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List of works by Kenneth H. Wolfe

A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast

scientific article published on 19 November 2007

A genome sequence survey shows that the pathogenic yeast Candida parapsilosis has a defective MTLa1 allele at its mating type locus

scientific article published on June 2005

A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach

scientific article

A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome

scientific article

A subset of conserved tRNA genes in plastid DNA of nongreen plants.

scientific article published on September 1998

Accelerated evolution of sites undergoing mRNA editing in plant mitochondria and chloroplasts

scientific article published in March 1997

Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome

scientific article published in May 2009

Allele-specific transcript isoforms in human

scientific article published in November 2004

An Evolutionary Perspective on Yeast Mating-Type Switching

scientific article

Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes

scientific article

Birth of a metabolic gene cluster in yeast by adaptive gene relocation

scientific article published on 12 June 2005

Carbon source requirements for mating and mating-type switching in the methylotrophic yeasts Ogataea (Hansenula) polymorpha and Komagataella phaffii (Pichia pastoris)

scientific article published on 06 January 2020

Cdc42p-interacting protein Bem4p regulates the filamentous-growth mitogen-activated protein kinase pathway

scientific article

Centromeres of the Yeast Komagataella phaffii (Pichia pastoris) Have a Simple Inverted-Repeat Structure

scientific article published on 6 August 2016

Changes in Alternative Splicing of Human and Mouse Genes Are Accompanied by Faster Evolution of Constitutive Exons

article

Chromosomal G + C content evolution in yeasts: systematic interspecies differences, and GC-poor troughs at centromeres

scientific article

Chromosomal location and evolutionary rate variation in enterobacterial genes

scientific article

Clade- and species-specific features of genome evolution in the Saccharomycetaceae

scientific article

Clusters of co-expressed genes in mammalian genomes are conserved by natural selection

scientific article

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

scientific article

Comparative genome analysis and gene finding in Candida species using CGOB.

scientific article published on 13 March 2013

Comparative genomics and genome evolution in yeasts

scientific article (publication date: 29 March 2006)

Comparative genomics of biotechnologically important yeasts

scientific article

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

scientific article published on 9 May 2006

Complete chloroplast genome sequence of a major allogamous forage species, perennial ryegrass (Lolium perenne L.).

scientific article published on 04 May 2009

Congruence of tissue expression profiles from Gene Expression Atlas, SAGEmap and TissueInfo databases

scientific article

Consequences of genome duplication

scientific article

Consistent patterns of rate asymmetry and gene loss indicate widespread neofunctionalization of yeast genes after whole-genome duplication

scientific article published on 28 December 2006

Coverage-Versus-Length Plots, a Simple Quality Control Step for Yeast Genome Sequence Assemblies

scientific article published on 07 March 2019

Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data

scientific article

Discovery of an unconventional centromere in budding yeast redefines evolution of point centromeres

scientific article published on 9 July 2015

Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse

scientific article published on October 2004

Draft Genome Sequence of a Highly Heterozygous Yeast Strain from the Metschnikowia pulcherrima Subclade, UCD127.

scientific article

Draft Genome Sequence of a Red Basidiomycete Yeast, Symmetrospora coprosmae Strain UCD350, Isolated from Soil in Ireland

scientific article published on 31 October 2019

Draft Genome Sequence of the Birch Tree Fungal Pathogen Taphrina betulina UCD315

scientific article published on 27 November 2019

Draft Genome Sequence of the Yeast Nadsonia starkeyi-henricii UCD142, Isolated from Forest Soil in Ireland.

scientific article

Draft Genome Sequences of Two Isolates of the Yeast Kazachstania servazzii Recovered from Soil in Ireland

scientific article published on 31 October 2019

Draft Genome Sequences of Two Natural Isolates of the Yeast Barnettozyma californica from Ireland, UCD09 and UCD89.

scientific article published on 21 June 2018

Ebb and flow of the chloroplast inverted repeat

scientific article

Elaboration, diversification and regulation of the Sir1 family of silencing proteins in Saccharomyces.

