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		Publications from the Wolfe Laboratory To see PubMed abstracts, click the checkbox beside the article(s) and then  Last update: June 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. (2018) Evolutionary instability of CUG-Leu in the genetic code of budding yeasts. Nat Commun. 9: 1887.   Ortiz-Merino RA, Varela JA, Coughlan AY, Hoshida H, da Silveira WB, Wilde C, Kuijpers NGA, Geertman JM, Wolfe KH, Morrissey JP. (2018) Ploidy Variation in Kluyveromyces marxianus Separates Dairy and Non-dairy Isolates. Front Genet. 9: 94.   Ortiz-Merino RA, Kuanyshev N, Byrne KP, Varela JA, Morrissey JP, Porro D, Wolfe KH, Branduardi P. (2018) Transcriptional Response to Lactic Acid Stress in the Hybrid Yeast Zygosaccharomyces parabailii. Appl Environ Microbiol. 84: e02294-17   Hanson SJ, Byrne KP, Wolfe KH. (2017) Flip/flop mating-type switching in the methylotrophic yeast Ogataea polymorpha is regulated by an Efg1-Rme1-Ste12 pathway. PLoS Genet. 13: e1007092.   Wolfe KH, Butler G. (2017) Evolution of Mating in the Saccharomycotina. Annu Rev Microbiol. 71: 197-214.   Ortiz-Merino RA, Kuanyshev N, Braun-Galleani S, Byrne KP, Porro D, Branduardi P, Wolfe KH (2017) Evolutionary restoration of fertility in an interspecies hybrid yeast, by whole-genome duplication after a failed mating-type switch. PLoS Biol. 15: e2002128.   Coughlan AY, Hanson SJ, Byrne KP, Wolfe KH. (2016) Centromeres of the Yeast Komagataella phaffii (Pichia pastoris) Have a Simple Inverted-Repeat Structure. Genome Biol Evol. 8: 2482-92.   Schröder MS, Martinez de San Vicente K, Prandini TH, Hammel S, Higgins DG, Bagagli E, Wolfe KH, Butler G. (2016) Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species. PLoS Genet. 12: e1006404.   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, Deshpande S, Douglass AP, Hanson SJ, Klenk HP, LaButti KM, Lapidus A, Lindquist EA, Lipzen AM, Meier-Kolthoff JP, Ohm RA, Otillar RP, Pangilinan JL, Peng Y, Rokas A, Rosa CA, Scheuner C, Sibirny AA, Slot JC, Stielow JB, Sun H, Kurtzman CP, Blackwell M, Grigoriev IV, Jeffries TW. (2016) Comparative genomics of biotechnologically important yeasts. Proc Natl Acad Sci U S A. 113: 9882-7.   Pryszcz LP, Németh T, Saus E, Ksiezopolska E, Hegedüsová E, Nosek J, Wolfe KH, Gacser A, Gabaldón T. (2015) The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis. PLoS Genet. 11: e1005626.   Wolfe KH. (2015) Origin of the Yeast Whole-Genome Duplication. PLoS Biol. 13: e1002221.   Kobayashi N, Suzuki Y, Schoenfeld LW, Müller CA, Nieduszynski C, Wolfe KH, Tanaka TU. (2015) Discovery of an unconventional centromere in budding yeast redefines evolution of point centromeres. Curr Biol. 25:m 2026-33.   Wolfe KH, Armisén D, Proux-Wera E, ÓhÉigeartaigh SS, Azam H, Gordon JL, Byrne KP. (2015) Clade- and species-specific features of genome evolution in the Saccharomycetaceae. FEMS Yeast Res. 15: fov035   Monerawela C, James TC, Wolfe KH, Bond U. (2015) Loss of lager specific genes and subtelomeric regions define two different Saccharomyces cerevisiae lineages for Saccharomyces pastorianus Group I and II strains. FEMS Yeast Res. 15.pii: fou008.   Pitoniak A, Chavel CA, Chow J, Smith J, Camara D, Karunanithi S, Li B, Wolfe KH, Cullen PJ. (2015) Cdc42p-interacting protein Bem4p regulates the filamentous-growth mitogen-activated protein kinase pathway. Mol Cell Biol. 35: 417-36.   