Laboratory of Gene Expression

High-throughput gene expression profiling and single-cell analysis using qPCR and RNA-Seq

Group leader: prof. Mikael Kubista, PhD

Detailed laboratory website: www.labgenexp.eu
 

Kubista's laboratory is Czech's leading academic laboratory specialized in high-throughput gene expression profiling and single-cell analysis using real-time quantitative PCR (qPCR) and RNA-sequencing. We have several basic research projects in the field of developmental biology and stem cells, and applied projects in cancer and neurological research. We also develop methods and applications for nucleic acid analyses and we are active in the area of standardization.

Methodology and Quality Controls:

  •        Single-cell expression profiling in research and diagnostics
  •        Quality control tools
  •        Method development and standardization

Developmental biology:

  •        Role of nitric oxide signaling during early development, regeneration and wound healing
  •        Comparison of gene expression and signaling pathways during regeneration and wound healing
  •        Localization of maternal RNAs in oocytes and their distribution among blastomeres during early development

Neurobiology:

  •        Characterization of glial cell following CNS injuries
  •        Glial cells - the key players in the progression of amyotrophic lateral sclerosis
  •        Single-cell transcriptomic analysis of Alexander disease
  •        Role and therapeutic applications of microRNAs in CNS injuries

Collaborators: University Medical Center Utrecht (UMCU) Brain Center, University of Gothenburg, University of Notre Dame USA, Czech Academy of Sciences (Institute of Experimental Medicine, Institute of Animal Physiology and Genetics), 2st Medical Faculty at the Charles University, FROV University of South Bohemia

Abaffy Pavel, Ing., Ph.D.
Benešová Zuzana, Mgr.
Benešová Šárka, Mgr.
Iegorova Viktoriia, M.Sc., Ph.D.
Kašparová Veronika
Klassen Ruslan Alexandrovič, Ing.
Kraus Daniel, Mgr.
Kubista Mikael, prof. Dr., Ph.D.
Naraine Ravindra
Netušil Jiří, Bc.
Šimková Kateřina, Bc.
Šindelka Radek, Mgr., Ph.D.
Valihrach Lukáš, Ing., Ph.D.
Žucha Daniel, Mgr.

2021

  • Andersson, D., Kristiansson, H., Kubista, M., Stahlberg, A. (2021) "Ultrasensitive circulating tumor DNA analysis enables precision medicine: experimental workflow considerations" Exp Rev of Mol Diag, DOI:10.1080/14737159.2021.1889371
  • Kralovicova, J., Borovska, I., Pengelly, R., Lee, E., Abaffy, P., Sindelka, R., Grutzner, F., & Vorechovsky, I. (2021)."Restriction of an intron size en route to endothermy." Nucleic Acids Research. https://doi.org/10.1093/nar/gkab046 

