Publications

Mujahid Ali Shah, Effrosyni Fatira, Viktoriia Iegorova, Xuan Xie, David Gela, Marek Rodina, Roman Franěk, Martin Pšenička, Taiju Saito. Blastomeres derived from the vegetal pole provide extra-embryonic nutrition to sturgeon (Acipenser) embryos: Transition from holoblastic to meroblastic cleavage. Aquaculture (2022). 551, 737899. https://doi.org/10.1016/j.aquaculture.2022.737899.

Valihrach L, Matusova Z, Zucha D, Klassen R, Benesova S, Abaffy P, Kubista M and Anderova M (2022) Recent advances in deciphering oligodendrocyte heterogeneity with single-cell transcriptomics. Front. Cell. Neurosci. 16:1025012. doi: 10.3389/fncel.2022.1025012

Iegorova V, Naraine R, Psenicka M, Zelazowska M and Sindelka R (2022) Comparison of RNA localization during oogenesis within Acipenser ruthenus and Xenopus laevis. Front. Cell Dev. Biol. 10:982732. doi: 10.3389/fcell.2022.982732

ISL1 is necessary for auditory neuron development and contributes toward tonotopic organization. Filova I, Pysanenko K, Tavakoli M, Vochyanova S, Dvorakova M, Bohuslavova R, Smolik O, Fabriciova V, Hrabalova P, Benesova S, Valihrach L, Cerny J, Yamoah EN, Syka J, Fritzsch B, Pavlinkova G. Proc Natl Acad Sci U S A. 2022 Sep 13;119(37):e2207433119. doi: 10.1073/pnas.2207433119.

Naraine R, Iegorova V, Abaffy P, Franek R, Soukup V, Psenicka M, Sindelka R. Evolutionary conservation of maternal RNA localization in fishes and amphibians revealed by TOMO-Seq. Dev Biol. 2022 Jun 22:S0012-1606(22)00130-0. doi: 10.1016/j.ydbio.2022.06.013.

Gazo I, Naraine R, Lebeda I, Tomčala A, Dietrich M, Franěk R, Pšenička M, Šindelka R. Transcriptome and Proteome Analyses Reveal Stage-Specific DNA Damage Response in Embryos of Sturgeon (Acipenser ruthenus). International Journal of Molecular Sciences. 2022; 23(12):6392. https://doi.org/10.3390/ijms23126392

Smieszek A, Marcinkowska K, Pielok A, Sikora M, Valihrach L, Carnevale E, Marycz K. Obesity Affects the Proliferative Potential of Equine Endometrial Progenitor Cells and Modulates Their Molecular Phenotype Associated with Mitochondrial Metabolism. Cells. 2022; 11(9):1437. https://doi.org/10.3390/cells11091437

Small RNA-Sequencing for Analysis of Circulating miRNAs: Benchmark Study. Androvic P, Benesova S, Rohlova E, Kubista M, Valihrach L. J Mol Diagn. 2022 Jan 23:S1525-1578(22)00011-3. doi: 10.1016/j.jmoldx.2021.12.006.

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.

Tureckova J, Kamenicka M, Kolenicova D, Filipi T, Hermanova Z, Kriska J, Meszarosova L, Pukajova B, Valihrach L, Androvic P, Zucha D, Chmelova M, Vargova L and Anderova M (2022) Compromised Astrocyte Swelling/Volume Regulation in the Hippocampus of the Triple Transgenic Mouse Model of Alzheimer’s Disease. Front. Aging Neurosci. 13:783120. doi: 10.3389/fnagi.2021.783120.

Isolation and Characterization of Highly Pure Type A Spermatogonia From Sterlet (Acipenser ruthenus) Using Flow-Cytometric Cell Sorting. Xie X, Tichopád T, Kislik G, Langerová L, Abaffy P, Šindelka R, Franěk R, Fučíková M, Steinbach C, Shah MA, Šauman I, Chen F, Pšenička M. Front Cell Dev Biol. 2021 Dec 10;9:772625. doi: 10.3389/fcell.2021.772625.

Zucha D, Kubista M, Valihrach L. Tutorial: Guidelines for Single-Cell RT-qPCR. Cells. 2021; 10(10):2607. https://doi.org/10.3390/cells10102607

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.

Benesova, S.; Kubista, M.; Valihrach, L. Small RNA-Sequencing: Approaches and Considerations for miRNA Analysis. Diagnostics 2021, 11, 964. https://doi.org/10.3390/diagnostics11060964.

Ultrasensitive circulating tumor DNA analysis enables precision medicine: experimental workflow considerations. Andersson D, Kristiansson H, Kubista M, Ståhlberg A. Expert Rev Mol Diagn. 2021 Mar 8:1-12. doi: 10.1080/14737159.2021.1889371.