scientific article published on 26 January 2009

Elusive origins of the extra genes in Aspergillus oryzae

scientific article

Estimation of synteny conservation and genome compaction between pufferfish (Fugu) and human

scientific article

Eukaryote genome duplication - where's the evidence?

scientific article published in December 1998

Evidence for a High Frequency of Simultaneous Double-Nucleotide Substitutions

scientific article published in Science

Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi

scientific article

Evidence from comparative genomics for a complete sexual cycle in the 'asexual' pathogenic yeast Candida glabrata

scientific article

EvoChromo: towards a synthesis of chromatin biology and evolution

scientific article published on 26 September 2019

Evolution of Mating in the Saccharomycotina

scientific article published on 28 June 2017

Evolution of gene order and chromosome number in Saccharomyces, Kluyveromyces and related fungi

scientific article

Evolution of the MAT locus and its Ho endonuclease in yeast species

scholarly article

Evolution of the plastid ribosomal RNA operon in a nongreen parasitic plant: accelerated sequence evolution, altered promoter structure, and tRNA pseudogenes

scientific article

Evolutionary Origins of the Fumonisin Secondary Metabolite Gene Cluster in Fusarium verticillioides and Aspergillus niger

scientific article published on 23 May 2011

Evolutionary biology: Speciation reversal

scientific article published in Nature

Evolutionary capture of viral and plasmid DNA by yeast nuclear chromosomes

scientific article published on 7 August 2009

Evolutionary erosion of yeast sex chromosomes by mating-type switching accidents

scientific article

Evolutionary genomics: yeasts accelerate beyond BLAST.

scientific article published on May 2004

Evolutionary instability of CUG-Leu in the genetic code of budding yeasts.

scientific article

Evolutionary mobility of the ribosomal DNA array in yeasts

scientific article

Evolutionary re-organisation of a large operon in adzuki bean chloroplast DNA caused by inverted repeat movement

scientific article published in October 2002

Evolutionary restoration of fertility in an interspecies hybrid yeast, by whole-genome duplication after a failed mating-type switch.

scientific article

Extensive genomic duplication during early chordate evolution

scientific article (publication date: 28 May 2002)

Extent of genomic rearrangement after genome duplication in yeast

scientific article

Flip/flop mating-type switching in the methylotrophic yeast Ogataea polymorpha is regulated by an Efg1-Rme1-Ste12 pathway

scientific article

Fourfold faster rate of genome rearrangement in nematodes than in Drosophila

scientific article

Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant

scientific article published on November 15, 1992

Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution

scientific article

Functional partitioning of yeast co-expression networks after genome duplication

scientific article

Gene Duplication and Gene Conversion in the Caenorhabditis elegans Genome

article

Gene duplication, exon gain and neofunctionalization of OEP16-related genes in land plants.

scientific article

Gene order evolution and paleopolyploidy in hemiascomycete yeasts

scientific article

Genome Sequence of Torulaspora microellipsoides CLIB 830T.

scientific article

Genome survey sequencing of the wine spoilage yeast Dekkera (Brettanomyces) bruxellensis

scientific article published on 2 February 2007

GenomeVx: simple web-based creation of editable circular chromosome maps

scientific article published on 28 January 2008

Genomic differences between Candida glabrata and Saccharomyces cerevisiae around the MRPL28 and GCN3 loci

scientific article

Genomic diversity and meiotic recombination among isolates of the biotech yeast Komagataella phaffii (Pichia pastoris)

scientific article published on 04 December 2019

Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus

scientific article

Giant GAL gene clusters for the melibiose-galactose pathway in Torulaspora

scientific article published on 03 November 2020

Identification of a Candida utilis gene encoding ribosomal protein L7: evidence for two divergent subclasses of the eukaryotic ribosomal protein L7 family

scientific article published in July 1993

Identification of functional open reading frames in chloroplast genomes

scientific article published in June 1988

Increased glycolytic flux as an outcome of whole-genome duplication in yeast

scientific article (publication date: 2007)

Increased glycolytic flux as an outcome of whole-genome duplication in yeast.

