2026

  • Słomian D, Jakimowicz M, Suchocki T, Szyda J. Comparison of BLUPF90IOD3 and MiXBLUP implementations of the single-step model applied to the Polish national dairy cattle evaluation. Journal of Dairy Research. 2026;93(2):218-222. doi:10.1017/S0022029926102088

  • Jakimowicz M, Sidorczuk K, Huyben D, Hildebrand F, Napora-Rutkowski L, Hajduk P, Sztuka M, Mielczarek M, Słomian D, Jarosz L, Szyda J. Supplementation with effective microorganisms in earthen ponds affects common carp growth and abundance of specific bacterial families. BMC Genomics2026

  • Słomian D, Żukowski K, Szyda J. A comparison of genomically enhanced breeding values predicted by different single-step approaches. Annals of Animal Science. 2026;26(3):789-796. doi:10.2478/aoas-2025-0088

2025

  • Kotlarz K, Słomian D, Zawadzka W, Szyda J. Feature Selection Strategies for Deep Learning-Based Classification in Ultra-High-Dimensional Genomic Data. International Journal of Molecular Sciences. 2025;26(16):7961. doi:10.3390/ijms26167961
  • Kotlarz K, Ziemnicka K, Budny B, Mielczarek M, Liu J, Wrotkowska E, Kaznowski J, Suchocki T, Kałużny J, Wierzbicka M, Dobosz P, Ruchała M, Szyda J. Are head and neck versus abdominal paragangliomas driven by different single nucleotide events? Journal of Applied Genetics. 2025. doi:10.1007/s13353-025-00994-0
  • Jakimowicz M, Szyda J, Jagusiak W, Topolski P, Suchocki T. Genome-wide association study and enrichment analysis for clinical health traits in Holstein-Friesian cattle. Animal. 2025;19(7):101545. doi:10.1016/j.animal.2025.101545

2024

  • Wojdak-Maksymiec K, Szyda J, Stanisławczyk A. The effects of LTF and TNFα genes on milk production are dependent on lactation state. Folia Pomeranae Universitatis Technologiae Stetinensis, Agricultura, Alimentaria, Piscaria et Zootechnica. 2024;372(71)3:51–62. doi:10.1111/fap.12000
  • Pareek C S, Sachajko M, Kalra G, Szyda J et al. Identification of trait-associated microRNA modules in liver transcriptome of pig fed with PUFAs-enriched supplementary diet. Journal of Applied Genetics. 2024. doi:10.1007/s13353-024-00800-0
  • Kotlarz K, Mielczarek M, Biecek P, Guldbrandtsen B, Szyda J. Exploring the impact of sequence context on errors in SNP genotype calling with whole genome sequencing data using AI-based autoencoder approach. NAR Genomics and Bioinformatics. 2024. doi:10.1093/nargab/lqae000
  • Kotlarz K, Mielczarek M, Biecek P, Wojdak-Maksymiec K, Suchocki T, Topolski P, Jagusiak W, Szyda J. An explainable deep learning classifier of bovine mastitis based on whole genome sequence data – circumventing the p>>n problem. International Journal of Molecular Sciences. 2024. doi:10.3390/ijms24131111
  • Sztuka M, Kotlarz K, Mielczarek M, Hajduk P, Liu J, Szyda J. NextFlow vs. plain Bash: Different approaches to the parallelisation of SNP calling from whole genome sequence data. NAR Genomics and Bioinformatics. 2024. doi:10.1093/nargab/lqae000
  • Hofman B, Szyda J, Frąszczak M, Mielczarek M. Long non-coding RNA variability in porcine skeletal muscle. Journal of Applied Genetics. 2024. doi:10.1002/ajmg.a.63400
  • Borowczyk M, Sypniewski M, Szyda J, Braszka M, Ziemnicka K, Ruchała M, Oszywa M, Król Z, Dobosz P. Genetic predisposition to differentiated thyroid cancer among Polish population. Polish Archives of Internal Medicine. 2024. doi:10.1007/s00439-024-02600-0

