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evolution (8) 8
genetics & heredity (8) 8
index medicus (8) 8
mutation (8) 8
saccharomyces cerevisiae - genetics (8) 8
evolution & development (7) 7
research (6) 6
yeast (6) 6
adaptation (5) 5
chemistry (5) 5
genetics (5) 5
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microbiology (5) 5
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population (5) 5
wine (5) 5
cloning (4) 4
environment (4) 4
evolution, molecular (4) 4
experiments (4) 4
genetic fitness (4) 4
genome, fungal (4) 4
genomics (4) 4
information and communication technology [ict] specially adaptedfor specific application fields (4) 4
saccharomyces-cerevisiae (4) 4
selection, genetic (4) 4
studies (4) 4
analysis (3) 3
beer (3) 3
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condition-responsive control in microbiological orenzymological processes (3) 3
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genes (3) 3
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materials science, multidisciplinary (3) 3
measuring or testing processes involving enzymes, nucleicacids or microorganisms (3) 3
metallurgy (3) 3
mutation or genetic engineering (3) 3
processes of preparing such compositions (3) 3
research article (3) 3
saccharomyces cerevisiae proteins - genetics (3) 3
spirits (3) 3
vinegar (3) 3
adaptation, biological (2) 2
adaptation, physiological - genetics (2) 2
adaptive evolution (2) 2
adaptor proteins, signal transducing - genetics (2) 2
adaptor proteins, signal transducing - metabolism (2) 2
article (2) 2
beneficial mutations (2) 2
biotechnology & applied microbiology (2) 2
confidence intervals (2) 2
directed molecular evolution (2) 2
ecology (2) 2
epistasis (2) 2
epistasis, genetic (2) 2
evolutionary biology (2) 2
gene (2) 2
gene dosage (2) 2
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glucose (2) 2
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nanopartikel (2) 2
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ratios (2) 2
saccharomyces cerevisiae - growth & development (2) 2
saccharomyces cerevisiae - metabolism (2) 2
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wineries & vineyards (2) 2
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1. Full Text Whole Genome, Whole Population Sequencing Reveals That Loss of Signaling Networks Is the Major Adaptive Strategy in a Constant Environment
by Kvitek, Daniel J and Sherlock, Gavin
PLoS Genetics, ISSN 1553-7390, 11/2013, Volume 9, Issue 11, p. e1003972
Molecular signaling networks are ubiquitous across life and likely evolved to allow organisms to sense and respond to environmental change in dynamic... 
YEAST SACCHAROMYCES-CEREVISIAE | ASEXUAL POPULATIONS | CLONAL INTERFERENCE | BENEFICIAL MUTATIONS | EXPERIMENTAL EVOLUTION | GLUCOSE | ADAPTATION | GENETICS & HEREDITY | LONG-TERM EXPERIMENT | CELL-GROWTH | ESCHERICHIA-COLI POPULATIONS | Genetic Fitness | Genome, Fungal | Adaptation, Physiological - genetics | Saccharomyces cerevisiae - genetics | Selection, Genetic | Environment | Signal Transduction - genetics | Mutation | Saccharomyces cerevisiae - growth & development | Evolution, Molecular | Cellular signal transduction | Research | Nucleotide sequencing | Population genetics | DNA sequencing | Studies | Genes | Cloning | Population | Genomes | Experiments | Evolution & development
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2. Full Text Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape
by Kvitek, Daniel J and Sherlock, Gavin
PLoS Genetics, ISSN 1553-7390, 04/2011, Volume 7, Issue 4, p. e1002056
The fitness landscape captures the relationship between genotype and evolutionary fitness and is a pervasive metaphor used to describe the possible... 
