li, Jingjing, Sheikh, Taha Majid Mahmood, Zhang, Qimeng, Wang, Xuehai, Zhang, Jinfeng, Fitzpatrick, David A., McGowan, Jamie, Shi, Xiujuan, Deng, Sheng, Jiu, Min, Zhou, Dongmei, Druzhinina, Irina S. and Wei, Lihui (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 (765872). pp. 1-14. ISSN 1664-302X

Moloney, Nicola M., Larkin, Annemarie, Xu, Linan, Fitzpatrick, David A., Crean, Holly L., Walshe, Kieran, Haas, Hubertus, Decristoforo, Clemens and Doyle, Sean (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. p. 114384. ISSN 0003-2697

Hanson, Sara J, Cinnéide, Eoin Ó, Salzberg, Letal I, Wolfe, Kenneth H, McGowan, Jamie, Fitzpatrick, David A., Matlin, Kate and Berman, J (2021) Genomic diversity, chromosomal rearrangements, and interspecies hybridization in the Ogataea polymorpha species complex. G3 Genes|Genomes|Genetics, 11 (8). pp. 1-18. ISSN 2160-1836

O'Connor, Eoin, Doyle, Sean, Amini, Aniça, Grogan, Helen and Fitzpatrick, David 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, 125 (9). pp. 704-717. ISSN 1878-6146

McGowan, Jamie, O'Hanlon, Richard, Owens, Rebecca A. and Fitzpatrick, David A. (2020) Comparative Genomic and Proteomic Analyses of Three Widespread Phytophthora Species: Phytophthora chlamydospora, Phytophthora gonapodyides and Phytophthora pseudosyringae. Microorganisms, 8 (5). ISSN 2076-2607

O'Connor, Eoin, Coates, Christopher J., Eastwood, Dan C., Fitzpatrick, David A. and Grogan, Helen (2020) FISHing in fungi: Visualisation of mushroom virus X in the mycelium of Agaricus bisporus by fluorescence in situ hybridisation. Journal of Microbiological Methods, 173. p. 105913. ISSN 01677012

O’Connor, Eoin, Owens, Rebecca A., Doyle, Sean, Amini, Aniça, Grogan, Helen and Fitzpatrick, David A. (2020) Proteomic investigation of interhyphal interactions between strains of Agaricus bisporus. Fungal Biology, 124 (6). pp. 579-591. ISSN 18786146

Waldron, Rose, McGowan, Jamie, Gordon, Natasha, Mitchell, E Bruce, Fitzpatrick, David A. and Doyle, Sean (2019) Characterisation of three novel ß-1,3 glucanases from the medically important house dust mite Dermatophagoides pteronyssinus (airmid). Insect Biochemistry and Molecular Biology, 115 (103242). ISSN 0965-1748

Sarikaya-Bayram, Ozlem, Dettmann, Anne, Karahoda, Betim, Moloney, Nicola M., Ormsby, Tereza, McGowan, Jamie, Cea-Sánchez, Sara, Miralles-Duran, Alejandro, Brancini, Guilherme T P, Luque, Eva, Fitzpatrick, David A., Canovas, David, Corrochano, Luis M, Doyle, Sean, Selker, Eric U, Seiler, Stephen and Bayram, Ozgur (2019) Control of development, secondary metabolism and light-dependent carotenoid biosynthesis by the velvet complex of Neurospora crassa. Genetics, 212 (3). pp. 691-710. ISSN 0016-6731

Zuniga-Soto, Evelyn, Fitzpatrick, David A., Doohan, Fiona M. and Mullins, Ewen (2019) Insights into the transcriptomic response of the plant engineering bacterium Ensifer adhaerens OV14 during transformation. Scientific Reports, 9 (10344). ISSN 2045-2322

McCarthy, Charley G.P. and Fitzpatrick, David A. (2019) Pan-genome analyses of model fungal species. Microbial Genomics, 5 (2). 000243. ISSN 2057-5858

McCarthy, Charley G.P. and Fitzpatrick, David A. (2019) Pangloss: A Tool for Pan-Genome Analysis of Microbial Eukaryotes. Genes, 10 (521). ISSN 2073-4425

