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Pavel Abaffy



Areas of expertise

  • Bioinformatics
  • NGS
  • RNA-Seq - experimental design, library preparation and data analysis
  • RT-qPCR
  • Work with Xenopus laevis experimental model
  • Biochemistry


I am a Ph.D. student in the group of Radek Sindelka. I study the process of embryonic wound healing and regeneration in the embryos of the frog model Xenopus laevis. I focus mainly on the method for the measurement of gene expression, especially using RNA-Seq. I assist people throughout each step of the process of this method – experimental design, sample preparation, library preparation, sequencing and data analysis. I like optimization of processes, especially those involving challenging samples (isolation in specific condition or from complicated tissue, usage of kits out of their declared limits) or “exotic” samples. Due to my interest in Informatics and Mathematics, I started to learn and explore many aspects about NGS (especially RNA-Seq) and now I assist people with their questions about this popular method. My big advantage is that I am well versed in all aspects of the RNA-Seq process, from the experimental design part, continuing with isolation and library preparation and finishing with verification of results, so I can help people with almost any crazy question they can have for their experiment.

Selected Publications

  1. The role of nitric oxide during embryonic epidermis development of Xenopus laevis. Tomankova S, Abaffy P, Sindelka R. Biol Open. 2017 Jun 15;6(6):862-871. doi: 10.1242/bio.023739
  2. Asymmetric distribution of biomolecules of maternal origin in the Xenopus laevis egg and their impact on the developmental plan. Sindelka, R., Abaffy, P., Qu, Y., Tomankova, S., Sidova, M., Naraine, R., Kolar, M., Peuchen, E., Sun, L., Dovichi, N., Kubista, M.  Scientific Reports, 8: 8315, 2018. doi: 10.1038/s41598-018-26592-1
  3. Effects of post-mortem and physical degradation on RNA integrity and quality. Sidova M, Tomankova S, Abaffy P, Kubista M, Sindelka R. Biomol Detect Quantif. 2015 Aug 21;5:3-9. doi: 10.1016/j.bdq.2015.08.002