1. RESEARCH ARTICLE Nature Communications, 15: 9190. Alternative sulphur metabolism in the fungal pathogen Candida parapsilosis Lombardi L, Salzberg LI, Ó Cinnéide E, O'Brien CE, Morio F, Turner SA, Byrne KP, Butler G (2024) DOI: 10.1038/s41467-024-53442-8 Citations: PubMed PMID: 39448588 Supplemental:   Information   Description   Data 1     Data 2   Data 3   Data 4

	2. GENOME ANNOUNCEMENT Microbiology Resource Announcements, 13: e01081-23. Genome sequences of two isolates of the yeast Candida zeylanoides: UCD849 from soil in Ireland, and AWD from an African Wild Dog McLaughlin RW, Hession C, Bergin S, Cosgrove A, Dowd A, Garvey N, Litovskich G, Osaigbovo E, Popa D, Thuku C, Butler G, Wolfe KH, Byrne KP (2024) DOI: 10.1128/mra.01081-23 Citations: PubMed PMID: 38334401

	3. GENOME ANNOUNCEMENT Microbiology Resource Announcements, 13: e01073-23. Draft genome sequence of the yeast Schwanniomyces capriottii strain UCD805, isolated from soil in Ireland Heneghan P, Ryan A, Ó Cinnéide E, Davies J, Bracken C, Ogundipe V, Doheny M, Lenihan L, Passalaris A, Walker R, Wolfe KH, Butler G, Byrne KP (2024) DOI: 10.1128/mra.01073-23 Citations: PubMed PMID: 38315016

	4. RESEARCH ARTICLE FEMS Yeast Research, 22: foac053. Identification of European isolates of the lager yeast parent Saccharomyces eubayanus Bergin SA, Allen S, Hession C, Ó Cinnéide E, Ryan A, Byrne KP, Ó Cróinín T, Wolfe KH and Butler G (2022) Award: Winner Best Paper of 2022 in FEMS Yeast Research Commentary: Sampaio JP (2022) FEMS Yeast Research, 22: foac058 DOI: 10.1093/femsyr/foac053 Citations: PubMed PMID: 36473696 Press: New York Times, RTÉ, Irish Times, The Sun, Daily Mail Science Press: New Scientist, Science News, Silicon Republic Press Release: butler.ucd.ie, UCD Research, UCD, NovaUCD Supplemental:   Files

	5. RESEARCH ARTICLE PLOS Biology, 20: e3001877. Identification of genetic variants of the industrial yeast Komagataella phaffii (Pichia pastoris) that contribute to increased yields of secreted heterologous proteins Offei B, Braun-Galleani S, Venkatesh A, Casey WT, O'Connor KE, Byrne KP and Wolfe KH (2022) Commentary: Swichkow CR, Bloom JS, Kruglyak L (2022) PLOS Biology, 20: e3001911 DOI: 10.1371/journal.pbio.3001877 Citations: PubMed PMID: 36520709 Supplemental:   Figure 1   Figure 2   Figure 3   Figure 4   Figure 5     Figure 6   Figure 7   Figure 8   Figure 9   Figure 10     Data 1   Data 2   Data 3   Data 4       Table 1   Table 2   Raw Images 1

	6. RESEARCH ARTICLE PLOS Genetics, 18: e1010525. A widespread inversion polymorphism conserved among Saccharomyces species is caused by recurrent homogenization of a sporulation gene family Salzberg LI, Martos AAR, Lombardi L, Jermiin LS, Blanco A, Byrne KP and Wolfe KH (2022) DOI: 10.1371/journal.pgen.1010525 Citations: PubMed PMID: 36441813 Supplemental:   Figure 1   Figure 2   Figure 3   Figure 4   Figure 5     Figure 6   Figure 7   Figure 8   Table 1   Table 2     Table 3   Table 4   Table5   File 1   Data 1

	7. GENOME ANNOUNCEMENT Microbiology Resource Announcements, 11: e00957-22. Draft genome sequence of the yeast Blastobotrys aristata strain UCD613, isolated from soil in Ireland Don A, Byrne KP, Alqaderi F, Mazhova A, O'Leary Chaney B, Redmond S, Allen A, Gao J, Ó Cinnéide E, Bergin SA, Hession C, Wolfe KH and Butler G (2022) DOI: 10.1128/mra.00957-22 Citations: PubMed PMID: 36222698

