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Kenneth Wolfe

Research Profile

Phenomena

Evolution, Molecular

Physiology

Genes & Molecular Sequences

Concepts & Ideas

Living Beings

Anatomy

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Publications

TOP 3
Sarah L Maguire; Peadar Ó Gaora; Seán S Ohéigeartaigh; Markus S Schröder; Kenneth H Wolfe; Kevin P Byrne; Geraldine Butler
Comparative Genome Analysis and Gene Finding in Candida Species Using CGOB.
Estelle Proux-Wéra; Kevin P Byrne; Kenneth H Wolfe
Evolutionary mobility of the ribosomal DNA array in yeasts.
Estelle Proux-Wéra; David Armisén; Kevin P Byrne; Kenneth H Wolfe
A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach.

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All Publications

2013: Sarah L Maguire; Peadar Ó Gaora; Seán S Ohéigeartaigh; Markus S Schröder; Kenneth H Wolfe; Kevin P Byrne; Geraldine Butler
Comparative Genome Analysis and Gene Finding in Candida Species Using CGOB.
Molecular biology and evolution 2013;30(6):1281-91.
2013: Estelle Proux-Wéra; Kevin P Byrne; Kenneth H Wolfe
Evolutionary mobility of the ribosomal DNA array in yeasts.
Genome biology and evolution 2013;5(3):525-31.
2012: Estelle Proux-Wéra; David Armisén; Kevin P Byrne; Kenneth H Wolfe
A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach.
BMC bioinformatics 2012;13():237.
2011: Jonathan L Gordon; Kevin P Byrne; Kenneth H Wolfe
Mechanisms of chromosome number evolution in yeast.
PLoS genetics 2011;7(7):e1002190.
2011: Seán S OhÉigeartaigh; David Armisén; Kevin P Byrne; Kenneth H Wolfe
Systematic discovery of unannotated genes in 11 yeast species using a database of orthologous genomic segments.
BMC genomics 2011;12():377.
2010: Alan M Magee; Sue Aspinall; Danny W Rice; Brian P Cusack; Marie Sémon; Antoinette S Perry; Sasa Stefanović; Dan Milbourne; Susanne Barth; Jeffrey D Palmer; John C Gray; Tony A Kavanagh; Kenneth H Wolfe
Localized hypermutation and associated gene losses in legume chloroplast genomes.
Genome research 2010;20(12):1700-10.
2010: Nora Khaldi; Fayaz T Seifuddin; Geoff Turner; Daniel Haft; William C Nierman; Kenneth H Wolfe; Natalie Fedorova Abrams
SMURF: Genomic mapping of fungal secondary metabolite clusters.
Fungal genetics and biology : FG & B 2010;47(9):736-41.
2009: A Carolin Frank; Kenneth H Wolfe
Evolutionary capture of viral and plasmid DNA by yeast nuclear chromosomes.
Eukaryotic cell 2009;8(10):1521-31.
2009: Jonathan L Gordon; Kevin P Byrne; Kenneth H Wolfe
Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome.
PLoS genetics 2009;5(5):e1000485.
2009: Jennifer E G Gallagher; Joshua E Babiarz; Leonid Teytelman; Kenneth H Wolfe; Jasper Rine
Elaboration, diversification and regulation of the Sir1 family of silencing proteins in Saccharomyces.
Genetics 2009;181(4):1477-91.
2009: Tom A Williams; Kenneth H Wolfe; Mario A Fares
No rosetta stone for a sense-antisense origin of aminoacyl tRNA synthetase classes.
Molecular biology and evolution 2009;26(2):445-50.
2008: Gavin C Conant; Kenneth H Wolfe
Probabilistic cross-species inference of orthologous genomic regions created by whole-genome duplication in yeast.
Genetics 2008;179(3):1681-92.
2008: Marie Sémon; Kenneth H Wolfe
Preferential subfunctionalization of slow-evolving genes after allopolyploidization in Xenopus laevis.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(24):8333-8.
2008: Jonathan L Gordon; Kenneth H Wolfe
Recent allopolyploid origin of Zygosaccharomyces rouxii strain ATCC 42981.
Yeast (Chichester, England) 2008;25(6):449-56.
2008: Gavin C Conant; Kenneth H Wolfe
GenomeVx: simple web-based creation of editable circular chromosome maps.
Bioinformatics (Oxford, England) 2008;24(6):861-2.
2008: Nora Khaldi; Kenneth H Wolfe
Elusive origins of the extra genes in Aspergillus oryzae.
PloS one 2008;3(8):e3036.
