Research Topics
| K H WolfeSummaryAffiliation: Trinity College Country: Ireland Publications
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Publications
A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approachEstelle Proux-Wéra
Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
BMC Bioinformatics 13:237. 2012..However, the annotation of genomes presents a major bottleneck for de novo projects, because it still relies on a process that is largely manual...- Evidence for horizontal transfer of a secondary metabolite gene cluster between fungiNora Khaldi
Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
Genome Biol 9:R18. 2008..It has long been suspected that clusters can be transferred horizontally between species, but few concrete examples have been described so far... - Evidence from comparative genomics for a complete sexual cycle in the 'asexual' pathogenic yeast Candida glabrataSimon Wong
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
Genome Biol 4:R10. 2003..Parallel evolution in the two lineages as they adopted mammalian hosts resulted in separate but analogous switches from overtly sexual to cryptically sexual life cycles, possibly in response to defense by the host immune system... - Rewiring the transcriptional regulatory circuits of cellsDevin R Scannell
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
Genome Biol 5:206. 2004..New data from yeast species show that both processes can happen... - Systematic discovery of unannotated genes in 11 yeast species using a database of orthologous genomic segmentsSeán S Ohéigeartaigh
Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
BMC Genomics 12:377. 2011..This principle has often been used in investigations of particular genes or genomic regions, but to our knowledge it has never been implemented systematically... - Congruence of tissue expression profiles from Gene Expression Atlas, SAGEmap and TissueInfo databasesLukasz Huminiecki
Department of Genetics, Smurfit Institute, University of Dublin Trinity College, Dublin 2, Ireland
BMC Genomics 4:31. 2003..However, database meta-analysis is complicated by differences in experimental technologies, data post-processing, database formats, and inconsistent gene and sample annotation... 
Molecular evolution meets the genomics revolutionKenneth H Wolfe
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
Nat Genet 33:255-65. 2003....- Evolutionary genomics: yeasts accelerate beyond BLASTKen Wolfe
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
Curr Biol 14:R392-4. 2004..This left a legacy of about 500 pairs of duplicated genes, many of which contribute to this yeast's ability to ferment glucose anaerobically; a few have been evolving so quickly they retain almost no sequence similarity to each other... - Comparative genomics and genome evolution in yeastsKenneth H Wolfe
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
Philos Trans R Soc Lond B Biol Sci 361:403-12. 2006..One of the most interesting emerging areas is the growing number of events such as gene losses, gene displacements and gene relocations that can be attributed to the action of natural selection... - Yesterday's polyploids and the mystery of diploidizationK H Wolfe
Department of Genetics, Smurfit Institute, Trinity College, University of Dublin, Dublin 2, Republic of Ireland
Nat Rev Genet 2:333-41. 2001..The greatest mystery is the molecular basis of diploidization, the evolutionary process by which a polyploid genome turns into a diploid one... - Molecular evidence for an ancient duplication of the entire yeast genomeK H Wolfe
Department of Genetics, University of Dublin, Trinity College, Ireland
Nature 387:708-13. 1997..Tetraploidy may have facilitated the evolution of anaerobic fermentation in Saccharomyces... - Sequence of 29 kb around the PDR10 locus on the right arm of Saccharomyces cerevisiae chromosome XV: similarity to part of chromosome IA G Parle McDermott
Department of Genetics, University of Dublin, Trinity College, Ireland
Yeast 12:999-1004. 1996..This sequence contig forms part of a region of extended similarity to part of the left arm of chromosome I, which is a relic of an ancient duplicated chromosomal region... - Accelerated evolution of sites undergoing mRNA editing in plant mitochondria and chloroplastsD C Shields
Department of Genetics, Trinity College, Dublin, Ireland
Mol Biol Evol 14:344-9. 1997..Whatever the cause, the rapid rate of evolution indicates that editing confers little selective advantage at most sites... - Ebb and flow of the chloroplast inverted repeatS E Goulding
Department of Genetics, University of Dublin, Trinity College, Ireland
Mol Gen Genet 252:195-206. 1996..Nicotiana acuminata chloroplast DNA contains a "molecular fossil' of the IR-LSC junction that existed prior to this dramatic rearrangement... - Similarity between putative ATP-binding sites in land plant plastid ORF2280 proteins and the FtsH/CDC48 family of ATPasesK H Wolfe
Department of Genetics, University of Dublin, Trinity College, Ireland
Curr Genet 25:379-83. 1994..coli FtsH. Phylogenetic analysis suggests that the red and green plastid genes are not true homologues (orthologues) but distinct members of an ancient gene family... - When gene marriages don't work out: divorce by subfunctionalizationBrian P Cusack
Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
Trends Genet 23:270-2. 2007..Mangrove retains the alternatively spliced chimeric gene, but in poplar it underwent duplication and complete subfunctionalization, through complementary structural degeneration, to re-form separate RPL32 and SODcp genes... - Yeast genome evolution--the origin of the speciesDevin R Scannell
Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
Yeast 24:929-42. 2007.... - Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplicationDevin R Scannell
Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
Proc Natl Acad Sci U S A 104:8397-402. 2007..The apparent low initial sequence divergence of the gene pairs leads us to propose that the yeast WGD was probably an autopolyploidization... - Gene order evolution and paleopolyploidy in hemiascomycete yeastsSimon Wong
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
Proc Natl Acad Sci U S A 99:9272-7. 2002..cerevisiae lineage after polyploidization. This finding is confirmed by sequences around the C. glabrata TRP1 and IPP1 loci, which show that it contains sister regions derived from the same duplication event as that of S. cerevisiae... - Genome survey sequencing of the wine spoilage yeast Dekkera (Brettanomyces) bruxellensisMegan Woolfit
Department of Genetics, Smurfit Institute, Trinity College Dublin, Dublin 2, Ireland
Eukaryot Cell 6:721-33. 2007..These data provide a resource for further analyses of the population genetics and evolution of D. bruxellensis and of the genetic bases of its physiological capabilities... - Rearrangement rate following the whole-genome duplication in teleostsMarie Semon
Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
Mol Biol Evol 24:860-7. 2007..We show that there does appear to be an increase in rearrangement rate after WGD, but that there is also a great deal of additional variability in rearrangement rates across species... - Consistent patterns of rate asymmetry and gene loss indicate widespread neofunctionalization of yeast genes after whole-genome duplicationKevin P Byrne
Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
Genetics 175:1341-50. 2007..These results suggest that a significant fraction of the retained ohnologs in yeast species underwent neofunctionalization soon after duplication... - Not born equal: increased rate asymmetry in relocated and retrotransposed rodent gene duplicatesBrian P Cusack
Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
Mol Biol Evol 24:679-86. 2007..Finally, we demonstrate that the faster sequence evolution of retrogenes correlates with the profound alteration of their expression pattern that is precipitated by retrotransposition... - Gene duplication, exon gain and neofunctionalization of OEP16-related genes in land plantsSinéad C Drea
Plant Molecular Genetics Laboratory, Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
Plant J 46:723-35. 2006..Our results indicate that gene duplication, exon gain and regulatory sequence evolution each played a role in the divergence of OEP16 homologues in plants... - Positive darwinian selection at the imprinted MEDEA locus in plantsCharles Spillane
Institute of Plant Biology and Zurich Basel Plant Science Center, University of Zurich, Ch 8008 Zurich, Switzerland
Nature 448:349-52. 2007..The evolution of MEA suggests a late origin of genomic imprinting within the Brassicaceae, whereas imprinting is thought to have originated early within the mammalian lineage... - Increased glycolytic flux as an outcome of whole-genome duplication in yeastGavin C Conant
Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin, Ireland
Mol Syst Biol 3:129. 2007..We also show theoretically that increased fermentative capacity is of greatest advantage when glucose resources are both large and dense, an observation potentially related to the appearance of angiosperms around the time of WGD... - Extensive genomic duplication during early chordate evolutionAoife McLysaght
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
Nat Genet 31:200-4. 2002..Considering the incompleteness of the sequence data and the antiquity of the event, the results are compatible with at least one round of polyploidy... - Probabilistic cross-species inference of orthologous genomic regions created by whole-genome duplication in yeastGavin C Conant
Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
Genetics 179:1681-92. 2008..We suggest that while duplicate copies of some genes may be lost neutrally after WGD, another set of genes may be initially preserved in duplicate by natural selection for reasons including dosage... - Preferential subfunctionalization of slow-evolving genes after allopolyploidization in Xenopus laevisMarie Semon
Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
Proc Natl Acad Sci U S A 105:8333-8. 2008..laevis, the orthologous pair is more likely to have been retained in duplicate in zebrafish, suggesting that similar factors, among them subfunctionalization, determined which gene pairs survived in duplicate after the two WGDs... 