YEAST | GENE INTERACTIONS | POPULATION | PERSPECTIVE | SPECIATION | ESCHERICHIA-COLI | ADAPTATION | SEX | GENETICS & HEREDITY | EVOLUTIONARY PATHS | SACCHAROMYCES-CEREVISIAE | Saccharomyces cerevisiae - genetics | Gene Frequency | Selection, Genetic | Adaptation, Biological | Saccharomyces cerevisiae Proteins - genetics | Sequence Analysis, DNA | Genetic Fitness | Genome, Fungal | Epistasis, Genetic | Adaptor Proteins, Signal Transducing - genetics | Saccharomyces cerevisiae Proteins - metabolism | Adaptor Proteins, Signal Transducing - metabolism | Monosaccharide Transport Proteins - metabolism | Codon, Nonsense - genetics | Evolution, Molecular | Monosaccharide Transport Proteins - genetics | Evolution | Genetic aspects | Research | Gene mutations | Brewer's yeast | Confidence intervals | Genotype & phenotype | Cloning | Genetics | Population | Genomes | Mutation | Experiments | Evolution & development
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3. Full Text Heterozygote Advantage Is a Common Outcome of Adaptation inSaccharomyces cerevisiae
by Sellis, Diamantis and Kvitek, Daniel J and Dunn, Barbara and Sherlock, Gavin and Petrov, Dmitri A
Genetics, ISSN 0016-6731, 07/2016, Volume 203, Issue 3, pp. 1401 - 1413
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4. Full Text Whole Genome, Whole Population Sequencing Reveals That Loss of Signaling Networks Is the Major Adaptive Strategy in a Constant Environment
: e1003972
by Daniel J Kvitek and Gavin Sherlock
PLoS Genetics, ISSN 1553-7390, 11/2013, Volume 9, Issue 11
  Molecular signaling networks are ubiquitous across life and likely evolved to allow organisms to sense and respond to environmental change in dynamic... 
Studies | Genes | Cloning | Population | Genomes | Mutation | Experiments | Evolution & development | Cyclic AMP
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5. Full Text Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments
by Dunn, Barbara and Richter, Chandra and Kvitek, Daniel J and Pugh, Tom and Sherlock, Gavin
Genome Research, ISSN 1088-9051, 05/2012, Volume 22, Issue 5, pp. 908 - 924
Although the budding yeast Saccharomyces cerevisiae is arguably one of the most well-studied organisms on earth, the genome-wide variation within this... 
MOLECULAR CHARACTERIZATION | WINE | POPULATION | INTERSPECIES HYBRIDIZATION | MICROARRAY | BIOCHEMISTRY & MOLECULAR BIOLOGY | REARRANGEMENTS | INTROGRESSION | GENETIC DIVERSITY | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | SEQUENCE | GENETICS & HEREDITY | ADAPTIVE EVOLUTION | Saccharomyces cerevisiae - genetics | Chromosome Mapping | Sequence Analysis, DNA | DNA Copy Number Variations | Genetic Variation | Comparative Genomic Hybridization | Genome, Fungal | Hybridization, Genetic | Recombination, Genetic | DNA Transposable Elements - genetics | Plasmids - genetics | Genome, Mitochondrial | Principal Component Analysis | Cluster Analysis | Telomere - genetics | Yeast fungi | Genomes | Mitochondrial diseases | Genetic aspects | Research | Genetic regulation | Brewer's yeast | Health aspects
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6. Full Text Variations in stress sensitivity and genomic expression in diverse S. cerevisiae isolates
by Kvitek, Daniel J and Will, Jessica L and Gasch, Audrey P
PLoS Genetics, ISSN 1553-7390, 10/2008, Volume 4, Issue 10, p. e1000223
Interactions between an organism and its environment can significantly influence phenotypic evolution. A first step toward understanding this process is to... 
STRAINS | POPULATION GENETIC-VARIATION | WINE | ANEUPLOIDY | EVOLUTION | BUDDING YEAST | GENETICS & HEREDITY | QUANTITATIVE TRAIT LOCUS | COPPER RESISTANCE | MICROARRAYS | SACCHAROMYCES-CEREVISIAE | Genetic Variation | Gene Expression | Phenotype | Saccharomyces cerevisiae - physiology | Genome, Fungal | Saccharomyces cerevisiae - genetics | Ecosystem | Environment | Gene Dosage | Phylogeny | Saccharomyces cerevisiae - isolation & purification | Studies | Ratios | Yeast | Microbiology | Genomics | Biology | Standard deviation | Hybridization | Gene expression | Wineries & vineyards | Evolution & development
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7. Full Text Reciprocal Sign Epistasis between Frequently Experimentally Evolved Adaptive Mutations Causes a Rugged Fitness Landscape
: e1002056
by Daniel J Kvitek and Gavin Sherlock
PLoS Genetics, ISSN 1553-7390, 04/2011, Volume 7, Issue 4
  The fitness landscape captures the relationship between genotype and evolutionary fitness and is a pervasive metaphor used to describe the possible... 
