Kevin Byrne

1. RESEARCH ARTICLE

Preprint, In Review

Intracellular acidification by bacteria-derived valeric acid is a mechanism of trans-kingdom ecology against Candida parapsilosis colonization
Yasuma-Mitobe K, Liao C, Nemeth T, Byrne KP, Billips A, Ramos R, Salinas CN, Chan E, Perissinoto M, Sidebottom AM, Plitas G, Butler G, Cross JR, Pamer EG, Gacser A, Xavier JB, Hohl TM (2025)

DOI: 10.1101/2025.09.12.675697

2. RESEARCH ARTICLE

Preprint, In Review

Centromeres in budding yeasts are conserved in chromosomal location but not in structure
Hession C, Byrne KP, Wolfe KH, Butler G (2025)

DOI: 10.1101/2025.07.24.666568

3. RESEARCH ARTICLE

International Journal of Systematic and Evolutionary Microbiology, 75: 006898.

Cyberlindnera hibernica sp. nov. and Barnettozyma discipulorum sp. nov., isolated from forest soil in Ireland
Ryan AP, Carvalho C, Zhao Y, Decuseara J, Osborne M, Heneghan P, Byrne KP, Ó Cróinín T, Wolfe KH, Sampaio JP, Butler G (2025)

DOI: 10.1099/ijsem.0.006898
Citations: PubMed
PMID: 40924470

Supplemental: Supplemental Information Information

4. GENOME ANNOUNCEMENT

Microbiology Resource Announcements, 14: e01168-24.

Genome sequence of the yeast Candida solani UCD1087, isolated from soil in Ireland
Osborne M, Hession C, Behnass S, Biju C, Dennison J, Faulkner A, Flynn A, Haugh J, Magner S, O'Reilly S, Saoud R , Ó Cróinín T, Wolfe KH, Butler G, Byrne KP (2025)

DOI: 10.1128/mra.01168-24
Citations: PubMed
PMID: 40152880

5. GENOME ANNOUNCEMENT

Microbiology Resource Announcements, 14: e01162-24.

Genome sequence of the yeast Cyberlindnera sylvatica UCD1060, isolated from soil in Ireland
Heneghan PG, Ryan AP, Bergin SA, Caka M, Coughlin A, Decuseara J, Gora M, Hudov D, McLoughlin A, Osadolor S, Saeed Maguire I, Swistowska W, Wolfe KH, Butler G, Byrne KP (2025)

DOI: 10.1128/mra.01162-24
Citations: PubMed
PMID: 40130933

6. 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: Supplemental Information Information Supplemental Information Description Supplemental Information Data 1
Supplemental Information Data 2 Supplemental Information Data 3 Supplemental Information Data 4

7. 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

8. 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

9. 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: Supplemental Information Files

10. 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: Supplemental Information Figure 1 Supplemental Information Figure 2 Supplemental Information Figure 3 Supplemental Information Figure 4 Supplemental Information Figure 5
Supplemental Information Figure 6 Supplemental Information Figure 7 Supplemental Information Figure 8 Supplemental Information Figure 9 Supplemental Information Figure 10
Supplemental Information Data 1 Supplemental Information Data 2 Supplemental Information Data 3 Supplemental Information Data 4
Supplemental Information Table 1 Supplemental Information Table 2 Supplemental Information Raw Images 1

11. 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: Supplemental Information Figure 1 Supplemental Information Figure 2 Supplemental Information Figure 3 Supplemental Information Figure 4 Supplemental Information Figure 5
Supplemental Information Figure 6 Supplemental Information Figure 7 Supplemental Information Figure 8 Supplemental Information Table 1 Supplemental Information Table 2
Supplemental Information Table 3 Supplemental Information Table 4 Supplemental Information Table5 Supplemental Information File 1 Supplemental Information Data 1

12. 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

13. 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

14. 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

15. 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

16. 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: Supplemental Information File 1 Supplemental Information File 2 Supplemental Information File 3

17. 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: Supplemental Information File 1 Supplemental Information File 2 Supplemental Information File 3 Supplemental Information File 4

18. 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

19. 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

20. 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

21. 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: Supplemental Information Information MGOB Website Website

22. 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: Supplemental Information Information

23. 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: Supplemental Information Figure 1 Supplemental Information Figure 2

24. 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: Supplemental Information Information

