Kenneth H. Wolfe, PhD - Publications

Affiliations: 
Smurfit Institute of Genetics University of Dublin, Trinity College 
Area:
yeast, bioinformatics, evolution
Website:
http://wolfe.gen.tcd.ie/

168 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Venkatesh A, Murray AL, Coughlan AY, Wolfe KH. Giant GAL gene clusters for the melibiose-galactose pathway in Torulaspora. Yeast (Chichester, England). PMID 33141945 DOI: 10.1002/yea.3532  0.32
2020 Coughlan AY, Lombardi L, Braun-Galleani S, Martos AA, Galeote V, Bigey F, Dequin S, Byrne KP, Wolfe KH. The yeast mating-type switching endonuclease HO is a domesticated member of an unorthodox homing genetic element family. Elife. 9. PMID 32338594 DOI: 10.7554/Elife.55336  0.52
2020 Coughlan AY, Lombardi L, Braun-Galleani S, Martos AA, Galeote V, Bigey F, Dequin S, Byrne KP, Wolfe KH. Author response: The yeast mating-type switching endonuclease HO is a domesticated member of an unorthodox homing genetic element family Elife. DOI: 10.7554/Elife.55336.Sa2  0.52
2019 Douglass AP, O'Brien CE, Offei B, Coughlan AY, Ortiz-Merino RA, Butler G, Byrne KP, Wolfe KH. Coverage-Versus-Length Plots, a Simple Quality Control Step for de Novo Yeast Genome Sequence Assemblies. G3 (Bethesda, Md.). 9: 879-887. PMID 33575767 DOI: 10.1534/g3.118.200745  0.52
2019 Douglass AP, O'Brien CE, Offei B, Coughlan AY, Ortiz-Merino RA, Butler G, Byrne KP, Wolfe KH. Coverage-Versus-Length Plots, a Simple Quality Control Step for de Novo Yeast Genome Sequence Assemblies. G3 (Bethesda, Md.). 9: 879-887. PMID 33575767 DOI: 10.1534/g3.118.200745  0.52
2019 Braun-Galleani S, Dias JA, Coughlan AY, Ryan AP, Byrne KP, Wolfe KH. Genomic diversity and meiotic recombination among isolates of the biotech yeast Komagataella phaffii (Pichia pastoris). Microbial Cell Factories. 18: 211. PMID 31801527 DOI: 10.1186/S12934-019-1260-4  0.52
2019 Heneghan P, Ryan AP, Nimmo D, Duggan C, Kumar P, O'Gaora P, Ó 'Cinnéide E, Byrne KP, Wolfe KH, O'Brien CE, Butler G. Draft Genome Sequence of the Birch Tree Fungal Pathogen Taphrina betulina UCD315. Microbiology Resource Announcements. 8. PMID 31776224 DOI: 10.1128/MRA.01255-19  0.52
2019 Faherty L, Lewis C, McElheron M, Garvey N, Duggan R, Shovlin B, Ó Cróinín T, Byrne KP, O'Brien CE, Wolfe KH, Butler G. Draft Genome Sequences of Two Isolates of the Yeast Kazachstania servazzii Recovered from Soil in Ireland. Microbiology Resource Announcements. 8. PMID 31672753 DOI: 10.1128/MRA.01257-19  0.52
2019 Almasoud J, McArdle L, Henne R, Mathews K, O'Connor Í, McLoughlin LE, Ó'Gaora P, Byrne KP, O'Brien CE, Wolfe KH, Butler G. Draft Genome Sequence of a Red Basidiomycete Yeast, Symmetrospora coprosmae Strain UCD350, Isolated from Soil in Ireland. Microbiology Resource Announcements. 8. PMID 31672752 DOI: 10.1128/MRA.01256-19  0.52
2019 Douglass AP, Byrne KP, Wolfe KH. The Methylotroph Gene Order Browser (MGOB) reveals conserved synteny and ancestral centromere locations in the yeast family Pichiaceae. Fems Yeast Research. PMID 31397853 DOI: 10.1093/Femsyr/Foz058  0.52
2019 Krassowski T, Kominek J, Shen XX, Opulente DA, Zhou X, Rokas A, Hittinger CT, Wolfe KH. Multiple Reinventions of Mating-type Switching during Budding Yeast Evolution. Current Biology : Cb. PMID 31353182 DOI: 10.1016/J.Cub.2019.06.056  0.32
2019 Palmer-Brown W, Miranda-CasoLuengo R, Wolfe KH, Byrne KP, Murphy CD. The CYPome of the model xenobiotic-biotransforming fungus Cunninghamella elegans. Scientific Reports. 9: 9240. PMID 31239505 DOI: 10.1038/S41598-019-45706-X  0.52
2019 Douglass AP, O'Brien CE, Offei B, Coughlan AY, Ortiz-Merino RA, Butler G, Byrne KP, Wolfe KH. Coverage-Versus-Length Plots, a Simple Quality Control Step for Yeast Genome Sequence Assemblies. G3 (Bethesda, Md.). PMID 30674538 DOI: 10.1534/G3.118.200745  0.52
2018 Coughlan AY, Wolfe KH. The reported point centromeres of Scheffersomyces stipitis are retrotransposon LTRs. Yeast (Chichester, England). PMID 30557459 DOI: 10.1002/Yea.3375  0.32
2018 Douglass AP, Offei B, Braun-Galleani S, Coughlan AY, Martos AAR, Ortiz-Merino RA, Byrne KP, Wolfe KH. Population genomics shows no distinction between pathogenic Candida krusei and environmental Pichia kudriavzevii: One species, four names. Plos Pathogens. 14: e1007138. PMID 30024981 DOI: 10.1371/Journal.Ppat.1007138  0.52
2018 Venkatesh A, Murray AL, Boyle AB, Quinn Farrington L, Maher TJ, Ó'Gaora P, Wolfe KH, O'Brien CE, Butler G. Draft Genome Sequence of a Highly Heterozygous Yeast Strain from the Metschnikowia pulcherrima Subclade, UCD127. Genome Announcements. 6. PMID 29930059 DOI: 10.1128/Genomea.00550-18  0.32