Confidence intervals | Genotype & phenotype | Cloning | Genetics | Evolution | Population | Genomes | Mutation | Experiments | Evolution & development
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8. PHENOTYPIC AND GENOTYPIC CONVERGENCES ARE INFLUENCED BY HISTORICAL CONTINGENCY AND ENVIRONMENT IN YEAST
by Spor, Ayme and Kvitek, Daniel J and Nidelet, Thibault and Martin, Juliette and Legrand, Judith and Dillmann, Christine and Bourgais, Aurelie and de Vienne, Dominique and Sherlock, Gavin and Sicard, Delphine
Evolution, ISSN 0014-3820, 03/2014, Volume 38, Issue 3, pp. 772 - 772
Different organisms have independently and recurrently evolved similar phenotypic traits at different points throughout history. This phenotypic convergence... 
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9. Full Text PHENOTYPIC AND GENOTYPIC CONVERGENCES ARE INFLUENCED BY HISTORICAL CONTINGENCY AND ENVIRONMENT IN YEAST
: MULTIPLE LIFE-HISTORY TRAITS CONVERGENCE IN YEAST
by Spor, Aymé and Kvitek, Daniel J and Nidelet, Thibault and Martin, Juliette and Legrand, Judith and Dillmann, Christine and Bourgais, Aurélie and de Vienne, Dominique and Sherlock, Gavin and Sicard, Delphine
Evolution, ISSN 0014-3820, 03/2014, Volume 68, Issue 3, pp. 772 - 790
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10. Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments
by Dunn, Barbara and Richter, Chandra and Kvitek, Daniel J and Pugh, Tom and Sherlock, Gavin
Genome Research, ISSN 1088-9051, 01/2012, Volume 22, Issue 5, pp. 908 - 924
Although the budding yeast Saccharomyces cerevisiae is arguably one of the most well-studied organisms on earth, the genome-wide variation within this... 
Journal Article
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11. Full Text Heterozygote advantage is a common outcome of adaptation in Saccharomyces cerevisiae
by Sellis, Diamantis and Kvitek, Daniel J and Dunn, Barbara and Sherlock, Gavin and Petrov, Dmitri A
Genetics, ISSN 0016-6731, 07/2016, Volume 203, Issue 3, pp. 1401 - 1413
Adaptation in diploids is predicted to proceed via mutations that are at least partially dominant in fitness. Recently, we argued that many adaptive mutations... 
Diploid | Experimental evolution | Heterozygote advantage | Adaptation | experimental evolution | HAPLOIDY | adaptation | POPULATIONS | DRUG-RESISTANCE | GENOME | MATHEMATICAL-THEORY | diploid | ARTIFICIAL SELECTION | EVOLUTION | GENE | GENETICS & HEREDITY | heterozygote advantage | COPY NUMBER VARIATION | EXPRESSION | Haploidy | Genetic Fitness | Adaptation, Physiological - genetics | Saccharomyces cerevisiae - genetics | Heterozygote | DNA Copy Number Variations - genetics | Directed Molecular Evolution | Mutation | Saccharomyces cerevisiae - growth & development | Selection, Genetic - genetics | Genetic aspects | Heterozygosis | Research | Adaptation (Biology) | Brewer's yeast | Heterozygosity | Proteins | Enzymes | Genotype & phenotype | Laboratories | Genes | Evolution & development | Life Sciences | Investigations
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12. Full Text PHENOTYPIC AND GENOTYPIC CONVERGENCES ARE INFLUENCED BY HISTORICAL CONTINGENCY AND ENVIRONMENT IN YEAST
by Aymé Spor and Daniel J. Kvitek and Thibault Nidelet and Juliette Martin and Judith Legrand and Christine Dillmann and Aurélie Bourgais and Dominique de Vienne and Gavin Sherlock and Delphine Sicard
Evolution, ISSN 0014-3820, 3/2014, Volume 68, Issue 3, pp. 772 - 790
Different organisms have independently and recurrently evolved similar phenotypic traits at different points throughout history. This phenotypic convergence... 