Recent allopolyploid origin of Zygosaccharomyces rouxii strain ATCC 42981Jonathan L Gordon
Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
Yeast 25:449-56. 2008..Instead, we conclude that ATCC 42981 is a Z. rouxii-Z. pseudorouxii interspecies hybrid that was formed so recently that its genome has not had time to decay...- GenomeVx: simple web-based creation of editable circular chromosome mapsGavin C Conant
Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin 2, Ireland
Bioinformatics 24:861-2. 2008..Output is in the Adobe Portable Document Format (PDF) and can be edited by programs such as Adobe Illustrator. AVAILABILITY: GenomeVx is available at http://wolfe.gen.tcd.ie/GenomeVx.. - Functional partitioning of yeast co-expression networks after genome duplicationGavin C Conant
Department of Genetics, Trinity College, University of Dublin, Dublin, Ireland
PLoS Biol 4:e109. 2006.... - A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeastDevin R Scannell
Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
Genome Res 18:137-47. 2008..We discuss the contribution of neofunctionalization to duplicate gene preservation and propose that a form of subfunctionalization mediated by coding region activity-reducing mutations is likely to have played an important role... - Consequences of genome duplicationMarie Semon
Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
Curr Opin Genet Dev 17:505-12. 2007..We have a growing understanding of the relationship between whole genome duplication and speciation. Further, recent studies are providing insights into why some gene pairs survive in duplicate, whereas others do not... - Complete DNA sequences of the mitochondrial genomes of the pathogenic yeasts Candida orthopsilosis and Candida metapsilosis: insight into the evolution of linear DNA genomes from mitochondrial telomere mutantsPeter Kosa
Department of Biochemistry, Faculty of Natural Sciences, Comenius University Mlynska dolina, CH-1 and B-1, 842 15, Bratislava, Slovak Republic
Nucleic Acids Res 34:2472-81. 2006.... - Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeastsDevin R Scannell
Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
Nature 440:341-5. 2006..We propose a simple, unified model in which a single mechanism--passive gene loss-enabled whole--genome duplication and led to the rapid emergence of new yeast species... - A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genomeGuillaume Blanc
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
Genome Res 13:137-44. 2003.... - Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolutionGuillaume Blanc
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, 2, Ireland
Plant Cell 16:1679-91. 2004..Together, these results suggest that functional diversification of the surviving duplicated genes is a major feature of the long-term evolution of polyploids... - Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genesGuillaume Blanc
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, 2, Ireland
Plant Cell 16:1667-78. 2004..However, the unusual age profile of tandem gene duplications in Arabidopsis indicates that other scenarios, such as variation in the rate at which duplicated genes are deleted, must also be considered... - Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouseLukasz Huminiecki
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
Genome Res 14:1870-9. 2004..We conclude that gene duplication is a major driving force behind the emergence of divergent gene expression patterns... - A genome sequence survey shows that the pathogenic yeast Candida parapsilosis has a defective MTLa1 allele at its mating type locusMary E Logue
Department of Biochemistry, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
Eukaryot Cell 4:1009-17. 2005..It is therefore likely that all (or at least the majority) of C. parapsilosis isolates have a mating pathway that is either defective or substantially different from that of C. albicans... - The 2R hypothesis and the human genome sequenceKarsten Hokamp
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
J Struct Funct Genomics 3:95-110. 2003..We find evidence for extensive duplication of parts of the genome. We also question the validity of the 'parsimony test' that has been used in other analyses... - Positive selection and subfunctionalization of duplicated CCT chaperonin subunitsMario A Fares
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin, Ireland
Mol Biol Evol 20:1588-97. 2003.... - Changes in alternative splicing of human and mouse genes are accompanied by faster evolution of constitutive exonsBrian P Cusack
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin, Ireland
Mol Biol Evol 22:2198-208. 2005..These results suggest that alterations in alternative splicing pattern can have knock-on effects in terms of accelerated sequence evolution in constant regions of the protein... - The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid speciesKevin P Byrne
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