2008: Nora Khaldi; Jérôme Collemare; Marc-Henri Lebrun; Kenneth H Wolfe
Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi.
Genome biology 2008;9(1):R18.
2008: Devin R Scannell; Kenneth H Wolfe
A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast.
Genome research 2008;18(1):137-47.
2007: Marie Sémon; Kenneth H Wolfe
Consequences of genome duplication.
Current opinion in genetics & development 2007;17(6):505-12.
2007: Devin R Scannell; Geraldine Butler; Kenneth H Wolfe
Yeast genome evolution--the origin of the species.
Yeast (Chichester, England) 2007;24(11):929-42.
2007: Brian P Cusack; Kenneth H Wolfe
When gene marriages don't work out: divorce by subfunctionalization.
Trends in genetics : TIG 2007;23(6):270-2.
2007: Devin R Scannell; A Carolin Frank; Gavin C Conant; Kevin P Byrne; Megan Woolfit; Kenneth H Wolfe
Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(20):8397-402.
2007: Megan Woolfit; Elzbieta Rozpedowska; Jure Piskur; Kenneth H Wolfe
Genome survey sequencing of the wine spoilage yeast Dekkera (Brettanomyces) bruxellensis.
Eukaryotic cell 2007;6(4):721-33.
2007: Marie Sémon; Kenneth H Wolfe
Reciprocal gene loss between Tetraodon and zebrafish after whole genome duplication in their ancestor.
Trends in genetics : TIG 2007;23(3):108-12.
2007: Marie Sémon; Kenneth H Wolfe
Rearrangement rate following the whole-genome duplication in teleosts.
Molecular biology and evolution 2007;24(3):860-7.
2007: Kevin P Byrne; Kenneth H Wolfe
Consistent patterns of rate asymmetry and gene loss indicate widespread neofunctionalization of yeast genes after whole-genome duplication.
Genetics 2007;175(3):1341-50.
2007: Brian P Cusack; Kenneth H Wolfe
Not born equal: increased rate asymmetry in relocated and retrotransposed rodent gene duplicates.
Molecular biology and evolution 2007;24(3):679-86.
2007: Gavin C Conant; Kenneth H Wolfe
Increased glycolytic flux as an outcome of whole-genome duplication in yeast.
Molecular systems biology 2007;3():129.
2006: Sinéad C Drea; Nga T Lao; Kenneth H Wolfe; Tony A Kavanagh
Gene duplication, exon gain and neofunctionalization of OEP16-related genes in land plants.
The Plant journal : for cell and molecular biology 2006;46(5):723-35.
2006: Gavin C Conant; Kenneth H Wolfe
Functional partitioning of yeast co-expression networks after genome duplication.
PLoS biology 2006;4(4):e109.
2006: Kenneth H Wolfe
Comparative genomics and genome evolution in yeasts.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2006;361(1467):403-12.
2006: Devin R Scannell; Kevin P Byrne; Jonathan L Gordon; Simon Wong; Kenneth H Wolfe
Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts.
Nature 2006;440(7082):341-5.
2006: Mario A Fares; Kevin P Byrne; Kenneth H Wolfe
Rate asymmetry after genome duplication causes substantial long-branch attraction artifacts in the phylogeny of Saccharomyces species.
Molecular biology and evolution 2006;23(2):245-53.
2006: Kevin P Byrne; Kenneth H Wolfe
Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser.
Nucleic acids research 2006;34(Database issue):D452-5.
2005: Brian P Cusack; Kenneth H Wolfe
Changes in alternative splicing of human and mouse genes are accompanied by faster evolution of constitutive exons.
Molecular biology and evolution 2005;22(11):2198-208.
2005: Kevin P Byrne; Kenneth H Wolfe
The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species.
Genome research 2005;15(10):1456-61.
2005: Simon Wong; Kenneth H Wolfe
Birth of a metabolic gene cluster in yeast by adaptive gene relocation.
Nature genetics 2005;37(7):777-82.
2005: Gregory A C Singer; Andrew T Lloyd; Lukasz Huminiecki; Kenneth H Wolfe
Clusters of co-expressed genes in mammalian genomes are conserved by natural selection.
Molecular biology and evolution 2005;22(3):767-75.
2004: Victoria Nembaware; Kenneth H Wolfe; Fabiana Bettoni; Janet Kelso; Cathal Seoighe
