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Pavel Abaffy, PhD


Pavel Abaffy

Pavel Abaffy, PhD


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. Spatiotemporal transcriptomic map of ischemic brain injury. Zucha D, Abaffy P, Kirdajova D, Jirak D, Anderova M, Kubista M, Valihrach L. BioRxiv 2023.03.28.534553; doi: 10.1101/2023.03.28.534553.
  2. NEUROD1 reinforces endocrine cell fate acquisition in pancreatic development. Bohuslavova R, Fabriciova V, Smolik O, Lebrón-Mora L, Abaffy P, Benesova S, Zucha D, Valihrach L, Berkova Z, Saudek F, Pavlinkova G. Nat Commun. 2023 Sep 9;14(1):5554. doi: 10.1038/s41467-023-41306-6.
  3. Complement C3a treatment accelerates recovery after stroke via modulation of astrocyte reactivity and cortical connectivity. Stokowska A, Aswendt M, Zucha D, Lohmann S, Wieters F, Moran Suarez J, Atkins AL, Li Y, Miteva M, Lewin J, Wiedermann D, Diedenhofen M, Torinsson Naluai Å, Abaffy P, Valihrach L, Kubista M, Hoehn M, Pekny M, Pekna M. J Clin Invest. 2023 Mar 30:e162253. doi: 10.1172/JCI162253. IF = 19.456.
  4. Cortical glia in SOD1(G93A) mice are subtly affected by ALS-like pathologyFilipi T, Matusova Z, Abaffy P, Vanatko O, Tureckova J, Benesova S, Kubiskova M, Kirdajova D, Zahumensky J, Valihrach L, Anderova M.Sci Rep. 2023 Apr 21;13(1):6538. doi: 10.1038/s41598-023-33608-y.
  5. Glioblastoma and cerebral organoids: development and analysis of an in vitro model for glioblastoma migrationFedorova V, Pospisilova V, Vanova T, Cerna KA, Abaffy P, Sedmik J, Raska J, Vochyanova S, Matusova Z, Houserova J, Valihrach L, Hodny Z, Bohaciakova D.Mol Oncol. 2023 Feb 6. doi: 10.1002/1878-0261.13389.
  6. Mitochondrial respiration supports autophagy to provide stress resistance during quiescence. Magalhaes-Novais S, Blecha J, Naraine R, Mikesova J, Abaffy P, Pecinova A, Milosevic M, Bohuslavova R, Prochazka J, Khan S, Novotna E, Sindelka R, Machan R, Dewerchin M, Vlcak E, Kalucka J, Stemberkova Hubackova S, Benda A, Goveia J, Mracek T, Barinka C, Carmeliet P, Neuzil J, Rohlenova K, Rohlena J. Autophagy. 2022 Mar 8:1-18. doi: 10.1080/15548627.2022.2038898.
  7. 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.
  8. 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.
  9. 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.
  10. 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.