Conferences – THETA 2.0

2026
AI in Veterinary Medicine Congress
J. Liu, M. Sztuka, M. Jakimowicz and J. Szyda Application of AutoEncoder architectures to the analysis of fish gut microbiome
WCGALP 2026
M. Sztuka and J. Szyda Comparative Deep Learning Architectures for Exploring High-Dimensional, Small-Sample Data
J. Szyda, M. Sztuka, M. Jakimowicz, K. Sidorczuk, D. Słomian, and Ł. Napora-Rutkowski Deep Learning and feature selection in the bioinformatic modelling of functionally annotated microbial communities in aquaculture
W. Zawadzka, J. Szyda, and M. Frąszczak Inferring Missing Genotypes from Partially Observed SNP Data Using Deep Learning-Based Architectures
D. Słomian, K. Żukowski, M. Skarwecka, J. Ten Napel, J. Vandenplas and J.Szyda Modelling missing parents in single-step test-day SNP-BLUP evaluation of dairy cattle
2025
Ai4AS-EAAP
M. Sztuka M. Jakimowicz. J.Szyda Deep learning in the bioinformatic modelling of taxonomically annotated microbial communities in aquaculture (poster)
J. Szyda, J. Liu, M. Sztuka, M. Frąszczak Does SNP imputation require attention?
J. Liu, M. Sztuka, M. Jakimowicz, J. Szyda Application of AutoEncoder architectures to the analysis of fish gut microbiome
DAGStat
T. Suchocki, J. Szyda Random regression model for longitudinal data.
M.Jakimowicz, T. Suchocki, W. Jagusiak, J. Szyda Investigating relationships between health traits on Holstein Friedman cattle with Structural equation modeling.
D. Schulze, J. Liu Cross-over trials in clinical psychology – rarely a good idea.
J. Szyda, D. Słomian, K. Kotlarz Approaches to dimensionality reduction for ultrahigh dimensional data.
M. Sztuka M. Jakimowicz. J.Szyda Deep Learning in the bioinformatic modelling of taxonomically annotated microbial communities in aquaculture
P. Mierzejewski, K. Kotlarz, J. Szyda, W. Dragan, M. Frąszczak Investigation of the temporal changes in brain activity based on functional Magnetic Resonance Imaging data
2024
Genetic Days
M. Jakimowicz, T. Suchocki, W. Jagusiak, P. Topolski, J. Szyda Genome-wide genomic and functional association study for health traits in Holstein cattle.
J. Szyda , THETA Biostatistic Group (Artificial) intelligent and non intelligent methods to explore multidimensional genomic data
M. Mielczarek, M. Ussowicz, K. Bogunia-Kubik, K. Kotlarz, B. Czech, R. Stępień, K. Adamiak, J. Szyda. NGS-based approach in the service of human disease diagnostics
M. Frąszczak, J. Liu, M. Mielczarek, P. Dobosz, J. Szyda. Exploring the distribution of single nucleotide polymorphisms across human exons and introns
M. Frąszczak, J. Szyda, B. Nowak, M. Kaźmierczak, M. Mielczarek. Trios-Based Inquiry into CNVs in Swine Genome
PTBI
J.Liu, D.Słomian, J.Szyda, K.Kotlarz, P.Dobosz. A three-level modeling for identifying important predictor variables in genome-wide association studies suffering from p >> n
M. Sztuka, M. Jakimowicz, K. Kotlarz, M. Mielczarek, D. Huyben, Ł. Napora-Rutkowski, P. Hajduk, J. Szyda Deep Learning in the bioinformatic modelling of functionally annotated microbial communities in aquaculture