25. 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: Supplemental Information Figure 1 Supplemental Information Figure 2 Supplemental Information Figure 3 Supplemental Information Figure 4
Supplemental Information Table 1 Supplemental Information Table 2 Supplemental Information File 1

26. 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"

27. 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: Supplemental Information Info Supplemental Information Data 1 Supplemental Information Data 2 Supplemental Information Data 3
Supplemental Information Data 4 Supplemental Information Data 5 Supplemental Information Data 6 Supplemental Information Data 7

28. 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: Supplemental Information Figure 1 Supplemental Information Figure 2 Supplemental Information Figure 3 Supplemental Information Figure 4 Supplemental Information Figure 5
Supplemental Information Figure 6 Supplemental Information Figure 7 Supplemental Information Figure 8 Supplemental Information Figure 9 Supplemental Information Figure 10
Supplemental Information Table 1 Supplemental Information Table 2 Supplemental Information Table 3 Supplemental Information Table 4 Supplemental Information Table 5
Supplemental Information Table 6 Supplemental Information Table 7

29. 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: Supplemental Information Figure 1 Supplemental Information Figure 2 Supplemental Information Data 1
Supplemental Information Table 1 Supplemental Information Table 2 Supplemental Information Table 3

30. 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: Supplemental Information Information

31. 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

32. 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: Supplemental Information Information

33. 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: Supplemental Information File 1

34. 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: Supplemental Table 1 Table 1

35. 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

36. 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: Supplemental Information Methods

37. 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

38. 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

39. 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"

40. 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: Supplemental Information / Supplemental Information Information

41. 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: Supplemental Information Dataset 1 Supplemental Information Figure 1 Supplemental Information Figure 2 Supplemental Information Figure 3 Supplemental Information Table 1
Supplemental Information Table 2 Supplemental Information Table 3 Supplemental Information Table 4 Supplemental Information Table 5 Supplemental Information Table 6

42. 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: Supplemental Information File 1

43. 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年11月29日0
Citations: PubMed
PMID: 20459735

Supplemental: Supplemental Information File 1 Supplemental Information File 2 Supplemental Information File 3 Supplemental Information File 4 Supplemental Information File 5 CGOB Website Website

44. 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: Supplemental Information Figure 1 Supplemental Information Table 1 Supplemental Information Table 2

45. 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: Supplemental Information / Supplemental Information Information

46. 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: Supplemental Information Information

47. 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: Supplemental Table 1 - Biased representation of Gene Ontology (GO) terms in gene loss classes Table 1 Supplemental Note 2 - Phylogenetic relationship among S. castellii, S. cerevisiae and C. glabrata Note 2 Supplemental Note 3 - Estimation of relative timing of speciation events Note 3 Supplemental Note 4 - Model-based estimation of the number of genes still duplicated at phylogenetic nodes Note 4 Supplemental Note 5 - Overrepresentation of slowly evolving genes and genes involved in highly conserved biological processes among genes that underwent RGL Note 5

48. 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

49. 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: Supplemental Table 1 - Distances and ratios of distances from each S. cerevisiae ohnolog to their C. albicans ortholog Table 1

50. REVIEW ARTICLE

Current Bioinformatics, 1: 131-146.

Computational analyses of ancient polyploidy
Byrne KP and Blanc G (2006)

DOI: 10.2174/157489306777011897

51. 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: Supplemental Methods Methods Supplemental Table 1 - Gene sets, homology, tandem repeats and ohnologs Table 1 Supplemental Table 2 - Full Ohnolog Lists from S. cerevisiae, S. castellii and C. glabrata Table 2 YGOB Data Data YGOB Website Website

52. 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
Dr Kevin Byrne
Conway Institute
UCD School of Medicine
University College Dublin
Belfield
Dublin 4
Ireland
email:
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Ph.D. Thesis

Post-polyploidy evolution
in yeasts
Kevin Byrne (2007)

Trinity College Library Dublin
THESIS 8198

Supervisor: Prof. Kenneth H. Wolfe
Department of Genetics,
Trinity College, Dublin 2, Ireland.

M.Sc. Thesis

Single spin asymmetry for proton-carbon scattering
Kevin Byrne (2002)

Trinity College Library Dublin
THESIS 6706

Supervisor: Dr. Nigel H. Buttimore
School of Mathematics,
Trinity College, Dublin 2, Ireland.

0000-0002-6368-154X

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