K H Wolfe

Summary

Affiliation: Trinity College
Country: Ireland

Publications

  1. pmc A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach
    Estelle Proux-Wéra
    Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
    BMC Bioinformatics 13:237. 2012
  2. pmc Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi
    Nora Khaldi
    Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
    Genome Biol 9:R18. 2008
  3. pmc Evidence from comparative genomics for a complete sexual cycle in the 'asexual' pathogenic yeast Candida glabrata
    Simon Wong
    Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
    Genome Biol 4:R10. 2003
  4. pmc Rewiring the transcriptional regulatory circuits of cells
    Devin R Scannell
    Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
    Genome Biol 5:206. 2004
  5. pmc Systematic discovery of unannotated genes in 11 yeast species using a database of orthologous genomic segments
    Seán S Ohéigeartaigh
    Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
    BMC Genomics 12:377. 2011
  6. pmc Congruence of tissue expression profiles from Gene Expression Atlas, SAGEmap and TissueInfo databases
    Lukasz Huminiecki
    Department of Genetics, Smurfit Institute, University of Dublin Trinity College, Dublin 2, Ireland
    BMC Genomics 4:31. 2003
  7. ncbi request reprint Molecular evolution meets the genomics revolution
    Kenneth H Wolfe
    Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
    Nat Genet 33:255-65. 2003
  8. ncbi request reprint Evolutionary genomics: yeasts accelerate beyond BLAST
    Ken Wolfe
    Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
    Curr Biol 14:R392-4. 2004
  9. pmc Comparative genomics and genome evolution in yeasts
    Kenneth 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
  10. ncbi request reprint Yesterday's polyploids and the mystery of diploidization
    K H Wolfe
    Department of Genetics, Smurfit Institute, Trinity College, University of Dublin, Dublin 2, Republic of Ireland
    Nat Rev Genet 2:333-41. 2001