2018 O'Boyle S, Bergin SA, Hussey ÉE, McLaughlin AD, Riddell LR, Byrne KP, Wolfe KH, O'Brien CE, Butler G. Draft Genome Sequence of the Yeast Nadsonia starkeyi-henricii UCD142, Isolated from Forest Soil in Ireland. Genome Announcements. 6. PMID 29930058 DOI: 10.1128/Genomea.00549-18  0.52
2018 Mullen AA, Lynch CD, Hill SM, Holohan CP, Ó Cróinín T, Wolfe KH, O'Brien CE, Butler G. Draft Genome Sequences of Two Natural Isolates of the Yeast Barnettozyma californica from Ireland, UCD09 and UCD89. Genome Announcements. 6. PMID 29930057 DOI: 10.1128/Genomea.00548-18  0.32
2018 Donovan PD, Holland LM, Lombardi L, Coughlan AY, Higgins DG, Wolfe KH, Butler G. TPP riboswitch-dependent regulation of an ancient thiamin transporter in Candida. Plos Genetics. 14: e1007429. PMID 29852014 DOI: 10.1371/Journal.Pgen.1007429  0.6
2018 Krassowski T, Coughlan AY, Shen XX, Zhou X, Kominek J, Opulente DA, Riley R, Grigoriev IV, Maheshwari N, Shields DC, Kurtzman CP, Hittinger CT, Rokas A, Wolfe KH. Evolutionary instability of CUG-Leu in the genetic code of budding yeasts. Nature Communications. 9: 1887. PMID 29760453 DOI: 10.1038/S41467-018-04374-7  0.92
2018 Ortiz-Merino RA, Varela JA, Coughlan AY, Hoshida H, da Silveira WB, Wilde C, Kuijpers NGA, Geertman JM, Wolfe KH, Morrissey JP. Ploidy Variation in Separates Dairy and Non-dairy Isolates. Frontiers in Genetics. 9: 94. PMID 29619042 DOI: 10.3389/Fgene.2018.00094  0.32
2017 Ortiz-Merino RA, Kuanyshev N, Byrne KP, Varela JA, Morrissey JP, Porro D, Wolfe KH, Branduardi P. Transcriptional response to lactic acid stress in the hybrid yeast Zygosaccharomyces parabailii. Applied and Environmental Microbiology. PMID 29269498 DOI: 10.1128/Aem.02294-17  0.52
2017 Hanson SJ, Byrne KP, Wolfe KH. Flip/flop mating-type switching in the methylotrophic yeast Ogataea polymorpha is regulated by an Efg1-Rme1-Ste12 pathway. Plos Genetics. 13: e1007092. PMID 29176810 DOI: 10.1371/Journal.Pgen.1007092  0.52
2017 Wolfe KH, Butler G. Evolution of Mating in the Saccharomycotina. Annual Review of Microbiology. PMID 28657889 DOI: 10.1146/Annurev-Micro-090816-093403  0.32
2017 Ortiz-Merino RA, Kuanyshev N, Braun-Galleani S, Byrne KP, Porro D, Branduardi P, Wolfe KH. Evolutionary restoration of fertility in an interspecies hybrid yeast, by whole-genome duplication after a failed mating-type switch. Plos Biology. 15: e2002128. PMID 28510588 DOI: 10.1371/Journal.Pbio.2002128  0.52
2016 Schröder MS, Martinez de San Vicente K, Prandini TH, Hammel S, Higgins DG, Bagagli E, Wolfe KH, Butler G. Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species. Plos Genetics. 12: e1006404. PMID 27806045 DOI: 10.1371/Journal.Pgen.1006404  0.6
2016 Riley R, Haridas S, Wolfe KH, Lopes MR, Hittinger CT, Göker M, Salamov AA, Wisecaver JH, Long TM, Calvey CH, Aerts AL, Barry KW, Choi C, Clum A, Coughlan AY, et al. Comparative genomics of biotechnologically important yeasts. Proceedings of the National Academy of Sciences of the United States of America. PMID 27535936 DOI: 10.1073/Pnas.1603941113  1
2016 Coughlan AY, Hanson SJ, Byrne KP, Wolfe KH. Centromeres of the yeast Komagataella phaffii (Pichia pastoris) have a simple inverted-repeat structure. Genome Biology and Evolution. PMID 27497317 DOI: 10.1093/Gbe/Evw178  0.52
2015 Pryszcz LP, Németh T, Saus E, Ksiezopolska E, Hegedűsová E, Nosek J, Wolfe KH, Gacser A, Gabaldón T. The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis. Plos Genetics. 11: e1005626. PMID 26517373 DOI: 10.1371/Journal.Pgen.1005626  1
2015 Wolfe KH. Origin of the Yeast Whole-Genome Duplication. Plos Biology. 13: e1002221. PMID 26252643 DOI: 10.1371/Journal.Pbio.1002221  1
2015 Wolfe KH, Armisén D, Proux-Wera E, ÓhÉigeartaigh SS, Azam H, Gordon JL, Byrne KP. Clade- and species-specific features of genome evolution in the Saccharomycetaceae. Fems Yeast Research. 15. PMID 26066552 DOI: 10.1093/Femsyr/Fov035  1
2014 Hanson SJ, Byrne KP, Wolfe KH. Mating-type switching by chromosomal inversion in methylotrophic yeasts suggests an origin for the three-locus Saccharomyces cerevisiae system. Proceedings of the National Academy of Sciences of the United States of America. 111: E4851-8. PMID 25349420 DOI: 10.1073/Pnas.1416014111  1
2014 Óhéigeartaigh SS, Armisén D, Byrne KP, Wolfe KH. SearchDOGS bacteria, software that provides automated identification of potentially missed genes in annotated bacterial genomes. Journal of Bacteriology. 196: 2030-42. PMID 24659774 DOI: 10.1128/Jb.01368-13  1
2014 Maguire SL, Wang C, Holland LM, Brunel F, Neuvéglise C, Nicaud JM, Zavrel M, White TC, Wolfe KH, Butler G. Zinc finger transcription factors displaced SREBP proteins as the major Sterol regulators during Saccharomycotina evolution. Plos Genetics. 10: e1004076. PMID 24453983 DOI: 10.1371/Journal.Pgen.1004076  1