Hanson SJ, Byrne KP, Wolfe KH. (2014) Mating-type switching by chromosomal inversion in methylotrophic yeasts suggests an origin for the three-locus Saccharomyces cerevisiae system. Proc Natl Acad Sci U S A. 111: E4851-8   OhÉigeartaigh SS, Armisén D, Byrne KP, Wolfe KH. (2014) SearchDOGS bacteria, software that provides automated identification of potentially missed genes in annotated bacterial genomes. J Bacteriol. 196: 2030-42.   Maguire SL, Wang C, Holland LM, Brunel F, Neuvéglise C, Nicaud JM, Zavrel M, White TC, Wolfe KH, Butler G. (2014) Zinc finger transcription factors displaced SREBP proteins as the major Sterol regulators during Saccharomycotina evolution. PLoS Genet. 10: e1004076.   Maguire S.L., OhÉigeartaigh S.S., Byrne K.P., Schröder M.S., O'Gaora P., Wolfe K.H. Butler G. (2013) Comparative genome analysis and gene finding in Candida species using CGOB. Mol Biol Evol. 30: 1281-91.   Proux-Wéra E., Byrne K.P., Wolfe K.H. (2013) Evolutionary mobility of the ribosomal DNA array in yeasts. Genome Biol Evol. 5: 525-31.   Proux-Wéra E., Armisén D., Byrne K.P., Wolfe K.H. (2012) A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach. BMC Bioinformatics. 13: 237   Riccombeni A., Vidanes G., Proux-Wéra E., Wolfe K.H., Butler G. (2012) Sequence and analysis of the genome of the pathogenic yeast Candida orthopsilosis. PLoS One. 7: e35750. Gordon J.L., Armisién D., Proux-Wéra E., ÓhÉigeartaigh S.S., Byrne K.P. & Wolfe K.H. (2011) Evolutionary erosion of yeast sex chromosomes by mating-type switching accidents. Proc Natl Acad Sci U S A. 108: 20024-9. Gordon J.L., Byrne K.P. & Wolfe K.H. (2011) Mechanisms of chromosome number evolution in yeast. PLoS Genet. 7, e1002190. OhÉigeartaigh S.S., Armisén D., Byrne K.P. & Wolfe K.H. (2011) Systematic discovery of unannotated genes in 11 yeast species using a database of orthologous genomic segments. BMC Genomics. 12, 377. Lane M.M., Burke N., Karreman R., Wolfe K.H., O'Byrne C.P. & Morrissey J.P. (2011) Physiological and metabolic diversity in the yeast Kluyveromyces marxianus. Antonie Van Leeuwenhoek. 2011. Khaldi N. & Wolfe K.H. (2011) Evolutionary Origins of the Fumonisin Secondary Metabolite Gene Cluster in Fusarium verticillioides and Aspergillus niger. Int J Evol Biol. 2011, 423821. Magee A.M., Aspinall S., Rice D.W., Cusack B.P., Sémon M., Perry A.S., Stefanovic S., Milbourne D., Barth S., Palmer J.D., Gray J.C., Kavanagh T.A. & Wolfe K.H. (2010) Localized hypermutation and associated gene losses in legume chloroplast genomes. Genome Res. 20, 1700-10. Khaldi N., Seifuddin F.T., Turner G., Haft D., Nierman W.C., Wolfe K.H. & Fedorova N.D. (2010) SMURF: Genomic mapping of fungal secondary metabolite clusters. Fungal Genet Biol. 47, 736-41. Lynch D.B., Logue M.E., Butler G. & Wolfe K.H. (2010) Chromosomal G + C content evolution in yeasts: systematic interspecies differences, and GC-poor troughs at centromeres. Genome Biol Evol. 2, 572-83. Drinnenberg I.A., Weinberg D.E., Xie K.T., Mower J.P., Wolfe K.H., Fink G.R. & Bartel D.P. (2009) RNAi in budding yeast. Science. 326, 544-50. Frank A.C. & Wolfe K.H. (2009) Evolutionary capture of viral and plasmid DNA by yeast nuclear chromosomes. Eukaryot Cell. 8i, 1521-31. Diekmann K., Hodkinson T.R., Wolfe K.H., van den Bekerom R., Dix P.J. & Barth S. (2009) Complete chloroplast genome sequence of a major allogamous forage species, perennial ryegrass (Lolium perenne L.). DNA Res. 16, 165-76. Gordon J.L., Byrne K.P. & Wolfe K.H. (2009) Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome. PLoS Genet. 