1. 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)

Citations: PubMed Central
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 

2. 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)

Citations: PubMed Central
PMID: 27497317

Supplemental:  Supplemental Information  Information 

3. 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)

Citations: PubMed Central
PMID: 26066552

4. 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)

Citations: PubMed Central
PMID: 25349420

Supplemental:  Supplemental Information  Information 

5. 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)

Citations: Google Scholar | PubMed Central
PMID: 24659774

Supplemental:  Supplemental Information  File 1 

6. 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)

Citations: Google Scholar | PubMed Central
PMID: 23486613

Supplemental:  Supplemental Table 1  Table 1 

7. 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)

Citations: Google Scholar | PubMed Central
PMID: 23419706

8. 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)

Citations: Google Scholar | PubMed Central
PMID: 22984983

9. 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)

Citations: Google Scholar | PubMed Central
PMID: 22123960

Supplemental:  Supplemental Information  /  Supplemental Information  Information

10. 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
Citations: Google Scholar | PubMed Central
PMID: 21811419

• Media: Branwen Morgan, Australian Broastcasting Corporation, 22nd July 2011
  "Scientists trace yeast's gene shuffle"

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

11. 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)

Citations: Google Scholar | PubMed Central
PMID: 21791067

Supplemental:  Supplemental Information  File 1 

12. 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)

Citations: Google Scholar | PubMed Central
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 

13. 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
Faculty of 1000: Recommended (3.0)
Citations: Google Scholar | PubMed Central
PMID: 19436716

Supplemental:  Supplemental Information  Figure 1  Supplemental Information  Table 1  Supplemental Information  Table 2

14. 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)

Faculty of 1000: Must Read (6.0)
Citations: Google Scholar | PubMed Central
PMID: 17494770

Supplemental:  Supplemental Information  /  Supplemental Information  Information

15. 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
Citations: Google Scholar | PubMed Central
PMID: 17194778

Supplemental:  Supplemental Information  Information

16. 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)

Faculty of 1000: Must Read (6.5)
Citations: Google Scholar | PubMed Central
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 

17. 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)

Citations: Google Scholar | PubMed Central
PMID: 16381909

18. 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)

Faculty of 1000: Must Read (6.0)
Citations: Google Scholar | PubMed Central
PMID: 16207937

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

19. REVIEW ARTICLE

Current Bioinformatics, 1: 131-146.

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

Citations: Google Scholar

20. 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)

Citations: Google Scholar | PubMed Central
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 
Dr Kevin Byrne
Conway Institute
School of Medicine
University College Dublin
Dublin 4
Ireland



Curriculum
Vitae

request access

PubMed
Scholar
database listings

Genomics & Bioinformatics
Political Science
High Energy Physics
show all categories

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.

PRINTABLE LIST

© Kevin Byrne 2017