2014 Magee AM, Aspinall S, Rice DW, Cusack BP, Sémon M, Perry AS, Stefanović S, Milbourne D, Barth S, Palmer JD, Gray JC, Kavanagh TA, Wolfe KH. Localized hypermutation and associated gene losses in legume chloroplast genomes (Genome Research (2010) 20, (1700-1710)) Genome Research. 24: 1052.  1
2013 Maguire SL, ÓhÉigeartaigh SS, Byrne KP, Schröder MS, O'Gaora P, Wolfe KH, Butler G. Comparative genome analysis and gene finding in Candida species using CGOB. Molecular Biology and Evolution. 30: 1281-91. PMID 23486613 DOI: 10.1093/Molbev/Mst042  1
2013 Proux-Wéra E, Byrne KP, Wolfe KH. Evolutionary mobility of the ribosomal DNA array in yeasts. Genome Biology and Evolution. 5: 525-31. PMID 23419706 DOI: 10.1093/Gbe/Evt022  1
2012 Proux-Wéra E, Armisén D, Byrne KP, Wolfe KH. A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach. Bmc Bioinformatics. 13: 237. PMID 22984983 DOI: 10.1186/1471-2105-13-237  1
2012 Riccombeni A, Vidanes G, Proux-Wéra E, Wolfe KH, Butler G. Sequence and analysis of the genome of the pathogenic yeast Candida orthopsilosis. Plos One. 7: e35750. PMID 22563396 DOI: 10.1371/Journal.Pone.0035750  1
2012 Wolfe K, Wayne ML, Makova K, Steen TY, Uyenoyama M, Takahata N. SMBE proposal to the government of Japan. Molecular Biology and Evolution. 29: 441. PMID 22080475 DOI: 10.1093/Molbev/Msr209  1
2011 Gordon JL, Armisén D, Proux-Wéra E, ÓhÉigeartaigh SS, Byrne KP, Wolfe KH. Evolutionary erosion of yeast sex chromosomes by mating-type switching accidents. Proceedings of the National Academy of Sciences of the United States of America. 108: 20024-9. PMID 22123960 DOI: 10.1073/Pnas.1112808108  1
2011 Gordon JL, Byrne KP, Wolfe KH. Mechanisms of chromosome number evolution in yeast. Plos Genetics. 7: e1002190. PMID 21811419 DOI: 10.1371/Journal.Pgen.1002190  1
2011 OhÉigeartaigh SS, Armisén D, Byrne KP, Wolfe KH. Systematic discovery of unannotated genes in 11 yeast species using a database of orthologous genomic segments. Bmc Genomics. 12: 377. PMID 21791067 DOI: 10.1186/1471-2164-12-377  1
2011 Khaldi N, Wolfe KH. Evolutionary Origins of the Fumonisin Secondary Metabolite Gene Cluster in Fusarium verticillioides and Aspergillus niger. International Journal of Evolutionary Biology. 2011: 423821. PMID 21716743 DOI: 10.4061/2011/423821  0.4
2011 Lane MM, Burke N, Karreman R, Wolfe KH, O'Byrne CP, Morrissey JP. Physiological and metabolic diversity in the yeast Kluyveromyces marxianus. Antonie Van Leeuwenhoek. 100: 507-19. PMID 21674230 DOI: 10.1007/S10482-011-9606-X  1
2011 Rozpedowska E, Piškur J, Wolfe KH. Genome sequences of saccharomycotina: Resources and applications in phylogenomics The Yeasts. 1: 145-157. DOI: 10.1016/B978-0-444-52149-1.00011-2  1
2010 Magee AM, Aspinall S, Rice DW, Cusack BP, Sémon M, Perry AS, Stefanović S, Milbourne D, Barth S, Palmer JD, Gray JC, Kavanagh TA, Wolfe KH. Localized hypermutation and associated gene losses in legume chloroplast genomes. Genome Research. 20: 1700-10. PMID 20978141 DOI: 10.1101/Gr.111955.110  1
2010 Lynch DB, Logue ME, Butler G, Wolfe KH. Chromosomal G + C content evolution in yeasts: systematic interspecies differences, and GC-poor troughs at centromeres. Genome Biology and Evolution. 2: 572-83. PMID 20693156 DOI: 10.1093/Gbe/Evq042  1
2010 Khaldi N, Seifuddin FT, Turner G, Haft D, Nierman WC, Wolfe KH, Fedorova ND. SMURF: Genomic mapping of fungal secondary metabolite clusters. Fungal Genetics and Biology : Fg & B. 47: 736-41. PMID 20554054 DOI: 10.1016/J.Fgb.2010.06.003  1
2009 Drinnenberg IA, Weinberg DE, Xie KT, Mower JP, Wolfe KH, Fink GR, Bartel DP. RNAi in budding yeast. Science (New York, N.Y.). 326: 544-50. PMID 19745116 DOI: 10.1126/science.1176945  1
2009 Frank AC, Wolfe KH. Evolutionary capture of viral and plasmid DNA by yeast nuclear chromosomes. Eukaryotic Cell. 8: 1521-31. PMID 19666779 DOI: 10.1128/Ec.00110-09  1
2009 Gordon JL, Byrne KP, Wolfe KH. Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome. Plos Genetics. 5: e1000485. PMID 19436716 DOI: 10.1371/Journal.Pgen.1000485  1
2009 Diekmann K, Hodkinson TR, Wolfe KH, van den Bekerom R, Dix PJ, Barth S. Complete chloroplast genome sequence of a major allogamous forage species, perennial ryegrass (Lolium perenne L.). Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. 16: 165-76. PMID 19414502 DOI: 10.1093/Dnares/Dsp008  1
2009 Gallagher JE, Babiarz JE, Teytelman L, Wolfe KH, Rine J. Elaboration, diversification and regulation of the Sir1 family of silencing proteins in Saccharomyces. Genetics. 181: 1477-91. PMID 19171939 DOI: 10.1534/Genetics.108.099663  1
