Mikhail Kolmogorov

A comprehensive assessment of tandem repeat genotyping methods for Nanopore long-read genomes

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.

APOBEC3-driven neoantigen-rich cancers co-opt 1q23.3 amplification for tumor-intrinsic immune cloaking

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.

A near-complete human pancreatic cancer genome

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.

Chromosome-arm-specific telomere length governs dual modes of structural genome evolution in IDH-mutant astrocytoma

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

Wakhan: reconstruction of chromosome-scale copy number profiles of tumor genomes with long-read sequencing

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

DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies

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

Long-read sequencing of single cell-derived melanoma subclones reveals divergent and parallel genomic and epigenomic evolutionary trajectories

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

Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair

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.

Diploid genome assembly of human fibroblast cell lines enables clone specific variant calling, improved read mapping and accurate phasing

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

Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads

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

Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection

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.

Haplotype-Resolved Long-Read Sequencing in Hundreds of Diverse Brains Identifies Structural Variant Impacts on Expression and Allele-Specific Methylation

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

Successful classification of clinical pediatric leukemia genetic subtypes via structural variant detection using HiFi long-read sequencing

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

Genetic regulation of TERT splicing contributes to reduced or elevated cancer risk by altering cellular longevity and replicative potential

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.

Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation

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: phasing and assembly of strain haplotypes from long-read metagenome sequencing

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

Personalized Pangenome References

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

Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation

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.

Automated assembly of high-quality diploid human reference genomes

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.

Critical Assessment of Metagenome Interpretation - the second round of challenges

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.

The complete sequence of a human genome

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.

Assembling Long Accurate Reads Using Multiplex de Bruijn Graphs

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

Haplotype-aware variant calling enables high accuracy in nanopore long-reads using deep neural networks

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: scalable long-read metagenome assembly using repeat graphs

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.

Assembly of Long Error-Prone Reads Using Repeat Graphs

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.

Chromosome assembly of large and complex genomes using multiple references

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.

Culture-free generation of microbial genomes from human and marine microbiomes

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.

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

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.

Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci

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.

Assembly of Long Error-Prone Reads Using de Bruijn Graphs

This paper introduces a de Bruijn graph-based assembler for long error-prone reads, achieving more accurate genome reconstructions than existing methods.