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 Feb 8:gkab046. doi: 10.1093/nar/gkab046.

Shah, M.A., Saito, T., Šindelka, R. et al. Novel technique for definite blastomere inhibition and distribution of maternal RNA in sterlet Acipenser ruthenus embryo. Fish Sci (2021).

Ancient Sturgeons Possess Effective DNA Repair Mechanisms: Influence of Model Genotoxicants on Embryo Development of Sterlet, Acipenser ruthenus. Gazo I, Franěk R, Šindelka R, Lebeda I, Shivaramu S, Pšenička M, Steinbach C. Int J Mol Sci. 2020 Dec 22;22(1):E6. doi: 10.3390/ijms22010006.

Cautionary note on contamination of reagents used for molecular detection of SARS-CoV-2. Huggett JF, Benes V, Bustin SA, Garson JA, Harris K, Kammel M, Kubista M, McHugh TD, Moran-Gilad J, Nolan T, Pfaffl MW, Salit M, Shipley G, Vallone PM, Vandesompele J, Wittwer C, Zeichhardt H. Clin Chem. 2020 Sep 7:hvaa214. doi: 10.1093/clinchem/hvaa214.

The Digital MIQE Guidelines Update: Minimum Information for Publication of Quantitative Digital PCR Experiments for 2020. dMIQE Group. Clin Chem. 2020 Aug 1;66(8):1012-1029. doi: 10.1093/clinchem/hvaa125.

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.

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.

Pre-analytical factors affecting the establishment of a single tube assay for multiparameter liquid biopsy detection in melanoma patients. Schneegans S, Lück L, Besler K, Bluhm L, Stadler JC, Staub J, Greinert R, Volkmer B, Kubista M, Gebhardt C, Sartori A, Irwin D, Serkkola E, Af Hällström T, Lianidou E, Sprenger-Haussels M, Hussong M, Mohr P, Schneider SW, Shaffer J, Pantel K, Wikman H. Mol Oncol. 2020 May;14(5):1001-1015. doi: 10.1002/1878-0261.12669.

Liquid biopsy analysis in cancer diagnostics. Andersson D, Kubista M, Ståhlberg A. Mol Aspects Med. 2020 Apr;72:100839. doi: 10.1016/j.mam.2019.100839.

Multicenter Evaluation of Circulating Cell-Free DNA Extraction and Downstream Analyses for the Development of Standardized (Pre)analytical Work Flows. Lampignano R, Neumann MHD, ..., Kubista M, Ammerlaan W, Sprenger-Haussels M, Schlange T, Heitzer E; Innovative Medicines Initiative CANCER-ID Consortium. Clin Chem. 2019 Oct 18. pii: clinchem.2019.306837. doi: 10.1373/clinchem.2019.306837.

Performance Comparison of Reverse Transcriptases for Single-Cell Studies. Daniel Zucha, Peter Androvic, Mikael Kubista, Lukas Valihrach.Clin Chem. 2020 Jan 1;66(1):217-228. doi: 10.1373/clinchem.2019.307835.

The role of nitric oxide during embryonic wound healing. Pavel Abaffy, Silvie Tomankova, Ravindra Naraine, Mikael Kubista & Radek Sindelka. BMC Genomics volume 20, Article number: 815 (2019).

High potassium exposure reveals the altered ability of astrocytes to regulate their volume in the aged hippocampus of GFAP/EGFP mice. D. Kolenicova, J. Tureckova, B. Pukajova, L. Harantova, J. Kriska, D. Kirdajova, I. Vorisek, M. Kamenicka, L. Valihrach, P. Androvic, M. Kubista, L. Vargova, M. Anderova. Neurobiol Aging. 2020 Feb;86:162-181. doi: 10.1016/j.neurobiolaging.2019.10.009. Epub 2019 Oct 22.

Valihrach L, Androvic P, Kubista M. Circulating miRNA analysis for cancer diagnostics and therapy. Mol Aspects Med. 2020 Apr;72:100825. doi: 10.1016/j.mam.2019.10.002.

Kloten V, Neumann MHD, Di Pasquale F, Sprenger-Haussels M, Shaffer JM, Schlumpberger M, Herdean A, Betsou F, Ammerlaan W, Af Hällström T, Serkkola E, Forsman T, Lianidou E, Sjöback R, Kubista M, Bender S, Lampignano R, Krahn T, Schlange T; CANCER-ID consortium. Clin Chem. 2019 Jun 24. pii: clinchem.2019.303271. doi: 10.1373/clinchem.2019.303271.