Konstantin Yu. Popadin

From life history to proteome via mutagenesis: an ecological footprint in genome evolution

The paper examines how mutational pressures from life history and ecology shape mitochondrial genome and proteome evolution by comparing long-lived termites with short-lived cockroaches.

Positive germline selection of mtDNA: evidence from the oocyte.

The paper analyzes mtDNA mutation dynamics in human oocytes and finds evidence of positive selection for noncoding and coding mutations, suggesting a shift from positive to purifying selection upon inheritance.

Mutational bias shapes protein evolution across RNA viruses

The paper quantifies how mutational biases shape protein evolution in RNA viruses by analyzing SARS-CoV-2 and 34 other species, showing that mutational spectra predict amino acid composition changes and deviations indicate selection pressures.

BacNeMu: neutral mutation spectra reconstruction pipeline for bacteria

BacNeMu reconstructs bacterial neutral mutation spectra using phylogenetic analysis and open databases, matching mutation accumulation experiments with less time.

Are mitochondrial DNA mutations under purifying selection in somatic tissues?

The paper reanalyzes mtDNA mutation data to determine if somatic mutations are under purifying selection, finding that apparent selection signals are due to germline mutations and most somatic mutations are neutral.

Rare variants in infection response protein pathways associated with sepsis in children.

The paper identifies genetic pathways and variants associated with sepsis susceptibility in children through genomic analysis of a paediatric cohort.

Mitochondrial Deletions and Healthspan: Lessons from the Common Repeat

The paper investigates the role of mitochondrial DNA repeats in aging and healthspan, finding that disrupting the common repeat reduces somatic deletions and improves healthspan.

Evolutionary mismatch between nuclear and mitochondrial genomes does not promote reversion mutations in mtDNA.

The paper shows that apparent reversion mutations in mtDNA are not real but result from sample cross-contamination and NUMTs.

NeMu: A Comprehensive Pipeline for Accurate Reconstruction of Neutral Mutation Spectra from Evolutionary Data

NeMu is a pipeline that reconstructs neutral mutation spectra from evolutionary data by analyzing all mutations on an evolutionary timescale.

Harnessing Stress: balancing the Burden of Slightly-Deleterious Variants by a Handicap

The paper shows that organisms with fewer slightly-deleterious variants are more likely to survive stress, leading to purifying selection on populations.

Selection of different parameters to study epistatic effect between heat shock and slightly deleterious mutations in the most fragile stage of embryogenesis Cyprinus carpio L.

The paper investigates epistatic effects between heat shock and slightly deleterious mutations in Cyprinus carpio L. embryos using mutagenesis and temperature stress to improve genetic quality in fish populations.

Mitochondrial mutation spectrum in Chordates: damage versus replication signatures, causes, and dynamics

The paper analyzes the mitochondrial mutation spectrum in chordates, identifying three main mutation signatures and their underlying causes, with implications for age-related disease prevention.

A novel, wave-shaped profile of germline selection of pathogenic mtDNA mutations is discovered by bypassing a classical statistical bias.

This paper reveals a wave-shaped germline selection profile of mtDNA mutations by correcting for regression to the mean bias, showing how mutations are filtered in the germline.

Reanalysis of mtDNA mutations of human primordial germ cells (PGCs) reveals NUMT contamination and suggests that selection in PGCs may be positive

The paper reanalyzes mtDNA mutation data from human primordial germ cells, identifies NUMT contamination, and suggests that selection in PGCs may be positive rather than negative.

Risk of mitochondrial deletions is affected by the global secondary structure of the human mitochondrial genome

The paper identifies a contact zone in the human mitochondrial genome where deletions are more likely, linking it to aging and lifespan.

The 'Stem' and the 'Workers' of the mtDNA population of the cell. Evidence from mutational analysis.

The paper proposes the existence of 'stem' and 'worker' mtDNA subpopulations based on mutational analysis and HiFi read data, suggesting differential roles in replication and oxidative phosphorylation.

Improving genome quality through artificial truncating purifying selection using heat shock: case of carps

The paper investigates using heat shock to induce purifying selection in carp to reduce deleterious mutations, finding that fitness drops more in mutated lines but with weak and unstable effects.

Isolation of highly purified genomic material from mitochondria of muscle tissue cells

The paper describes a method for isolating highly purified mitochondrial DNA from muscle tissue and evaluates its purity to avoid contamination from nuclear DNA.

Buffering role of HSP shapes the molecular evolution of mammalian and human genomes at short and long-term scales

This study shows that HSP90 buffering of slightly deleterious variants affects molecular evolution across species, tissues, and genes, with implications for predicting variant effects in the human genome.

Aneuploidy in human embryos is associated with a maternal age- independent increase in mitochondrial DNA content and an enrichment of ultra-rare mitochondrial DNA variants

The paper finds that aneuploidy in human embryos is linked to higher mitochondrial DNA content and more ultra-rare mtDNA variants, independent of maternal age.

Direction mutation pressure of SARS-CoV-2 helps to understand the past and predict the future evolution: C>U and G>U biased mutagenesis forces the majority of amino-acid substitutions to be from CG-rich losers to U-rich gainers

The paper analyzes SARS-CoV-2 mutagenesis, showing C>U and G>U biases drive amino-acid substitutions from CG-rich losers to U-rich gainers, with implications for vaccine design.

A mitochondria-specific mutational signature of aging: increased rate of A>G substitutions on a heavy chain.

The paper identifies an AH>GH substitution signature in mtDNA linked to aging and TSSS, showing higher frequency in species with longer generation lengths.

Nuclear DNA-encoded fragments of mitochondrial DNA (mtDNA) confound analysis of selection of mtDNA mutations in human primordial germ cells.

The paper re-analyzes mtDNA mutation data from primordial germ cells and finds that many variants are artifacts from nuclear mitochondrial DNA fragments, invalidating previous conclusions about purifying selection.

Mammalian mitochondrial mutational spectrum as a hallmark of cellular and organismal aging.

The paper investigates mtDNA mutational spectra across species and tissues, finding a correlation between AH>GH substitutions and longevity, suggesting it as a potential oxidative damage signature in mtDNA.

Dynamics of the most common pathogenic mtDNA variant m.3243A>G demonstrate frequency-dependency in blood and positive selection in the germline.

This paper shows that the m.3243A>G mtDNA mutation levels in blood change in a bi-phasic way with age, requiring an age correction dependent on mutation level, and finds evidence for positive germline selection of this mutation.

A>G substitutions on a heavy chain of mitochondrial genome marks an increased level of aerobic metabolism in warm versus cold vertebrates .

The paper examines A>G substitutions in mtDNA across vertebrates, finding higher rates in warm-blooded species, suggesting temperature influences oxidative damage and mutational patterns.

Intra- and inter-chromosomal chromatin interactions mediate genetic effects on regulatory networks

The paper combines regulatory element activity, gene expression, and genetic variation data across cell types to show how chromatin structure influences regulatory networks and genetic effects.

Mitochondrial pseudogenes suggest repeated inter-species hybridization in hominid evolution.

The paper identifies mitochondrial pseudogenes in hominids, suggesting repeated inter-species hybridization during human evolution.