Kateryna D. Makova

Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures

The paper presents a population-scale Y chromosome reference panel with 142 assemblies, revealing structural and epigenetic variation across 180,000 years of evolution.

The complete genome of a songbird

This paper presents the first fully phased, diploid, telomere-to-telomere genome of the zebra finch, revealing new genes and structural features.

A Complete Genome for the Common Marmoset

The paper presents the first telomere-to-telomere genome for the common marmoset, revealing genomic features and a pangenome resource for biomedical research.

Direct detection of alternative DNA conformations with long-read sequencing and machine learning approaches

This study uses long-read sequencing and machine learning to detect alternative DNA conformations, achieving ~90% accuracy in distinguishing G4 from B-form DNA.

The Vertebrate Genomes Project Phase I: A global reference genome resource

The Vertebrate Genomes Project Phase I provides high-quality reference genomes for 816 species, enabling evolutionary and conservation insights across vertebrates.

Variation and selection at predicted G-quadruplexes across the human pangenome

The paper analyzes G-quadruplexes across the human pangenome, finding that they show distinct selection patterns and influence gene expression.

Uncertainty-aware benchmarking reveals ambiguous transcripts in mRNA-lncRNA classification

The paper benchmarks transcript classifiers to identify ambiguous mRNA-lncRNA classifications by analyzing uncertainty and feature contributions.

Substitution spectrum and selection at G-quadruplexes in great ape telomere-to-telomere genomes

This study analyzes substitution patterns and selection at G-quadruplexes in great ape genomes, finding stronger purifying selection on stems than loops, especially in regulatory regions.

Comparative analysis of single-stranded and non-canonical DNA formation in human and other ape cells with telomere-to-telomere genomes

The paper analyzes single-stranded DNA (ssDNA) formation in human and non-human ape telomere-to-telomere genomes to identify non-B DNA structures and their functional roles.

Non-canonical DNA and sequencing challenges in bird genomes

The paper analyzes non-B DNA motifs in bird genomes, showing differences in distribution across chromosome types and their potential regulatory roles, while highlighting sequencing challenges.

Mitochondrial DNA mutations in human oocytes undergo frequency-dependent selection but do not increase with age

The paper detects mtDNA mutations in oocytes, blood, and saliva across ages and finds mutations increase in blood and saliva but not in oocytes, with age-related differences in mutation frequency distribution.

Evolutionary Dynamics of G-Quadruplexes in Human and Other Great Ape Telomere-to-Telomere Genomes

The paper analyzes G-quadruplexes in T2T genomes of great apes, finding shared and species-specific G4s, their methylation patterns, and their potential role in gene regulation and adaptation.

Nuclear Mitochondrial Sequences in Great Ape Telomere-to-Telomere Genomes

The paper studies NUMTs in great ape T2T genomes, showing they recapitulate species tree topology and are enriched in non-functional regions.

Non-canonical DNA in human and other ape telomere-to-telomere genomes

The paper characterizes non-B DNA motifs in T2T genomes of apes, showing their enrichment in specific genomic regions and potential roles in genome function.

The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes

The paper produces gapless assemblies of ape sex chromosomes for five great apes and a lesser ape, revealing divergence in Y chromosomes and evolutionary dynamics.

How and why ampliconic genes survive on the human Y chromosome

The paper investigates how multicopy gene families on the human Y chromosome survive despite lack of recombination, showing that homogenization via palindromes and arrays, along with purifying selection, preserve protein structure essential for fertility.

Methylation profiles at birth linked to early childhood obesity

The paper links methylation profiles at birth to early childhood obesity by analyzing 48 infants and identifying 23 and 10 genes in cord blood and placenta associated with weight outcomes.

In vivo detection of DNA secondary structures using Permanganate/S1 Footprinting with Direct Adapter Ligation and Sequencing (PDAL-Seq)

The paper introduces PDAL-Seq, a method to detect DNA secondary structures in vivo, and provides a standardized analysis pipeline.

Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes

The paper analyzes transcript isoform diversity of Y-chromosomal ampliconic genes in six great ape species using long-read sequencing and identifies evolutionary patterns and pseudogenization trends.

The complete sequence of a human Y chromosome

The paper presents the complete sequence of a human Y chromosome, correcting errors in the GRCh38 reference and adding over 30 million base pairs.

Distinct sequencing success at non-B-DNA motifs

This study examines how non-B DNA motifs affect sequencing error rates across three technologies and proposes a method to estimate false-positive SNVs.

Towards complete and error-free genome assemblies of all vertebrate species

The paper summarizes methods and lessons from assembling 16 vertebrate genomes, highlights the importance of long-read sequencing, and introduces the Vertebrate Genomes Project to generate complete reference genomes for all vertebrate species.

Family reunion via error correction: An efficient analysis of duplex sequencing data

The paper corrects errors in duplex sequencing data to reunite reads and improve the efficiency of variant detection.

Polygenic risk score based on weight gain trajectories is a strong predictor of childhood obesity

This paper develops a polygenic risk score for childhood obesity using longitudinal weight gain data and shows it predicts obesity risk better than adult GWAS-based scores.

Noise-Cancelling Repeat Finder: Uncovering tandem repeats in error-prone long-read sequencing data

The paper introduces NCRF, a tool for identifying tandem repeats in noisy long-read sequencing data, showing improved performance over existing methods.

Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate

The paper uses long-read sequencing to analyze how non-B DNA structures affect DNA polymerization speed and error rates across the human genome.

Correcting palindromes in long reads after whole-genome amplification

Pacasus corrects artificial palindromic errors in long reads after whole-genome amplification, improving mapping and assembly results.

IsoCon: Deciphering highly similar multigene family transcripts from Iso-Seq data

IsoCon improves transcript reconstruction of highly similar multigene family transcripts using long-read sequencing, detecting rare variants and novel isoforms in Y ampliconic gene families.

Mito-nuclear effects uncovered in admixed populations

The paper investigates mito-nuclear incompatibility in admixed populations, finding that mtDNA copy number decreases with increasing discordance between nuclear and mitochondrial ancestry.

A population phylogenetic view of mitochondrial heteroplasmy

The paper develops a population-genetic framework to model mitochondrial heteroplasmy inheritance and applies it to infer genetic drift and mutation rates during human development.