2020

  • Andersson, D., Kubista, M., & Stahlberg, A. (2020). "Liquid biopsy analysis in cancer diagnostics." Mol Aspects Med, 72, 100839
  • Androvic, P., Kirdajova, D., Tureckova, J., Zucha, D., Rohlova, E., Abaffy, P., Kriska, J., Valny, M., Anderova, M., Kubista, M., & Valihrach, L. (2020). "Decoding the Transcriptional Response to Ischemic Stroke in Young and Aged Mouse Brain." Cell Rep, 31(11), 107777.
  • dMIQE Group & Huggett, J. F. (2020). "The Digital MIQE Guidelines Update: Minimum Information for Publication of Quantitative Digital PCR Experiments for 2020." Clin Chem, 66(8), 1012-1029
  • Gazo, I., Franek, R., Sindelka, R., Lebeda, I., Shivaramu, S., Psenicka, M., & Steinbach, C. (2020). "Ancient Sturgeons Possess Effective DNA Repair Mechanisms: Influence of Model Genotoxicants on Embryo Development of Sterlet, Acipenser ruthenus." Int J Mol Sci, 22(1).
  • Grigg, I., Ivashko-Pachima, Y., Hait, T. A., Korenkova, V., Touloumi, O., Lagoudaki, R., Van Dijck, A., Marusic, Z., Anicic, M., Vukovic, J., Kooy, R. F., Grigoriadis, N., & Gozes, I. (2020, Jul 13). Tauopathy in the young autistic brain: novel biomarker and therapeutic target. Transl Psychiatry, 10(1), 228.
  • Huggett, J. F., Benes, V., Bustin, S. A., Garson, J. A., Harris, K., Kammel, M., Kubista, M., McHugh, T. D., Moran-Gilad, J., Nolan, T., Pfaffl, M. W., Salit, M., Shipley, G., Vallone, P. M., Vandesompele, J., Wittwer, C., & Zeichhardt, H. (2020). "Cautionary note on contamination of reagents used for molecular detection of SARS-CoV-2." Clin Chem.
  • Kolenicova, D., Tureckova, J., Pukajova, B., Harantova, L., Kriska, J., Kirdajova, D., Vorisek, I., Kamenicka, M., Valihrach, L., Androvic, P., Kubista, M., Vargova, L., & Anderova, M. (2020). "High potassium exposure reveals the altered ability of astrocytes to regulate their volume in the aged hippocampus of GFAP/EGFP mice." Neurobiol Aging, 86, 162-181
  • Lampignano, R., Neumann, M. H. D., Weber, S., Kloten, V., Herdean, A., Voss, T., Groelz, D., Babayan, A., Tibbesma, M., Schlumpberger, M., Chemi, F., Rothwell, D. G., Wikman, H., Galizzi, J. P., Riise Bergheim, I., Russnes, H., Mussolin, B., Bonin, S., Voigt, C., Musa, H., Pinzani, P., Lianidou, E., Brady, G., Speicher, M. R., Pantel, K., Betsou, F., Schuuring, E., Kubista, M., Ammerlaan, W., Sprenger-Haussels, M., Schlange, T., & Heitzer, E. (2020). Multicenter Evaluation of Circulating Cell-Free DNA Extraction and Downstream Analyses for the Development of Standardized (Pre)analytical Work Flows. Clin Chem, 66(1), 149-160.
  • Naraine, R., Abaffy, P., Sidova, M., Tomankova, S., Pocherniaieva, K., Smolik, O., Kubista, M., Psenicka, M., & Sindelka, R. (2020). "NormQ: RNASeq normalization based on RT-qPCR derived size factors." Comput Struct Biotechnol J, 18, 1173-1181
  • Schneegans, S., Luck, L., Besler, K., Bluhm, L., Stadler, J. C., Staub, J., Greinert, R., Volkmer, B., Kubista, M., Gebhardt, C., Sartori, A., Irwin, D., Serkkola, E., Af Hallstrom, T., Lianidou, E., Sprenger-Haussels, M., Hussong, M., Mohr, P., Schneider, S. W., Shaffer, J., Pantel, K., & Wikman, H. (2020). "Pre-analytical factors affecting the establishment of a single tube assay for multiparameter liquid biopsy detection in melanoma patients." Mol Oncol, 14(5), 1001-1015.
  • Valihrach, L., P. Androvic and M. Kubista (2020). "Circulating miRNA analysis for cancer diagnostics and therapy." Mol Aspects Med 72: 100825.

2019

  • Abaffy, P., S. Tomankova, R. Naraine, M. Kubista and R. Sindelka (2019). "The role of nitric oxide during embryonic wound healing." Bmc Genomics 20(1).

  • Androvic, P., N. Romanyuk, L. Urdzikova-Machova, E. Rohlova, M. Kubista and L. Valihrach (2019). "Two-tailed RT-qPCR panel for quality control of circulating microRNA studies." Sci Rep 9(1): 4255.

