Article

Petersen, Celine and Sørensen, Trine and Nielsen, Mikkel R. and Sondergaard, Teis E. and Sørensen, Jens L. and Fitzpatrick, David A. and 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

Dwyer, Kelly and Bentley, Ian S. and Fitzpatrick, David A. and Saleh, Aliabbas A. and Tighe, Emma and McGleenan, Eibhilin and 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 and Grogan, Helen and 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 and Grogan, Helen and 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 and Sarikaya Bayram, Özlem and Bayram, Ozgur and Karahoda, Betim and Meister, Cindy and Köhler, Anna M. and Thieme, Sabine and Elramli, Nadia and Frawley, Dean and McGowan, Jamie and Fitzpatrick, David A. and Schmitt, Kerstin and de Assis, Leandro Jose and Valerius, Oliver and 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 and Sarikaya Bayram, Özlem and Bayram, Ozgur and Karahoda, Betim and Meister, Cindy and Köhler, Anna M. and Thieme, Sabine and Elramli, Nadia and Frawley, Dean and McGowan, Jamie and Fitzpatrick, David A. and Schmitt, Kerstin and de Assis, Leandro Jose and Valerius, Oliver and 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 and Zhou, Dongmei and Shen, Danyu and Chen, Yifan and Xue, Taiqiang and Chen, Siqiao and Zhang, Qimeng and Zhang, Jinfeng and McGowan, Jamie and Cai, Feng and Pang, Guan and Wang, Nan and Sheikh, Taha Majid Mahmood and Deng, Sheng and Li, Jingjing and Soykam, Hüseyin Okan and Kara, Irem and Fitzpatrick, David A. and Druzhinina, Irina S. and Bayram Akcapinar, Günseli and Wei, Lihui and 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