EAAP 2024
D. Słomian, K. Żukowski, M. Skarwecka, K. Kotlarz, J.Szyda
Genome-wide association study for stature for Holstein cattle based on whole genome sequence, using a mixed linear model
International Conference of Quantitative Genetics (ICQG 2024)
K. Kotlarz, D. Słomian, J. Szyda
Rank aggregation-based feature selection for comprehensive multi-breed cattle classification
J.Szyda, M. Jakimowicz, M. Sztuka
Toward a biological interpretation of the effect of probiotic supplementation expressed by the microbiome composition of the fish gut microbiome
M. Jakimowicz, Ł. Napora-Rutkowski, T. Kaminska-Gibas, T. Suchocki, J. Szyda
Influence of Effective Microorganism Supplementation on the Water and on Gut Microbiome of Common Carp
European Human Genetics Conference (ESHG 2024)
M. Fraszczak, J. Liu, M. Mielczarek, Paula D., J. Szyda
The distribution of single nucleotide polymorphisms across consecutive exons and introns of the human genome
M. Mielczarek, B. Czech, R. Stępień, J. Szyda
The effect of transcriptomic annotations in breast cancer differential gene expression study
K. Kotlarz, B. Hofman, M. Mielczarek, Y. Wang, J. Szyda
Differences in cell type composition in the liver by the linear mixed model in the deconvolution method under thermal stress conditions
J. Liu, D. Słomian, P. Dobosz, J. Szyda
A three-level modeling for identifying important predictor
variables in genome-wide association studies suffering
from p >> n
Interbull meeting & iCAR 2024
D. Słomian, K. Żukowski, M. Skarwecka, J. Ten Napel, J. Vandenplas, J. Szyda. Differential handling of missing parents in genetic evaluation of dairy cattle using single step test day SNP-BLUP model
XXIX Winter School of Cattle Breeding
B. Czech, J. Szyda. The composition of intestinal microbiota and gene expression in Holstein cattle under heat stress
2023
19th International Symposium on Bioinformatics and Applications
R. Stępień, J. Szyda, B. Czech, M. Mielczarek. The effect of transcriptomic annotations in breast cancer differential gene expression study
PTBI 2023
J. Liu, J.Szyda, M.Frąszczak, M.Mielczarek, Exploring the distribution of SNPs amongst subsequent exons and introns in the human genome
B. Hofman, M. Frąszczak, J. Szyda, M,Mielczarek, LncRNAs Variability in Porcine Skeletal Muscle
M.Kaźmierczak, M.Mielczarek, B.Nowak, J.Szyda, M.Frąszczak, Analysis of CNV distribution in swine genome
P. Leśniak, M.Mielczarek, B.Nowak, J.Szyda, T.Strzała, M.Frąszczak, Analysis of the CNV detection based on combined Illumina and Nanopore data
Japan-Poland Joint Seminar 2023
B. Jaśkowski, B. Czech, W. Niżański Evaluation of the size of the recipient’s corpus luteum after synchronization as an additional criterion for increasing the pregnancy rate after an embryo transfer in cattle
17th International Symposium on Integrative Bioinformatics
J. Liu, K.Kotlarz, M.Mielczarek, W.Dragan, J.Szyda, Modelling the interplay between early life stress, recent stress and genome methylation pattern with the focus on whole-genome significance testing.