	8. GENOME ANNOUNCEMENT Microbiology Resource Announcements, 11: e00952-22. Draft genome sequence of the yeast Torulaspora quercuum strain UCD657, isolated from soil in Ireland Blessing I, Byrne KP, Ghnewa H, Davey R, Fubara A, Welc J, Oubihi S, Moore L, Smith C, Ó Cinnéide E, Bergin SA, Hession C, Wolfe KH and Butler G (2022) DOI: 10.1128/mra.00952-22 Citations: PubMed PMID: 36214680

	9. GENOME ANNOUNCEMENT Microbiology Resource Announcements, 10: e00736-21. Draft genome sequence of the yeast Ogataea degrootiae strain UCD465, isolated from soil in Ireland Ó Cinnéide E, Jones M, Bahate E, Boyd E, Clavero R, Doherty H, Drozdz I, Dumana M, Gonzales C, Kennedy J, Khan M, Maher S, McGurk C, Moreau K, Neville R, Norton J, Ó Cróinín T, O'Gorman E, Olliff JC, Orimaco R, Quinn E, Webb Kennedy S, Bergin SA, Byrne KP, Wolfe KH, and Butler G (2021) DOI: 10.1128/MRA.00736-21 Citations: PubMed PMID: 34591679

	10. GENOME ANNOUNCEMENT Microbiology Resource Announcements, 10: e00761-21. Draft genome sequences of a diploid and hybrid Candida species, Candida sanyaensis UCD423, isolated from compost in Ireland Ryan A, Ó Cinnéide E, Bergin SA, Alhajeri G, Almotawaa H, Daly I, Heneghan S, Horan K, Kavanagh R, Keane C, Martin A, McDonagh A, O'Leary J, Osborne M, Watson E, Byrne KP, Wolfe KH, and Butler G (2021) DOI: 10.1128/MRA.00761-21 Citations: PubMed PMID: 34553994

	11. RESEARCH ARTICLE eLife, 9: e55336. The yeast mating-type switching endonuclease HO is a domesticated member of an unorthodox homing genetic element family Coughlan AY, Lombardi L, Braun-Galleani S, Martos AAR, Galeote V, Bigey F, Dequin S, Byrne KP and Wolfe KH (2020) Insight: Rusche L (2020) eLife, 9: e58403 DOI: 10.7554/eLife.55336 Citations: PubMed PMID: 32338594 Supplemental:   File 1   File 2   File 3

	12. RESEARCH ARTICLE Microbial Cell Factories, 18: 211. Genomic diversity and meiotic recombination among isolates of the biotech yeast Komagataella phaffii (Pichia pastoris) Braun-Galleani S, Dias JA, Coughlan AY, Ryan AP, Byrne KP and Wolfe KH (2019) DOI: 10.1186/s12934-019-1260-4 Citations: PubMed PMID: 31801527 Supplemental:   File 1   File 2   File 3   File 4

	13. GENOME ANNOUNCEMENT Microbiology Resource Announcements, 8: e01255-19. Draft genome sequence of the birch tree fungal pathogen Taphrina betulina UCD315 Heneghan P, Ryan AP, Nimmo D, Duggan C, Kumar P, O'Gaora P, Ó Cinnéide E, Byrne KP, Wolfe KH, O'Brien CE and Butler G (2019) DOI: 10.1128/MRA.01255-19 Citations: PubMed PMID: 31776224

	14. GENOME ANNOUNCEMENT Microbiology Resource Announcements, 8: e01257-19. Draft genome sequences of two isolates of the yeast Kazachstania servazzii recovered from soil in Ireland Faherty L, Lewis C, McElheron M, Garvey N, Duggan R, Shovlin B, Ó Cróinín T, Byrne KP, O'Brien CE, Wolfe KH and Butler G (2019) DOI: 10.1128/MRA.01257-19 Citations: PubMed PMID: 31672753

	15. GENOME ANNOUNCEMENT Microbiology Resource Announcements, 8: e01256-19. Draft genome sequence of a red basidiomycete yeast, Symmetrospora coprosmae strain UCD350, isolated from soil in Ireland Almasoud J, McArdle L, Henne R, Mathews K, O'Connor Í, McLoughlin LE, O'Gaora P, Byrne KP, O'Brien CE, Wolfe KH and Butler G (2019) DOI: 10.1128/MRA.01256-19 Citations: PubMed PMID: 31672752

	16. RESEARCH ARTICLE FEMS Yeast Research, 19: foz058. The Methylotroph Gene Order Browser (MGOB) reveals conserved synteny and ancestral centromere locations in the yeast family Pichiaceae Douglass AP, Byrne KP and Wolfe KH (2019) DOI: 10.1093/femsyr/foz058 Citations: PubMed PMID: 31397853 Supplemental:   Information   Website