  • Bajzikova, M., J. Kovarova, A. R. Coelho, S. Boukalova, S. Oh, K. Rohlenova, D. Svec, S. Hubackova, B. Endaya, K. Judasova, A. Bezawork-Geleta, K. Kluckova, L. Chatre, R. Zobalova, A. Novakova, K. Vanova, Z. Ezrova, G. J. Maghzal, S. M. Novais, M. Olsinova, L. Krobova, Y. J. An, E. Davidova, Z. Nahacka, M. Sobol, T. Cunha-Oliveira, C. Sandoval-Acuna, H. Strnad, T. C. Zhang, T. Huynh, T. L. Serafim, P. Hozak, V. A. Sardao, W. J. H. Koopman, M. Ricchetti, P. J. Oliveira, F. Kolar, M. Kubista, J. Truksa, K. Dvorakova-Hortova, K. Pacak, R. Gurlich, R. Stocker, Y. Q. Zhou, M. V. Berridge, S. Park, L. F. Dong, J. Rohlena and J. Neuzil (2019). "Reactivation of Dihydroorotate Dehydrogenase-Driven Pyrimidine Biosynthesis Restores Tumor Growth of Respiration-Deficient Cancer Cells." Cell Metabolism 29(2): 399-+.

  • Bartos, O., J. Roslein, J. Kotusz, J. Paces, L. Pekarik, M. Petrtyl, K. Halacka, E. Stefkova Kasparova, J. Mendel, A. Boron, D. Juchno, A. Leska, O. Jablonska, V. Benes, M. Sidova and K. Janko (2019). "The Legacy of Sexual Ancestors in Phenotypic Variability, Gene Expression, and Homoeolog Regulation of Asexual Hybrids and Polyploids." Mol Biol Evol 36(9): 1902-1920.

  • Detavernier, A., A. Azouz, H. Shehade, M. Splittgerber, L. Van Maele, M. Nguyen, S. Thomas, Y. Achouri, D. Svec, E. Calonne, F. Fuks, G. Oldenhove and S. Goriely (2019). "Monocytes undergo multi-step differentiation in mice during oral infection by Toxoplasma gondii." Commun Biol 2(1): 472.

  • Kloten, V., M. H. D. Neumann, F. Di Pasquale, M. Sprenger-Haussels, J. M. Shaffer, M. Schlumpberger, A. Herdean, F. Betsou, W. Ammerlaan, T. A. Hallstrom, E. Serkkola, T. Forsman, E. Lianidou, R. Sjoback, M. Kubista, S. Bender, R. Lampignano, T. Krahn, T. Schlange and C.-I. Consortium (2019). "Multicenter Evaluation of Circulating Plasma MicroRNA Extraction Technologies for the Development of Clinically Feasible Reverse Transcription Quantitative PCR and Next-Generation Sequencing Analytical Work Flows." Clinical Chemistry 65(9): 1132-1140.

  • Kumar, J., D. Chudasama, C. Roberts, M. Kubista, R. Sjoback, J. Chatterjee, V. Anikin, E. Karteris and M. Hall (2019). "Detection of Abundant Non-Haematopoietic Circulating Cancer-Related Cells in Patients with Advanced Epithelial Ovarian Cancer." Cells 8(7).

  • Smieszek, A., K. Kornicka, J. Szlapka-Kosarzewska, P. Androvic, L. Valihrach, L. Langerova, E. Rohlova, M. Kubista and K. Marycz (2019). "Metformin Increases Proliferative Activity and Viability of Multipotent Stromal Stem Cells Isolated from Adipose Tissue Derived from Horses with Equine Metabolic Syndrome." Cells 8(2).

  • Zucha, D., P. Androvic, M. Kubista and L. Valihrach (2019). "Performance Comparison of Reverse Transcriptases for Single-Cell Studies." Clin Chem.

2018

  • Andersson, D., D. Svec, C. Pedersen, J. R. Henriksen and A. Stahlberg (2018). "Preamplification with dUTP and Cod UNG Enables Elimination of Contaminating Amplicons." Int J Mol Sci 19(10).

