Mammalian evolution of human cis-regulatory elements and transcription factor binding sites
Understanding the regulatory landscape of the human genome is a long-standing objective
of modern biology. Using the reference-free alignment across 241 mammalian genomes …
of modern biology. Using the reference-free alignment across 241 mammalian genomes …
Evolutionary constraint and innovation across hundreds of placental mammals
Zoonomia is the largest comparative genomics resource for mammals produced to date. By
aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect …
aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect …
A genomic timescale for placental mammal evolution
The precise pattern and timing of speciation events that gave rise to all living placental
mammals remain controversial. We provide a comprehensive phylogenetic analysis of …
mammals remain controversial. We provide a comprehensive phylogenetic analysis of …
The functional and evolutionary impacts of human-specific deletions in conserved elements
Conserved genomic sequences disrupted in humans may underlie uniquely human
phenotypic traits. We identified and characterized 10,032 human-specific conserved …
phenotypic traits. We identified and characterized 10,032 human-specific conserved …
Relating enhancer genetic variation across mammals to complex phenotypes using machine learning
Protein-coding differences between species often fail to explain phenotypic diversity,
suggesting the involvement of genomic elements that regulate gene expression such as …
suggesting the involvement of genomic elements that regulate gene expression such as …
DNA language models are powerful predictors of genome-wide variant effects
The expanding catalog of genome-wide association studies (GWAS) provides biological
insights across a variety of species, but identifying the causal variants behind these …
insights across a variety of species, but identifying the causal variants behind these …
Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs
We reconstruct the phenotype of Balto, the heroic sled dog renowned for transporting
diphtheria antitoxin to Nome, Alaska, in 1925, using evolutionary constraint estimates from …
diphtheria antitoxin to Nome, Alaska, in 1925, using evolutionary constraint estimates from …
[HTML][HTML] Identification of constrained sequence elements across 239 primate genomes
Noncoding DNA is central to our understanding of human gene regulation and complex
diseases,, and measuring the evolutionary sequence constraint can establish the functional …
diseases,, and measuring the evolutionary sequence constraint can establish the functional …
Using evolutionary constraint to define novel candidate driver genes in medulloblastoma
A Roy, S Sakthikumar, SV Kozyrev… - Proceedings of the …, 2023 - National Acad Sciences
Current knowledge of cancer genomics remains biased against noncoding mutations. To
systematically search for regulatory noncoding mutations, we assessed mutations in …
systematically search for regulatory noncoding mutations, we assessed mutations in …
Bayesian estimation of gene constraint from an evolutionary model with gene features
Measures of selective constraint on genes have been used for many applications including
clinical interpretation of rare coding variants, disease gene discovery, and studies of …
clinical interpretation of rare coding variants, disease gene discovery, and studies of …