2009 Williams TA, Wolfe KH, Fares MA. No rosetta stone for a sense-antisense origin of aminoacyl tRNA synthetase classes. Molecular Biology and Evolution. 26: 445-50. PMID 19037009 DOI: 10.1093/Molbev/Msn267  1
2008 Conant GC, Wolfe KH. Turning a hobby into a job: how duplicated genes find new functions. Nature Reviews. Genetics. 9: 938-50. PMID 19015656 DOI: 10.1038/Nrg2482  1
2008 Khaldi N, Wolfe KH. Elusive origins of the extra genes in Aspergillus oryzae. Plos One. 3: e3036. PMID 18725939 DOI: 10.1371/Journal.Pone.0003036  1
2008 Conant GC, Wolfe KH. Probabilistic cross-species inference of orthologous genomic regions created by whole-genome duplication in yeast. Genetics. 179: 1681-92. PMID 18562662 DOI: 10.1534/Genetics.107.074450  1
2008 Sémon M, Wolfe KH. Preferential subfunctionalization of slow-evolving genes after allopolyploidization in Xenopus laevis. Proceedings of the National Academy of Sciences of the United States of America. 105: 8333-8. PMID 18541921 DOI: 10.1073/Pnas.0708705105  1
2008 Gordon JL, Wolfe KH. Recent allopolyploid origin of Zygosaccharomyces rouxii strain ATCC 42981. Yeast (Chichester, England). 25: 449-56. PMID 18509846 DOI: 10.1002/Yea.1598  1
2008 Fedorova ND, Khaldi N, Joardar VS, Maiti R, Amedeo P, Anderson MJ, Crabtree J, Silva JC, Badger JH, Albarraq A, Angiuoli S, Bussey H, Bowyer P, Cotty PJ, Dyer PS, ... ... Wolfe KH, et al. Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. Plos Genetics. 4: e1000046. PMID 18404212 DOI: 10.1371/Journal.Pgen.1000046  1
2008 Conant GC, Wolfe KH. GenomeVx: simple web-based creation of editable circular chromosome maps. Bioinformatics (Oxford, England). 24: 861-2. PMID 18227121 DOI: 10.1093/Bioinformatics/Btm598  1
2008 Khaldi N, Collemare J, Lebrun MH, Wolfe KH. Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi. Genome Biology. 9: R18. PMID 18218086 DOI: 10.1186/Gb-2008-9-1-R18  1
2008 Scannell DR, Wolfe KH. A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast. Genome Research. 18: 137-47. PMID 18025270 DOI: 10.1101/Gr.6341207  1
2008 Conant GC, Wolfe KH. Increased glycolytic flux as an outcome of whole-genome duplication in yeast (Molecular Systems Biology (2007) 3 (129) DOI: 10.1038/msb4100170) Molecular Systems Biology. 4. DOI: 10.1038/msb.2008.46  1
2007 Sémon M, Wolfe KH. Consequences of genome duplication. Current Opinion in Genetics & Development. 17: 505-12. PMID 18006297 DOI: 10.1016/J.Gde.2007.09.007  1
2007 Conant GC, Wolfe KH. Increased glycolytic flux as an outcome of whole-genome duplication in yeast. Molecular Systems Biology. 3: 129. PMID 17667951 DOI: 10.1038/Msb4100170  1
2007 Spillane C, Schmid KJ, Laoueillé-Duprat S, Pien S, Escobar-Restrepo JM, Baroux C, Gagliardini V, Page DR, Wolfe KH, Grossniklaus U. Positive darwinian selection at the imprinted MEDEA locus in plants. Nature. 448: 349-52. PMID 17637669 DOI: 10.1038/Nature05984  1
2007 Scannell DR, Butler G, Wolfe KH. Yeast genome evolution--the origin of the species. Yeast (Chichester, England). 24: 929-42. PMID 17621376 DOI: 10.1002/Yea.1515  1
2007 Scannell DR, Frank AC, Conant GC, Byrne KP, Woolfit M, Wolfe KH. 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. 104: 8397-402. PMID 17494770 DOI: 10.1073/Pnas.0608218104  1
2007 Cusack BP, Wolfe KH. When gene marriages don't work out: divorce by subfunctionalization. Trends in Genetics : Tig. 23: 270-2. PMID 17418444 DOI: 10.1016/J.Tig.2007.03.010  1
2007 Woolfit M, Rozpedowska E, Piskur J, Wolfe KH. Genome survey sequencing of the wine spoilage yeast Dekkera (Brettanomyces) bruxellensis. Eukaryotic Cell. 6: 721-33. PMID 17277171 DOI: 10.1128/Ec.00338-06  1
2007 Sémon M, Wolfe KH. Reciprocal gene loss between Tetraodon and zebrafish after whole genome duplication in their ancestor. Trends in Genetics : Tig. 23: 108-12. PMID 17275132 DOI: 10.1016/J.Tig.2007.01.003  1
2007 Sémon M, Wolfe KH. Rearrangement rate following the whole-genome duplication in teleosts. Molecular Biology and Evolution. 24: 860-7. PMID 17218642 DOI: 10.1093/Molbev/Msm003  1
2007 Byrne KP, Wolfe KH. Consistent patterns of rate asymmetry and gene loss indicate widespread neofunctionalization of yeast genes after whole-genome duplication. Genetics. 175: 1341-50. PMID 17194778 DOI: 10.1534/Genetics.106.066951  1
2007 Cusack BP, Wolfe KH. Not born equal: increased rate asymmetry in relocated and retrotransposed rodent gene duplicates. Molecular Biology and Evolution. 24: 679-86. PMID 17179139 DOI: 10.1093/Molbev/Msl199  1
2006 Drea SC, Lao NT, Wolfe KH, Kavanagh TA. Gene duplication, exon gain and neofunctionalization of OEP16-related genes in land plants. The Plant Journal : For Cell and Molecular Biology. 46: 723-35. PMID 16709189 DOI: 10.1111/J.1365-313X.2006.02741.X  1