	17. RESEARCH ARTICLE Scientific Reports, 9: 9240. The CYPome of the model xenobiotic-biotransforming fungus Cunninghamella elegans Palmer-Brown W, Miranda-CasoLuengo R, Wolfe KH, Byrne KP and Murphy CD (2019) DOI: 10.1038/s41598-019-45706-x Citations: PubMed PMID: 31239505 Supplemental:   Information

	18. RESEARCH ARTICLE G3, 9: 879-887. Coverage-versus-Length plots, a simple quality control step for de novo yeast genome sequence assemblies Douglass AP, O'Brien CE, Offei B, Coughlan AY, Ortiz-Merino RA, Butler G, Byrne KP and Wolfe KH (2019) DOI: 10.1534/g3.118.200745 Citations: PubMed PMID: 30674538 Supplemental:   Figure 1   Figure 2

	19. RESEARCH ARTICLE Genome Biology and Evolution, 11: 189-206. Comparative analysis of Oomycete genome evolution using the Oomycete Gene Order Browser (OGOB) McGowan J, Byrne KP and Fitzpatrick DA (2019) DOI: 10.1093/gbe/evy267 Citations: PubMed PMID: 30535146 Supplemental:   Information

	20. RESEARCH ARTICLE PLOS Pathogens, 14: e1007138. Population genomics shows no distinction between pathogenic Candida krusei and environmental Pichia kudriavzevii: One species, four names Douglass AP, Offei B, Braun-Galleani S, Coughlan AY, Martos AAR, Ortiz-Merino RA, Byrne KP and Wolfe KH (2018) DOI: 10.1371/journal.ppat.1007138 Citations: PubMed PMID: 30024981 • Media: "Two Fungal Species - One Pathogenic, One Benign - Are Actually the Same", The Scientist, 19th July 2018 • Media: "We've Been Putting A Potentially Dangerous, Drug-resistant Yeast in Food for Centuries", Discover Magazine, 19th July 2018 Supplemental:   Figure 1   Figure 2   Figure 3   Figure 4     Table 1   Table 2   File 1

	21. GENOME ANNOUNCEMENT Genome Announcements, 6: e00549-18. Draft genome sequence of the yeast Nadsonia starkeyi-henricii UCD142, isolated from forest soil in Ireland O'Boyle S, Bergin SA, Hussey ÉE, McLaughlin AD, Riddell LR, Byrne KP, Wolfe KH, O'Brien CE and Butler G (2018) DOI: 10.1128/genomeA.00549-18 Citations: PubMed PMID: 29930058 • Press Release: "Undergraduate Genetics and Microbiology students isolate and name new yeast species from soil"

	22. RESEARCH ARTICLE Applied and Environmental Microbiology, 84: e02294-17. Transcriptional response to lactic acid stress in the hybrid yeast Zygosaccharomyces parabailii Ortiz-Merino RA, Kuanyshev N, Byrne KP, Varela JA, Morrissey JP, Porro D, Wolfe KH and Branduardi P (2018) DOI: 10.1128/AEM.02294-17 Citations: PubMed PMID: 29269498 Supplemental:   Info   Data 1   Data 2   Data 3     Data 4   Data 5   Data 6   Data 7

	23. RESEARCH ARTICLE PLOS Genetics, 13: e1007092. Flip/flop mating-type switching in the methylotrophic yeast Ogataea polymorpha is regulated by an Efg1-Rme1-Ste12 pathway Hanson SJ, Byrne KP and Wolfe KH (2017) DOI: 10.1371/journal.pgen.1007092 Citations: PubMed PMID: 29176810 Supplemental:   Figure 1   Figure 2   Figure 3   Figure 4   Figure 5     Figure 6   Figure 7   Figure 8   Figure 9   Figure 10     Table 1   Table 2   Table 3   Table 4   Table 5     Table 6   Table 7

	24. RESEARCH ARTICLE PLOS Biology, 15: e2002128. Evolutionary restoration of fertility in an interspecies hybrid yeast, by whole-genome duplication after a failed mating-type switch Ortiz-Merino RA, Kuanyshev N, Braun-Galleani S, Byrne KP, Porro D, Branduardi P and Wolfe KH (2017) DOI: 10.1371/journal.pbio.2002128 Citations: PubMed PMID: 28510588 Supplemental:   Figure 1   Figure 2   Data 1     Table 1   Table 2   Table 3