M. Frąszczak, M. Mielczarek, M. Kaźmierczak, B. Nowak, J. Szyda, Inheritance analysis of copy number variation polymorphisms in swine genome
M. Sztuka, P. Hajduk, J. Liu, K. Kotlarz, M. Mielczarek and J. Szyda Nextflow vs Naïve Bash Different approaches to SNP calling parallelisation on the Whole Genome Bovine Sequence talk
P. Hajduk
J. Szyda, M. Mielczarek Mining the K-mer patterns in whole-genome sequences of Holstein-Friesian cows
R. Stępień, J. Szyda, B. Czech, M. Mielczarek The effect of transcriptomic annotations in breast cancer differential gene expression study
EAAP 2023
A. Brzoza, Ł. Napora-Rutkowski, M. Mielczarek,T. Kamińska-Gibas, T.Suchocki, J. Szyda The impact of probiotic supplementation in aquaculture – bioinformatic modeling
M. Sztuka, P. Hajduk, J. Liu, K. Kotlarz, M. Mielczarek and J. Szyda Nextflow vs Naïve Bash Different approaches to SNP calling parallelisation on the Whole Genome Bovine Sequence
Kotlarz K., Mielczarek M., Biecek P., Guldbrandtsen B. and Szyda J. Enhancing bovine genome SNP call accuracy with autoencoder analysis of nucleotide impact with AI
Słomian D., Szyda J., Żukowski K. The heterogenity in convergence behaviour of a single step SNP-BLUP model across effects and animal groups
Słomian D., Szyda J. Choose your model wisely – the comparison of genomically enhanced breeding values predicted by different single-step models
D. Słomian, M. Jakimowicz, T.Suchocki , J. Szyda. Comparison of two software to estimate breeding values in cattle by single-step approach
PTBI 2022
Jakimowicz M. , Suchocki T., Zarnecki A., Skarwecka M., Szyda J., Jagusiak W. Using structural equation models to increase of accuracy of QTL estimation in cattle
EAAP 2022
M. Frąszczak, M. Mielczarek, M. Kaźmierczak, T. Strzała, B. Nowak, J.Szyda Analysis of the CNV inheritance in swine genome based on combined Illumina and Nanopore data
J. Szyda, M. Mielczarek Mining the K-mer patterns in whole-genome sequences of Holstein-Friesian cows
K. Kotlarz, M. Mielczarek, P. Biecek J. Szyda Classification of mastitis in cows using deep learning approach with model regularization
B.Czech, J. Szyda, Y. Wang Host transcriptome and microbiome data integration in Chinese Holstein cattle under heat stress
WCGALP 2022
B. Hofman, J.Szyda, M. Frąszczak, M.Mielczarek. LncRNAs_variability in skeletal muscle of Polish Landrace boars
K. Kotlarz, B. Kosinska-Selbi, Z. Cai, G. Sahana and J. Szyda
The application of mixed linear models (LMM) for the estimation of functional effects on bovine stature based on SNP summary statistics from a whole-genome association study
T. Suchocki, B. Kosinska-Selbi, M. Jakimowicz, J. Szyda
Genome-wide genomic and functional association study for workability and calving traits in Holstein cattle: PDF
2021
PTBI 2021
M. Mielczarek, M. Frąszczak, A. Zielak-Steciwko, B. Nowak, B. Hofman, J. Pierścińska, J. Szyda. Impact of Copy Number Variation on gene expression
J. Liu, T. Suchocki, J. Szyda. Bioinformatic modelling of SARS-CoV-2 pandemic with a focus on country-specific dynamics
K. Kotlarz, M. Mielczarek, T. Suchocki, J. Dou, Y. Wang Y, J. Szyda. Identification of heat stress responsive transcripts in Sprague-Dawley rats using mixed linear models
B. Hofman, J. Szyda. M. Mielczarek. Identification and characteristics of lncRNAs in Polish Landrace boars
EAAP 2021
M. Jakimowicz, T. Suchocki, A. Żarnecki, M. Skarwecka, J. Szyda Investigating relationships between fertility traits in Holstein Friesian cattle using Structural Equation Modelling
M. Jakimowicz, T. Suchocki, J. Szyda, S. Nyman, D.-J. De Koning Influence of pedigree on effective population size in European Red Dairy Cattle
K. Kotlarz, J. Szyda, M. Mielczarek, T. Suchocki, J. Dou, Y. Wang. Identification of heat stress responsive transcripts in Sprague-Dawley rats using mixed linear models
B. Czech, K. Wang, S. Chen, Y. Wang, J. Szyda. Faecal microbiota and their association with heat stress in Bos taurus
B. Czech, K. Wang, S. Chen, Y. Wang, J. Szyda. Challenges of 16S rRNA gene analysis in Chinese Holstein cows under heat stress condition
M. Mielczarek, M. Frąszczak, A. Zielak-Steciwko, B. Nowak, B. Hofman, J. Pierścińska, J. Szyda. CNV impact on gene expression
M. Kołomański, M. Frąszczak, M. Mielczarek. Impact of NGS data trimming on differential gene expression analysis in two groups of bees
M. Frąszczak, M. Mielczarek, P. Grzesiak, J. Szyda The exploration of Single Nucleotide Polymorphisms density in Bos taurus genomes reveals their role in the immune response
B. Kosinska-Selbi, Z. Cai, J. Szyda, K. Kotlarz, G. Sahana Estimation of Kegg pathways effects on stature usisng GWAS summary statistics
S. Marasinskiene, R. Sveistiene, M. Kargo, B. Kosinska-Selbi, Ch. Schmidtmann, V. Juskiene Aplication of a bio-economic model for economic estimation of Lithuanian dairy breeds