2006 Kosa P, Valach M, Tomaska L, Wolfe KH, Nosek J. 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. Nucleic Acids Research. 34: 2472-81. PMID 16684995 DOI: 10.1093/Nar/Gkl327  1
2006 Conant GC, Wolfe KH. Functional partitioning of yeast co-expression networks after genome duplication. Plos Biology. 4: e109. PMID 16555924 DOI: 10.1371/Journal.Pbio.0040109  1
2006 Scannell DR, Byrne KP, Gordon JL, Wong S, Wolfe KH. Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature. 440: 341-5. PMID 16541074 DOI: 10.1038/Nature04562  1
2006 Wolfe KH. Comparative genomics and genome evolution in yeasts. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 361: 403-12. PMID 16524829 DOI: 10.1098/Rstb.2005.1799  1
2006 Byrne KP, Wolfe KH. Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser. Nucleic Acids Research. 34: D452-5. PMID 16381909 DOI: 10.1093/Nar/Gkj041  1
2006 Fares MA, Byrne KP, Wolfe KH. Rate asymmetry after genome duplication causes substantial long-branch attraction artifacts in the phylogeny of Saccharomyces species. Molecular Biology and Evolution. 23: 245-53. PMID 16207937 DOI: 10.1093/Molbev/Msj027  1
2006 Wong S, Wolfe KH. Duplication of genes and genomes in yeasts Topics in Current Genetics. 15: 79-99. DOI: 10.1007/b105770  1
2005 Byrne KP, Wolfe KH. The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Research. 15: 1456-61. PMID 16169922 DOI: 10.1101/Gr.3672305  1
2005 Cusack BP, Wolfe KH. Changes in alternative splicing of human and mouse genes are accompanied by faster evolution of constitutive exons. Molecular Biology and Evolution. 22: 2198-208. PMID 16049198 DOI: 10.1093/Molbev/Msi218  1
2005 Wong S, Wolfe KH. Birth of a metabolic gene cluster in yeast by adaptive gene relocation. Nature Genetics. 37: 777-82. PMID 15951822 DOI: 10.1038/Ng1584  1
2005 Logue ME, Wong S, Wolfe KH, Butler G. A genome sequence survey shows that the pathogenic yeast Candida parapsilosis has a defective MTLa1 allele at its mating type locus. Eukaryotic Cell. 4: 1009-17. PMID 15947193 DOI: 10.1128/Ec.4.6.1009-1017.2005  1
2005 Woolfit M, Wolfe K. The gene duplication that greased society's wheels Nature Genetics. 37: 566-567. PMID 15920515 DOI: 10.1038/Ng0605-566  1
2005 Singer GA, Lloyd AT, Huminiecki LB, Wolfe KH. Clusters of co-expressed genes in mammalian genomes are conserved by natural selection. Molecular Biology and Evolution. 22: 767-75. PMID 15574806 DOI: 10.1093/Molbev/Msi062  1
2004 Nembaware V, Wolfe KH, Bettoni F, Kelso J, Seoighe C. Allele-specific transcript isoforms in human. Febs Letters. 577: 233-8. PMID 15527791 DOI: 10.1016/J.Febslet.2004.10.018  1
2004 Huminiecki L, Wolfe KH. Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse. Genome Research. 14: 1870-9. PMID 15466287 DOI: 10.1101/Gr.2705204  1
2004 Coghlan A, Wolfe KH. Origins of recently gained introns in Caenorhabditis. Proceedings of the National Academy of Sciences of the United States of America. 101: 11362-7. PMID 15243155 DOI: 10.1073/Pnas.0308192101  1
2004 Hokamp K, Wolfe KH. PubCrawler: keeping up comfortably with PubMed and GenBank. Nucleic Acids Research. 32: W16-9. PMID 15215341 DOI: 10.1093/Nar/Gkh453  1
2004 Blanc G, Wolfe KH. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. The Plant Cell. 16: 1667-78. PMID 15208399 DOI: 10.1105/Tpc.021345  1
2004 Blanc G, Wolfe KH. Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. The Plant Cell. 16: 1679-91. PMID 15208398 DOI: 10.1105/Tpc.021410  1
2004 Wolfe K. Evolutionary genomics: Yeasts accelerate beyond BLAST Current Biology. 14: R392-R394. PMID 15186766 DOI: 10.1016/J.Cub.2004.05.015  1
2004 Scannell DR, Wolfe K. Rewiring the transcriptional regulatory circuits of cells Genome Biology. 5. PMID 14759249 DOI: 10.1186/Gb-2004-5-2-206  1
2004 Butler G, Kenny C, Fagan A, Kurischko C, Gaillardin C, Wolfe KH. Evolution of the MAT locus and its Ho endonuclease in yeast species. Proceedings of the National Academy of Sciences of the United States of America. 101: 1632-7. PMID 14745027 DOI: 10.1073/Pnas.0304170101  1
2003 Huminiecki L, Lloyd AT, Wolfe KH. Congruence of tissue expression profiles from Gene Expression Atlas, SAGEmap and TissueInfo databases. Bmc Genomics. 4: 31. PMID 12885301 DOI: 10.1186/1471-2164-4-31  1
2003 Hokamp K, McLysaght A, Wolfe KH. The 2R hypothesis and the human genome sequence. Journal of Structural and Functional Genomics. 3: 95-110. PMID 12836689 DOI: 10.1023/A:1022661917301  1
2003 Fares MA, Wolfe KH. Positive selection and subfunctionalization of duplicated CCT chaperonin subunits. Molecular Biology and Evolution. 20: 1588-97. PMID 12832642 DOI: 10.1093/Molbev/Msg160  1