5, e1000485. Gallagher J.E., Babiarz J.E., Teytelman L., Wolfe K.H. & Rine J. (2009) Elaboration, diversification and regulation of the Sir1 family of silencing proteins in Saccharomyces. Genetics. 181, 1477-91. Williams T.A., Wolfe K.H. & Fares M.A. (2009) No rosetta stone for a sense-antisense origin of aminoacyl tRNA synthetase classes. Mol Biol Evol. 26, 445-50. Conant G.C. & Wolfe K.H. (2008) Turning a hobby into a job: how duplicated genes find new functions. Nat Rev Genet. 9, 938-50. Khaldi, N. & Wolfe, K. H. (2008) Elusive origins of the extra genes in Aspergillus oryzae. PLoS ONE 3, e3036. Conant, G.C. & Wolfe, K.H. (2008) Probabilistic cross-species inference of orthologous genomic regions created by whole-genome duplication in yeast. Genetics 179, 1681-92. Semon, M. & Wolfe, K. H. (2008) Preferential subfunctionalization of slow-evolving genes in Xenopus laevis. Proc. Natl. Acad. Sci. USA 105, 8333-8338. Gordon, J. L. & Wolfe, K. H. (2008) Recent allopolyploid origin of Zygosaccharomyces rouxii strain ATCC 42981. Yeast 25, 449-456. Fedorova, N. D., Khaldi, N., Joardar, V. S., Maiti, R., Amedeo, P., Anderson, M. J., Crabtree, J., Silva, J. C., Badger, J. H., Albarraq, A., Angiuoli, S., Bussey, H., Bowyer, P., Cotty, P. J., Dyer, P. S., Egan, A., Galens, K., Fraser-Liggett, C. M., Haas, B. J., Inman, J. M., Kent, R., Lemieux, S., Malavazi, I., Orvis, J., Roemer, T., Ronning, C. M., Sundaram, J. P., Sutton, G., Turner, G., Venter, J. C., White, O. R., Whitty, B. R., Youngman, P., Wolfe, K. H., Goldman, G. H., Wortman, J. R., Jiang, B., Denning, D. W. & Nierman, W. C. (2008) Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genet. 4, e1000046. Conant, G. C. & Wolfe, K. H. (2008) GenomeVx: simple web-based creation of editable circular chromosome maps. Bioinformatics 24, 861-862. Khaldi, N., Collemare, J., Lebrun, M. H. & Wolfe, K. H. (2008) Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi. Genome Biol. 9, R18. Scannell, D. R. & Wolfe, K. H. (2008) A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast. Genome Res. 18, 137-147. Semon, M. & Wolfe, K. H. (2007) Consequences of genome duplication. Curr. Opin. Genet. Devel. 17, 505-512. Conant, G.C. & Wolfe, K.H. (2007) Increased glycolytic flux as an outcome of whole-genome duplication in yeast. Mol. Syst. Biol. 3: 129. Spillane, C., Schmid, K.J., Laoueille-Duprat, S., Pien, S., Escobar-Restrepo, J.M., Baroux, C., Gagliardini, V., Page, D.R., Wolfe, K.H. & Grossniklaus, U. (2007) Positive darwinian selection at the imprinted MEDEA locus in plants. Nature 448: 349-52. Scannell, D.R., Butler, G. & Wolfe, K.H. (2007) Yeast genome evolution-the origin of the species. Yeast 24: 929-42. Scannell, D.R., Frank, A.C., Conant, G.C., Byrne, K.P., Woolfit, M. & Wolfe, K.H. (2007) Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication. Proc. Natl. Acad. Sci. U S A 104: 8397-402. Cusack, B.P. & Wolfe, K.H. (2007) When gene marriages don't work out: divorce by subfunctionalization. Trends Genet. 23: 270-2. Woolfit, M., Rozpedowska, E., Piskur, J. & Wolfe, K.H. (2007) Genome survey sequencing of the wine spoilage yeast Dekkera (Brettanomyces) bruxellensis. Eukaryot. Cell 6: 721-33. Semon, M. & Wolfe, K.H. (2007) Reciprocal gene loss between Tetraodon and zebrafish after whole genome duplication in their ancestor. Trends Genet. 