Yeasts | Phenotypes | Ecological life histories | Population characteristics | Evolution | Evolutionary genetics | Nonsense | Convergent evolution | Genetic mutation | Phenotypic traits | 14‐3‐3 protein | experimental evolution | pleiotropy | life‐history evolution | Adaptive landscape | 14-3-3 protein | Pleiotropy | Experimental evolution | Life-history evolution | PARALLEL EVOLUTION | PATHWAYS | CLONAL INTERFERENCE | MOLECULAR EVOLUTION | SACCHAROMYCES | POPULATIONS | STRATEGIES | EVOLUTIONARY BIOLOGY | life-history evolution | ADAPTATION | GENETICS & HEREDITY | GENE-EXPRESSION | ECOLOGY | ADAPTIVE EVOLUTION | Saccharomyces cerevisiae - metabolism | Saccharomyces cerevisiae - genetics | Selection, Genetic | Environment | Genotype | Mutation | Saccharomyces cerevisiae Proteins - genetics | Gene-Environment Interaction | 14-3-3 Proteins - genetics | Evolution, Molecular | Research | Adaptation (Biology) | adaptive landscape | BMH1 | Saccharomyces cerevisiae
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13. Full Text Variations in Stress Sensitivity and Genomic Expression in Diverse S. cerevisiae Isolates
: e1000223
by Daniel J Kvitek and Jessica L Will and Audrey P Gasch
PLoS Genetics, ISSN 1553-7390, 10/2008, Volume 4, Issue 10
  Interactions between an organism and its environment can significantly influence phenotypic evolution. A first step toward understanding this process is to... 
Studies | Ratios | Yeast | Microbiology | Genomics | Biology | Standard deviation | Hybridization | Gene expression | Wineries & vineyards | Evolution & development
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14. Full Text The Valley-of-Death: Reciprocal sign epistasis constrains adaptive trajectories in a constant, nutrient limiting environment
by Chiotti, Kami E and Kvitek, Daniel J and Schmidt, Karen H and Koniges, Gregory and Schwartz, Katja and Donckels, Elizabeth A and Rosenzweig, Frank and Sherlock, Gavin
Genomics, ISSN 0888-7543, 12/2014, Volume 104, Issue 6, pp. 431 - 437
The fitness landscape is a powerful metaphor for describing the relationship between genotype and phenotype for a population under selection. However,... 
Evolution | Epistasis | Yeast | Genomics | EMPIRICAL FITNESS LANDSCAPES | PROTEIN | CLONAL INTERFERENCE | BENEFICIAL MUTATIONS | SACCHAROMYCES-CEREVISIAE | GENE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | ADAPTATION | GENETICS & HEREDITY | DNA-SEQUENCING DATA | Saccharomyces cerevisiae - genetics | Selection, Genetic | Adaptation, Biological | Directed Molecular Evolution | Gene Dosage | Saccharomyces cerevisiae Proteins - genetics | Saccharomyces cerevisiae - metabolism | Genetic Fitness | Epistasis, Genetic | Adaptor Proteins, Signal Transducing - genetics | Glucose - chemistry | Saccharomyces cerevisiae Proteins - metabolism | Glucose - metabolism | Mutation | Adaptor Proteins, Signal Transducing - metabolism | Culture Media - chemistry | Evolution, Molecular | Glucose metabolism | Dextrose | Glucose | genomics | epistasis | yeast
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15. PHENOTYPIC AND GENOTYPIC CONVERGENCES ARE INFLUENCED BY HISTORICAL CONTINGENCY AND ENVIRONMENT IN YEAST
by Aymé Spor and Daniel J Kvitek and Thibault Nidelet and Juliette Martin and Judith Legrand and Christine Dillmann and Aurélie Bourgais and Dominique de Vienne and Gavin Sherlock and Delphine Sicard
Evolution, ISSN 0014-3820, 03/2014, Volume 68, Issue 3, p. 772
  Different organisms have independently and recurrently evolved similar phenotypic traits at different points throughout history. This phenotypic convergence... 
Genotype & phenotype | Yeast | Evolution | Organisms | Animal populations | Mutation | Convergence
Journal Article
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16. Full Text Transient Genotype-by-Environment Interactions Following Environmental Shock Provide a Source of Expression Variation for Essential Genes
by Eng, Kevin H and Kvitek, Daniel J and Keles, Sunduz and Gasch, Audrey P
Genetics, ISSN 0016-6731, 02/2010, Volume 184, Issue 2, pp. 587 - 593
Understanding complex genotype-by-environment interactions (GEIs) is crucial for understanding phenotypic variation. An important factor often overlooked in... 
