Trans2express - de novo transcriptome assembly pipeline optimized for gene expression analysis.

Background: As genomes of many eukaryotic species, especially plants, are large and complex, their de novo sequencing and assembly is still a difficult task despite progress in sequencing technologies. An alternative to genome assembly is the assembly of transcriptome, the set of RNA products of the expressed genes. While a bunch of de novo transcriptome assemblers exists, the challenges of transcriptomes (the existence of isoforms, the uneven expression levels across genes) complicates the generation of high-quality assemblies suitable for downstream analyses.

[Choledochal cysts: surgical treatment in newborns and infants].

Objective: To improve postoperative outcomes in newborns and infants with choledochal cysts and to determine the indications for surgery.

Material And Methods: There were 13 children aged 0-3 months with choledochal cyst who underwent reconstructive surgery between 2019 and 2023. In all children, choledochal cyst was associated with cholestasis.

Origin and diversity of Capsella bursa-pastoris from the genomic point of view.

Background: Capsella bursa-pastoris, a cosmopolitan weed of hybrid origin, is an emerging model object for the study of early consequences of polyploidy, being a fast growing annual and a close relative of Arabidopsis thaliana. The development of this model is hampered by the absence of a reference genome sequence.

Results: We present here a subgenome-resolved chromosome-scale assembly and a genetic map of the genome of Capsella bursa-pastoris.

The genome of the toxic invasive species Heracleum sosnowskyi carries an increased number of genes despite absence of recent whole-genome duplications.

Heracleum sosnowskyi, belonging to a group of giant hogweeds, is a plant with large effects on ecosystems and human health. It is an invasive species that contributes to the deterioration of grassland ecosystems. The ability of H.

Interspecific comparison of gene expression profiles using machine learning.

Interspecific gene comparisons are the keystones for many areas of biological research and are especially important for the translation of knowledge from model organisms to economically important species. Currently they are hampered by the low resolution of methods based on sequence analysis and by the complex evolutionary history of eukaryotic genes. This is especially critical for plants, whose genomes are shaped by multiple whole genome duplications and subsequent gene loss.