Alexander Platt
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View article: Apollo: A comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell
Apollo: A comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell Open
Modern sequencing instruments bring unprecedented opportunity to study within-host viral evolution in conjunction with viral transmissions between hosts. However, no computational simulators are available to assist the characterization of …
View article: Reviewer #2 (Public Review): Analyses of allele age and fitness impact reveal human beneficial alleles to be older than neutral controls
Reviewer #2 (Public Review): Analyses of allele age and fitness impact reveal human beneficial alleles to be older than neutral controls Open
A classic population genetic prediction is that alleles experiencing directional selection should swiftly traverse allele frequency space, leaving detectable reductions in genetic variation in linked regions. However, despite this expectat…
View article: Reviewer #1 (Public Review): Analyses of allele age and fitness impact reveal human beneficial alleles to be older than neutral controls
Reviewer #1 (Public Review): Analyses of allele age and fitness impact reveal human beneficial alleles to be older than neutral controls Open
A classic population genetic prediction is that alleles experiencing directional selection should swiftly traverse allele frequency space, leaving detectable reductions in genetic variation in linked regions. However, despite this expectat…
View article: Analyses of allele age and fitness impact reveal human beneficial alleles to be older than neutral controls
Analyses of allele age and fitness impact reveal human beneficial alleles to be older than neutral controls Open
A classic population genetic prediction is that alleles experiencing directional selection should swiftly traverse allele frequency space, leaving detectable reductions in genetic variation in linked regions. However, despite this expectat…
View article: Reviewer #3 (Public Review): Analyses of allele age and fitness impact reveal human beneficial alleles to be older than neutral controls
Reviewer #3 (Public Review): Analyses of allele age and fitness impact reveal human beneficial alleles to be older than neutral controls Open
A classic population genetic prediction is that alleles experiencing directional selection should swiftly traverse allele frequency space, leaving detectable reductions in genetic variation in linked regions. However, despite this expectat…
View article: Analyses of allele age and fitness impact reveal human beneficial alleles to be older than neutral controls
Analyses of allele age and fitness impact reveal human beneficial alleles to be older than neutral controls Open
A classic population genetic prediction is that alleles experiencing directional selection should swiftly traverse allele frequency space, leaving detectable reductions in genetic variation in linked regions. However, despite this expectat…
View article: cLD: Rare-variant linkage disequilibrium between genomic regions identifies novel genomic interactions
cLD: Rare-variant linkage disequilibrium between genomic regions identifies novel genomic interactions Open
Linkage disequilibrium (LD) is a fundamental concept in genetics; critical for studying genetic associations and molecular evolution. However, LD measurements are only reliable for common genetic variants, leaving low-frequency variants un…
View article: Analyses of allele age and fitness impact reveal human beneficial alleles to be older than neutral controls
Analyses of allele age and fitness impact reveal human beneficial alleles to be older than neutral controls Open
A classic population genetic prediction is that alleles experiencing directional selection should swiftly traverse allele frequency space, leaving detectable reductions in genetic variation in linked regions. However, despite this expectat…
View article: Genetic architecture and evolution of color variation in American black bears
Genetic architecture and evolution of color variation in American black bears Open
SUMMARY Color variation is a frequent evolutionary substrate for camouflage in small mammals but the underlying genetics and evolutionary forces that drive color variation in natural populations of large mammals are mostly unexplained. The…
View article: cLD: Rare-variant disequilibrium between genomic regions identifies novel genomic interactions
cLD: Rare-variant disequilibrium between genomic regions identifies novel genomic interactions Open
Linkage disequilibrium (LD) is a fundamental concept in genetics; critical for studying genetic associations and molecular evolution. However, LD measurements are only reliable for common genetic variants, leaving low-frequency variants un…
View article: EIA volume 36 issue 2 Cover and Front matter
EIA volume 36 issue 2 Cover and Front matter Open
An abstract is not available for this content so a preview has been provided. As you have access to this content, a full PDF is available via the ‘Save PDF’ action button.
View article: EIA volume 36 issue 3 Cover and Front matter
EIA volume 36 issue 3 Cover and Front matter Open
An abstract is not available for this content so a preview has been provided. As you have access to this content, a full PDF is available via the ‘Save PDF’ action button.
View article: EIA volume 36 issue 1 Cover and Front matter
EIA volume 36 issue 1 Cover and Front matter Open
An abstract is not available for this content so a preview has been provided. As you have access to this content, a full PDF is available via the ‘Save PDF’ action button.
View article: EIA volume 36 issue 4 Cover and Front matter
EIA volume 36 issue 4 Cover and Front matter Open
An abstract is not available for this content so a preview has been provided. As you have access to this content, a full PDF is available via the ‘Save PDF’ action button.
View article: EIA volume 35 issue 4 Cover and Front matter
EIA volume 35 issue 4 Cover and Front matter Open
An abstract is not available for this content so a preview has been provided. As you have access to this content, a full PDF is available via the ‘Save PDF’ action button.
View article: Phantom histories of misspecified pasts
Phantom histories of misspecified pasts Open
A bstract The observation that even a tiny sample of genome sequences from a natural population contains a plethora of information about the history of the population has enticed researchers to use these data to fit complex demographic his…
View article: EIA volume 34 issue 3 Cover and Front matter
EIA volume 34 issue 3 Cover and Front matter Open
An abstract is not available for this content so a preview has been provided. As you have access to this content, a full PDF is available via the ‘Save PDF’ action button.
View article: An estimator of first coalescent time reveals selection on young variants and large heterogeneity in rare allele ages among human populations
An estimator of first coalescent time reveals selection on young variants and large heterogeneity in rare allele ages among human populations Open
Allele age has long been a focus of population genetic research, primarily because it can be an important clue to the fitness effects of an allele. By virtue of their effects on fitness, alleles under directional selection are expected to …
View article: OCMA: Fast, Memory-Efficient Factorization of Prohibitively Large Relationship Matrices
OCMA: Fast, Memory-Efficient Factorization of Prohibitively Large Relationship Matrices Open
Matrices representing genetic relatedness among individuals (i.e., Genomic Relationship Matrices, GRMs) play a central role in genetic analysis. The eigen-decomposition of GRMs (or its alternative that generates fewer top singular values u…
View article: Adaptive Landscape of Protein Variation in Human Exomes
Adaptive Landscape of Protein Variation in Human Exomes Open
The human genome contains hundreds of thousands of missense mutations. However, only a handful of these variants are known to be adaptive, which implies that adaptation through protein sequence change is an extremely rare phenomenon in hum…
View article: Adaptive landscape of protein variation in human exomes
Adaptive landscape of protein variation in human exomes Open
The human genome contains hundreds of thousands of missense mutations. However, only a handful of these variants are known to be adaptive, which implies that adaptation through protein sequence change is an extremely rare phenomenon in hum…
View article: Age distributions of rare lineages reveal recent demographic history and selection
Age distributions of rare lineages reveal recent demographic history and selection Open
The age of an allele of a given frequency offers insight into both its function and origin, and the distribution of ages of alleles in a population conveys significant information about its history. The rarer the allele the more likely it …
View article: Protein evolution depends on multiple distinct population size parameters
Protein evolution depends on multiple distinct population size parameters Open
That population size affects the fate of new mutations arising in genomes, modulating both how frequently they arise and how efficiently natural selection is able to filter them, is well established. It is therefore clear that these distin…
View article: EIA volume 32 issue 4 Cover and Front matter
EIA volume 32 issue 4 Cover and Front matter Open
An abstract is not available for this content so a preview has been provided. As you have access to this content, a full PDF is available via the ‘Save PDF’ action button.