2020
EAAP 2020
M. Mielczarek, S.L. Rodriguez-Zas, J. Szyda, B. Southey. Group specific CNVs in scouts and recruits of honeybee.
Video here
K. Kotlarz, J. Szyda, B. Czech, M. Mielczarek, T. Suchocki, B. Guldbrandtsen. Don’t play too much! Deep learning to classify true and false positive SNPs in whole genome sequence.
Video here
J. Szyda, B. Czech, K. Wang, S. Chen, Y. Wang. The application of mixed linear models for the analysis of microbiome influence on heat stress in Chinese Holstein cows.
Video here
B. Czech, J. Szyda, K. Wang, S. Chen, Y. Wang. The effect of pipelines and databases on the analysis of the fecal microbiota of dairy cattle.
Video here
B. Kosińska-Selbi, M. Jakimowicz, T. Suchocki, M. Skarwecka, A. Żarnecki, W. Jagusiak, J. Szyda. Genome-Wide Association Study for Milking Speed and Temperament in Holstein-Friesian bulls.
Video here
B. Kosińska-Selbi, Ch. Schmidtmann, M. Kargo, J. F. Ettema, J. Szyda. Estimation of economical values for Polish Holstein, Polish Red and Scandinavian Red.
Video here
M. Jakimowicz, T. Suchocki, B. Kosińska-Selbi, A. Żarnecki, W. Jagusiak, M. Kopeć-Morek and J. Szyda. Genome-wide genomic and functional association study for direct calving ease in Holstein cattle.
Video here
T. Suchocki, A. Żarnecki, M. Jakimowicz and J. Szyda. Impact of rare SNP variants on the genomic evaluation for conception rate.
Video here
PTBI 2020
B. Czech, J. Szyda, B. Guldbrandtsen. Patterns of DNA variation between the autosomes, the X chromosome and the Y chromosome in Bos taurus genome.
M. Kołomański, J. Szyda, M. Frąszczak, M. Mielczarek. DNA sequence features underlying large-scale duplications and deletions in humans.
K. Kotlarz, M. Mielczarek, T. Suchocki, B. Czech, B. Guldbrandtsen, J. Szyda. Deep learning algorithms for the imbalanced classification of correct and incorrect SNP genotypes from WGS pipelines.