  • Bezawork-Geleta, A., H. Wen, L. F. Dong, B. Yan, J. Vider, S. Boukalova, L. Krobova, K. Vanova, R. Zobalova, M. Sobol, P. Hozak, S. M. Novais, V. Caisova, P. Abaffy, R. Naraine, Y. Pang, T. Zaw, P. Zhang, R. Sindelka, M. Kubista, S. Zuryn, M. P. Molloy, M. V. Berridge, K. Pacak, J. Rohlena, S. Park and J. Neuzil (2018). "Alternative assembly of respiratory complex II connects energy stress to metabolic checkpoints." Nature Communications 9.

  • Cerychova, R., R. Bohuslavova, F. Papousek, D. Sedmera, P. Abaffy, V. Benes, F. Kolar and G. Pavlinkova (2018). "Adverse effects of Hif1a mutation and maternal diabetes on the offspring heart." Cardiovasc Diabetol 17(1): 68.

  • Kubista, M., J. Dreyer-Lamm and A. Stahlberg (2018). "The secrets of the cell." Molecular Aspects of Medicine 59: 1-4.

  • Pivonkova, H., Z. Hermanova, D. Kirdajova, T. Awadova, J. Malinsky, L. Valihrach, D. Zucha, M. Kubista, A. Galisova, D. Jirak and M. Anderova (2018). "The Contribution of TRPV4 Channels to Astrocyte Volume Regulation and Brain Edema Formation." Neuroscience 394: 127-143.

  • Pocherniaieva, K., M. Sidova, M. Havelka, T. Saito, M. Psenicka, R. Sindelka and V. Kaspar (2018). "Comparison of oocyte mRNA localization patterns in sterlet Acipenser ruthenus and African clawed frog Xenopus laevis." J Exp Zool B Mol Dev Evol 330(3): 181-187.

  • Sindelka, R., P. Abaffy, Y. Qu, S. Tomankova, M. Sidova, R. Naraine, M. Kolar, E. Peuchen, L. Sun, N. Dovichi and M. Kubista (2018). "Asymmetric distribution of biomolecules of maternal origin in the Xenopus laevis egg and their impact on the developmental plan." Sci Rep 8(1): 8315.

  • Skerenova, M., V. Mikulova, O. Capoun, D. Svec, K. Kolostova, V. Soukup, H. Honova, T. Hanus and T. Zima (2018). "Gene Expression Analysis of Immunomagnetically Enriched Circulating Tumor Cell Fraction in Castration-Resistant Prostate Cancer." Mol Diagn Ther 22(3): 381-390.

  • Stahlberg, A. and M. Kubista (2018). "Technical aspects and recommendations for single-cell qPCR." Molecular Aspects of Medicine 59: 28-35.

  • Svec, D., S. Dolatabadi, C. Thomsen, N. Cordes, M. Shannon, P. Fitzpatrick, G. Landberg, P. Aman and A. Stahlberg (2018). "Identification of inhibitors regulating cell proliferation and FUS-DDIT3 expression in myxoid liposarcoma using combined DNA, mRNA, and protein analyses." Lab Invest 98(7): 957-967.

  • Valihrach, L., P. Androvic and M. Kubista (2018). "Platforms for Single-Cell Collection and Analysis." International Journal of Molecular Sciences 19(3).

  • Valny, M., P. Honsa, E. Waloschkova, H. Matuskova, J. Kriska, D. Kirdajova, P. Androvic, L. Valihrach, M. Kubista and M. Anderova (2018). "A single-cell analysis reveals multiple roles of oligodendroglial lineage cells during post-ischemic regeneration." Glia 66(5): 1068-1081.

2017

  • Aaltonen, K. E., V. Novosadova, P. O. Bendahl, C. Graffman, A. M. Larsson and L. Ryden (2017). "Molecular characterization of circulating tumor cells from patients with metastatic breast cancer reflects evolutionary changes in gene expression under the pressure of systemic therapy." Oncotarget 8(28): 45544-45565.

