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Pavel Abaffy



Areas of expertise

  • Bioinformatics
  • NGS
  • RNA-Seq
  • Single-cell RNA-Seq
  • Spatial transcriptomics
  • RT-qPCR


I finished my PhD in the group of Radek Sindelka, where I was studying processes of embryonic wound healing and regeneration in the embryos of Xenopus laevis. During my PhD study, I started to learn new methods for study of transcriptomics – bulk RNA-seq, single-cell RNA-seq and spatial transcriptomics. When I finished PhD, I started to work in the group of Lukas Valihrach on the projects of neurodegeneration and acute brain injury using all the knowledge on RNA-seq methods. I guide my colleagues and our collaborators throughout each step of the process of transcriptomics methods – experimental design, sample preparation, library preparation, sequencing and data analysis. I love process of optimization, especially those involving challenging samples (isolation in specific condition or from complicated tissue, usage of kits out of their declared limits etc.) 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. Transient astrocyte-like NG2 glia subpopulation emerges solely following permanent brain ischemia. Kirdajova D, Valihrach L, Valny M, Kriska J, Krocianova D, Benesova S, Abaffy P, Zucha D, Klassen R, Kolenicova D, Honsa P, Kubista M, Anderova M. Glia. 2021 Jul 27. doi: 10.1002/glia.24064.

  2. Restriction of an intron size en route to endothermy. Královičová J, Borovská I, Pengelly R, Lee E, Abaffy P, Šindelka R, Grutzner F, Vořechovský I. Nucleic Acids Res. 2021 Mar 18;49(5):2460-2487. doi: 10.1093/nar/gkab046.

  3. Decoding the Transcriptional Response to Ischemic Stroke in Young and Aged Mouse Brain. Androvic P, Kirdajova D, Tureckova J, Zucha D, Rohlova E, Abaffy P, Kriska J, Valny M, Anderova M, Kubista M, Valihrach L. Cell Rep. 2020 Jun 16;31(11):107777. doi: 10.1016/j.celrep.2020.107777.

  4. NormQ: RNASeq normalization based on RT-qPCR derived size factors. Naraine R, Abaffy P, Sidova M, Tomankova S, Pocherniaieva K, Smolik O, Kubista M, Psenicka M, Sindelka R. Comput Struct Biotechnol J. 2020 May 14;18:1173-1181. doi: 10.1016/j.csbj.2020.05.010. eCollection 2020.

  5. The role of nitric oxide during embryonic wound healing. Abaffy P, Tomankova S, Naraine R, Kubista M, Sindelka R. BMC Genomics. 2019 Nov 6;20(1):815. doi: 10.1186/s12864-019-6147-6.

  6. Alternative assembly of respiratory complex II connects energy stress to metabolic checkpoints. Bezawork-Geleta A, Wen H, Dong L, Yan B, Vider J, Boukalova S, Krobova L, Vanova K, Zobalova R, Sobol M, Hozak P, Novais SM, Caisova V, Abaffy P, Naraine R, Pang Y, Zaw T, Zhang P, Sindelka R, Kubista M, Zuryn S, Molloy MP, Berridge MV, Pacak K, Rohlena J, Park S, Neuzil J. Nat Commun. 2018 Jun 7;9(1):2221. doi: 10.1038/s41467-018-04603-z.

  7. 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. Sci Rep. 2018 May 29;8(1):8315. doi: 10.1038/s41598-018-26592-1.

  8. Adverse effects of Hif1a mutation and maternal diabetes on the offspring heart. Cerychova R, Bohuslavova R, Papousek F, Sedmera D, Abaffy P, Benes V, Kolar F, Pavlinkova G. Cardiovasc Diabetol. 2018 May 12;17(1):68. doi: 10.1186/s12933-018-0713-0.

  9. 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.

  10. Asymmetric Localization and Distribution of Factors Determining Cell Fate During Early Development of Xenopus laevis. Sindelka R, Sidova M, Abaffy P, Kubista M. Results Probl Cell Differ. 2017;61:229-241. doi: 10.1007/978-3-319-53150-2_10.

  11. 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.