David Porubskỳ

Verkko automates telomere-to-telomere diploid genome assembly using long-read sequencing and graph-based methods, achieving high accuracy in chromosome assembly.

GAVISUNK validates genome assemblies by comparing distances between k-mers in HiFi assemblies and Oxford Nanopore reads to detect misassemblies.

The paper evaluates sequencing and assembly methods to create high-quality diploid human genome assemblies, finding that long reads and haplotype sorting improve accuracy and completeness.

The paper analyzes inversion polymorphisms in a complete human genome assembly, showing improved detection and orientation accuracy with the T2T reference compared to GRCh38.

The paper assesses SNVs within human segmental duplications, finding increased mutation rates and interlocus gene conversion, along with distinct mutational spectra.

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

The paper presents a comprehensive analysis of segmental duplications in a complete human genome, revealing their distribution, variation, and evolutionary significance.

The paper identifies recurrent inversions in human genomes and links them to genomic disorders through mutational recurrence and structural diversity.

This paper introduces scNOVA, a method to analyze somatic structural variants in single-cell multiomics data, revealing their functional impacts on gene regulation and cancer pathways.

Mako detects complex structural variants using a graph-based pattern growth approach, achieving 70% validation rate on real data and identifying 15 CSV types including two novel ones.

FALCON-Phase uses long-read sequencing and Hi-C data to create phased diploid genome assemblies, achieving high accuracy in non-human species but lower accuracy in humans.

This paper completes the linear assembly of human chromosome 8, resolves long-standing gaps, and analyzes the evolutionary history of its centromeric regions across great apes.

The paper presents 64 haplotype-resolved human genomes using long-read sequencing and identifies structural variants, SV-eQTLs, and adaptive selection candidates.

This paper presents a fully phased de novo genome assembly of an individual using Strand-seq and HiFi reads, achieving high accuracy and contiguity with low switch error rates.

The paper presents a gapless, telomere-to-telomere assembly of the human X chromosome using ultra-long-read nanopore sequencing and complementary technologies.

This paper introduces scTRIP, a method to detect structural variations in single cells, revealing new SV classes and mutational processes in cancer samples.

This study compares HiFi and CLR long-read sequencing for human genome assembly, finding HiFi provides better continuity and accuracy in complex regions but not centromeres or segmental duplications.

This study identifies a large number of structural variants in human genomes using multiple sequencing technologies and presents them as a gold standard for future studies.

This study uses Strand-seq to show that most spontaneous sister chromatid exchanges in yeast are not caused by DNA double-strand breaks.

This paper introduces an integrative phasing strategy to generate dense and accurate whole-chromosome haplotypes using Strand-seq and long-read sequencing technologies.