1. RESEARCH ARTICLE Preprint, In review 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: 10.21203/rs.3.rs-3951443/v1

	2. 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

	3. 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

	4. 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

	5. 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

	6. 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

	7. 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

	8. 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

	9. 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

	10. 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

	11. 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

	12. 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

	13. 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

	14. 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

	15. 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

	16. 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

	17. 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

	18. 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

	19. 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

	20. 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

	21. 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

	22. 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

	23. 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

	24. 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

	25. 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

	26. 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

	27. 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

	28. 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

	29. 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

	30. 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

	31. 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

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

	33. 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