YEAST | EVOLVABILITY | GENOMIC EXPRESSION | EVOLUTION | CANALIZATION | NATURAL-SELECTION | GENETICS & HEREDITY | CONSEQUENCES | MICROARRAYS | SACCHAROMYCES-CEREVISIAE | PLASTICITY | Phenotype | Saccharomyces cerevisiae - physiology | Time Factors | Saccharomyces cerevisiae - genetics | Environment | Genotype | Gene Expression Regulation, Fungal - genetics | Genes, Essential - genetics | Heat-Shock Response - genetics | Cell culture | Research | Gene expression | Genetic regulation | Analysis | Protein-protein interactions | Genotype & phenotype | Genetics | Investigations
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17. Methods, systems and processes of identifying genetic variation in highly similar genes
by Gafni, Erik and Kvitek, Daniel J
08/2019
Provided herein are novel methods, systems and processes for mapping sequence reads to a modified reference genome and determining the presence or absence of a... 
TESTING | INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIRCHEMICAL OR PHYSICAL PROPERTIES | MEASURING | PHYSICS | INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTEDFOR SPECIFIC APPLICATION FIELDS
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18. METHODS, SYSTEMS AND PROCESSES OF IDENTIFYING GENETIC VARIATION IN HIGHLY SIMILAR GENES
by KVITEK, Daniel, J and GAFNI, Erik
12/2018
Provided herein are novel methods, systems and processes for mapping sequence reads to a modified reference genome and determining the presence or absence of a... 
WINE | MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEICACIDS OR MICROORGANISMS | ENZYMOLOGY | COMPOSITIONS OR TEST PAPERS THEREFOR | MICROBIOLOGY | COMPUTING | COUNTING | INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTEDFOR SPECIFIC APPLICATION FIELDS | BEER | MUTATION OR GENETIC ENGINEERING | SPIRITS | METALLURGY | PROCESSES OF PREPARING SUCH COMPOSITIONS | BIOCHEMISTRY | CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL ORENZYMOLOGICAL PROCESSES | CHEMISTRY | PHYSICS | VINEGAR | ELECTRIC DIGITAL DATA PROCESSING | CALCULATING
Patent
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19. METHODS, SYSTEMS AND PROCESSES OF IDENTIFYING GENETIC VARIATION IN HIGHLY SIMILAR GENES
by KVITEK, Daniel, J and GAFNI, Erik
02/2018
Provided herein are novel methods, systems and processes for mapping sequence reads to a modified reference genome and determining the presence or absence of a... 
WINE | MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEICACIDS OR MICROORGANISMS | ENZYMOLOGY | COMPOSITIONS OR TEST PAPERS THEREFOR | MICROBIOLOGY | COMPUTING | COUNTING | INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTEDFOR SPECIFIC APPLICATION FIELDS | BEER | MUTATION OR GENETIC ENGINEERING | SPIRITS | METALLURGY | PROCESSES OF PREPARING SUCH COMPOSITIONS | BIOCHEMISTRY | CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL ORENZYMOLOGICAL PROCESSES | CHEMISTRY | PHYSICS | VINEGAR | ELECTRIC DIGITAL DATA PROCESSING | CALCULATING
Patent
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20. METHODS, SYSTEMS AND PROCESSES OF IDENTIFYING GENETIC VARIATION IN HIGHLY SIMILAR GENES
by GAFNI, ERIK and KVITEK, DANIEL J
10/2016
Provided herein are novel methods, systems, and processes for mapping sequence reads to a modified reference genome and determining the presence or absence of... 
WINE | MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEICACIDS OR MICROORGANISMS | ENZYMOLOGY | COMPOSITIONS OR TEST PAPERS THEREFOR | MICROBIOLOGY | COMPUTING | COUNTING | INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTEDFOR SPECIFIC APPLICATION FIELDS | BEER | MUTATION OR GENETIC ENGINEERING | SPIRITS | METALLURGY | PROCESSES OF PREPARING SUCH COMPOSITIONS | BIOCHEMISTRY | CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL ORENZYMOLOGICAL PROCESSES | CHEMISTRY | PHYSICS | VINEGAR | ELECTRIC DIGITAL DATA PROCESSING | CALCULATING
Patent
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