Wojciech Makałowski

TEclass2 classifies transposable elements using a Transformer-based deep learning model, offering reliable results and a user-friendly tool for TE annotation.

The paper introduces a data management system for gut microbiome studies in children small for gestational age, enhancing quality control and data sharing through a web interface.

The paper investigates Alu-driven DNA transductions in primate genomes and finds no evidence of Alu-mediated transductions in humans, chimpanzees, or rhesus monkeys.

The paper shows that the orientation of the first cleavage in mouse oocytes follows the shorter diameter of the unfertilized oocyte, leading to segregation of animal and vegetal hemispheres and explaining differences in monozygotic twins.

The paper presents the complete sequence of a human Y chromosome, correcting errors in the GRCh38 reference and adding over 30 million base pairs.

The paper presents the first de novo repeat discovery and annotation of a complete human reference genome, identifying novel satellite arrays and characterizing new classes of complex repeats.

The paper evaluates de novo transposon detection tools using simulated and curated data, finding that model-based tools outperform k-mer counting methods but still struggle with fragmented or small TEs.

This paper presents a high-quality genome assembly and annotation of the California harvester ant Pogonomyrmex californicus, enabling studies on social polymorphism and adaptation to arid environments.

The paper introduces MetaG, a tool for metagenomic analysis of short and long reads, showing high accuracy in classifying viral isolates and outperforming existing methods.

The paper integrates multi-omics data to analyze gene expression dynamics in mouse embryos, revealing discrepancies between transcript and protein levels during early development.