2023

  • Słomian D, Żukowski K, Szyda J. Heterogeneity in convergence behaviour of the single-step SNP-BLUP model across different effects and animal groups. Genetics, Selection, Evolution. 2023;55:82. doi:10.1186/s12863-023-01182-5
  • Liu J, Suchocki T, Szyda J. Bioinformatic modelling of SARS-CoV-2 pandemic with a focus on country-specific dynamics. BMC Public Health. 2023;23:148. doi:10.1186/s12889-023-15148-4
  • Lancman G, Parsa K, Kotlarz K, Avery L, Lurie A, Lieberman-Cribbin A, Cho HJ, Parekh SS, Richard S, Richter J, Rodriguez C, Rossi A, Sanchez LJ, Thibaud S, Jagannath S, Chari A. IVIg Use Associated with Ten-Fold Reduction of Serious Infections in Multiple Myeloma Patients Treated with Anti-BCMA Bispecific Antibodies. Blood Cancer Discovery. 2023;4:440–451. doi:10.1182/bloodcancerdiscov.2023.440451
  • Prochowska S, Napierkowska S, Czech B, Niżański W. Feline sperm head morphometry in relation to male pedigree and fertility. Theriogenology. 2023;208:119–125. doi:10.1016/j.theriogenology.2023.119125
  • Mroczek M, Liu J, Sypniewski M, Pieńkowski T, Itrych B, Stojak J, Pronobis-Szczylik B, Stępień M, Kaja E, Dąbrowski M, Suchocki T, Wojtaszewska M, Zawadzki P, Mach A, Sztromwasser P, Król ZJ, Szyda J, Dobosz P. The cancer-risk variant frequency among Polish population reported by the first national whole-genome sequencing study. Frontiers in Oncology. 2023;13:1045817. doi:10.3389/fonc.2023.1045817
  • Slomian D, Szyda J, Dobosz P, Stojak J, Michalska-Foryszewska A, Sypniewski M, Liu J, Kotlarz K, Suchocki T, Mroczek M, Stępień M, Sztromwasser P, Król ZJ. Better safe than sorry—Whole-genome sequencing indicates that missense variants are significant in susceptibility to COVID-19. PLoS ONE. 2023;18:e0279356. doi:10.1371/journal.pone.0279356
  • Liu J, Mroczek M, Mach A, Stępień M, Aplas A, Pronobis-Szczylik B, Bukowski S, Mielczarek M, Gajewska E, Topolski P, Król ZJ, Szyda J, Dobosz P. Genetics, Genomics and Emerging Molecular Therapies of Pancreatic Cancer. Cancers. 2023;15:779. doi:10.3390/cancers15030779
  • Kwasnik M, Socha W, Czech B, Wasiak M, Rola J, Rozek W. Protein-Coding Region Derived Small RNA in Exosomes from Influenza A Virus–Infected Cells. International Journal of Molecular Sciences. 2023;24:867. doi:10.3390/ijms24010867