	25. RESEARCH ARTICLE Genome Biology and Evolution, 8: 2482-92. Centromeres of the yeast Komagataella phaffii (Pichia pastoris) have a simple inverted-repeat structure Coughlan AY, Hanson SJ, Byrne KP and Wolfe KH (2016) DOI: 10.1093/gbe/evw178 Citations: PubMed PMID: 27497317 Supplemental:   Information

	26. REVIEW ARTICLE FEMS Yeast Research, 15: fov035. Clade- and species-specific features of genome evolution in the Saccharomycetaceae Wolfe KH, Armisén D, Proux-Wera E, ÓhÉigeartaigh SS, Azam H, Gordon JL and Byrne KP (2015) DOI: 10.1093/femsyr/fov035 Citations: PubMed PMID: 26066552

	27. RESEARCH ARTICLE PNAS, 111: E4851-8. Mating type switching by chromosomal inversion in methylotrophic yeasts suggests an origin for the three-locus Saccharomyces cerevisiae system Hanson SJ, Byrne KP and Wolfe KH (2014) DOI: 10.1073/pnas.1416014111 Citations: PubMed PMID: 25349420 Supplemental:   Information

	28. RESEARCH ARTICLE Journal of Bacteriology, 196: 2030-2042. SearchDOGS Bacteria, software that provides automated identification of potentially missed genes in annotated bacterial genomes ÓhÉigeartaigh SS, Armisén D, Byrne KP and Wolfe KH (2014) DOI: 10.1128/JB.01368-13 Citations: PubMed PMID: 24659774 Supplemental:   File 1

	29. RESEARCH ARTICLE Molecular Biology and Evolution, 30: 1281-1291. Comparative genome analysis and gene finding in Candida species using CGOB Maguire S, ÓhÉigeartaigh SS, Byrne KP, Schroeder M, O'Gaora P, Wolfe KH and Butler G (2013) DOI: 10.1093/molbev/mst042 Citations: PubMed PMID: 23486613 Supplemental:   Table 1

	30. RESEARCH ARTICLE Genome Biology and Evolution, 5: 525-531. Evolutionary mobility of the ribosomal DNA array in yeasts Proux-Wéra E, Byrne KP and Wolfe KH (2013) DOI: 10.1093/gbe/evt022 Citations: PubMed PMID: 23419706

	31. RESEARCH ARTICLE Party Politics, 19: 985-997. What's in a name? Using surnames as data for party research Kevin Byrne and Eoin O'Malley (2013) DOI: 10.1177/1354068811436032 Supplemental:   Methods

	32. RESEARCH ARTICLE Irish Political Studies, 28: 130-139. The two types of Ulster unionism: Testing an ethnic explanation for the unionist/loyalist divide Kevin Byrne and Eoin O'Malley (2013) DOI: 10.1080/07907184.2012.732573

	33. RESEARCH ARTICLE BMC Bioinformatics, 13: 237. A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach Proux-Wéra E, Armisén D, Byrne KP and Wolfe KH (2012) DOI: 10.1186/1471-2105-13-237 Citations: PubMed PMID: 22984983

	34. RESEARCH ARTICLE British Journal of Politics and International Relations, 14: 613-629. Politics with Hidden Bases: Unearthing the deep roots of party systems Kevin Byrne and Eoin O'Malley (2012) DOI: 10.1111/j.1467-856X.2011.00478.x • TV: The Week In Politics, RTÉ1, 26th June 2011   "Irish political surnames may indicate party affiliation" • Press: Stephen Collins, Political Editor, Irish Times, 27th June 2011   "FF and FG tribal split traced back to 12th century" • Press: Paul O'Brien, Political Editor, Irish Examiner, 27th June 2011   "Tribal split between 'Gaelic' FF and 'English' FG names" • Op-ed: Kevin Byrne and Eoin O'Malley, Sunday Business Post, 3rd July 2011   "Tribal rift between FF and FG goes deeper than the Civil War"

	35. RESEARCH ARTICLE PNAS, 108: 20024-20029. Evolutionary erosion of yeast sex chromosomes by mating-type switching accidents Gordon JL, Armisén D, Proux-Wéra E, ÓhÉigeartaigh SS, Byrne KP and Wolfe KH (2011) DOI: 10.1073/pnas.1112808108 Citations: PubMed PMID: 22123960 Supplemental:   /   Information