Waldron, Rose, McGowan, Jamie, Gordon, Natasha, McCarthy, Charley G.P., Mitchell, E. Bruce and Fitzpatrick, David A. (2019) Proteome and allergenome of the European house dust mite Dermatophagoides pteronyssinus. PLoS ONE, 14 (5). e0216171. ISSN 1932-6203

O'Connor, Eoin, McGowan, Jamie, McCarthy, Charley G.P., Amini, Anica, Grogan, Helen and Fitzpatrick, David A. (2019) Whole Genome Sequence of the Commercially Relevant Mushroom Strain Agaricus bisporus var. bisporus ARP23. G3, 9. pp. 3057-3066. ISSN 2160-1836

McGowan, Jamie, Byrne, Kevin P. and Fitzpatrick, David A. (2018) Comparative Analysis of Oomycete Genome Evolution Using the Oomycete Gene Order Browser (OGOB). Genome Biology and Evolution, 11 (1). pp. 189-206. ISSN 1759-6653

Rahman, Farzana, Hassan, Mehedi, Hanano, Abdulsamie, Fitzpatrick, David A., McCarthy, Charley G.P. and Murphy, Denis (2018) Evolutionary, structural and functional analysis of the caleosin/peroxygenase gene family in the Fungi. BMC Genomics, 19 (976). ISSN 1471-2164

O'Brien, Caoimhe E., McCarthy, Charley G.P., Walshe, Annie E., Shaw, Dennis R., Sumski, Deirdre A., Krassowski, Tadeusz, Fitzpatrick, David A. and Butler, Geraldine (2018) Genome analysis of the yeast Diutina catenulata, a member of the Debaryomycetaceae/Metschnikowiaceae (CTG-Ser) clade. PLoS ONE, 13 (6). e0198957. ISSN 1932-6203

McNamara, Louise, Griffin, Christine, Fitzpatrick, David A., Kavanagh, Kevin and Carolan, James C. (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, 101. pp. 1-13. ISSN 0965-1748

Cullen, Louise, O'Connor, Andrew, McCormack, Sarah, Owens, Rebecca A., Holt, Giles S., Collins, Cassandra, Callaghan, Maire, Doyle, Sean, Smith, Darren, Schaffer, Kirsten, Fitzpatrick, David A. and McClean, Siobhan (2018) The involvement of the low-oxygen-activated locus of Burkholderia cenocepacia in adaptation during cystic fibrosis infection. Scientific Reports, 8 (1). p. 13386. ISSN 2045-2322

McCarthy, Charley G.P. and Fitzpatrick, David A. (2017) Multiple Approaches to Phylogenomic Reconstruction of the Fungal Kingdom. Advances in genetics, 100. pp. 211-266. ISSN 0065-2660

McCarthy, Charley G.P. and Fitzpatrick, David A. (2017) Phylogenomic Reconstruction of the Oomycete Phylogeny Derived from 37 Genomes. Msphere, 2 (2). ISSN 2379-5042

Waldron, Rose, McGowan, Jamie, Gordon, Natasha, McCarthy, Charley G.P., Mitchell, E. Bruce, Doyle, Sean and Fitzpatrick, David A. (2017) Draft Genome Sequence of Dermatophagoides pteronyssinus, the European House Dust Mite. Genome Announcments, 5 (2). e00789-17. ISSN 2169-8287

McGill, Lorraine M., Fitzpatrick, David A., Pisani, Davide and Burnell, Ann (2017) Estimation of phylogenetic divergence times in Panagrolaimidae and other nematodes using relaxed molecular clocks calibrated with insect and crustacean fossils. Nematology, 19 (8). pp. 899-913. ISSN 1568-5411