Allele-specific transcript isoforms in human.
FEBS letters 2004;577(1-2):233-8.
2004: Lukasz Huminiecki; Kenneth H Wolfe
Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse.
Genome research 2004;14(10A):1870-9.
2004: Avril Coghlan; Kenneth H Wolfe
Origins of recently gained introns in Caenorhabditis.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(31):11362-7.
2004: Karsten Hokamp; Kenneth H Wolfe
PubCrawler: keeping up comfortably with PubMed and GenBank.
Nucleic acids research 2004;32(Web Server issue):W16-9.
2004: Guillaume Blanc; Kenneth H Wolfe
Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes.
The Plant cell 2004;16(7):1667-78.
2004: Guillaume Blanc; Kenneth H Wolfe
Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution.
The Plant cell 2004;16(7):1679-91.
2003: Mario A Fares; Kenneth H Wolfe
Positive selection and subfunctionalization of duplicated CCT chaperonin subunits.
Molecular biology and evolution 2003;20(10):1588-97.
2003: Lukasz Huminiecki; Andrew T Lloyd; Kenneth H Wolfe
Congruence of tissue expression profiles from Gene Expression Atlas, SAGEmap and TissueInfo databases.
BMC genomics 2003;4(1):31.
2003: Kenneth H Wolfe; Wen-Hsiung Li
Molecular evolution meets the genomics revolution.
Nature genetics 2003;33 Suppl():255-65.
2003: Karsten Hokamp; Denis C Shields; Kenneth H Wolfe; Daniel R Caffrey
Wrapping up BLAST and other applications for use on Unix clusters.
Bioinformatics (Oxford, England) 2003;19(3):441-2.
2003: Guillaume Blanc; Karsten Hokamp; Kenneth H Wolfe
A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome.
Genome research 2003;13(2):137-44.
2003: Karsten Hokamp; Aoife McLysaght; Kenneth H Wolfe
The 2R hypothesis and the human genome sequence.
Journal of structural and functional genomics 2003;3(1-4):95-110.
2003: Simon Wong; Mario A Fares; Wolfgang Zimmermann; Geraldine Butler; Kenneth H Wolfe
Evidence from comparative genomics for a complete sexual cycle in the 'asexual' pathogenic yeast Candida glabrata.
Genome biology 2003;4(2):R10.
2002: Antoinette S Perry; Kenneth H Wolfe
Nucleotide substitution rates in legume chloroplast DNA depend on the presence of the inverted repeat.
Journal of molecular evolution 2002;55(5):501-8.
2002: Antoinette S Perry; Sinéad Brennan; David J Murphy; Tony A Kavanagh; Kenneth H Wolfe
Evolutionary re-organisation of a large operon in adzuki bean chloroplast DNA caused by inverted repeat movement.
DNA research : an international journal for rapid publication of reports on genes and genomes 2002;9(5):157-62.
2002: Simon Wong; Geraldine Butler; Kenneth H Wolfe
Gene order evolution and paleopolyploidy in hemiascomycete yeasts.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(14):9272-7.
2002: Avril Coghlan; Kenneth H Wolfe
Fourfold faster rate of genome rearrangement in nematodes than in Drosophila.
Genome research 2002;12(6):857-67.
2002: Aoife McLysaght; Karsten Hokamp; Kenneth H Wolfe
Extensive genomic duplication during early chordate evolution.
Nature genetics 2002;31(2):200-4.
2001: Kenneth H Wolfe
Yesterday's polyploids and the mystery of diploidization.
Nature reviews. Genetics 2001;2(5):333-41.
2001: R S Millen; R G Olmstead; Keith L Adams; Jeffrey D Palmer; Nga T Lao; Laura Heggie; T A Kavanagh; Julian M Hibberd; John C Gray; C W Morden; P J Calie; L S Jermiin; Kenneth H Wolfe
Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus.
The Plant cell 2001;13(3):645-58.
2000: Cathal Seoighe; Nancy A Federspiel; Ted Jones; N Hansen; V Bivolarovic; R Surzycki; Raquel Tamse; Caridad Komp; L Huizar; Ronald W Davis; Stewart Scherer; E Tait; Duncan J Shaw; D Harris; Lee Murphy; K Oliver; K Taylor; Marie-Adele Rajandream; Bart Barrell; Kenneth H Wolfe
Prevalence of small inversions in yeast gene order evolution.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(26):14433-7.