2022

  • Mielczarek M, Frąszczak M, Zielak-Steciwko A E, Nowak B, Hofman B, Pierścińska J, Kruszyński W, Szyda J. An effect of large-scale deletions and duplications on transcript expression. Functional & Integrative Genomics. 2022;23:19.
  • Kotlarz K, Kosinska-Selbi B, Cai Z, Sahana G, Szyda J. Application of mixed linear models for the estimation of functional effects on bovine stature based on SNP summary statistics from a whole-genome association study. Genetics Selection Evolution. 2022;54:80.
  • Czech B, Wang Y, Wang K, Luo H, Hu L, Szyda J. Host transcriptome and microbiome interactions in Holstein cattle under heat stress condition. Frontiers in Microbiology. 2022;13.
  • Jakimowicz M, Suchocki T, Liu J, Szyda J. Modeling the spatial distribution of COVID-19 infections in Europe reveals no similarities between countries during the first year of the pandemic. Biostatistics & Epidemiology. 2022.
  • Sypniewski M, Król Z J, Szyda J, Kaja E, Mroczek M, Suchocki T, Lejman A, Stępień M, Topolski P, Dąbrowski M, Kotlarz K, Aplas A, Wasiak M, Wojtaszewska M, Zawadzki P, Pawlak A, Gil R, Dobosz P, Stojak J. Gene variants related to cardiovascular and pulmonary diseases may correlate with severe outcome of COVID-19. International Journal of Molecular Sciences. 2022;23:8696.
  • Wełeszczuk J, Kosińska-Selbi B, Cholewińska P. Prediction of Polish Holstein’s economical index and calving interval using machine learning. Livestock Science. 2022;264:105039.
  • Marašinskienė Š, Šveistienė R, Kosińska-Selbi B, Schmidtmann C, Ettema J F, Juškienė V, Kargo M. Application of a bio-economic model to demonstrate the importance of health traits in herd management of Lithuanian dairy breeds. Animals. 2022;12:1926.
  • Czech B, Szyda J, Wang K, Luo H, Wang Y. Fecal microbiota and their association with heat stress in Bos taurus. BMC Microbiology. 2022;22:171.
  • Suchocki T, Jakimowicz M, Żarnecki A, Dziech A, Szyda J. The impact of rare single nucleotide polymorphism variants on the genomic evaluation of dairy cattle. Animal Science Papers and Reports. 2022;40:135–146.
  • Szyda J, Dobosz P, Stojak J, Sypniewski M, Suchocki T, Kotlarz K, Mroczek M, Stępień M, Słomian D, Butkiewicz S, Sztromwasser P, Liu J, Król Z J. Beyond GWAS—Could genetic differentiation within the allograft rejection pathway shape natural immunity to COVID-19? International Journal of Molecular Sciences. 2022;23:6272.
  • Kołomański M, Szyda J, Frąszczak M, Mielczarek M. DNA sequence features underlying large-scale duplications and deletions in human. Journal of Applied Genetics. 2022;63:527–533.
  • Jakimowicz M, Szyda J, Żarnecki A, Jagusiak W, Morek-Kopeć M, Kosińska-Selbi B, Suchocki T. Genome-wide genomic and functional association study for workability and calving traits in Holstein cattle. Animals. 2022;12:1127.
  • Kosińska-Selbi B, Schmidtmann C, Ettema J F, Szyda J, Kargo M. Breeding goals for conservation and active Polish dairy cattle breeds derived with a bio-economic model. Livestock Science. 2022;255:104809.
  • Kotlarz K, Mielczarek M, Wang Y, Dou J, Suchocki T, Szyda J. Identification of functional features underlying heat stress response in Sprague–Dawley rats using mixed linear models. Scientific Reports. 2022;12:7671.
  • Kaja E, Lejman A, Sielski D, Sypniewski M, Gambin T, Dawidziuk M, Suchocki T, Golik P, Wojtaszewska M, Mroczek M, Stępień M, Szyda J, Lisiak-Teodorczyk K, Wolbach F, Kołodziejska D, Ferdyn K, Dąbrowski M, Woźna A, Żytkiewicz M et al. The Thousand Polish Genomes—A database of Polish variant allele frequencies. International Journal of Molecular Sciences. 2022;23:4532.
  • Sokolski M, Reszka K, Suchocki T, Adamik B, Doroszko A, Drobnik J, et al. History of heart failure in patients hospitalized due to COVID-19: relevant factor of in-hospital complications and all-cause mortality up to six months. Journal of Clinical Medicine. 2022;11:241.

2021

  • Wojtaszewska M, Stępień R, Woźna A, Piernik M, Sztromwasser P, Dąbrowski M, Gniot M, Szymański S, Socha M, Kasprzak P, Matkowski R, Zawadzki P. Validation of HER2 Status in Whole Genome Sequencing Data of Breast Cancers with the Ploidy-Corrected Copy Number Approach. Molecular Diagnosis & Therapy. 2021;26(1):105–116. doi:10.1007/s40291-021-00571-1
  • Sierpiński R, Franczuk P, Tkaczyszyn M, Suchocki T, Krekora J, Opolski G, Maggioni A, Poloński L, Ponikowski P, Jankowska E A. Burden of multimorbidity in a Polish cohort of ambulatory and hospitalized heart failure patients from two large European registry programs: prognostic implications. Polish Archives of Internal Medicine. 2021. doi:10.20452/pamw.16101
  • Suchocki T, Czech B, Duniławska A, Sławińska A, Derebecka N, Wesoły J, Siwek M, Szyda J. SNP prioritization in targeted sequencing data associated with humoral immune responses in chicken. Poultry Science. 2021;100(11):101433.
  • Tkaczyszyn M, Comín-Colet J, Voors A A, van der Meer P, Veldhuisen D J, Enjuanes C, Moliner P, Drozd M, Sierpiński R, Rozentryt P, Nowak J, Suchocki T, Banasiak W, Ponikowski P, Jankowska E A. Iron deficiency contributes to resistance to endogenous erythropoietin in anaemic heart failure patients. European Journal of Heart Failure. 2021;23(10):1677–1686. doi:10.1002/ejhf.2253
  • Sztromwasser P, Skrzypczak D, Michalak A, Fendler W. Remus: A Web Application for Prioritization of Regulatory Regions and Variants in Monogenic Diseases. Frontiers in Genetics. 2021. doi:10.3389/fgene.2021.638960