  • Androvic, P., L. Valihrach, J. Elling, R. Sjoback and M. Kubista (2017). "Two-tailed RT-qPCR: a novel method for highly accurate miRNA quantification." Nucleic Acids Research 45(15).

  • Bredemeier, M., P. Edimiris, P. Mach, M. Kubista, R. Sjoback, E. Rohlova, K. Kolostova, S. Hauch, B. Aktas, M. Tewes, R. Kimmig and S. Kasimir-Bauer (2017). "Gene Expression Signatures in Circulating Tumor Cells Correlate with Response to Therapy in Metastatic Breast Cancer." Clinical Chemistry 63(10): 1585-1593.

  • Dong, L. F., J. Kovarova, M. Bajzikova, A. Bezawork-Geleta, D. Svec, B. Endaya, K. Sachaphibulkij, A. R. Coelho, N. Sebkova, A. Ruzickova, A. S. Tan, K. Kluckova, K. Judasova, K. Zamecnikova, Z. Rychtarcikova, V. Gopalan, L. Andera, M. Sobol, B. Yan, B. Pattnaik, N. Bhatraju, J. Truksa, P. Stopka, P. Hozak, A. K. Lam, R. Sedlacek, P. J. Oliveira, M. Kubista, A. Agrawal, K. Dvorakova-Hortova, J. Rohlena, M. V. Berridge and J. Neuzil (2017). "Horizontal transfer of whole mitochondria restores tumorigenic potential in mitochondrial DNA-deficient cancer cells." Elife 6.

  • Forootan, A., R. Sjoback, J. Bjorkman, B. Sjogreen, L. Linz and M. Kubista (2017). "Methods to determine limit of detection and limit of quantification in quantitative real-time PCR (qPCR)." Biomol Detect Quantif 12: 1-6.

  • Hanoteau, A., C. Henin, D. Svec, C. Bisilliat Donnet, S. Denanglaire, D. Colau, P. Romero, O. Leo, B. Van den Eynde and M. Moser (2017). "Cyclophosphamide treatment regulates the balance of functional/exhausted tumor-specific CD8(+) T cells." Oncoimmunology 6(8): e1318234.

  • Hillreiner, M., C. Schmautz, I. Ballweg, V. Korenkova, M. W. Pfaffl and H. Kliem (2017). "Gene expression profiling in pbMEC - in search of molecular biomarkers to predict immunoglobulin production in bovine milk." BMC Vet Res 13(1): 369.

  • Rychtarcikova, Z., S. Lettlova, V. Tomkova, V. Korenkova, L. Langerova, E. Simonova, P. Zjablovskaja, M. Alberich-Jorda, J. Neuzil and J. Truksa (2017). "Tumor-initiating cells of breast and prostate origin show alterations in the expression of genes related to iron metabolism." Oncotarget 8(4): 6376-6398.

  • Šindelka, R., Šídová, M., Abaffy, P., Kubista, M. (2017). Asymmetric Localization and Distribution of Factors Determining Cell Fate During Early Development of Xenopus laevis. Asymmetric Cell Division in Development, Differentiation and Cancer. J. Tassan, Kubiak, J., Springer International Publishing AG. 61: 229-241.

  • Tomankova, S., P. Abaffy and R. Sindelka (2017). "The role of nitric oxide during embryonic epidermis development of Xenopus laevis." Biol Open 6(6): 862-871.

2016

  • Aman, P., S. Dolatabadi, D. Svec, E. Jonasson, S. Safavi, D. Andersson, P. Grundevik, C. Thomsen and A. Stahlberg (2016). "Regulatory mechanisms, expression levels and proliferation effects of the FUS-DDIT3 fusion oncogene in liposarcoma." J Pathol 238(5): 689-699.

  • Bjorkman, J., D. Svec, E. Lott, M. Kubista and R. Sjoback (2016). "Differential amplicons (DeltaAmp)-a new molecular method to assess RNA integrity." Biomol Detect Quantif 6: 4-12.