2nd CiBreed Fall Workshop 2020
J. Liu, T. Suchocki, J. Szyda. Tuning the genomic evaluation system of Holstein-Friesian cattle
2019
ReDiverse 2019
B. Kosińska-Selbi, Ch. Schmidtmann, S. Marasinskiene, M. Kargo Derivation of economic values for Red breeds
XIX International Congress of ISAH
B. Kosińska-Selbi, M. Frąszczak, T.Suchocki, Ch. Egger-Danner, H. Schwarzernbacher, J. Szyda. Genetic variants underlying hoof diseases in Braunvieh and Fleckvieh cattle
EAAP 2019
B. Kosińska-Selbi, M. Frąszczak, T.Suchocki, Ch. Egger-Danner, H. Schwarzernbacher, J. Szyda. Genome-Wide Association Study for Leg Disorders in Austrian Braunvieh and Fleckvieh
T. Suchocki, B. Czech, M. Siwek and J. Szyda SNP prioritisation for immune responses traits in chicken
M. Mielczarek, M. Frąszczak, J. Szyda. Modulation of gene expression by CNVs
B. Czech, B. Guldbrandtsen, J. Szyda. Patterns of genetic variation between autosomes and sex chromosomes in Bos taurus genome
B. Czech, T.Suchocki, J. Szyda. SNP prioritisation in GWAS with dense marker sets
BIT19
B. Kosińska-Selbi, M. Frąszczak, T.Suchocki, Ch. Egger-Danner, H. Schwarzernbacher, J. Szyda. Differences in genomic structure between two cattle breeds
IGB Fellows Symposium
J.Szyda, M. Mielczarek, M. Frąszczak, G. Minozzi, R. Giannico, JL. Williams, K. Wojdak-Maksymiec.The genetic background of clinical mastitis in Holstein-Friesian cattle
2018
XXVIIth Genetic Days 2018
B. Kosińska-Selbi, J. Szyda, Ch. Egger-Danner, H. Schwarzernbacher, Comparison of LD structure between Braunvieh and Fleckvieh cattle population based on single nucleotide polymorphism
PTBI 2018
J. Szyda M. Mielczarek, M. Frąszczak, G. Minozzi, J. Williams, K. Wojdak-Maksymiec. Unraveling the genetic background of clinical mastitis in dairy cattle using WGS
B. Kosińska-Selbi, J. Szyda, M. Frąszczak, T. Suchocki, Ch. Egger-Danner, H. Schwarzenbacher Genome-wide analysis of single nucleotide polymorphism underlying feet and leg disorders for Austrian Braunvieh cattle
EAAP 2018
M. Mielczarek, M. Frąszczak, J.Szyda Impact of copy number polymorphisms on gene expression
M. Frąszczak, M. Mielczarek, N. Czerwik, E. Nicolazzi, J.L. Williams, J.Szyda Analysis of copy number variation regions in bovine genome
B. Czech, M. Mielczarek, M. Frąszczak, J. Szyda Breed specific reference genomes in cattle
J.Szyda, M. Mielczarek Single Nucleotide Polymorphisms underlying mastitis predisposition in Polish-Holstein Friesian cows
Why R ? 2018
B.Kosińska-Selbi, J.Szyda RNA-seq sequence analysis with R/Bioconductor
WCGALP 2018
M.Mielczarek, M. Frąszczak, E.L. Nicolazzi, J. L.Williams, J. Szyda. Copy number variations within and among diverse cattle breeds.
J. Szyda, P. Barski, M. Mielczarek & M. Frąszczak Assessing DNA sequence features underlying copy number variants.
T. Suchocki, Ch. Egger-Danner, H. Schwarzenbacher, M. Mielczarek & J. Szyda Combining SNP-chip and whole genome sequence data towards the identification of causal mutations underlying feet and leg disorders in cattle .
2017
DGfZ Tagung 2017
B. Czech, E. Dobkowski, M. Mielczarek, M. Frąszczak, J. Szyda. The construction of Bos taurus breed specific reference genomes for Fleckvieh, Simmental, Guernsey and Brown Swiss.
EAAP 2017
J.Szyda, M. Mielczarek, M. Frąszczak, G. Minozzi, R. Giannico, JL. Williams, K. Wojdak-Maksymiec. Unravelling the Genetic Background of Clinical Mastitis in Cattle Using Whole Genome Sequence.
M. Mielczarek, M. Frąszczak, J. Szyda. False Positives structural deletions.
CEN-ISBS 2017
J. Szyda. Beyond GWAS the application of SNP-chips in genomic selection.
M. Frąszczak, M. Mielczarek, J.Szyda, the G2F Consortium memebers. The analysis of CNV regions in five breeds of bulls