23: 108-12. Semon, M. & Wolfe, K.H. (2007) Rearrangement rate following the whole-genome duplication in teleosts. Mol. Biol. Evol. 24: 860-7. Byrne, K.P. & Wolfe, K.H. (2007) Consistent patterns of rate asymmetry and gene loss indicate widespread neofunctionalization of yeast genes after whole-genome duplication. Genetics 175: 1341-50. Cusack, B.P. & Wolfe, K.H. (2007) Not born equal: increased rate asymmetry in relocated and retrotransposed rodent gene duplicates. Mol. Biol. Evol. 24: 679-86. Drea, S.C., Lao, N.T., Wolfe, K.H. &, Kavanagh, T.A. (2006) Gene duplication, exon gain and neofunctionalization of OEP16-related genes in land plants. Plant J. 46: 723-35. Kosa, P., Valach, M., Tomaska, L., Wolfe, K.H. & Nosek, J. (2006) 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 Res. 34: 2472-81. Conant, G. C. & Wolfe, K. H. (2006). Functional partitioning of yeast co-expression networks after genome duplication. PLoS Biol. 4, e109. Scannell, D. R.*, Byrne, K. P.*, Gordon, J. L., Wong, S. & Wolfe, K. H. (2006). Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature 440, 341-345. Byrne, K. P. & Wolfe, K. H. (2006). Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser. Nucleic Acids Res. 34, D452-455. Fares, M. A., Byrne, K. P. & Wolfe, K. H. (2006). Rate asymmetry after genome duplication causes substantial long-branch attraction artifacts in the phylogeny of Saccharomyces species. Mol. Biol. Evol. 23, 245-253. Wolfe, K. H. (2006). Comparative genomics and genome evolution in yeasts. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 361, 403-412. Wong, S. & Wolfe, K. H. (2006). Duplication of genes and genomes in yeasts. In Comparative genomics (Sunnerhagen, P. & Piskur, J., eds.), Vol. 15, pp. 78-99. Springer-Verlag, Heidelberg. Byrne, K. P. & Wolfe, K. H. (2005). The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res. 15, 1456-1461. Cusack, B. P. & Wolfe, K. H. (2005). Changes in alternative splicing of human and mouse genes are accompanied by faster evolution of constitutive exons. Mol. Biol. Evol. 22, 2198-2208. Haber, J. E. & Wolfe, K. H. (2005). Evolution and function of HO and VDE endonucleases in fungi. In Inteins and homing endonucleases (Belfort, M., Derbyshire, V., Stoddard, B. & Wood, D., eds.), pp. 161-176. Springer-Verlag, Berlin. Logue, M. E., Wong, S., Wolfe, K. H. & Butler, G. (2005). A genome sequence survey shows that the pathogenic yeast Candida parapsilosis has a defective MTLa1 at its mating type locus. Eukaryot. Cell 4, 1009-1017. Singer, G. A. C., Lloyd, A. T., Huminiecki, L. B. & Wolfe, K. H. (2005). Clusters of co-expressed genes in mammalian genomes are conserved by natural selection. Mol. Biol. Evol. 22, 767-775. Wong, S. & Wolfe, K. H. (2005). Birth of a metabolic gene cluster in yeast by adaptive gene relocation. Nature Genet. 37, 777-782. Woolfit, M. & Wolfe, K. (2005). The gene duplication that greased society's wheels. Nature Genet. 37, 566-567. Hokamp, K. & Wolfe, K. H. (2004). PubCrawler: keeping up comfortably with PubMed and GenBank. Nucleic Acids Res. 32, W16-W19. Huminiecki, L. & Wolfe, K. H. (2004). Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse. Genome Res. 14, 1870-1879. Nembaware, V., Wolfe, K. H., Bettoni, F., Kelso, J. & Seoighe, C. (2004). Allele-specific transcript isoforms in human. FEBS Lett. 577, 233-238. Blanc, G. & Wolfe, K. H. (2004a). Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell. 16, 1667-1678 Blanc, G. & Wolfe, K. H. (2004b). Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell. 16, 1679-1691 Coghlan, A. & Wolfe, K. H. (2004). Origins of recently gained introns in Caenorhabditis. Proc. Natl. Acad. Sci. USA. 101, 11362-11367 Butler, G., Kenny, C., Fagan, A., Kurischko, C., Gaillardin, C. & Wolfe, K. H. (2004). Evolution of the MAT locus and its Ho endonuclease in yeast species. Proc. Natl. Acad. Sci. USA 101, 1632-1637 Wolfe, K. (2004). Evolutionary genomics: Yeasts accelerate beyond BLAST. Curr. Biol. 14, R392-R394 Scannell, D.R. & Wolfe, K. H. (2004). Rewiring the transcriptional regulatory circuits of cells. Genome Biol. 5: 206. Fares, M.A. & Wolfe, K. H. (2003). Positive Selection and Sub-Functionalisation of Duplicated CCT Chaperonin Subunits. Mol. Biol. Evol. 20, 1588-1597 Huminiecki, L., Lloyd, A.T. & Wolfe, K. H. (2003). Congruence of tissue expression profiles from Gene Expression Atlas, SAGEmap and TissueInfo databases. BMC Genomics 4, 31 Hokamp, K., McLysaght, A. & Wolfe, K. H. (2003). The 2R hypothesis and the human genome sequence. Journal of Structural and Functional Genomics. 3: 95-110. Wong, S., Fares M.A., Zimmermann W., Butler G. & Wolfe, K. H. (2003). Evidence from comparative genomics for a complete sexual cycle in the 'asexual' pathogenic yeast Candida glabrata. Genome Biol. 4(2), R1O. Wolfe, K. H. & Li, W.H. (2003). Molecular evolution meets the genomics revolution. Nat Genet. 33 Suppl, 255-265. Hokamp, K., Shields D.C., Wolfe K.H. & Caffrey D.R. (2003). Wrapping up BLAST and other applications for use on Unix clusters. Bioinformatics 19(3), 441-442. Blanc, G., Hokamp, K. & Wolfe, K. H. (2003). A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res. 13(2), 137-144. Perry, A. S. & Wolfe, K. H. (2002). Nucleotide substitution rates in legume chloroplast DNA depend on the presence of the inverted repeat. J Mol Evol 55, 501-508. Perry, A. S., Brennan, S., Murphy, D. J., Kavanagh, T. A. & Wolfe, K. H. (2002). Evolutionary re-organisation of a large operon in adzuki bean chloroplast DNA caused by inverted repeat movement. DNA Res 9, 157-162. Walsh, D. W., Wolfe, K. H. & Butler, G. (2002). Genomic differences between Candida glabrata and Saccharomyces cerevisiae at the MRPL28 and GCN3 loci. Yeast 19, 991-994. Wong, S., Butler, G. and Wolfe, K.H. (2002). Gene order evolution and paleopolyploidy in hemiascomycete yeasts. Proc. Natl. Acad. Sci. USA 99(14), 9272-9277. McLysaght, A., Hokamp K, and Wolfe, K.H. (2002). Extensive genomic duplication during early chordate evolution. Nat Genet 31(2), 200-204. Coghlan, A. and Wolfe, K.H. (2002). Fourfold faster rate of genome rearrangement in nematodes than in Drosophila. Genome Res 12(6), 857-867. Coghlan, A., Mac Donaill, D.A. and Buttimore, N.H. (2001). Representation of amino acids as five-bit or three-bit patterns for filtering protein databases. Bioinformatics 17, 676-685. Millen, R.S., Olmstead, R.G., Adams, K.L., Palmer, J.D., Lao, N.T., Heggie, L., Kavanagh, T.A., Hibberd, J.M., Gray, J.C., Morden, C.W., Calie, P.J., Jermiin, L.S. and Wolfe, K.H. (2001). Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus. Plant Cell 13, 645-658. Wolfe, K.H. (2001). Yesterday's polyploids and the mystery of diploidization. Nature Reviews Genet. 