Andrzej Zieleziński

First community challenge for automated virus taxonomy

This paper organizes a community challenge to develop automated virus taxonomy classification tools and evaluates their performance on a combined dataset of expert-curated and metagenomic sequences.

Cosmopolitan gut bacteriophages expand the phenotype of health-related bacteria

The paper identifies cosmopolitan gut bacteriophages that expand the functional repertoire of health-related bacteria across diverse populations.

FAMSA2 enables accurate multiple sequence alignment at protein-universe scale

FAMSA2 provides high-accuracy multiple sequence alignments for large-scale protein datasets with significantly improved speed.

Insufficiency of 40S ribosomal proteins, RPS26 and RPS25, negatively affects biosynthesis of polyglycine-containing proteins in fragile-X associated conditions

The paper identifies RPS26 and RPS25 as modifiers of RAN translation in fragile X conditions, showing their depletion reduces FMRpolyG production and toxicity.

Ultrafast and accurate sequence alignment and clustering of viral genomes

Vclust clusters viral genomes efficiently and accurately using Lempel-Ziv parsing for average nucleotide identity, outperforming existing tools.

Bacterial Lytic Polysaccharide Monooxygenases negatively affect insect larvae growth

This study shows that bacterial LPMOs inhibit Spodoptera exigua larvae growth by 30-69 percentage points when administered per os.

A ligand-receptor interactome atlas of the zebrafish

The paper creates a zebrafish ligand-receptor interactome atlas using physical interaction data and provides tools for studying cellular communication.

TRGdb: a universal resource for exploration of taxonomically restricted genes in bacteria

TRGdb provides a database of taxonomically restricted genes in bacteria, offering sequence information and features for research.

PHIST: fast and accurate prediction of prokaryotichosts from metagenomic viral sequences

PHIST predicts prokaryotic hosts of viruses from their genomic sequences, improving accuracy and speed over existing methods.

Taxonomy-aware, sequence similarity ranking reliably predicts phage-host relationships

Phirbo improves phage-host relationship prediction by integrating sequence similarity and bacterial relatedness, outperforming existing tools in precision and recall.

RaFAH: A superior method for virus-host prediction

RaFAH is a machine-learning method for virus-host prediction that outperforms existing methods with an F1-score of 0.97 at the phylum level, discovering new archaeal virus lineages and auxiliary metabolic genes.

Benchmarking of alignment-free sequence comparison methods

This paper benchmarks alignment-free sequence comparison methods across five research applications and provides a web resource for evaluating and comparing these methods.