  • Conrad, S., H. Azizi, M. Hatami, M. Kubista, M. Bonin, J. Hennenlotter, K. D. Sievert and T. Skutella (2016). "Expression of Genes Related to Germ Cell Lineage and Pluripotency in Single Cells and Colonies of Human Adult Germ Stem Cells." Stem Cells International.

  • Dzamba, D., L. Valihrach, M. Kubista and M. Anderova (2016). "The correlation between expression profiles measured in single cells and in traditional bulk samples." Scientific Reports 6.

  • Gorges, T. M., A. Kuske, K. Rock, O. Mauermann, V. Muller, S. Peine, K. Verpoort, V. Novosadova, M. Kubista, S. Riethdorf and K. Pantel (2016). "Accession of Tumor Heterogeneity by Multiplex Transcriptome Profiling of Single Circulating Tumor Cells." Clinical Chemistry 62(11): 1504-1515.

  • Hensler, M., I. Vancurova, E. Becht, O. Palata, P. Strnad, P. Tesarova, M. Cabinakova, D. Svec, M. Kubista, J. Bartunkova, R. Spisek and L. Sojka (2016). "Gene expression profiling of circulating tumor cells and peripheral blood mononuclear cells from breast cancer patients." Oncoimmunology 5(4).

  • Honsa, P., M. Valny, J. Kriska, H. Matuskova, L. Harantova, D. Kirdajova, L. Valihrach, P. Androvic, M. Kubista and M. Anderova (2016). "Generation of Reactive Astrocytes from NG2 Cells is Regulated by Sonic Hedgehog." Glia 64(9): 1518-1531.

  • Korenkova, V., J. Slyskova, V. Novosadova, S. Pizzamiglio, L. Langerova, J. Bjorkman, O. Vycital, V. Liska, M. Levy, K. Veskrna, P. Vodicka, L. Vodickova, M. Kubista and P. Verderio (2016). "The focus on sample quality: Influence of colon tissue collection on reliability of qPCR data." Scientific Reports 6.

  • Tlapakova, T., T. M. Nguyen, M. Vegrichtova, M. Sidova, K. Strnadova, M. Blahova and V. Krylov (2016). "Identification and characterization of Xenopus tropicalis common progenitors of Sertoli and peritubular myoid cell lineages." Biol Open 5(9): 1275-1282.

  • Virant-Klun, I., A. Stahlberg, M. Kubista and T. Skutella (2016). "MicroRNAs: From Female Fertility, Germ Cells, and Stem Cells to Cancer in Humans." Stem Cells International.

2015

  • Andersson, D., N. Akrap, D. Svec, T. E. Godfrey, M. Kubista, G. Landberg and A. Stahlberg (2015). "Properties of targeted preamplification in DNA and cDNA quantification." Expert Review of Molecular Diagnostics 15(8): 1085-1100.

  • Dzamba, D., P. Honsa, M. Valny, J. Kriska, L. Valihrach, V. Novosadova, M. Kubista and M. Anderova (2015). "Quantitative Analysis of Glutamate Receptors in Glial Cells from the Cortex of GFAP/EGFP Mice Following Ischemic Injury: Focus on NMDA Receptors." Cellular and Molecular Neurobiology 35(8): 1187-1202.

  • Kap, M., A. M. Sieuwerts, M. Kubista, M. Oomen, S. Arshad and P. Riegman (2015). "The Influence of Tissue Procurement Procedures on RNA Integrity, Gene Expression, and Morphology in Porcine and Human Liver Tissue." Biopreservation and Biobanking 13(3): 200-206.

  • Korenkova, V., J. Scott, V. Novosadova, M. Jindrichova, L. Langerova, D. Svec, M. Sidova and R. Sjoback (2015). "Pre-amplification in the context of high-throughput qPCR gene expression experiment." BMC Mol Biol 16: 5.