2, 333-341. McLysaght, A., Seoighe, C. and Wolfe, K. (2000). High frequency of inversions during eukaryote gene order evolution. In Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families (Sankoff, D. & Nadeau, J. H., eds.), pp. 47-58. Kluwer Academic Press, Dordrecht. Lander, E.S. et al. (2001) Initial sequencing and analysis of the human genome. Nature 409, 860-921. Seoighe, C., Federspiel, N., Jones, T., Hansen, N., Bivolarovic, V., Surzycki, R., Tamse, R., Komp, C., Huizar, L., Davis, R.W., Scherer, S., Tait, E., Shaw, D.J., Harris, D., Murphy, L., Oliver, K., Taylor, K., Rajandream, M.-A., Barrell, B.G. & Wolfe, K.H. (2000) Prevalence of small inversions in yeast gene order evolution. Proc. Natl. Acad. Sci. USA 97, 14433-14437. Coghlan, A. & Wolfe, K.H. (2000) Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast 16, 1131-1145. McLysaght, A., Enright, A.J., Skrabanek, L. & Wolfe, K.H. (2000) Estimation of synteny conservation and genome compaction between pufferfish (Fugu) and human. Yeast 17, 22-36. Averof, M., Rokas, A., Wolfe, K.H. & Sharp, P.M. (2000) Evidence for a high frequency of simultaneous double-nucleotide substitutions. Science 287, 1283-1286. Hokamp, K. and Wolfe, K.H. (1999) What's new in the library? What's new in GenBank? Let PubCrawler tell you. Trends Genet. 15, 471-472. Seoighe, C. and Wolfe, K.H. (1999). Updated map of duplicated regions in the yeast genome. Gene 238, 253-261. Seoighe, C. and Wolfe, K.H. (1999) Yeast genome evolution in the post-genome era. Curr. Opin. Microbiol. 2, 548-554. Bradnam, K.R., Seoighe, C., Sharp, P.M. and Wolfe, K.H. (1999). G+C content variation along and among Saccharomyces cerevisiae chromosomes. Mol. Biol. Evol. 16, 666-675. Tort, J., Brindey, P. J., Knox, D., Wolfe, K. H. and Dalton, J. P. (1999) Proteinases and associated genes of parasitic helminths. Advances in Parasitology 43, 161-266. Semple, C. and Wolfe, K.H. (1999) Gene duplication and gene conversion in the Caenorhabditis elegans genome. J. Mol. Evol. 48, 555-564. Lafay, B., Lloyd, A.T., McLean, M.J., Devine, K.M., Sharp, P.M. and Wolfe, K.H. (1999) Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutation biases. Nucleic Acids Res. 27, 1642-1649. McLean, M.J., Wolfe, K.H. and Devine, K.M. (1998) Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes. J. Mol. Evol. 47, 691-696. Skrabanek, L and Wolfe, K.H. (1998) Eukaryote genome duplication - where's the evidence? Curr. Opin. Genet. Devel. 8, 694-700. Lohan, A.J. and Wolfe, K.H. (1998) A subset of conserved tRNA genes in plastid DNA of nongreen plants. Genetics 150, 425-433. Seoighe, C. and Wolfe, K.H. (1998) Extent of genomic rearrangement after genome duplication in yeast. Proc. Natl. Acad. Sci. USA 95, 4447-4452. Keogh, R.S., Seoighe, C and Wolfe, K.H. (1998) Evolution of gene order and chromosome number in Saccharomyces, Kluyveromyces and related fungi. Yeast 14, 443-457. Wolfe, K.H. and Shields, D.C. (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387, 708-713. Dujon, B. et al. (1997) The nucleotide sequence of Saccharomyces cerevisiae chromosome XV. Nature 387 (suppl.) 98-102. Shields, D.C. and Wolfe, K.H. (1997) Accelerated evolution of sites undergoing mRNA editing in plant mitochondria and chloroplasts. Mol. Biol. Evol. 14, 344-349. Parle-McDermott, A.G., Hand, N.J., Goulding, S.E. and Wolfe, K.H. (1996) Sequence of 29 kb around the PDR10 locus on the right arm of Saccharomyces cerevisiae chromosome XV: similarity to part of chromosome I. Yeast 12, 999-1004. Goulding, S.E., Olmstead, R.G., Morden, C.W. and Wolfe, K.H. (1996) Ebb and Flow of the Chloroplast Inverted Repeat. Mol. Gen. Genet. 