Sipos, György, Prasanna, Arun N., Walter, Mathias C., Krizsán, Krisztina, Kiss, Brigitta, Hess, Jaqueline, Varga, Torda, Slot, Jason, Riley, Robert, Bóka, Bettina, Rigling, Daniel, Barry, Kerrie, Lee, Juna, Mihaltcheva, Sirma, LaButti, Kurt, Lipzen, Anna, Waldron, Rose, Moloney, Nicola M., Sperisen, Christoph, Kredics, László, Vágvölgyi, Csaba, Patrignani, Andrea, Fitzpatrick, David A., Nagy, István, Doyle, Sean, Anderson, James B., Grigoriev, Igor V., Münsterkötter, Martin and Nagy, László (2017) Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria. Nature Ecology & Evolution, 1. pp. 1931-1941. ISSN 2397-334X

McGowan, Jamie and Fitzpatrick, David A. (2017) Genomic, Network, and Phylogenetic Analysis of the Oomycete Effector Arsenal. Msphere, 2 (6). e00408-17. ISSN 2379-5042

Collins, Cassandra, Hurley, Rachel, Almutlagah, Nada, O'Keeffe, Grainne, Keane, Thomas M., Fitzpatrick, David A. and Owens, Rebecca A. (2017) Proteomic Characterization of Armillaria mellea Reveals Oxidative Stress Response Mechanisms and Altered Secondary Metabolism Profiles. Microorganisms, 5 (3). p. 60. ISSN 2076-2607

McNamara, Louise, Carolan, James C., Griffin, Christine, Fitzpatrick, David A. and Kavanagh, Kevin (2017) The effect of entomopathogenic fungal culture filtrate on the immune response of the greater wax moth, Galleria mellonella. Journal of Insect Physiology, 100. pp. 82-92. ISSN 0022-1910

McCarthy, Charley G.P. and Fitzpatrick, David A. (2016) Systematic Search for Evidence of Interdomain Horizontal Gene Transfer from Prokaryotes to Oomycete Lineages. Msphere, 1 (5). ISSN 2379-5042

Fitzpatrick, David A. and Walsh, Fiona (2016) Antibiotic resistance genes across a wide variety of metagenomes. FEMS Microbiology Ecology, 92 (2). fiv168. ISSN 1574-6941

An, Lu, Fitzpatrick, David A. and Harrison, Paul M. (2016) Emergence and evolution of yeast prion and prion-like proteins. BMC Evolutionary Biology, 16 (24). ISSN 1471-2148

Smith, Elizabeth B., Dolan, Stephen K., Fitzpatrick, David A., Doyle, Sean and Jones, Gary W. (2016) Towards understanding the gliotoxin detoxification mechanism: in vivo thiomethylation protects yeast from gliotoxin cytotoxicity. Microbial Cell, 3 (3). pp. 120-125. ISSN 2311-2638

Owens, Rebecca A., O'Keeffe, Grainne, Smith, Elizabeth B., Dolan, Stephen K., Hammel, Stephen, Sheridan, Kevin J., Fitzpatrick, David A., Keane, Thomas M. and Doyle, Sean (2015) Interplay between Gliotoxin Resistance, Secretion, and the Methyl/ Methionine Cycle in Aspergillus fumigatus. Eukaryotic Cell, 14 (9). pp. 941-957. ISSN 1535-9786

Reardon, Wesley, Gallagher, Pauline, Nolan, Katie M., Wright, Hayley, Carde-nosa-Rubio, Maria Cruz, Bragalini, Claudia, Lee, Chui-Sang, Fitzpatrick, David A., Corcoran, Killian, Wolff, Kirsten and Nugent, Jacqueline M. (2014) Different outcomes for the MYB floral symmetry genes DIVARICATA and RADIALIS during the evolution of derived actinomorphy in Plantago. New Phytologist, 202 (2). pp. 716-725. ISSN 0028-646X

Hasin, Naushaba, Cusack, Sarah, Ali, Shahin S., Fitzpatrick, David A. and Jones, Gary W. (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 (194). pp. 1-12. ISSN 1471-2164

Haggerty, Leanne S., Jachiet, Pierre-Alain, Hanage, William P., Fitzpatrick, David A., Lopez, Philippe, O'Connell, Mary J., Pisani, Davide, Wilkinson, Mark, Bapteste, Eric and McInerney, James O. (2014) A Pluralistic Account of Homology: Adapting the Models to the Data. Molecular Biology and Evolution, 31 (3). pp. 501-506. ISSN 0737-4038