older …

  • 2020
  • Mielczarek M, Czech B, Stańczyk J, Szyda J, Guldbrandtsen B. Extraordinary Command Line: Basic Data Editing Tools for Biologists Dealing with Sequence Data. The Open Bioinformatics Journal. 2020;13(1):137–145. doi:10.2174/1875036202013010137.
  • Sierpiński R, Josiak K, Suchocki T, et al. High soluble transferrin receptor in patients with heart failure. European Journal of Heart Failure. 2020;23(6):919–932. doi:10.1002/ejhf.2036.
  • Kosińska-Selbi B, Suchocki T, Egger-Danner C, et al. Hoof disorders in cattle. Frontiers in Genetics. 2020;11:577116. doi:10.3389/fgene.2020.577116.
  • Sierpiński R, Sokolska JM, Suchocki T, et al. Heart failure hospitalization trends. ESC Heart Failure. 2020;7(6):3365–3373. doi:10.1002/ehf2.13060.
  • Kotlarz K, Szyda J, Żarnecki A. Genetic trends in Holstein cattle. Wiadomości Zootechniczne. 2020;2:3–12.
  • Kotlarz K, Mielczarek M, Suchocki T, et al. Deep learning SNP genotype classification. Journal of Applied Genetics. 2020;61(4):607–616. doi:10.1007/s13353-020-00586-0.
  • Czech B, Guldbrandtsen B, Szyda J. DNA variation patterns in Bos taurus. Scientific Reports. 2020;10:70380. doi:10.1038/s41598-020-70380-9.
  • Liu J, Suchocki T, Szyda J. Genomic evaluation tuning. Computers and Electronics in Agriculture. 2020;175:105594. doi:10.1016/j.compag.2020.105594.
  • Kosińska-Selbi B, Mielczarek M, Szyda J. lncRNA in livestock review. Animal. 2020;14(10):2003–2013. doi:10.1017/s1751731120000841.
  • Suchocki T, Egger-Danner C, Schwarzenbacher H, Szyda J. GWAS hoof disorders. Journal of Dairy Science. 2020;103(5):4483–4494. doi:10.3168/jds.2019-17542.
  • 2019
  • Barski P, Mielczarek M, Frąszczak M, Szyda J. Copy number variants. Acta Scientiarum Polonorum Zootechnica. 2019;18:25–30.
  • Szyda J, Mielczarek M, Frąszczak M, et al. Mastitis genetics. Animal. 2019;13:2156–2163.
  • 2018
  • Czech B, Frąszczak M, Mielczarek M, Szyda J. Breed-specific SNPs. PLoS ONE. 2018;13:e0198419.
  • Mielczarek M, Frąszczak M, Williams JL, et al. CNV landscape in cattle. BMC Genomics. 2018;19:410.
  • Lewczuk D, et al. Osteochondrosis selection in horses. Journal of Applied Genetics. 2018;59:225–230.
  • 2017
  • Szyda J, Suchocki T, Qanbari S, Liu Z, Simianer H. Holstein population stratification. Journal of Applied Genetics. 2017;58:521–526.
  • Mielczarek M, Frąszczak M, Giannico R, et al. CNV in dairy cattle. Journal of Dairy Science. 2017;100:5515–5525.
  • Suchocki T, Liu Z, Żarnecki A, Szyda J. Genomic evaluation model. Animal Science Papers and Reports. 2017;35:193–198.
  • Lewczuk D, et al. Horse SNP osteochondrosis. Animal Production Science. 2017;57:608–613.
  • Chung NC, Szyda J, Frąszczak M. Bull genome structure. Scientific Reports. 2017;7:40688.
  • 2016
  • Jankowska EA, Tkaczyszyn M, et al. Iron therapy meta-analysis. European Journal of Heart Failure. 2016;18(7):786–795.
