An expanded sequence context model broadly explains variability in polymorphism levels across the human genome

V Aggarwala, BF Voight - Nature genetics, 2016 - nature.com
The rate of single-nucleotide polymorphism varies substantially across the human genome
and fundamentally influences evolution and incidence of genetic disease. Previous studies …

Extremely rare variants reveal patterns of germline mutation rate heterogeneity in humans

J Carlson, AE Locke, M Flickinger… - Nature …, 2018 - nature.com
A detailed understanding of the genome-wide variability of single-nucleotide germline
mutation rates is essential to studying human genome evolution. Here, we use~ 36 million …

Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes

AY Panchin, YV Panchin - PeerJ, 2020 - peerj.com
Background SARS-CoV-2 is a novel coronavirus that causes COVID-19 infection, with a
closest known relative found in bats. For this virus, hundreds of genomes have been …

Fibrodysplasia ossificans progressiva in Spain: epidemiological, clinical, and genetic aspects

A Morales-Piga, J Bachiller-Corral, MJ Trujillo-Tiebas… - Bone, 2012 - Elsevier
We aimed to investigate the epidemiological determinants, clinical features, and genetic
pattern of FOP in our country by evaluating the entire population of patients identified …

Interaction-based evolution: how natural selection and nonrandom mutation work together

A Livnat - Biology direct, 2013 - Springer
Background The modern evolutionary synthesis leaves unresolved some of the most
fundamental, long-standing questions in evolutionary biology: What is the role of sex in …

Heterogeneity of the Transition/Transversion Ratio in Drosophila and Hominidae Genomes

VB Seplyarskiy, P Kharchenko… - Molecular biology …, 2012 - academic.oup.com
Mutation rate varies between sites in the genome. Part of this variation can be explained by
well-recognized short nucleotide contexts, but a large component of this variation remains …

Preservation of methylated CpG dinucleotides in human CpG islands

AY Panchin, VJ Makeev, YA Medvedeva - Biology direct, 2016 - Springer
Background CpG dinucleotides are extensively underrepresented in mammalian genomes.
It is widely accepted that genome-wide CpG depletion is predominantly caused by an …

The somatic autosomal mutation matrix in cancer genomes

NA Temiz, DE Donohue, A Bacolla, KM Vasquez… - Human Genetics, 2015 - Springer
DNA damage in somatic cells originates from both environmental and endogenous sources,
giving rise to mutations through multiple mechanisms. When these mutations affect the …

Neighbor preferences of amino acids and context-dependent effects of amino acid substitutions in human, mouse, and dog

M Fu, Z Huang, Y Mao, S Tao - International journal of molecular sciences, 2014 - mdpi.com
Amino acids show apparent propensities toward their neighbors. In addition to preferences
of amino acids for their neighborhood context, amino acid substitutions are also considered …

Comparative Analysis of Context‐Dependent Mutagenesis Using Human and Mouse Models

SA Medvedeva, AY Panchin… - BioMed Research …, 2013 - Wiley Online Library
Substitution rates strongly depend on their nucleotide context. One of the most studied
examples is the excess of C> T mutations in the CG context in various groups of organisms …