O’Keeffe, Grainne, Hammel, Stephen, Owens, Rebecca A., Keane, Thomas M., Fitzpatrick, David A., Jones, Gary W. and Doyle, Sean (2014) RNA-seq reveals the pan-transcriptomic impact of attenuating the gliotoxin self-protection mechanism in Aspergillus fumigatus. BMC Genomics, 15 (894). pp. 1-26. ISSN 1471-2164

Dolan, Stephen K., Owens, Rebecca A., O'Keefe, Grainne, Hammel, Stephen, Fitzpatrick, David A., Jones, Gary W. and Doyle, Sean (2014) Regulation of Nonribosomal Peptide Synthesis: bis-Thiomethylation Attenuates Gliotoxin Biosynthesis in Aspergillus fumigatus. Chemistry and Biology, 21 (8). pp. 999-2012. ISSN 1074-5521

Jones, Gary W., Doyle, Sean and Fitzpatrick, David A. (2014) The evolutionary history of the genes involved in the biosynthesis of the antioxidant ergothioneine. Gene, 549 (1). pp. 161-170. ISSN 0378-1119

Culleton, Bridget A., Lall, Patrick, Kinsella, Gemma K., Doyle, Sean, McCaffrey, John G., Fitzpatrick, David A. and Burnell, Ann (2014) A role for the Parkinson’s disease protein DJ-1 as a chaperone and antioxidant in the anhydrobiotic nematode Panagrolaimus superbus. Cell Stress & Chaperones, 20 (1). pp. 121-137. ISSN 1355-8145

Gildea, Sarah, Fitzpatrick, David A. and Cullinane, Ann (2013) Epidemiological and virological investigations of equine influenza outbreaks in Ireland (2010–2012). Influenza and Other Respiratory Viruses, 7 (S.4). pp. 61-74. ISSN 1750-2659

Clarke, Michael, Lohan, Amanda, Liu, Bernard, Lagkouvardos, Ilias, Roy, Scott, Zafar, Nikhat, Bertelli, Claire, Schilde, Christina, Kianianmomeni, Arash, Burglin, Thomas R., Frech, Christian, Turcotte, Bernard, Kopec, Klaus O., Synnott, John M., Choo, Caleb, Paponov, Ivan, Finkler, Aliza, Soon Heng Tan, Chris, Hutchins, Andrew P., Weinmeier, Thomas, Ratteri, Thomas, Chu, Jeffery SC, Gimenez, Gregory, Irimia, Manuel, Rigden, Daniel J., Fitzpatrick, David A., Lorenzo-Morales, Jacob, Baterman, Alex, Chiu, Cheng-Hsun, Tang, Petrus, Hegemann, Peter, Fromm, Hillel, Raoult, Didier, Greub, Gilbert, Miranda-Saavedra, Diego, Chen, Nansheng, Nash, Piers, Ginger, Michael L., Horn, Matthias, Schaap, Pauline, Caler, Lis and Loftus, Brendan J. (2013) Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling. Genome Biology, 14 (R11). ISSN 1465-6906

Collins, Cassandra, Keane, Thomas M., Turner, Daniel J., O'Keefe, Grainne, Fitzpatrick, David A. and Doyle, Sean (2013) Genomic and Proteomic Dissection of the Ubiquitous Plant Pathogen, Armillaria mellea: Toward a New Infection Model System. Journal of Proteome Research, 12. pp. 2552-2570. ISSN 1535-3893

Sharma, Visha, He, Chao, Sacca-Schaeffer, Julian, Brzozowski, Eric, Martin-Herranz, Daniel E., Mendelowitz, Zelda, Fitzpatrick, David A. and O'Halloran, Damien M. (2013) Insight into the Family of Na+/Ca2+ Exchangers of Caenorhabditis elegans. Genetics, 195. pp. 611-619. ISSN 0016-6731

He, Chao, Fitzpatrick, David A. and O'Halloran, Damien M. (2013) A comparative study of the molecular evolution of signalling pathway members across olfactory, gustatory and photosensory modalities. Journal of Genetics, 92 (2). pp. 327-334. ISSN 0022-1333