2003 Wolfe K. Speciation reversal Nature. 422: 25-26. PMID 12621415 DOI: 10.1038/422025A  1
2003 Wong S, Fares MA, Zimmermann W, Butler G, Wolfe KH. Evidence from comparative genomics for a complete sexual cycle in the 'asexual' pathogenic yeast Candida glabrata. Genome Biology. 4: R10. PMID 12620120 DOI: 10.1186/Gb-2003-4-2-R10  1
2003 Wolfe KH, Li WH. Molecular evolution meets the genomics revolution. Nature Genetics. 33: 255-65. PMID 12610535 DOI: 10.1038/Ng1088  1
2003 Hokamp K, Shields DC, Wolfe KH, Caffrey DR. Wrapping up BLAST and other applications for use on Unix clusters. Bioinformatics (Oxford, England). 19: 441-2. PMID 12584141 DOI: 10.1093/Bioinformatics/Btg007  1
2003 Blanc G, Hokamp K, Wolfe KH. A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Research. 13: 137-44. PMID 12566392 DOI: 10.1101/Gr.751803  1
2002 Perry AS, Brennan S, Murphy DJ, Kavanagh TA, Wolfe KH. 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. 9: 157-62. PMID 12465715 DOI: 10.1093/Dnares/9.5.157  1
2002 Perry AS, Wolfe KH. Nucleotide substitution rates in legume chloroplast DNA depend on the presence of the inverted repeat. Journal of Molecular Evolution. 55: 501-8. PMID 12399924 DOI: 10.1007/S00239-002-2333-Y  1
2002 Walsh DW, Wolfe KH, Butler G. Genomic differences between Candida glabrata and Saccharomyces cerevisiae around the MRPL28 and GCN3 loci. Yeast (Chichester, England). 19: 991-4. PMID 12125055 DOI: 10.1002/Yea.890  1
2002 Wong S, Butler G, Wolfe KH. Gene order evolution and paleopolyploidy in hemiascomycete yeasts. Proceedings of the National Academy of Sciences of the United States of America. 99: 9272-7. PMID 12093907 DOI: 10.1073/Pnas.142101099  1
2002 Coghlan A, Wolfe KH. Fourfold faster rate of genome rearrangement in nematodes than in Drosophila. Genome Research. 12: 857-67. PMID 12045140 DOI: 10.1101/Gr.172702  1
2002 McLysaght A, Hokamp K, Wolfe KH. Extensive genomic duplication during early chordate evolution. Nature Genetics. 31: 200-4. PMID 12032567 DOI: 10.1038/Ng884  1
2001 Wolfe KH. Yesterday's polyploids and the mystery of diploidization. Nature Reviews. Genetics. 2: 333-41. PMID 11331899 DOI: 10.1038/35072009  1
2001 Millen RS, Olmstead RG, Adams KL, Palmer JD, Lao NT, Heggie L, Kavanagh TA, Hibberd JM, Gray JC, Morden CW, Calie PJ, Jermiin LS, Wolfe KH. Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus. The Plant Cell. 13: 645-58. PMID 11251102 DOI: 10.1105/Tpc.13.3.645  1
2001 Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, Fitzhugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, ... ... Wolfe KH, et al. Erratum: Initial sequencing and analysis of the human genome: International Human Genome Sequencing Consortium (Nature (2001) 409 (860-921)) Nature. 412: 565-566. DOI: 10.1038/35087627  0.56
2000 Seoighe C, Federspiel N, Jones T, Hansen N, Bivolarovic V, Surzycki R, Tamse R, Komp C, Huizar L, Davis RW, Scherer S, Tait E, Shaw DJ, Harris D, Murphy L, ... ... Wolfe KH, et al. Prevalence of small inversions in yeast gene order evolution. Proceedings of the National Academy of Sciences of the United States of America. 97: 14433-7. PMID 11087826 DOI: 10.1073/Pnas.240462997  1
2000 Coghlan A, Wolfe KH. Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast (Chichester, England). 16: 1131-45. PMID 10953085 DOI: 10.1002/1097-0061(20000915)16:12<1131::Aid-Yea609>3.0.Co;2-F  1
2000 Wolfe K. Robustness - It's not where you think it is Nature Genetics. 25: 3-4. PMID 10802639 DOI: 10.1038/75560  1
2000 McLysaght A, Enright AJ, Skrabanek L, Wolfe KH. Estimation of synteny conservation and genome compaction between pufferfish (Fugu) and human. Yeast (Chichester, England). 17: 22-36. PMID 10797599 DOI: 10.1002/(Sici)1097-0061(200004)17:1<22::Aid-Yea5>3.0.Co;2-S  0.56
2000 Averof M, Rokas A, Wolfe KH, Sharp PM. Evidence for a high frequency of simultaneous double-nucleotide substitutions. Science (New York, N.Y.). 287: 1283-6. PMID 10678838 DOI: 10.1126/Science.287.5456.1283  1
2000 McLysaght A, Enright AJ, Skrabanek L, Wolfe KH. Estimation of synteny conservation and genome compaction between pufferfish (Fugu) and human Yeast. 17: 22-36.  1
1999 Seoighe C, Wolfe KH. Updated map of duplicated regions in the yeast genome. Gene. 238: 253-61. PMID 10571001 DOI: 10.1016/S0378-1119(99)00319-4  1
1999 Hokamp K, Wolfe K. What's new in the library? What's new in GenBank? Let PubCrawler tell you Trends in Genetics. 15: 471-472. PMID 10529811 DOI: 10.1016/S0168-9525(99)01808-9  1
1999 Seoighe C, Wolfe KH. Yeast genome evolution in the post-genome era. Current Opinion in Microbiology. 2: 548-54. PMID 10508730 DOI: 10.1016/S1369-5274(99)00015-6  1