scientific article

Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication

scientific article

Initial sequencing and analysis of the human genome

scientific article published on 15 February 2001

Ins and outs of plastid genome evolution

scientific article published on December 1991

Lack of a functional plastid tRNA(Cys) gene is associated with loss of photosynthesis in a lineage of parasitic plants

scientific article

Localized hypermutation and associated gene losses in legume chloroplast genomes

scientific article

Loss of lager specific genes and subtelomeric regions define two different Saccharomyces cerevisiae lineages for Saccharomyces pastorianus Group I and II strains

scientific article published on March 2015

Mammalian DNA replication: mutation biases and the mutation rate

scientific article published in April 1991

Mammalian gene evolution: nucleotide sequence divergence between mouse and rat

scientific article

Many Parallel Losses of infA from Chloroplast DNA during Angiosperm Evolution with Multiple Independent Transfers to the Nucleus

scientific article published on 01 March 2001

Mating-type switching by chromosomal inversion in methylotrophic yeasts suggests an origin for the three-locus Saccharomyces cerevisiae system

scientific article

Mechanisms of Chromosome Number Evolution in Yeast

scientific article published on July 21, 2011

Molecular cloning of multiple bovine aspartyl protease genes

scientific article

Molecular evidence for an ancient duplication of the entire yeast genome

scientific article (publication date: 12 June 1997)

Molecular evolution meets the genomics revolution

scientific article

Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species

scientific article (publication date: November 2016)

Multiple Reinventions of Mating-type Switching during Budding Yeast Evolution

scientific article published on 25 July 2019

Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts

scientific article

Mutation rates differ among regions of the mammalian genome

scientific article

Ninety extra nucleotide in ndhF gene of tobacco chloroplast DNA: a summary of revisions to the 1986 genome sequence

scientific article

No rosetta stone for a sense-antisense origin of aminoacyl tRNA synthetase classes

scientific article published on 26 November 2008

Not Born Equal: Increased Rate Asymmetry in Relocated and Retrotransposed Rodent Gene Duplicates

article

Nucleotide Substitution Rates in Legume Chloroplast DNA Depend on the Presence of the Inverted Repeat

article

Origin of Lactose Fermentation in Kluyveromyces lactis by Interspecies Transfer of a Neo-functionalized Gene Cluster during Domestication

scientific article published on 05 December 2019

Origin of the Yeast Whole-Genome Duplication

scientific article

Origins of recently gained introns in Caenorhabditis

scholarly article

Physiological and metabolic diversity in the yeast Kluyveromyces marxianus

scientific article

Plastid translation and transcription genes in a non-photosynthetic plant: intact, missing and pseudo genes

scientific article published on November 1991

Ploidy Variation in Kluyveromyces marxianus Separates Dairy and Non-dairy Isolates

scientific article published on 21 March 2018

Polymorphic centromere locations in the pathogenic yeast Candida parapsilosis

scientific article published on 18 May 2020

Population genomics shows no distinction between pathogenic Candida krusei and environmental Pichia kudriavzevii: One species, four names

scientific article published on 19 July 2018

Positive darwinian selection at the imprinted MEDEA locus in plants

scientific article published in Nature

Positive selection and subfunctionalization of duplicated CCT chaperonin subunits

scientific article published on 27 June 2003

Preferential subfunctionalization of slow-evolving genes after allopolyploidization in Xenopus laevis

scholarly article

Prevalence of small inversions in yeast gene order evolution

scientific article published in December 2000

Probabilistic cross-species inference of orthologous genomic regions created by whole-genome duplication in yeast

scientific article published on 18 June 2008

Proteinases and associated genes of parasitic helminths

scientific article

PubCrawler: keeping up comfortably with PubMed and GenBank

scientific article

RNAi in budding yeast

scientific article

Rapid evolution of the plastid translational apparatus in a nonphotosynthetic plant: loss or accelerated sequence evolution of tRNA and ribosomal protein genes

scientific article

Rate asymmetry after genome duplication causes substantial long-branch attraction artifacts in the phylogeny of Saccharomyces species

scientific article published on 5 October 2005

Rearrangement rate following the whole-genome duplication in teleosts.