Fitzpatrick, David A. and O'Halloran, Damien M. (2012) Investigating the Relationship between Topology and Evolution in a Dynamic Nematode Odor Genetic Network. International Journal of Evolutionary Biology, 2012 (548081). ISSN 2090-052X

O'Hanlon, Karen, Margison, Geoffrey P., Hatch, Amy, Fitzpatrick, David A., Owens, Rebecca A., Doyle, Sean and Jones, Gary W. (2012) Molecular characterization of an adaptive response to alkylating agents in the opportunistic pathogen Aspergillus fumigatus. Nucleic Acids Research, 40 (16). pp. 7806-7820. ISSN 0305-1048

Fitzpatrick, David A., O'Brien, Jennifer, Moran, Ciara, Hasin, Naushaba, Kenny, Elaine, Cormican, Paul, Gates, Amy, Morris, Derek W. and Jones, Gary W. (2011) Assessment of Inactivating Stop Codon Mutations in Forty Saccharomyces cerevisiae Strains: Implications for [PSI+] Prion-Mediated Phenotypes. PLoS ONE, 6 (12). e28684. ISSN 1932-6203

Creevey, Christopher J., Doerks, Tobias, Fitzpatrick, David A., Raes, Jeroen and Bork, Peer (2011) Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer. PLoS ONE, 6 (8). ISSN 1932-6203

Ding, Chen, Yin, Jun, Tovar, Edgar Mauricio Medina, Fitzpatrick, David A., Higgins, Desmond G. and Thiele, Dennis J. (2011) The Cu regulon of the human fungal pathogen Cryptococcus neoformans H99: Cuf1 activates distinct genes in response to both Cu excess and deficiency. Molecular Microbiology, 81 (6). pp. 1560-1576. ISSN 0950-382X

Fitzpatrick, David A. (2011) Horizontal gene transfer in fungi. Microbiology Letters.

Medina, Edgar M., Jones, Gary W. and Fitzpatrick, David A. (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 (3-4). pp. 116-133. ISSN 0022-2844

Fitzpatrick, David A., O'Gaora, Peadar, Byrne, Kevin P. and Butler, Geraldine (2010) Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser. BMC Genomics, 11 (290). pp. 1-14. ISSN 1471-2164

Reardon, Wesley, Fitzpatrick, David A., Fares, Mario A. and Nugent, Jacqueline M. (2009) Evolution of flower shape in Plantago lanceolata. Plant Molecular Biology, 71 (3). pp. 241-250. ISSN 0167-4412

Butler, Geraldine, Rasmussen, Matthew D., Lin, Michael F., Santos, Manuel A., Sakthikumar, Sharadha, Munro, Carol A., Rheinbay, Esther, Grabherr, Manfred, Forche, Anja, Reedy, Jennifer L., Agrafioti, Ino, Arnaud, Martha B., Bates, Steven, Brown, Alistair J.P., Brunke, Sascha, Costanzo, Maria C., Fitzpatrick, David A., de Groot, Piet W. J., Harris, David, Hoyer, Lois L., Hube, Bernhard, Klis, Frans M., Kodira, Chinnappa, Lennard, Nicola, Logue, Mary E., Martin, Ronny, Neiman, Aaron M., Nikolaou, Elissavet, Quail, Michael A., Quinn, Janet, Santos, Maria C., Schmitzberger, Florian F., Sherlock, Gavin, Shah, Prachi, Silverstein, Kevin A.T., Skrzypek, Marek S., Soll, David, Staggs, Rodney, Stansfield, Ian, Stumpf, Michael P.H., Sudbery, Peter E., Srikantha, Thyagarajan, Zeng, Qiandong, Berman, Judith, Berriman, Matthew, Heitman, Joseph, Gow, Neil A.R., Lorenz, Michael C., Birren, Bruce W., Kellis, Manolis and Cuomo, Christina A. (2009) Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature, 459. pp. 657-662. ISSN 1476-4687

Haggerty, Leanne S., Martin, Fergal J., Fitzpatrick, David A. and McInerney, James O. (2009) Gene and genome trees conflict at many levels. Philosophical Transactions of the Royal Society B, 364 (1527). pp. 2209-2219. ISSN 0080-4622