  • Kubista, M., R. Sjoback, M. Jindrichova, E. Rohlova, V. Rusnakova, K. Kolostova, S. Hauch, B. Aktas, M. Tewes, M. Bredemeier and S. Kasimir-Bauer (2015). "Expression profiling of circulating tumor cells." International Journal of Molecular Medicine 36: S72-S72.

  • Sidova, M., S. Tomankova, P. Abaffy, M. Kubista and R. Sindelka (2015). "Effects of post-mortem and physical degradation on RNA integrity and quality." Biomol Detect Quantif 5: 3-9.

  • Sidova, M., R. Sindelka, M. Castoldi, V. Benes and M. Kubista (2015). "Intracellular microRNA profiles form in the Xenopus laevis oocyte that may contribute to asymmetric cell division." Scientific Reports 5.

  • Slyskova, J., F. Cordero, B. Pardini, V. Korenkova, V. Vymetalkova, L. Bielik, L. Vodickova, P. Pitule, V. Liska, V. M. Matejka, M. Levy, T. Buchler, M. Kubista, A. Naccarati and P. Vodicka (2015). "Post-Treatment Recovery of Suboptimal DNA Repair Capacity and Gene Expression Levels in Colorectal Cancer Patients." Molecular Carcinogenesis 54(9): 769-778.

  • Svec, D., A. Tichopad, V. Novosadova, M. W. Pfaffl and M. Kubista (2015). "How good is a PCR efficiency estimate: Recommendations for precise and robust qPCR efficiency assessments." Biomol Detect Quantif 3: 9-16.

2014

  • Anderova, M., J. Benesova, M. Mikesova, D. Dzamba, P. Honsa, J. Kriska, O. Butenko, V. Novosadova, L. Valihrach, M. Kubista, L. Dmytrenko, M. Cicanic and L. Vargova (2014). "Altered Astrocytic Swelling in the Cortex of alpha-Syntrophin-Negative GFAP/EGFP Mice." Plos One 9(11).

  • Conrad, S., H. Azizi, M. Hatami, M. Kubista, M. Bonin, J. Hennenlotter, M. Renninger and T. Skutella (2014). "Differential Gene Expression Profiling of Enriched Human Spermatogonia after Short- and Long-Term Culture." Biomed Research International.

  • Honsa, P., H. Pivonkova, L. Harantova, O. Butenko, J. Kriska, D. Dzamba, V. Rusnakova, L. Valihrach, M. Kubista and M. Anderova (2014). "Increased Expression of Hyperpolarization-Activated Cyclic Nucleotide-Gated (HCN) Channels in Reactive Astrocytes Following Ischemia." Glia 62(12): 2004-2021.

  • Jacox, L., R. Sindelka, J. Chen, A. Rothman, A. Dickinson and H. Sive (2014). "The extreme anterior domain is an essential craniofacial organizer acting through Kinin-Kallikrein signaling." Cell Rep 8(2): 596-609.

  • Kubista, M., R. Sjoback, M. Jindrichova, E. Rohlova, V. Rusnakova, S. Hauch, B. Aktas, M. Tewes, M. Bredemeier and S. Kasimir-Bauer (2014). "High Throughput Few and Single Cell Expression Profiling and the Characterization of Circulating Tumor Cells." Anticancer Research 34(10): 6014-6014.

  • Malentacchi, F., M. Pazzagli, L. Simi, C. Orlando, R. Wyrich, K. Gunther, P. Verderio, S. Pizzamiglio, C. M. Ciniselli, H. Zhang, V. Korenkova, L. Rainen, T. Bar, M. Kubista and S. Gelmini (2014). "SPIDIA-RNA: Second External Quality Assessment for the Pre-Analytical Phase of Blood Samples Used for RNA Based Analyses." Plos One 9(11).

