Conferences

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

2024

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.

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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.

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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.

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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.

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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.

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B. Kosińska-Selbi, Ch. Schmidtmann, M. Kargo, J. F. Ettema, J. Szyda. Estimation of economical values for Polish Holstein, Polish Red and Scandinavian Red.

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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.

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T. Suchocki, A. Żarnecki, M. Jakimowicz and J. Szyda. Impact of rare SNP variants on the genomic evaluation for conception rate.

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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