Doyle, Sean and Cuskelly, Daragh D. and Conlon, Niall and Fitzpatrick, David A. and Gilmartin, Ciara B. and 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 and Fitzpatrick, David A. and 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 and Chen, Siqiao and Xue, Taiqiang and Li, Jingjing and Sheikh, Taha Majid Mahmood and Zhang, Qimeng and Wang, Xuehai and Zhang, Jinfeng and Fitzpatrick, David A. and McGowan, Jamie and Shi, Xiujuan and Deng, Sheng and Jiu, Min and Zhou, Dongmei and 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. and Larkin, Annemarie and Xu, Linan and Fitzpatrick, David A. and Crean, Holly L. and Walshe, Kieran and Haas, Hubertus and 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 and Cinnéide, Eoin Ó and Salzberg, Letal I and Wolfe, Kenneth H and McGowan, Jamie and Fitzpatrick, David A. and 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 and Doyle, Sean and Amini, Aniça and 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 and O'Hanlon, Richard and 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 and Coates, Christopher J. and Eastwood, Dan C. and 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 and Owens, Rebecca A. and Doyle, Sean and Amini, Aniça and 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 and McGowan, Jamie and Gordon, Natasha and Mitchell, E Bruce and 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 and Dettmann, Anne and Karahoda, Betim and Moloney, Nicola M. and Ormsby, Tereza and McGowan, Jamie and Cea-Sánchez, Sara and Miralles-Duran, Alejandro and Brancini, Guilherme T P and Luque, Eva and Fitzpatrick, David A. and Canovas, David and Corrochano, Luis M and Doyle, Sean and Selker, Eric U and 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 and Fitzpatrick, David A. and 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 and McGowan, Jamie and Gordon, Natasha and McCarthy, Charley G.P. and 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 and McGowan, Jamie and McCarthy, Charley G.P. and Amini, Anica and 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 and 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 and Hassan, Mehedi and Hanano, Abdulsamie and Fitzpatrick, David A. and 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. and McCarthy, Charley G.P. and Walshe, Annie E. and Shaw, Dennis R. and Sumski, Deirdre A. and Krassowski, Tadeusz and 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 and Griffin, Christine and Fitzpatrick, David A. and 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 and O'Connor, Andrew and McCormack, Sarah and Owens, Rebecca A. and Holt, Giles S. and Collins, Cassandra and Callaghan, Maire and Doyle, Sean and Smith, Darren and Schaffer, Kirsten and 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 and McGowan, Jamie and Gordon, Natasha and McCarthy, Charley G.P. and Mitchell, E. Bruce and 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. and Fitzpatrick, David A. and 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 and Prasanna, Arun N. and Walter, Mathias C. and Krizsán, Krisztina and Kiss, Brigitta and Hess, Jaqueline and Varga, Torda and Slot, Jason and Riley, Robert and Bóka, Bettina and Rigling, Daniel and Barry, Kerrie and Lee, Juna and Mihaltcheva, Sirma and LaButti, Kurt and Lipzen, Anna and Waldron, Rose and Moloney, Nicola M. and Sperisen, Christoph and Kredics, László and Vágvölgyi, Csaba and Patrignani, Andrea and Fitzpatrick, David A. and Nagy, István and Doyle, Sean and Anderson, James B. and Grigoriev, Igor V. and 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 and Hurley, Rachel and Almutlagah, Nada and O'Keeffe, Grainne and Keane, Thomas M. and 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 and Carolan, James C. and Griffin, Christine and 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 and 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. and Dolan, Stephen K. and Fitzpatrick, David A. and 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. and O'Keeffe, Grainne and Smith, Elizabeth B. and Dolan, Stephen K. and Hammel, Stephen and Sheridan, Kevin J. and Fitzpatrick, David A. and 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 and Gallagher, Pauline and Nolan, Katie M. and Wright, Hayley and Carde-nosa-Rubio, Maria Cruz and Bragalini, Claudia and Lee, Chui-Sang and Fitzpatrick, David A. and Corcoran, Killian and 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 and Cusack, Sarah and Ali, Shahin S. and 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. and Jachiet, Pierre-Alain and Hanage, William P. and Fitzpatrick, David A. and Lopez, Philippe and O'Connell, Mary J. and Pisani, Davide and Wilkinson, Mark and 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 and Hammel, Stephen and Owens, Rebecca A. and Keane, Thomas M. and Fitzpatrick, David A. and 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. and Owens, Rebecca A. and O'Keefe, Grainne and Hammel, Stephen and Fitzpatrick, David A. and 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. and 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. and Lall, Patrick and Kinsella, Gemma K. and Doyle, Sean and McCaffrey, John G. and 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 and 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 and Lohan, Amanda and Liu, Bernard and Lagkouvardos, Ilias and Roy, Scott and Zafar, Nikhat and Bertelli, Claire and Schilde, Christina and Kianianmomeni, Arash and Burglin, Thomas R. and Frech, Christian and Turcotte, Bernard and Kopec, Klaus O. and Synnott, John M. and Choo, Caleb and Paponov, Ivan and Finkler, Aliza and Soon Heng Tan, Chris and Hutchins, Andrew P. and Weinmeier, Thomas and Ratteri, Thomas and Chu, Jeffery SC and Gimenez, Gregory and Irimia, Manuel and Rigden, Daniel J. and Fitzpatrick, David A. and Lorenzo-Morales, Jacob and Baterman, Alex and Chiu, Cheng-Hsun and Tang, Petrus and Hegemann, Peter and Fromm, Hillel and Raoult, Didier and Greub, Gilbert and Miranda-Saavedra, Diego and Chen, Nansheng and Nash, Piers and Ginger, Michael L. and Horn, Matthias and Schaap, Pauline and 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 and Keane, Thomas M. and Turner, Daniel J. and O'Keefe, Grainne and 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 and He, Chao and Sacca-Schaeffer, Julian and Brzozowski, Eric and Martin-Herranz, Daniel E. and Mendelowitz, Zelda and 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 and 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 and Margison, Geoffrey P. and Hatch, Amy and Fitzpatrick, David A. and Owens, Rebecca A. and 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. and O'Brien, Jennifer and Moran, Ciara and Hasin, Naushaba and Kenny, Elaine and Cormican, Paul and Gates, Amy and 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. and Doerks, Tobias and Fitzpatrick, David A. and 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 and Yin, Jun and Tovar, Edgar Mauricio Medina and Fitzpatrick, David A. and 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. and 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. and O'Gaora, Peadar and 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 and Fitzpatrick, David A. and 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 and Rasmussen, Matthew D. and Lin, Michael F. and Santos, Manuel A. and Sakthikumar, Sharadha and Munro, Carol A. and Rheinbay, Esther and Grabherr, Manfred and Forche, Anja and Reedy, Jennifer L. and Agrafioti, Ino and Arnaud, Martha B. and Bates, Steven and Brown, Alistair J.P. and Brunke, Sascha and Costanzo, Maria C. and Fitzpatrick, David A. and de Groot, Piet W. J. and Harris, David and Hoyer, Lois L. and Hube, Bernhard and Klis, Frans M. and Kodira, Chinnappa and Lennard, Nicola and Logue, Mary E. and Martin, Ronny and Neiman, Aaron M. and Nikolaou, Elissavet and Quail, Michael A. and Quinn, Janet and Santos, Maria C. and Schmitzberger, Florian F. and Sherlock, Gavin and Shah, Prachi and Silverstein, Kevin A.T. and Skrzypek, Marek S. and Soll, David and Staggs, Rodney and Stansfield, Ian and Stumpf, Michael P.H. and Sudbery, Peter E. and Srikantha, Thyagarajan and Zeng, Qiandong and Berman, Judith and Berriman, Matthew and Heitman, Joseph and Gow, Neil A.R. and Lorenz, Michael C. and Birren, Bruce W. and 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. and Martin, Fergal J. and 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. and Dolan, K.M. and Fitzpatrick, David A. and Browne, J.A. and 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. and 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. and O'Dushlaine, Colm and Fitzpatrick, David A. and 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. and Logue, Mary E. and 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. and 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. and 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. and Fitzpatrick, David A. and McCormack, Grace P. and 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. and 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. and Browne, John A. and Boyd, Jacqueline and 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. and Fitzpatrick, David A. and Philip, Gayle K. and Kinsella, Rhoda J. and O'Connell, Mary J. and Pentony, Melissa M. and Travers, Simon A. and 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. and Fitzpatrick, David A. and 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