Ivan Liachko

Haplotype-phased genomes of the barley leaf rust pathogen reveal evidence of repeat element expansion and somatic hybridization

The paper presents haplotype-phased, chromosome-scale genomes of Puccinia hordei isolates, revealing repeat expansion, somatic hybridization, and genome plasticity.

GuFi phages represent the most prevalent viral family-level clusters in the human gut microbiome

The paper identifies GuFi phages as prevalent gut viral families using long-read sequencing and shows their broad host ranges and underappreciated impact on the microbiome.

A molecular inventory of the faecal microbiomes of 23 marsupial species

This paper presents a comprehensive analysis of the faecal microbiomes of 23 marsupial species, revealing novel microbial genomes and highlighting the influence of host phylogeny on microbiome composition.

Analysis and culturing of the prototypic crAssphage reveals a phage-plasmid lifestyle

This study characterizes the crAssphage lifestyle as a phage-plasmid, demonstrating its persistence in the gut microbiome without causing host lysis or chromosomal integration.

Comparative genomics of the sexually transmitted parasite Trichomonas vaginalis reveals relaxed and convergent evolution and genes involved in spillover from birds to humans

This study compares the genomics of seven Trichomonas species, revealing convergent genome size expansions in human-infecting lineages and genes involved in host-switching from birds to humans.

Proxi-RIMS-seq2 applied to native microbiomes uncovers hundreds of known and novel m5C methyltransferase specificities.

The paper applies Proxi-RIMS-seq2 to native microbiomes to identify m5C methylation motifs and their cognate methyltransferases, revealing over 1900 motifs including a novel 8-base recognition site.

Mobile genetic elements exhibit increased sequence diversity with increasing host range within the gut microbiome of the Western Honey bee

The paper shows that mobile genetic elements in honey bee gut microbiomes show increased sequence diversity with broader host range.

Highly accurate metagenome-assembled genomes from human gut microbiota using long-read assembly, binning, and consolidation methods

This study improves metagenome-assembled genomes from human gut microbiota using long-read sequencing and novel assembly methods, yielding more high-quality MAGs and uncovering uncultured diversity.

A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.)

The paper presents a contiguous de novo genome assembly of sugar beet EL10 using long-read sequencing and scaffolding, showing high congruence with the reference genome and reduced gene copy number variation.

Accurate viral genome reconstruction and host assignment with proximity-ligation sequencing

The paper develops a platform using proximity-ligation sequencing to reconstruct viral genomes and assign hosts from metagenomic data, showing high accuracy and efficiency.

Extended haplotype phasing of de novo genome assemblies with FALCON-Phase

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.

Differential Expression of α,β, and γ Protocadherin Isoforms During Differentiation, Aging, and Cancer

The paper examines the differential expression of α, β, and γ protocadherin isoforms across differentiation, aging, and cancer using human embryonic stem cells and cancer cell lines.

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise

This study evaluates sequencing technologies and assembly strategies to improve genome completeness in a non-model organism, focusing on resolving dark matter regions like transposable elements and GC-rich areas.

Degradation of recalcitrant polyurethane and xenobiotic additives by a selected landfill microbial community and its biodegradative potential revealed by proximity ligation-based metagenomic analysis

The paper investigates PU degradation by a landfill microbial community using metagenomic analysis, identifying metabolic pathways and enzymes involved in breaking down polyurethanes and xenobiotic additives.

Divergent selection following speciation in two ectoparasitic honey bee mites

The paper examines the evolutionary divergence of two honey bee mite species, identifying gene families under divergent selection and suggesting species-specific strategies for parasite control.

Chromosome-scale de novo assembly and phasing of a Chinese indigenous pig genome

The paper presents a high-quality phased chromosome-scale genome assembly of a Chinese indigenous pig and identifies genetic differences between this breed and Duroc pigs.

The Genome of the Zebra Mussel, Dreissena polymorpha: A Resource for Invasive Species Research

This paper presents the genome of the zebra mussel, Dreissena polymorpha, providing insights into its invasive success and creating a resource for invasive species research.

Repeat elements organize 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae

The paper investigates how repeat elements shape 3D genome structure and transcription in the fungus Epichloë festucae, revealing a unique patchwork genome with repeat-rich blocks that regulate gene expression in symbiosis.

Hi-C deconvolution of a human gut microbiome yields high-quality draft genomes and reveals plasmid-genome interactions.

Hi-C contacts assign assembled contigs to the cell they came from: 50 near-complete genomes among 252 clusters from one human fecal sample, plus plasmid-host links.

Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer sample using Hi-C

The paper uses Hi-C to assemble genomes from a mixed beer sample, identifying a novel yeast hybrid between Pichia membranifaciens and an undescribed yeast.

The dynamic three-dimensional organization of the diploid yeast genome

This study examines the 3D genome organization in diploid yeast, finding dynamic homolog proximity and environment-induced gene relocalization.

Differential paralog divergence modulates evolutionary outcomes in yeast

This study shows that differential paralog divergence in yeast species leads to distinct evolutionary trajectories under sulfate limitation.

Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes

This paper presents a de novo mammalian genome assembly for the domestic goat using long-read sequencing, short-read validation, and chromatin interaction mapping, achieving high contiguity and resolving repetitive regions.