Mikhail Kolmogorov

RawMod detects epigenetic DNA modifications without requiring control data or prior knowledge of modification types, achieving high accuracy across multiple modification types.

This paper benchmarks 7 TR genotyping tools using Nanopore long-read data, finding that no single tool is best across all metrics, and that sequence-level accuracy is crucial for clinical and population studies.

The paper identifies a tumor-intrinsic immune-cloaking mechanism in neoantigen-rich cancers driven by APOBEC3 mutagenesis and 1q23.3 amplification, showing NECTIN4's role in suppressing immune responses.

This paper presents near-complete, haplotype-resolved assemblies of a pancreatic cancer genome and normal tissue, identifying extensive somatic variants and epigenetic changes in previously excluded regions.

This study uses long-read sequencing to show that telomere length differences between chromosome arms influence structural genome changes in IDH-mutant astrocytomas.

Wakhan reconstructs chromosome-scale copy number profiles of tumor genomes using long-read sequencing, showing better consistency with data than existing methods.

DeepSomatic is a deep learning method for detecting somatic variants from short-read and long-read sequencing data, outperforming existing callers, especially for indels.

The paper uses long-read sequencing to analyze genomic and epigenomic changes in melanoma subclones, revealing parallel evolutionary paths and lineage-specific methylation patterns.

The paper describes a comprehensive genomic dataset from a tumor-normal pair with broad consent, generated using multiple sequencing technologies for benchmarking somatic variant detection.

The paper presents diploid genome assemblies for two human fibroblast cell lines, enabling clone-specific variant calling, improved read mapping, and accurate phasing.

Severus detects and characterizes somatic structural variations in tumor genomes using long reads, outperforming existing methods in accuracy and revealing clinically relevant rearrangements.

This study evaluates the diagnostic yield of long-read nanopore sequencing in rare disease detection, finding it covers more genes and detects additional variants compared to short-read sequencing.

The paper uses long-read sequencing to identify structural variants and their impacts on gene expression and methylation in diverse human brain samples.

This study shows that HiFi long-read sequencing can detect clinically relevant structural variants in pediatric leukemia, improving subtype classification.

This study identifies VNTR6-1 and rs10069690 as regulators of TERT splicing and expression, influencing cancer risk and telomere dynamics through altered telomerase isoform ratios.

The paper uses long-read sequencing on 100 samples from the 1000 Genomes Project to identify structural variants and improve understanding of human genetic variation.

Strainy assembles and phases strain haplotypes from long-read metagenome data, outperforming existing methods in accuracy and completeness.

The paper introduces a personalized pangenome approach to improve short-read mapping and variant calling by reducing reference bias and errors.

This paper develops a scalable protocol for Oxford Nanopore long-read sequencing, achieving high SNP and structural variant detection with haplotype-resolved methylation calls, suitable for large-scale genomics projects.

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 evaluates metagenomic software tools using realistic datasets, highlighting improvements in assembly and taxon profiling while identifying remaining challenges in virus/archaea detection and reproducibility.

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.

This paper introduces LJA, an algorithm that improves genome assembly using long accurate reads by constructing multiplex de Bruijn graphs and reducing error rates.

The paper introduces a haplotype-aware variant calling pipeline for nanopore and PacBio HiFi data, achieving high accuracy in variant detection and de novo assembly polishing.

metaFlye improves metagenome assembly using long-read sequencing, producing more contiguous and accurate assemblies with better reconstruction of 16S RNA genes and novel plasmids/viruses.

Building the repeat graph from fast, possibly misassembled contigs lets Flye resolve repeats and produce more contiguous long-read assemblies, with fewer errors than Canu on human and worm genomes.

The paper introduces Ragout, a reference-assisted assembly tool that improves chromosome assembly for large and complex genomes, achieving high accuracy with less than 5% unlocalized sequence.

This paper introduces a read cloud metagenomic sequencing approach combined with a new assembler, Athena, to generate high-quality microbial genome drafts from human and marine microbiomes without culturing.

The paper compares genome assemblies of Mus caroli and Mus pahari with Mus musculus and Rattus norvegicus to reveal lineage-specific evolutionary mechanisms, particularly repeat-associated processes.

The paper presents full-length de novo genome assemblies for 16 inbred mouse strains, identifying strain-specific haplotypes and novel functional loci, including a large unannotated gene with potential developmental roles.