  • Suchocki T, Wojdak-Maksymiec K, Szyda J. Gene networks milk traits. Czech Journal of Animal Science. 2016;61:526–538.
  • Mielczarek M, Szyda J. SNP calling review. Journal of Applied Genetics. 2016;57:71–79.
  • Frąszczak M, Suchocki T, Szyda J. Gene network analysis. Journal of Applied Genetics. 2016;57:129–133.
  • Frąszczak M, Szyda J. GWAS SNP selection. Journal of Applied Genetics. 2016;57:207–213.
  • 2015
  • Szyda J, et al. Whole-genome variation cows. Mammalian Genome. 2015;28:658–665.
  • Suchocki T, Szyda J. GWAS semen traits. Journal of Dairy Science. 2015;98:5774–5780.
  • Siwek M, et al. Chicken immune QTL. Animal Genetics. 2015;46:247–254.
  • 2014
  • Szyda J, Komisarek J, Antkowiak I. Time-dependent gene effects. Animal Genetics. 2014;45:322–328.
  • 2013
  • Ponikowska B, et al. Iron status diabetes. Diabetes Care. 2013;36:4147–4156.
  • Gminterek A, et al. Porphyromonas gene marker. PLoS ONE. 2013;8:e67719.
  • Wojdak-Maksymiec K, Szyda J, Strabel T. Mastitis polymorphism. BMC Veterinary Research. 2013;9:114.
  • Jankowska EA, et al. Iron deficiency heart failure. JACC. 2013;61(Suppl):E749.
  • Silesian A, Szyda J. tagSNP selection. Animal. 2013;7:1227–1230.
  • Suchocki T, Szyda J, Zhang Q. QTL regression. Journal of Applied Genetics. 2013;54:49–60.
  • Szyda J, et al. SNP selection strategies. Czech Journal of Animal Science. 2013;58:136–145.
  • Moska M, et al. Common shrew genetics. Hereditas. 2013;149:197–206.
  • 2012
  • Bartoszewicz J, Frąszczak M. Stochastic order estimators. Probability and Mathematical Statistics. 2012;22:57–67.
  • Frąszczak M, Bartoszewicz J. Distribution invariance. Applicationes Mathematicae. 2012;39:283–292.
  • Wojdak-Maksymiec K, et al. Mastitis polymorphism. J Anim Vet Adv. 2012;11:2230–2237.
  • Zabolewicz T, et al. Lactoferrin gene. Livestock Science. 2012;149:267–274.
  • Mucha A, Wierzbicki H. QTL MAS models. BMC Proceedings. 2012;6:S11.
  • Siwek M, et al. Chicken QTL. Journal of Applied Genetics. 2012;53:115–119.
  • Oleński K, et al. Beta-casein SNP. Animal Science Papers and Reports. 2012;30:5–12.
  • 2011–2005 (selected)
  • Szyda J, et al. Genomic evaluation fitting. Journal of Applied Genetics. 2011;52:363–366.
  • Suchocki T, Szyda J. Growth modelling. Journal of Applied Genetics. 2011;52:95–100.
  • Szyda J, et al. Marker longevity traits. BMC Genetics. 2011;12:30.
  • Wierzbicki H, et al. Boar semen traits. Medycyna Weterynaryjna. 2010;66:765–769.
  • Oleński K, et al. Gene polymorphism milk traits. Livestock Science. 2010;131:137–140.
  • Suchocki T, Komisarek J, Szyda J. Candidate gene modelling. Journal of Dairy Science. 2007;90:2971–2979.
  • Viitala S, et al. Bovine receptor genes. Genetics. 2006;173:2151–2164.
  • Szyda J, Liu Z, Reinhardt F. QTL estimation. Journal of Dairy Science. 2005;88:356–367.