Fitzpatrick, David A. (2009) Lines of Evidence for Horizontal Gene Transfer of a Phenazine Producing Operon into Multiple Bacterial Species. Journal of Molecular Evolution, 68 (2). pp. 171-185. ISSN 0022-2844

Regeai, S.O., Dolan, K.M., Fitzpatrick, David A., Browne, J.A., Jones, J.T. and Burnell, Ann (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 (1). pp. 421-424. ISSN 1755-098X

Fitzpatrick, David A., Logue, Mary E. and Butler, Geraldine (2008) Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis. BMC Evolutionary Biology, 8. pp. 181-195. ISSN 1471-2148

Johnstone, Catriona R., O'Dushlaine, Colm, Fitzpatrick, David A., Edwards, Richard J. and Shields, Denis C. (2007) Evaluation of Whether Accelerated Protein Evolution in Chordates Has Occurred before, after, or Simultaneously with Gene Duplication. Molecular Biology and Evolution, 24 (1). pp. 315-323. ISSN 0737-4038

Fitzpatrick, David A., Logue, Mary E., Stajich, Jason E. and Butler, Geraldine (2006) A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evolutionary Biology, 6. pp. 99-113. ISSN 1471-2148

Fitzpatrick, David A., O'Halloran, Damien M. and Burnell, Ann (2006) Multiple lineage specific expansions within the guanylyl cyclase gene family. BMC Evolutionary Biology, 6. pp. 26-43. ISSN 1471-2148

Fitzpatrick, David A., Creevey, Christopher J. and McInerney, James O. (2006) Genome Phylogenies Indicate a Meaningful a-Proteobacterial Phylogeny and Support a Grouping of the Mitochondria with the Rickettsiales. Molecular Biology and Evolution, 23 (1). pp. 74-85.

O'Halloran, Damien M., Fitzpatrick, David A., McCormack, Grace P., McInerney, James O. and Burnell, Ann (2006) The molecular phylogeny of a nematode-specific clade of heterotrimeric G-protein alpha-subunit genes. Journal of Molecular Evolution, 63 (1). pp. 87-94. ISSN 0022-2844

Fitzpatrick, David A. and McInerney, James O. (2005) Evidence of Positive Darwinian Selection in Omp85, a Highly Conserved Bacterial Outer Membrane Protein Essential for Cell Viability. Journal of Molecular Evolution, 61 (1). pp. 90-98.

Fitzpatrick, David A., Creevey, Christopher J. and McInerney, James O. (2005) Evidence of Positive Darwinian Selection in Putative Meningococcal Vaccine Antigens. Journal of Molecular Evolution, 61 (1). pp. 90-98. ISSN 0022-2844

Shannon, Adam J., Browne, John A., Boyd, Jacqueline, Fitzpatrick, David A. and Burnell, Ann (2005) The anhydrobiotic potential and molecular phylogenetics of species and strains of Panagrolaimus (Nematoda, Panagrolaimidae). Journal of Experimental Biology, 208. pp. 2433-2445.

Creevey, Christopher J., Fitzpatrick, David A., Philip, Gayle K., Kinsella, Rhoda J., O'Connell, Mary J., Pentony, Melissa M., Travers, Simon A., Wilkinson, Mark and McInerney, James O. (2004) Does a tree-like phylogeny only exist at the tips in the prokaryotes? Proceedings of The Royal Society of London, Biology Series, 271 (1557). pp. 2551-2558.

Kinsella, Rhoda J., Fitzpatrick, David A., Creevey, Christopher J. and McInerney, James O. (2003) Fatty acid biosynthesis in Mycobacterium tuberculosis: Lateral gene transfer, adaptive evolution, and gene duplication. Proceedings of the National Academy of Sciences, 100 (18). pp. 10320-10325. ISSN 1091-6490

Thesis

Fitzpatrick, David A. (2004) A study of selection and recombination in microorganisms and a place for the mitochondrion among the a-proteobacteria. PhD thesis, National University of Ireland Maynooth.