1999 Bradnam KR, Seoighe C, Sharp PM, Wolfe KH. G+C content variation along and among Saccharomyces cerevisiae chromosomes. Molecular Biology and Evolution. 16: 666-75. PMID 10335660 DOI: 10.1093/Oxfordjournals.Molbev.A026149  1
1999 Semple C, Wolfe KH. Gene duplication and gene conversion in the Caenorhabditis elegans genome. Journal of Molecular Evolution. 48: 555-64. PMID 10198121 DOI: 10.1007/Pl00006498  1
1999 Lafay B, Lloyd AT, McLean MJ, Devine KM, Sharp PM, Wolfe KH. Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases. Nucleic Acids Research. 27: 1642-9. PMID 10075995 DOI: 10.1093/Nar/27.7.1642  1
1998 Skrabanek L, Wolfe KH. Eukaryote genome duplication - where's the evidence? Current Opinion in Genetics & Development. 8: 694-700. PMID 9914206 DOI: 10.1016/S0959-437X(98)80039-7  1
1998 McLean MJ, Wolfe KH, Devine KM. Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes. Journal of Molecular Evolution. 47: 691-6. PMID 9847411 DOI: 10.1007/Pl00006428  1
1998 Lohan AJ, Wolfe KH. A subset of conserved tRNA genes in plastid DNA of nongreen plants. Genetics. 150: 425-33. PMID 9725858  1
1998 Keogh RS, Seoighe C, Wolfe KH. Evolution of gene order and chromosome number in Saccharomyces, Kluyveromyces and related fungi. Yeast (Chichester, England). 14: 443-57. PMID 9559552 DOI: 10.1002/(Sici)1097-0061(19980330)14:5<443::Aid-Yea243>3.0.Co;2-L  1
1998 Seoighe C, Wolfe KH. Extent of genomic rearrangement after genome duplication in yeast. Proceedings of the National Academy of Sciences of the United States of America. 95: 4447-52. PMID 9539757 DOI: 10.1073/Pnas.95.8.4447  1
1997 Wolfe KH, Shields DC. Molecular evidence for an ancient duplication of the entire yeast genome. Nature. 387: 708-13. PMID 9192896 DOI: 10.1038/42711  1
1997 Dujon B, Albermann K, Aldea M, Alexandraki D, Ansorge W, Arino J, Benes V, Bohn C, Bolotin-Fukuhara M, Bordonné R, Boyer J, Camasses A, Casamayor A, Casas C, Chéret G, et al. The nucleotide sequence of Saccharomyces cerevisiae chromosome XV. Nature. 387: 98-102. PMID 9169874  1
1997 Shields DC, Wolfe KH. Accelerated evolution of sites undergoing mRNA editing in plant mitochondria and chloroplasts. Molecular Biology and Evolution. 14: 344-9. PMID 9066800 DOI: 10.1093/Oxfordjournals.Molbev.A025768  1
1996 Parle-McDermott AG, Hand NJ, Goulding SE, Wolfe KH. 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). 12: 999-1004. PMID 8896263 DOI: 10.1002/(Sici)1097-0061(199609)12:10B<999::Aid-Yea976>3.0.Co;2-E  1
1996 Goulding SE, Olmstead RG, Morden CW, Wolfe KH. Ebb and flow of the chloroplast inverted repeat. Molecular & General Genetics : Mgg. 252: 195-206. PMID 8804393 DOI: 10.1007/Bf02173220  1
1995 Ems SC, Morden CW, Dixon CK, Wolfe KH, dePamphilis CW, Palmer JD. Transcription, splicing and editing of plastid RNAs in the nonphotosynthetic plant Epifagus virginiana. Plant Molecular Biology. 29: 721-33. PMID 8541499 DOI: 10.1007/Bf00041163  1
1994 Wolfe KH, Lohan AJ. Sequence around the centromere of Saccharomyces cerevisiae chromosome II: similarity of CEN2 to CEN4. Yeast (Chichester, England). 10: S41-6. PMID 8091860 DOI: 10.1002/Yea.320100006  1
1994 Wolfe KH. Similarity between putative ATP-binding sites in land plant plastid ORF2280 proteins and the FtsH/CDC48 family of ATPases. Current Genetics. 25: 379-83. PMID 8082182 DOI: 10.1007/Bf00351493  1
1994 Downie SR, Katz-Downie DS, Wolfe KH, Calie PJ, Palmer JD. Structure and evolution of the largest chloroplast gene (ORF2280): internal plasticity and multiple gene loss during angiosperm evolution. Current Genetics. 25: 367-78. PMID 8082181 DOI: 10.1007/Bf00351492  1
1994 Butler G, Wolfe KH. Yeast homologue of mammalian Ran binding protein 1. Biochimica Et Biophysica Acta. 1219: 711-2. PMID 7948031 DOI: 10.1016/0167-4781(94)90233-X  1
1994 Feldmann H, Aigle M, Aljinovic G, André B, Baclet MC, Barthe C, Baur A, Bécam AM, Biteau N, Boles E, Brandt T, Brendel M, Brückner M, Bussereau F, Christiansen C, ... ... Wolfe KH, et al. Complete DNA sequence of yeast chromosome II. The Embo Journal. 13: 5795-809. PMID 7813418  1
1993 Olmstead RG, Sweere JA, Wolfe KH. Ninety extra nucleotide in ndhF gene of tobacco chloroplast DNA: a summary of revisions to the 1986 genome sequence. Plant Molecular Biology. 22: 1191-3. PMID 8400137 DOI: 10.1007/Bf00028992  1
1993 Sharp PM, Wolfe KH. 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. 21: 3577. PMID 8346035 DOI: 10.1093/Nar/21.15.3577  1
1993 Wolfe KH, Sharp PM. Mammalian gene evolution: nucleotide sequence divergence between mouse and rat. Journal of Molecular Evolution. 37: 441-56. PMID 8308912 DOI: 10.1007/Bf00178874  1
