A catalog of neutral and deleterious polymorphism in yeast (Q21563326)

19 August 2022

Scott W Doniger

1

Scott W

Doniger

1 reference

19 August 2022

Hyun Seok Kim

2

Hyun Seok

Kim

1 reference

19 August 2022

Devjanee Swain

3

Devjanee

Swain

1 reference

19 August 2022

Daniella Corcuera

4

Daniella

Corcuera

1 reference

19 August 2022

Morgan Williams

5

Morgan

Williams

1 reference

19 August 2022

Shiaw-Pyng Yang

6

Shiaw-Pyng

Yang

1 reference

Creative Commons Attribution 4.0 International

19 August 2022

language of work or name

English

0 references

publication date

August 2008

0 references

published in

PLOS Genetics

0 references

volume

4

0 references

issue

8

0 references

page(s)

e1000183

0 references

copyright license

start time

29 August 2008

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

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MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model

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Duplicated genes evolve slower than singletons despite the initial rate increase

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Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae

19 March 2017

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The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics

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Predicting deleterious amino acid substitutions

19 March 2017

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Genetic and physical maps of Saccharomyces cerevisiae

19 March 2017

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Evolution of genes and genomes on the Drosophila phylogeny

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Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

19 March 2017

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Initial sequence of the chimpanzee genome and comparison with the human genome

19 March 2017

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Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting

19 March 2017

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Sequencing and comparison of yeast species to identify genes and regulatory elements

19 March 2017

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Initial sequencing and comparative analysis of the mouse genome

19 March 2017

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Base-calling of automated sequencer traces using phred. II. Error probabilities

19 March 2017

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Transcriptional regulatory code of a eukaryotic genome

19 March 2017

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Sum1 and Ndt80 proteins compete for binding to middle sporulation element sequences that control meiotic gene expression

19 March 2017

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Aquaporin expression correlates with freeze tolerance in baker's yeast, and overexpression improves freeze tolerance in industrial strains

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Differential expression of two genes encoding isoforms of the ATPase involved in sodium efflux in Saccharomyces cerevisiae

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Predicting the effects of amino acid substitutions on protein function

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Slightly Deleterious Mutant Substitutions in Evolution

19 March 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Adaptive protein evolution at the Adh locus in Drosophila

19 March 2017

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HyPhy: hypothesis testing using phylogenies

19 March 2017

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Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level

24 March 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Distribution and intensity of constraint in mammalian genomic sequence

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Prediction of deleterious human alleles

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Identifying DNA and protein patterns with statistically significant alignments of multiple sequences

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Selection on amino acid substitutions in Arabidopsis

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Analysis of sequence conservation at nucleotide resolution

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Genetic variation in the cysteine biosynthesis pathway causes sensitivity to pharmacological compounds

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Accelerated rate of gene gain and loss in primates

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Mutational and selective effects on copy-number variants in the human genome

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Frequent gain and loss of functional transcription factor binding sites

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Evaluating the role of natural selection in the evolution of gene regulation.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Reduced variation in the yellow-achaete-scute region in natural populations of Drosophila melanogaster.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Frequencies of null alleles at enzyme Loci in natural populations of ponderosa and red pine.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Four linked genes participate in controlling sporulation efficiency in budding yeast

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Sequence diversity, reproductive isolation and species concepts in Saccharomyces

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Adaptive evolution by mutations in the FLO11 gene

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Variation within and among species in gene expression: raw material for evolution

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Enzyme null alleles in natural populations of Drosophila melanogaster: Frequencies in a North Carolina population

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

AN ESTIMATE OF THE MUTATIONAL DAMAGE IN MAN FROM DATA ON CONSANGUINEOUS MARRIAGES

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

An improved map of conserved regulatory sites for Saccharomyces cerevisiae

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Identifying the conserved network of cis-regulatory sites of a eukaryotic genome

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Copy correction and concerted evolution in the conservation of yeast genes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Genome-wide regulatory complexity in yeast promoters: separation of functionally conserved and neutral sequence

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Molecular characterization of a chromosomal rearrangement involved in the adaptive evolution of yeast strains.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Testing the neutral theory of molecular evolution with genomic data from Drosophila.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Adaptive protein evolution in Drosophila

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

The neutral theory in the genomic era.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Positive and negative selection on the human genome

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

DNA polymorphism in lycopersicon and crossing-over per physical length

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

DNA variability and recombination rates at X-linked loci in humans

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Patterns of DNA variability at X-linked loci in Mus domesticus

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Comparing mutational variabilities.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

How much do we know about spontaneous human mutation rates?

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Frequency of enzyme deficiency variants in erythrocytes of newborn infants

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Tandem gene amplification mediates copper resistance in yeast

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Genealogy of principal strains of the yeast genetic stock center

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Molecular genetic variation in the centromeric region of the X chromosome in three Drosophila ananassae populations. I. Contrasts between the vermilion and forked loci

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

The subtelomeric Y' repeat family in Saccharomyces cerevisiae: an experimental system for repeated sequence evolution.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Lack of polymorphism on the Drosophila fourth chromosome resulting from selection

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Homing of a DNA endonuclease gene by meiotic gene conversion in Saccharomyces cerevisiae

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Statistical analyses of Drosophila and human protein polymorphisms

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Noncoding sequences conserved in a limited number of mammals in the SIM2 interval are frequently functional

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

PCAP: a whole-genome assembly program

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Accounting for human polymorphisms predicted to affect protein function

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: structure-based assessment of amino acid variation

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Mutations affecting fitness in Drosophila populations

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Intragenic tandem repeats generate functional variability

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Identification of functional transcription factor binding sites using closely related Saccharomyces species

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Genetic diversity in yeast assessed with whole-genome oligonucleotide arrays

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Species and recombination effects on DNA variability in the tomato genus.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515631

Adaptive evolution of non-coding DNA in Drosophila

30 May 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000183

The cost of inbreeding in Arabidopsis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000183

Inference of positive and negative selection on the 5' regulatory regions of Drosophila genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000183

The Nearly Neutral Theory of Molecular Evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000183

Inbreeding Depression and its Evolutionary Consequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000183

Quantitative trait loci mapped to single-nucleotide resolution in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000183

Hypervariable noncoding sequences in Saccharomyces cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000183

A widespread transposable element masks expression of a yeast copper transport gene.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000183

Polymorphism of Saccharomyces cerevisiae aquaporins

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000183

Genetic events associated with an insertion mutation in yeast

21 January 2018

1 reference

12 December 2020

A method for detecting positive selection at single amino acid sites

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12 December 2020

A 'natural' mutation in Saccharomyces cerevisiae strains derived from S288c affects the complex regulatory gene HAP1 (CYP1)

1 reference

12 December 2020

Analysis and manipulation of yeast mitochondrial genes

1 reference

12 December 2020

Very low gene duplication rate in the yeast genome

1 reference

12 December 2020

10.1371/JOURNAL.PGEN.1000183

Identifiers

DOI

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1 reference

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