Aleksey V. Zimin

The paper introduces Verkko-Fillet, a tool for refining genome assemblies, and applies it to produce a telomere-to-telomere giraffe genome.

EviAnn improves eukaryotic genome annotation by using transcript alignments and protein homology, outperforming existing tools with less computational time.

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 presents three chromosome-level genome assemblies of Lomentospora prolificans, revealing a chromosomal translocation event between strains.

PSAURON assesses protein-coding gene annotations across species using a machine learning model trained on over 1000 genomes, providing scores to identify high-quality annotations and potential spurious proteins.

WheresWalker is a mutation mapping pipeline that rapidly identifies mutation-containing intervals in whole genome sequencing data, validated in zebrafish and maize.

The paper produces a high-quality genome sequence for whitebark pine and identifies NLR genes associated with resistance to white pine blister rust.

The paper assembles a gapless, reference-quality genome from a Southern Han Chinese individual and identifies gene-level differences compared to a reference genome.

This paper presents a chromosome-level genome assembly for Uloborus diversus, identifies sex chromosomes, and provides insights into spidroin genes and evolutionary biology.

KrakenUniq improves metagenomic classification on low-memory systems by processing databases in chunks without sacrificing accuracy.

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.

JASPER improves genome assembly accuracy and creates population-specific references by polishing with k-mer counts and integrating variant data from multiple individuals.

This study presents a high-quality genome and methylome analysis of Quercus lobata, identifying genomic features linked to oak evolutionary success, including gene duplications and methylation patterns.

SAMBA improves genome assembly contiguity using long-read data by scaffolding and gap-filling existing assemblies, outperforming other tools in accuracy and contiguity.

The paper presents a new reference genome, PR1, from a Puerto Rican individual, highlighting its completeness and annotations compared to existing genomes.

The paper assembles the Rocky Mountain elk genome and identifies nine putative immune system gene losses compared to cattle.

The paper introduces POLCA, a genome polishing tool that improves accuracy and speed in genome assembly correction using long-read and short-read data.

The paper assembles and annotates a population-specific Ashkenazi human reference genome, showing improved contiguity and completeness compared to GRCh38.

This paper presents a chromosome-scale walnut genome assembly, improving gene prediction and enabling better analysis of genetic diversity and proteomic changes.

The paper presents an updated wheat genome assembly, Triticum 4.0, which includes 15.07 gigabases of sequence and over 5700 new genes, improving upon previous assemblies.

This paper presents the first genome assembly of the giant sequoia, enabling analysis of disease resistance genes for conservation and evolutionary studies.

StringTie2 assembles error-prone long reads, recovering on average 8.3 and 2.6 times as many correct transcripts as FLAIR and Traphlor, and outperforms Scallop on short reads.

The paper presents the first near-complete assembly of the hexaploid bread wheat genome using a combination of short and long-read sequencing technologies.