Genome Res 15:1456-61. 2005..cerevisiae (551, including 22 previously unidentified), Saccharomyces castellii (599), and Candida glabrata (404)... - Rate asymmetry after genome duplication causes substantial long-branch attraction artifacts in the phylogeny of Saccharomyces speciesMario A Fares
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
Mol Biol Evol 23:245-53. 2006..Tests for adaptive evolution indicated that positive selection might be the cause of rate asymmetry in a substantial fraction (19%) of the paralog pairs... - Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order BrowserKevin P Byrne
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
Nucleic Acids Res 34:D452-5. 2006..This paper discusses the usage and utility of version 1.0 of YGOB, which is publicly available at http://wolfe.gen.tcd.ie/ygob... - Genomic differences between Candida glabrata and Saccharomyces cerevisiae around the MRPL28 and GCN3 lociDavid W Walsh
Department of Biochemistry and Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
Yeast 19:991-4. 2002..cerevisiae chromosome XI (including GCN3) followed by a four-gene cluster similar to chromosome XV (including HIS3). A small-scale rearrangement of gene order has occurred in the chromosome XI-like section... - Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatusNatalie D Fedorova
The J Craig Venter Institute, Rockville, Maryland, United States of America
PLoS Genet 4:e1000046. 2008.... - Wrapping up BLAST and other applications for use on Unix clustersKarsten Hokamp
Department of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
Bioinformatics 19:441-2. 2003..AVAILABILITY: The packages were developed in Perl on a 20-node Linux cluster and are provided together with a configuration script and documentation. They can be freely downloaded from http://wolfe.gen.tcd.ie/wrapper... - Evolution of the MAT locus and its Ho endonuclease in yeast speciesGeraldine Butler
Department of Biochemistry, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
Proc Natl Acad Sci U S A 101:1632-7. 2004.... - Fourfold faster rate of genome rearrangement in nematodes than in DrosophilaAvril Coghlan
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
Genome Res 12:857-67. 2002..The breakpoints of translocations are strongly associated with dispersed repeats and gene family members in the C. elegans genome... - Evolutionary re-organisation of a large operon in adzuki bean chloroplast DNA caused by inverted repeat movementAntoinette S Perry
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
DNA Res 9:157-62. 2002..Analysis of the endpoints of the rearrangement indicates that it probably occurred by means of a two-step process of expansion and contraction of the IR and not by a 78-kb inversion... - PubCrawler: keeping up comfortably with PubMed and GenBankKarsten Hokamp
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
Nucleic Acids Res 32:W16-9. 2004..A new output format and more flexibility for the email formatting help PubCrawler cope with increasing challenges arising from browser incompatibilities and mail filters, therefore making it suitable for a wide range of users... - Origins of recently gained introns in CaenorhabditisAvril Coghlan
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
Proc Natl Acad Sci U S A 101:11362-7. 2004..All of these similarities involve minisatellites or palindromes in the intron sequences. Our results suggest that at least some of the intron gains were caused by reverse splicing of a preexisting intron... - Clusters of co-expressed genes in mammalian genomes are conserved by natural selectionGregory A C Singer
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin, Ireland
Mol Biol Evol 22:767-75. 2005..Contrary to previous reports, we find that genes with high expression are not clustered to a greater extent than expected by chance and are not conserved during evolution... - Nucleotide substitution rates in legume chloroplast DNA depend on the presence of the inverted repeatAntoinette S Perry
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
J Mol Evol 55:501-8. 2002..We propose that this acceleration is a direct result of the decrease in the copy number of the sequence, rather than an intrinsic property of the genes normally located in the IR... - Reciprocal gene loss between Tetraodon and zebrafish after whole genome duplication in their ancestorMarie Semon
Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
Trends Genet 23:108-12. 2007..We estimate that thousands of genes that remained duplicated when Tetraodon and zebrafish diverged underwent reciprocal loss subsequently in these two species, probably contributing to reproductive isolation between them... - Birth of a metabolic gene cluster in yeast by adaptive gene relocationSimon Wong
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
Nat Genet 37:777-82. 2005..The DAL cluster is located in a domain of modified chromatin involving both H2A.Z histone exchange and Hst1-Sum1-mediated histone deacetylation, and it may be a coadapted gene complex formed by epistatic selection...