	36. RESEARCH ARTICLE PLOS Genetics, 7: e1002190. Mechanisms of chromosome number evolution in yeast Gordon JL, Byrne KP and Wolfe KH (2011) Community Choice: A story of chromosome number (2011) Nature, 477: 9 DOI: 10.1371/journal.pgen.1002190 Citations: PubMed PMID: 21811419 • Media: "Scientists trace yeast's gene shuffle", Australian Broastcasting Corporation, 22nd July 2011 Supplemental:   Dataset 1   Figure 1   Figure 2   Figure 3   Table 1    Table 2   Table 3   Table 4   Table 5   Table 6

	37. RESEARCH ARTICLE BMC Genomics, 12: 377. Systematic discovery of unannotated genes in 11 yeast species using a database of orthologous genomic segments OhEigeartaigh SS, Armisen D, Byrne KP and Wolfe KH (2011) DOI: 10.1186/1471-2164-12-377 Citations: PubMed PMID: 21791067 Supplemental:   File 1

	38. RESEARCH ARTICLE BMC Genomics, 11: 290. Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser Fitzpatrick DA, O'Gaora P, Byrne KP and Butler G (2010) DOI: 10.1186/1471-2164-11-290 Citations: PubMed PMID: 20459735 Supplemental:   File 1   File 2   File 3   File 4   File 5   Website

	39. RESEARCH ARTICLE PLOS Genetics, 5: e1000485. Additions, losses and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome Gordon JL, Byrne KP and Wolfe KH (2009) Perspective: Sankoff D (2009) PLOS Genetics, 5: e1000483 Highlights: Neame E (2009) Nature Reviews Genetics, 10: 426 DOI: 10.1371/journal.pgen.1000485 Citations: PubMed PMID: 19436716 Supplemental:   Figure 1   Table 1   Table 2

	40. RESEARCH ARTICLE PNAS, 104: 8397-8402. Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication Scannell DR, Frank AC, Conant GC, Byrne KP, Woolfit M and Wolfe KH (2007) DOI: 10.1073/pnas.0608218104 Citations: PubMed PMID: 17494770 Supplemental:   /   Information

	41. RESEARCH ARTICLE Genetics, 175: 1341-1350. Consistent patterns of rate asymmetry and gene loss indicate widespread neo-functionalization of yeast genes after whole-genome duplication Byrne KP and Wolfe KH (2007) Issue Highlights: Genetics, 2007; 175: NP DOI: 10.1534/genetics.106.066951 Citations: PubMed PMID: 17194778 Supplemental:   Information

	42. RESEARCH ARTICLE Nature, 440: 341-345. Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts Scannell DR*, Byrne KP*, Gordon JL, Wong S and Wolfe KH (2006) DOI: 10.1038/nature04562 Citations: PubMed PMID: 16541074 • Press: Dick Ahlstrom, Science Editor, Irish Times, 3rd March 2006   "Demonstrating the origin of a species" * These authors contributed equally to this work. Supplemental:   Table 1   Note 2   Note 3   Note 4   Note 5

	43. RESEARCH ARTICLE Nucleic Acids Research, 34: D452-455. Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser Byrne KP and Wolfe KH (2006) DOI: 10.1093/nar/gkj041 Citations: PubMed PMID: 16381909

	44. RESEARCH ARTICLE Molecular Biology and Evolution, 23: 245-253. Rate asymmetry and adaptive evolution after genome duplication causes substantial long branch attraction artifacts in the phylogeny of Saccharomyces species Fares MA, Byrne KP and Wolfe KH (2006) DOI: 10.1093/molbev/msj027 Citations: PubMed PMID: 16207937 Supplemental:   Table 1

	45. REVIEW ARTICLE Current Bioinformatics, 1: 131-146. Computational analyses of ancient polyploidy Byrne KP and Blanc G (2006) DOI: 10.2174/157489306777011897

	46. RESEARCH ARTICLE Genome Research, 15: 1456-1461. The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species Byrne KP and Wolfe KH (2005) DOI: 10.1101/gr.3672305 Citations: PubMed PMID: 16169922 Supplemental:   Methods   Table 1   Table 2   Data   Website

	47. CONFERENCE PROCEEDINGS Fifth Workshop on QCD, 346-353 The spin dependence of swift proton collisions AT Bates, NH Buttimore and KP Byrne (2000) Proceedings of the Fifth Workshop on Quantum Chromodynamics, (eds. HM Fried, B Muller and Y Gabellini), pp. 346-353. Villefranche-sur-Mer, France, 3-7 Jan 2000. World Scientific, Singapore. inSPIRE: 549767 DOI: 10.1142/4572