Collaborators

Detail Information

Publications59

  1. pmc A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach
    Estelle 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...
  2. pmc Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi
    Nora 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...
  3. pmc Evidence from comparative genomics for a complete sexual cycle in the 'asexual' pathogenic yeast Candida glabrata
    Simon Wong
    Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
    Genome Biol 4:R10. 2003
    ..We show here that the C. glabrata genome contains many genes apparently involved in sexual reproduction...
  4. pmc Rewiring the transcriptional regulatory circuits of cells
    Devin 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...
  5. pmc Systematic discovery of unannotated genes in 11 yeast species using a database of orthologous genomic segments
    Seán 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...
  6. pmc Congruence of tissue expression profiles from Gene Expression Atlas, SAGEmap and TissueInfo databases
    Lukasz 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...
  7. ncbi request reprint Molecular evolution meets the genomics revolution
    Kenneth H Wolfe
    Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
    Nat Genet 33:255-65. 2003
    ....
  8. ncbi request reprint Evolutionary genomics: yeasts accelerate beyond BLAST
    Ken 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...
  9. pmc Comparative genomics and genome evolution in yeasts
    Kenneth 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...
  10. ncbi request reprint Yesterday's polyploids and the mystery of diploidization
    K 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...
  11. ncbi request reprint Molecular evidence for an ancient duplication of the entire yeast genome
    K 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...
  12. ncbi request reprint Sequence of 29 kb around the PDR10 locus on the right arm of Saccharomyces cerevisiae chromosome XV: similarity to part of chromosome I
    A 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...
  13. ncbi request reprint Accelerated evolution of sites undergoing mRNA editing in plant mitochondria and chloroplasts
    D 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...
  14. ncbi request reprint Ebb and flow of the chloroplast inverted repeat
    S 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...
  15. ncbi request reprint Similarity between putative ATP-binding sites in land plant plastid ORF2280 proteins and the FtsH/CDC48 family of ATPases
    K 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...
  16. ncbi request reprint When gene marriages don't work out: divorce by subfunctionalization
    Brian 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...
  17. ncbi request reprint Yeast genome evolution--the origin of the species
    Devin R Scannell
    Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
    Yeast 24:929-42. 2007
    ....
  18. pmc Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication
    Devin 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...
  19. pmc Gene order evolution and paleopolyploidy in hemiascomycete yeasts
    Simon 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...
  20. pmc Genome survey sequencing of the wine spoilage yeast Dekkera (Brettanomyces) bruxellensis
    Megan 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...
  21. ncbi request reprint Rearrangement rate following the whole-genome duplication in teleosts
    Marie 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...
  22. pmc Consistent patterns of rate asymmetry and gene loss indicate widespread neofunctionalization of yeast genes after whole-genome duplication
    Kevin 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...
  23. ncbi request reprint Not born equal: increased rate asymmetry in relocated and retrotransposed rodent gene duplicates
    Brian 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...
  24. ncbi request reprint Gene duplication, exon gain and neofunctionalization of OEP16-related genes in land plants
    Sinéad 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...
  25. ncbi request reprint Positive darwinian selection at the imprinted MEDEA locus in plants
    Charles 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...
  26. pmc Increased glycolytic flux as an outcome of whole-genome duplication in yeast
    Gavin 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...
  27. ncbi request reprint Extensive genomic duplication during early chordate evolution
    Aoife 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...
  28. pmc Probabilistic cross-species inference of orthologous genomic regions created by whole-genome duplication in yeast
    Gavin 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...
  29. pmc Preferential subfunctionalization of slow-evolving genes after allopolyploidization in Xenopus laevis
    Marie 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...
  30. doi request reprint Recent allopolyploid origin of Zygosaccharomyces rouxii strain ATCC 42981
    Jonathan 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...
  31. doi request reprint GenomeVx: simple web-based creation of editable circular chromosome maps
    Gavin C Conant
    Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin 2, Ireland
    Bioinformatics 24:861-2. 2008
    ..In the latter case, features are automatically extracted and colored, an example of which is given. Output is in the Adobe Portable Document Format (PDF) and can be edited by programs such as Adobe Illustrator...
  32. pmc Functional partitioning of yeast co-expression networks after genome duplication
    Gavin C Conant
    Department of Genetics, Trinity College, University of Dublin, Dublin, Ireland
    PLoS Biol 4:e109. 2006
    ....
  33. pmc A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast
    Devin 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...
  34. ncbi request reprint Consequences of genome duplication
    Marie 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...
  35. pmc 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 mutants
    Peter 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
    ....
  36. ncbi request reprint Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts
    Devin 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...
  37. pmc A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome
    Guillaume Blanc
    Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
    Genome Res 13:137-44. 2003
    ....
  38. pmc Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution
    Guillaume 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...
  39. pmc Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes
    Guillaume 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...
  40. pmc Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse
    Lukasz 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...
  41. pmc A genome sequence survey shows that the pathogenic yeast Candida parapsilosis has a defective MTLa1 allele at its mating type locus
    Mary 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...
  42. ncbi request reprint The 2R hypothesis and the human genome sequence
    Karsten 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...
  43. ncbi request reprint Positive selection and subfunctionalization of duplicated CCT chaperonin subunits
    Mario A Fares
    Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin, Ireland
    Mol Biol Evol 20:1588-97. 2003
    ....
  44. ncbi request reprint Changes in alternative splicing of human and mouse genes are accompanied by faster evolution of constitutive exons
    Brian 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...
  45. pmc The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species
    Kevin 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)...
  46. ncbi request reprint Rate asymmetry after genome duplication causes substantial long-branch attraction artifacts in the phylogeny of Saccharomyces species
    Mario 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...
  47. pmc Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser
    Kevin 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...
  48. ncbi request reprint Genomic differences between Candida glabrata and Saccharomyces cerevisiae around the MRPL28 and GCN3 loci
    David 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...
  49. pmc Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus
    Natalie D Fedorova
    The J Craig Venter Institute, Rockville, Maryland, United States of America
    PLoS Genet 4:e1000046. 2008
    ..The role of duplication in the origin of lineage-specific genes is further underlined by the discovery of genomic islands that seem to function as designated "gene dumps" and, perhaps, simultaneously, as "gene factories"...
  50. ncbi request reprint Wrapping up BLAST and other applications for use on Unix clusters
    Karsten Hokamp
    Department of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
    Bioinformatics 19:441-2. 2003
    ..1) BLAST.pm, a new module for the 'MOLLUSC' package. (2) WRAPID, a simple tool for parallelizing large numbers of small instances of programs such as BLAST, FASTA and CLUSTALW...
  51. pmc Evolution of the MAT locus and its Ho endonuclease in yeast species
    Geraldine 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
    ....
  52. pmc Fourfold faster rate of genome rearrangement in nematodes than in Drosophila
    Avril 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...
  53. ncbi request reprint Evolutionary re-organisation of a large operon in adzuki bean chloroplast DNA caused by inverted repeat movement
    Antoinette 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...
  54. pmc PubCrawler: keeping up comfortably with PubMed and GenBank
    Karsten 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...
  55. pmc Origins of recently gained introns in Caenorhabditis
    Avril 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...
  56. ncbi request reprint Clusters of co-expressed genes in mammalian genomes are conserved by natural selection
    Gregory 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...
  57. ncbi request reprint Nucleotide substitution rates in legume chloroplast DNA depend on the presence of the inverted repeat
    Antoinette 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...
  58. ncbi request reprint Reciprocal gene loss between Tetraodon and zebrafish after whole genome duplication in their ancestor
    Marie 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...
  59. ncbi request reprint Birth of a metabolic gene cluster in yeast by adaptive gene relocation
    Simon 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...