Joanna Szyda

This study compares methods for handling missing parental information in genomic breeding value predictions for dairy cattle, finding that grouping missing parents as genetic groups is more robust for ungenotyped individuals in incomplete pedigrees.

This study shows that adding effective microorganisms to feed and pond water improves common carp growth without changing microbial communities.

The paper introduces a procedure to analyze gene panel data for complex traits, narrowing down SNPs with potential causal effects on protein structure.

This paper compares three feature selection methods for ultra-high-dimensional genomic data, finding that MD-SRA provides the best balance of classification accuracy and computational efficiency.

The paper uses an autoencoder to identify systematic errors in SNP genotype calling from WGS data by analyzing sequence context and quality metrics.

The paper develops a deep learning classifier for bovine mastitis susceptibility using whole genome sequence data, overcoming the p>>n problem through LASSO and deep learning integration.

This paper compares SNP calling workflow parallelisation using plain Bash and Nextflow, finding that multi-process Nextflow is faster but uses more RAM and disk space.

The paper analyzes SNP distribution across human exons and introns using a Polish population dataset, finding that outer exons and first introns have significantly more SNPs.

The paper estimates the functional effects of KEGG pathways on bovine stature using SNP summary statistics from GWAS and mixed linear models.

The paper identifies differentially expressed genes and microbiome interactions in Holstein cattle under heat stress, finding 1,851 shared genes linked to cytokine pathways and microbiome hubs influencing gene expression.

The paper describes the creation of a national database of Polish genomic variant allele frequencies using 1,079 whole genomes, identifying rare variants and confirming allele frequencies for known pathogenic variants.

The paper identifies fecal microbiota associated with heat stress in cattle using 16S rRNA sequencing and statistical analysis.

The paper analyzes DNA variation patterns across autosomes, X, and Y chromosomes in Bos taurus using a new genome assembly, finding differences in variant density, divergence, and Tajima's D.