The Department conducts research on the modeling and analysis of data from biological experiments as well as data processing structures and tools. Data from experiments using protocols such as next generation sequencing or chromatography are of particular interest. Due to numerous observations and the complementarity of these analyses in biological designs, particularly important issues of interest concern the integration of different data sets and phylogenomic approaches that take into account the interpretation of data in an evolutionary context.

Research profile

• basic research in the field of statistical, IT and bioinformatical methods in the analysis of the integrated biological experimental results, with particular emphasis on experiments performed in genetics, genomics of plants and plant-associated microorganisms, as well as in plant breeding,
• creating database standards and tools for storing and processing data from plant experiments,
• interdisciplinary research using molecular and experimental biology methods for the acquisition and interpretation of multiomic data

Methods

• analysis of biological data, in particular:
  • analysis of multiomic data, in particular the results of high-throughput DNA sequencing in transcriptomic and epigenomic experiments,
  • interpretation and integration of data from experiments using DNA sequencing and plant phenotyping,
  • design and verification of molecular plant diagnostics methods based on evolutionary and phylogenetic criteria
• statistical and (bio) information methods:
  • analysis of linear mixed models, functional data modeling, multivariate analysis,
  • standardization of experimental information and relational databases,
  • methods of phylogenetic tree reconciliation and analysis of protein domain architecture
   

Current reserach activities

• developing methods of processing and interpreting the results of experiments conducted to assess gene expression, protein and DNA interactions, and the state of chromatin,
• studies of the evolutionary origin of legume plants' ability to create a stable symbiosis with papillary bacteria,
• reconstruction of the probable origin of the ability of higher fungi to synthesize bioactive macrolactone polyketides
• development of semantic models for phenotypic data

Selected papers

• Czyż, K. B., 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.). International Journal of Molecular Sciences, 21(7), 2580
• Koczyk, G., Pawłowska, J., Muszewska, A. (2021) Terpenoid Biosynthesis Dominates among Secondary Metabolite Clusters in Mucoromycotina Genomes. Journal of Fungi (Basel, Switzerland), 7(4), 285
• Papoutsoglou EA, Faria D, Arend D, Arnaud E, Athanasiadis IN, Chaves I, Coppens F, Cornut G, Costa BV, Ćwiek-Kupczyńska H, Droesbeke B, Finkers R, Gruden K, Junker A, King GJ, Krajewski P, Lange M, Laporte MA, Michotey C, Oppermann M, Ostler R, Poorter H, Ramı Rez-Gonzalez R, Ramšak Ž, Reif JC, Rocca-Serra P, Sansone SA, Scholz U, Tardieu F, Uauy C, Usadel B, Visser RGF, Weise S, Kersey PJ, Miguel CM, Adam-Blondon AF, Pommier C. (2020) Enabling reusability of plant phenomic datasets with MIAPPE 1.1. New Phytologist; 227(1):260-273
• Tyrka M, Mokrzycka M, Bakera B, Tyrka D, Szeliga M, Stojałowski S, Matysik P, Rokicki M, Rakoczy-Trojanowska M, Krajewski P. (2021) Evaluation of genetic structure in European wheat cultivars and advanced breeding lines using high-density genotyping-by-sequencing approach. BMC Genomics; 22(1):81
• Winkelmüller TM, Entila F, Anver S, Piasecka A, Song B, Dahms E, Sakakibara H, Gan X, Kułak K, Sawikowska A, Krajewski P, Tsiantis M, Garrido-Oter R, Fukushima K, Schulze-Lefert P, Laurent S, Bednarek P, Tsuda K. (2021) Gene expression evolution in pattern-triggered immunity within Arabidopsis thaliana and across Brassicaceae species. Plant Cell; 33(6):1863–87

Research projects