2000: A Coghlan; Kenneth H Wolfe
Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae.
Yeast (Chichester, England) 2000;16(12):1131-45.
2000: Aoife McLysaght; A J Enright; Lucy Skrabanek; Kenneth H Wolfe
Estimation of synteny conservation and genome compaction between pufferfish (Fugu) and human.
Yeast (Chichester, England) 2000;17(1):22-36.
1999: Cathal Seoighe; Kenneth H Wolfe
Yeast genome evolution in the post-genome era.
Current opinion in microbiology 1999;2(5):548-54.
1999: Cathal Seoighe; Kenneth H Wolfe
Updated map of duplicated regions in the yeast genome.
Gene 1999;238(1):253-61.
1999: K R Bradnam; Cathal Seoighe; Paul M Sharp; Kenneth H Wolfe
G+C content variation along and among Saccharomyces cerevisiae chromosomes.
Molecular biology and evolution 1999;16(5):666-75.
1999: Bénédicte Lafay; Andrew T Lloyd; M J McLean; K M Devine; Paul M Sharp; Kenneth H Wolfe
Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases.
Nucleic acids research 1999;27(7):1642-9.
1998: Lucy Skrabanek; Kenneth H Wolfe
Eukaryote genome duplication - where's the evidence?
Current opinion in genetics & development 1998;8(6):694-700.
1998: M J McLean; Kenneth H Wolfe; K M Devine
Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes.
Journal of molecular evolution 1998;47(6):691-6.
1998: Amanda J Lohan; Kenneth H Wolfe
A subset of conserved tRNA genes in plastid DNA of nongreen plants.
Genetics 1998;150(1):425-33.
1998: Cathal Seoighe; Kenneth H Wolfe
Extent of genomic rearrangement after genome duplication in yeast.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(8):4447-52.
1998: R S Keogh; Cathal Seoighe; Kenneth H Wolfe
Evolution of gene order and chromosome number in Saccharomyces, Kluyveromyces and related fungi.
Yeast (Chichester, England) 1998;14(5):443-57.
1997: Kenneth H Wolfe; D C Shields
Molecular evidence for an ancient duplication of the entire yeast genome.
Nature 1997;387(6634):708-13.
1997: Kenneth H Wolfe; G Butler
Yeast's clickable chromosomes and other genome browsers.
Trends in genetics : TIG 1997;13(6):246-7.
1996: A G Parle-McDermott; N J Hand; S E Goulding; Kenneth H Wolfe
Sequence of 29 kb around the PDR10 locus on the right arm of Saccharomyces cerevisiae chromosome XV: similarity to part of chromosome I.
Yeast (Chichester, England) 1996;12(10B Suppl):999-1004.
1995: K M Devine; Kenneth H Wolfe
Bacterial genomes: a TIGR in the tank.
Trends in genetics : TIG 1995;11(11):429-31.
1994: Kenneth H Wolfe; Amanda J Lohan
Sequence around the centromere of Saccharomyces cerevisiae chromosome II: similarity of CEN2 to CEN4.
Yeast (Chichester, England) 1994;10 Suppl A():S41-6.
1993: Kenneth H Wolfe; P M Sharp
Mammalian gene evolution: nucleotide sequence divergence between mouse and rat.
Journal of molecular evolution 1993;37(4):441-56.
1993: Paul M Sharp; Kenneth H Wolfe
Identification of a Candida utilis gene encoding ribosomal protein L7: evidence for two divergent subclasses of the eukaryotic ribosomal protein L7 family.
Nucleic acids research 1993;21(15):3577.
1989: Paul M Sharp; D C Shields; Kenneth H Wolfe; W H Li
Chromosomal location and evolutionary rate variation in enterobacterial genes.
Science (New York, N.Y.) 1989;246(4931):808-10.
1989: Kenneth H Wolfe; Paul M Sharp; W H Li
Mutation rates differ among regions of the mammalian genome.
Nature 1989;337(6204):283-5.
1988: Q Lu; Kenneth H Wolfe; D J McConnell
Molecular cloning of multiple bovine aspartyl protease genes.
Gene 1988;71(1):135-46.
1988: Paul M Sharp; E Cowe; Desmond G Higgins; D C Shields; Kenneth H Wolfe; F Wright
Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity.
Nucleic acids research 1988;16(17):8207-11.
1988: Kenneth H Wolfe; Paul M Sharp
Identification of functional open reading frames in chloroplast genomes.
Gene 1988;66(2):215-22.