1992 Wolfe KH, Morden CW, Palmer JD. Small single-copy region of plastid DNA in the non-photosynthetic angiosperm Epifagus virginiana contains only two genes. Differences among dicots, monocots and bryophytes in gene organization at a non-bioenergetic locus. Journal of Molecular Biology. 223: 95-104. PMID 1731088 DOI: 10.1016/0022-2836(92)90718-Y  1
1992 Wolfe KH, Katz-Downie DS, Morden CW, Palmer JD. Evolution of the plastid ribosomal RNA operon in a nongreen parasitic plant: accelerated sequence evolution, altered promoter structure, and tRNA pseudogenes. Plant Molecular Biology. 18: 1037-48. PMID 1600142 DOI: 10.1007/Bf00047707  1
1992 Wolfe KH, Morden CW, Ems SC, Palmer JD. Rapid evolution of the plastid translational apparatus in a nonphotosynthetic plant: loss or accelerated sequence evolution of tRNA and ribosomal protein genes. Journal of Molecular Evolution. 35: 304-17. PMID 1404416 DOI: 10.1007/Bf00161168  1
1992 Wolfe KH, Morden CW, Palmer JD. Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant. Proceedings of the National Academy of Sciences of the United States of America. 89: 10648-52. PMID 1332054 DOI: 10.1073/Pnas.89.22.10648  1
1991 Bulmer M, Wolfe KH, Sharp PM. Synonymous nucleotide substitution rates in mammalian genes: implications for the molecular clock and the relationship of mammalian orders. Proceedings of the National Academy of Sciences of the United States of America. 88: 5974-8. PMID 2068073 DOI: 10.1073/Pnas.88.14.5974  1
1991 Wolfe KH. Mammalian DNA replication: mutation biases and the mutation rate. Journal of Theoretical Biology. 149: 441-51. PMID 2062104 DOI: 10.1016/S0022-5193(05)80092-X  1
1991 Morden CW, Wolfe KH, dePamphilis CW, Palmer JD. Plastid translation and transcription genes in a non-photosynthetic plant: intact, missing and pseudo genes. The Embo Journal. 10: 3281-8. PMID 1915295 DOI: 10.1002/J.1460-2075.1991.Tb04892.X  1
1991 Wolfe KH, Morden CW, Palmer JD. Ins and outs of plastid genome evolution. Current Opinion in Genetics & Development. 1: 523-9. PMID 1822284 DOI: 10.1016/S0959-437X(05)80202-3  1
1991 Taylor GW, Wolfe KH, Morden CW, dePamphilis CW, Palmer JD. Lack of a functional plastid tRNA(Cys) gene is associated with loss of photosynthesis in a lineage of parasitic plants. Current Genetics. 20: 515-8. PMID 1723664 DOI: 10.1007/Bf00334780  1
1989 Wolfe KH, Sharp PM, Li WH. Mutation rates differ among regions of the mammalian genome. Nature. 337: 283-5. PMID 2911369 DOI: 10.1038/337283A0  1
1989 Wolfe KH, Gouy M, Yang YW, Sharp PM, Li WH. Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proceedings of the National Academy of Sciences of the United States of America. 86: 6201-5. PMID 2762323 DOI: 10.1073/Pnas.86.16.6201  1
1989 Sharp PM, Shields DC, Wolfe KH, Li WH. Chromosomal location and evolutionary rate variation in enterobacterial genes. Science (New York, N.Y.). 246: 808-10. PMID 2683084 DOI: 10.1126/Science.2683084  1
1989 Wolfe KH. Compilation of sequences of protein-coding genes in chloroplast DNA including cyanelle and cyanobacterial homologues Plant Molecular Biology Reporter. 7: 30-48. DOI: 10.1007/Bf02669244  1
1989 Wolfe KH, Sharp PM, Li WH. Rates of synonymous substitution in plant nuclear genes Journal of Molecular Evolution. 29: 208-211. DOI: 10.1007/Bf02100204  1
1989 Li WH, Gouy M, Wolfe KH, Sharp PM. Angiosperm origins [9] Nature. 342: 131-132.  1
1988 Wolfe KH. The site of deletion of the inverted repeat in pea chloroplast DNA contains duplicated gene fragments. Current Genetics. 13: 97-9. PMID 3359497 DOI: 10.1007/Bf00365763  1
1988 Wolfe KH, Sharp PM. Identification of functional open reading frames in chloroplast genomes. Gene. 66: 215-22. PMID 3169573 DOI: 10.1016/0378-1119(88)90358-7  1
1988 Lu Q, Wolfe KH, McConnell DJ. Molecular cloning of multiple bovine aspartyl protease genes. Gene. 71: 135-46. PMID 3145907 DOI: 10.1016/0378-1119(88)90085-6  1
1988 Sharp PM, Cowe E, Higgins DG, Shields DC, Wolfe KH, Wright F. 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. 16: 8207-11. PMID 3138659 DOI: 10.1093/Nar/16.17.8207  1
1987 Wolfe KH, Li WH, Sharp PM. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proceedings of the National Academy of Sciences of the United States of America. 84: 9054-8. PMID 3480529 DOI: 10.1073/Pnas.84.24.9054  1
1987 Li WH, Wolfe KH, Sourdis J, Sharp PM. Reconstruction of phylogenetic trees and estimation of divergence times under nonconstant rates of evolution. Cold Spring Harbor Symposia On Quantitative Biology. 52: 847-56. PMID 3454293 DOI: 10.1101/Sqb.1987.052.01.092  1
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