scientific article published on 11 January 2007

Recent allopolyploid origin of Zygosaccharomyces rouxii strain ATCC 42981

scientific article published on 01 June 2008

Reciprocal gene loss between Tetraodon and zebrafish after whole genome duplication in their ancestor

article

Reconstruction of phylogenetic trees and estimation of divergence times under nonconstant rates of evolution

scientific article published on 01 January 1987

Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae

scientific article published on September 2000

Rewiring the transcriptional regulatory circuits of cells

scientific article

SMBE proposal to the government of Japan

scientific article published in 2012

SMURF: Genomic mapping of fungal secondary metabolite clusters

scientific article published on 8 June 2010

SearchDOGS bacteria, software that provides automated identification of potentially missed genes in annotated bacterial genomes

scientific article

Sequence and analysis of the genome of the pathogenic yeast Candida orthopsilosis

scientific article

Sequence around the centromere of Saccharomyces cerevisiae chromosome II: similarity of CEN2 to CEN4.

scientific article published on April 1994

Sequence of 29 kb around the PDR10 locus on the right arm of Saccharomyces cerevisiae chromosome XV: similarity to part of chromosome I.

scientific article published on September 1996

Significance of positive selection and gene duplication in adaptive evolution: in memory of Austin L. Hughes

scientific article

Similarity between putative ATP-binding sites in land plant plastid ORF2280 proteins and the FtsH/CDC48 family of ATPases

scientific article published in April 1994

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

scientific article published on January 1992

Snf2 controls pulcherriminic acid biosynthesis and antifungal activity of the biocontrol yeast Metschnikowia pulcherrima

scientific article published on 20 May 2019

Structure and evolution of the largest chloroplast gene (ORF2280): internal plasticity and multiple gene loss during angiosperm evolution

scientific article published in April 1994

Systematic discovery of unannotated genes in 11 yeast species using a database of orthologous genomic segments

scientific article

TPP riboswitch-dependent regulation of an ancient thiamin transporter in Candida.

scientific article published on 31 May 2018

The 2R hypothesis and the human genome sequence

scientific article

The CYPome of the model xenobiotic-biotransforming fungus Cunninghamella elegans

scientific article published on 25 June 2019

The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis

scientific article published on 30 October 2015

The Methylotroph Gene Order Browser (MGOB) reveals conserved synteny and ancestral centromere locations in the yeast family Pichiaceae

scientific article published on 01 September 2019

The gene duplication that greased society's wheels

scientific article published in June 2005

The reported point centromeres of Scheffersomyces stipitis are retrotransposon long terminal repeats

scientific article published on 29 January 2019

The site of deletion of the inverted repeat in pea chloroplast DNA contains duplicated gene fragments

scientific article published on January 1, 1988

The yeast mating-type switching endonuclease HO is a domesticated member of an unorthodox homing genetic element family

scientific article published on 27 April 2020

Transcription, splicing and editing of plastid RNAs in the nonphotosynthetic plant Epifagus virginiana

scientific article published in November 1995

Transcriptional response to lactic acid stress in the hybrid yeast Zygosaccharomyces parabailii.

scientific article published on 21 December 2017

Turning a hobby into a job: how duplicated genes find new functions

scientific article (publication date: December 2008)

Updated map of duplicated regions in the yeast genome

scientific article published on 01 September 1999

Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser

scientific article

When gene marriages don't work out: divorce by subfunctionalization

scientific article published on 5 April 2007

Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes

scientific article

Wrapping up BLAST and other applications for use on Unix clusters

scientific article published on 01 February 2003

Yeast genome evolution in the post-genome era.

scientific article

Yeast genome evolution--the origin of the species

scientific article published on November 2007

Yeast homologue of mammalian Ran binding protein 1.

scientific article published in November 1994

Zinc finger transcription factors displaced SREBP proteins as the major Sterol regulators during Saccharomycotina evolution

scientific article (publication date: 2014)

Zygosaccharomyces pseudobailii, another yeast interspecies hybrid that regained fertility by damaging one of its MAT loci

article by Stephanie Braun-Galleani et al published 1 November 2018 in FEMS Yeast Research