Biometrics and Bioinformatics Team

Leader

dr. hab. Grzegorz Koczyk

Members

prof. dr hab. Paweł Krajewski

dr Katarzyna Czyż

dr Dariusz Kruszka

dr inż. Monika Mokrzycka

mgr Maria Nuc (PhD student)

mgr Michał Kawaliło (PhD student)

lic. Michał Stanoch

From left to right: P. Krajewski, D. Kruszka, K. Czyż, M. Stanoch, M. Nuc, M. Kawaliło, M. Mokrzycka, G. Koczyk

Research profile

The Team conducts research on the modelling and analysis of data from biological experiments, phylogenomic annotation of reference and
newly sequenced taxa (plants and plant-associated microorganisms), as well as generalized data processing tools and structures. Our main
scope of interest lies in the data obtained from sequencing or chromatography experiments involving secondary metabolites, biotic and abiotic stimuli. Due to high input volumes and the complementarity of analyses in biological projects, the integration of diverse data sets plays a key role in our activities. For this purpose, we employ statistical, informatic and bioinformatic methods tailored to analysis of experimental data with special focus on the fields of genetics, genomics and plant breeding programs.

Our main achievements revealed that:

• The "minimum information" principle can be used for standardization of formatting and annotation of plant phenotypic data, as shown by the development of the Minimum Information About Plant Phenotypic Experiment (MIAPPE) recommendations (Krajewski et al., 2015; Ćwiek-Kupczyńska et al., 2016; Papoutsoglou et al., 2020; www.miappe.org; projects: TransPlant, EPPN2020)
• A significantly depleted representation across 13 plant gene families, shows that losses of genes involved in trichome development, defense and wounding responses were strongly associated with development of stable rhizobial symbiosis in legumes (Czyż et al. 2022; NCN/SONATA grant no. 2016/21/D/NZ8/01300).
• Semantic approach can be used to structure results of linear mixed model analyses and improve understanding of the experimental data and scientific conclusions (Ćwiek-Kupczyńska et al., 2020; projects: EPPN2020, NCN grant no. 2016/21/N/ST6/02358)
• Xanthomonas effector XopD manipulates the expression of Arabidopsis abscisic acid signalling-related genes and activates OSCA1.1, a gene encoding a calcium-permeable channel required for stomatal closure in response to osmotic stress (You et. al., 2023).
• A survey of 157 genomes of early-diverging fungi (Mucoromycotina) shows that a considerable representation of both terpene and nonribosomal peptide synthetase (NRPS)-like candidate secondary metabolite clusters (SMCs) exists in these (previously) underannotated taxa (Koczyk et al. 2021; NCN/OPUS grant no. 2016/21/B/NZ9/01875).
• Genome-wide association study provided information useful in procedures of hybrid breeding of wheat (Mokrzycka et al., 2022; Tyrka et al., 2021; project HYBRE)   
• Elevated temperature can cause genotype-specific changes in crown tissue of barley plants concerning gene expression, as studied by the high-throughput transcriptome sequencing (Mikołajczak et al., 2022; project NCN no. 2016/22/M/NZ9/00251).

Key words

linear mixed models, functional data modelling, multivariate analysis, phylogenomics, evolutionary bioinformatics, secondary metabolites, multiomic data integration, next generation sequencing data analysis  

Selected recent publications (see all in Scopus)

Matuszkiewicz M, Grądzielewska A, Święcicka M, Ozturk A, Mokrzycka M, Igbari AD, Song J, Kilian A, Rakoczy-Trojanowska M (2024). Identification of quantitative trait loci associated with leaf rust resistance in rye by precision mapping. BMC Plant Biology 24: 291 DOI 10.1186/s12870-024-04960-6

Filipia K, Klein D, Mokrzycka M (2024). Discrepancy between structured matrices in the power analysis of a separability test, Computational Statistics & Data Analysis 192: 107907 DOI 10.1016/j.csda.2023.107907.

You Y, Koczyk G, Nuc M, Morbitzer R, Holmes DR, von Roepenack-Lahaye E, Hou S, Giudicatti A, Gris C, Manavella PA, Noël LD, Krajewski P, Lahaye T (2023) The eINTACT system dissects bacterial exploitation of plant osmosignalling to enhance virulence. Nat. Plants 9, 128–141  DOI: 10.1038/s41477-022-01302-y

Czyż KB, Taylor CM, Kawaliło M, Koczyk G (2022) Gain or Loss? Evidence for Legume Predisposition to Symbiotic Interactions with Rhizobia via Loss of Pathogen-Resistance-Related Gene Families. Int J Mol Sci.; 23(24):16003. DOI: 10.3390/ijms232416003

Mokrzycka M, Stojałowski S, Tyrka M, Matysik P, Żmijewska B, Marcinkowski R, Woźna-Pawlak U, Martofel R, Rokicki M, Rakoczy-Trojanowska M, Krajewski P  (2022). Genome-Wide Association Analysis for Hybrid Breeding in Wheat. Int. J. Mol. Sci. 2022, 23, 15321, 10.3390/ijms232315321

Mikolajczak K, Kuczynska A, Ogrodowicz P, Kielbowicz-Matuk A, Cwiek-Kupczynska H, Daszkowska-Golec A, Szarejko I, Surma M, Krajewski P (2022). High-throughput sequencing data revealed genotype-specific changes evoked by heat stress in crown tissue of barley sdw1 near-isogenic lines. BMC Genomics 23, 1: 177, 10.1186/s12864-022-08410-1

Hall RD, D'Auria JC, Ferreira ACS, Gibon Y, Kruszka D, Mishra P, van de Zedde R (2022). High-throughput plant phenotyping: a role for metabolomics? Trends in Plant Science 27, 6: 549-563, 10.1016/j.tplants.2022.02.001

Koczyk G, Pawłowska J, Muszewska A (2021) Terpenoid Biosynthesis Dominates among Secondary Metabolite Clusters in Mucoromycotina Genomes. J Fungi (Basel).;7(4):285. DOI: 10.3390/jof7040285

Czyż KB, Książkiewicz M, Koczyk G, Szczepaniak A, Podkowiński J, Naganowska B (2020) A Tale of Two Families: Whole Genome and Segmental Duplications Underlie Glutamine Synthetase and Phosphoenolpyruvate Carboxylase Diversity in Narrow-Leafed Lupin (Lupinus angustifolius L.). Int J Mol Sci.;21(7):2580. DOI: 10.3390/ijms21072580

Ćwiek-Kupczyńska H, Filipiak K, Markiewicz A, Rocca-Serra Ph, Gonzalez-Beltran AN, Sansone SA, Millet EJ, van Eeuwijk F, Ławrynowicz A, Krajewski P (2020) Semantic concept schema of the linear mixed model of experimental observations. Scientific Data 7: 70. DOI: 10.1038/s41597-020-0409-7

Projects (finished recently or current)