252, 195-206. Wolfe, K.H. (1996) Molecular evolution of plants: more genomes, fewer generalities. In Molecular Genetics of Photosynthesis (J. Barber and B. Andersson, eds.), volume in Frontiers of Molecular Biology series (D. Hames and D. Glover, eds.). IRL Press, Oxford. Ems, S.C., Morden C.W., Dixon, C.K., Wolfe, K.H., dePamphilis, C.W. and Palmer, J.D. (1995) Transcription, splicing and editing of plastid RNAs in the nonphotosynthetic plant Epifagus virginiana. Plant Mol. Biol. 29, 721-733. Feldmann, H. et al. (1994) Complete DNA sequence of yeast chromosome II. EMBO J. 13, 5795-5809. Butler, G. and Wolfe, K.H. (1994) Yeast homologue of mammalian Ran binding protein 1. Biochim. Biophys. Acta 1219, 711-712. Wolfe, K.H. and Lohan, A.J.E. (1994) Sequence around the centromere of Saccharomyces cerevisiae chromosome II: similarity of CEN2 to CEN4. Yeast 10, S41-S46. Wolfe, K.H. (1994) Similarity between putative ATP-binding sites in land plant plastid ORF2280 proteins and the FtsH/CDC48 family of ATPases. Curr. Genet. 25, 379-383. Downie, S.R., Katz-Downie, D.S., Wolfe, K.H., Calie, P.J. and Palmer, J.D. (1994) Structure and evolution of the largest chloroplast gene (ORF2280): internal plasticity and multiple gene loss during angiosperm evolution. Curr. Genet. 25, 367-378. Sharp, P.M. and Wolfe, K.H. (1993) Identification of a Candida utilis gene encoding ribosomal protein L7: evidence for two divergent subclasses of the eukaryotic ribosomal protein L7 family. Nucleic Acids Res. 21, 3557. Wolfe, K.H. and Sharp, P.M. (1993) Mammalian gene evolution: Nucleotide sequence divergence between mouse and rat. J. Mol. Evol. 37, 441-456. Olmstead, R.G., Sweere, J.A. and Wolfe, K.H. (1993) Ninety extra nucleotides in ndhF gene of tobacco chloroplast DNA: a summary of revisions to the 1986 genome sequence. Plant Mol. Biol. 22, 1191-1193. Wolfe, K.H., Morden, C.W. and Palmer, J.D. (1992) Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant. Proc. Natl. Acad. Sci. USA 89, 10648-10652. 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Sharp, P.M., Cowe, E., Higgins, D.G., Shields, D.C., Wolfe, K.H. and Wright, F. (1988) Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe and Homo sapiens; a review of the considerable within-species diversity. Nucleic Acids Res. 16, 8207-8211. Wolfe, K.H. and Sharp, P.M. (1988) Identification of functional open reading frames in chloroplast genomes. Gene 66, 215-222. Wolfe, K.H. (1988) The site of deletion of the inverted repeat in pea chloroplast DNA contains duplicated gene fragments. Curr. Genet. 13, 97-99. Lu, Q., Wolfe, K.H. and McConnell, D.J. (1988) Molecular cloning of multiple bovine aspartyl protease genes. Gene 71, 135-146. Wolfe, K.H., Li, W.-H. and Sharp, P.M. (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast and nuclear DNAs. Proc. Natl. Acad. Sci. USA 84, 9054-9058. Li, W.-H., Wolfe, K.H., Sourdis, J. and Sharp, P.M. (1987) Reconstruction of phylogenetic trees and estimation of divergence times under nonconstant rates of evolution. Cold Spring Harbor Symp. Quant. Biol. 52, 847-856.
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