Biometry and Bioinformatics Team

Head
 
Staff
Katarzyna Czyż, PhD
Hanna Ćwiek-Kupczyńska, PhD
Monika Mokrzycka, PhD
Maria Nuc, MSc (PhD student)
Michał Kawaliło, MSc (PhD student)
 
 

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

Project number: 2016/22/M/NZ9/00251
Project title: Regulation of semi-dwarf sdw1/denso gene expression in barley (Hordeum vulgare L.) and its association with plant architecture and physiology
Project type: HARMONIA 8
Principal Investigator: Paweł Krajewski
Duration: 17 April 2017 - 16 April 2022
 
Project number: 7331013
Project title: European Plant Phenotyping Network 2020 (EPPN2020)
Project type: H2020-INFRAIA-2016-1
Principal Investigator: Francois Tardieu, INRA, Francja
Principal Investigator (IPG PAS): Paweł Krajewski
Duration: 1 May 2017 - 31 October 2021
 
Project number: BIOSTRATEG3/343665/6/NCBR/2017
Project title: An integrated strategy for reactivating Polish breeding of hybrid wheat (Acronym: HYBRE)
Principal Investigator: Stefan Malepszy (SGGW)
Principal Investigator (IPG PAS): Paweł Krajewski
Duration: 21 August 2017 -  30 April 2022
 
Project number: 2016/21/B/NZ9/01875
Project title: Origins and spread of the capacity towards synthesis of bioactive macrolactones in higher fungi
Project type: OPUS 11
Principal Investigator: Grzegorz Koczyk
Duration: 7 March 2017 -  6 March 2022
 
Project number: 2016/21/D/NZ8/01300
Project title: Genome dynamics underlying nodulation capacity of early diverging legumes
Project type: SONATA 11
Principal Investigator: Katarzyna Czyż (Wyrwa)
Duration: 3 March 2017 -  2 March 2022