  • Slyskova, J., Y. Lorenzo, A. Karlsen, M. H. Carlsen, V. Novosadova, R. Blomhoff, P. Vodicka and A. R. Collins (2014). "Both genetic and dietary factors underlie individual differences in DNA damage levels and DNA repair capacity." DNA Repair (Amst) 16: 66-73.

  • Stahlberg, A. and M. Kubista (2014). "The workflow of single-cell expression profiling using quantitative real-time PCR." Expert Review of Molecular Diagnostics 14(3): 323-331.

  • Vymetalkova, V. P., J. Slyskova, V. Korenkova, L. Bielik, L. Langerova, P. Prochazka, A. Rejhova, L. Schwarzova, B. Pardini, A. Naccarati and P. Vodicka (2014). "Molecular characteristics of mismatch repair genes in sporadic colorectal tumors in Czech patients." BMC Med Genet 15: 17.

  • Zatecka, E., L. Ded, F. Elzeinova, A. Kubatova, A. Dorosh, H. Margaryan, P. Dostalova, V. Korenkova, K. Hoskova and J. Peknicova (2014). "Effect of zearalenone on reproductive parameters and expression of selected testicular genes in mice." Reprod Toxicol 45: 20-30.

  • Zhang, H., V. Korenkova, R. Sjoback, D. Svec, J. Bjorkman, M. Kruhoffer, P. Verderio, S. Pizzamiglio, C. M. Ciniselli, R. Wyrich, U. Oelmueller, M. Kubista, T. Lindahl, A. Lonneborg and E. Rian (2014). "Biomarkers for monitoring pre-analytical quality variation of mRNA in blood samples." Plos One 9(11): e111644.

2013

  • Andersson, D., U. Wilhelmsson, M. Nilsson, M. Kubista, A. Stahlberg, M. Pekna and M. Pekny (2013). "Plasticity Response in the Contralesional Hemisphere after Subtle Neurotrauma: Gene Expression Profiling after Partial Deafferentation of the Hippocampus." Plos One 8(7).

  • Bustin, S. A., V. Benes, J. Garson, J. Hellemans, J. Huggett, M. Kubista, R. Mueller, T. Nolan, M. W. Pfaffl, G. Shipley, C. T. Wittwer, P. Schjerling, P. J. Day, M. Abreu, B. Aguado, J. F. Beaulieu, A. Beckers, S. Bogaert, J. A. Browne, F. Carrasco-Ramiro, L. Ceelen, K. Ciborowski, P. Cornillie, S. Coulon, A. Cuypers, S. De Brouwer, L. De Ceuninck, J. De Craene, H. De Naeyer, W. De Spiegelaere, K. Deckers, A. Dheedene, K. Durinck, M. Ferreira-Teixeira, A. Fieuw, J. M. Gallup, S. Gonzalo-Flores, K. Goossens, F. Heindryckx, E. Herring, H. Hoenicka, L. Icardi, R. Jaggi, F. Javad, M. Karampelias, F. Kibenge, M. Kibenge, C. Kumps, I. Lambertz, T. Lammens, A. Markey, P. Messiaen, E. Mets, S. Morais, A. Mudarra-Rubio, J. Nakiwala, H. Nelis, P. A. Olsvik, C. Perez-Novo, M. Plusquin, T. Remans, A. Rihani, P. Rodrigues-Santos, P. Rondou, R. Sanders, K. Schmidt-Bleek, K. Skovgaard, K. Smeets, L. Tabera, S. Toegel, T. Van Acker, W. Van den Broeck, J. Van der Meulen, M. Van Gele, G. Van Peer, M. Van Poucke, N. Van Roy, S. Vergult, J. Wauman, M. Tshuikina-Wiklander, E. Willems, S. Zaccara, F. Zeka and J. Vandesompele (2013). "The need for transparency and good practices in the qPCR literature." Nature Methods 10(11): 1063-1067.

  • Dusatkova, L., H. Zamrazilova, B. Sedlackova, J. Vcelak, P. Hlavaty, I. Aldhoon Hainerova, V. Korenkova, O. Bradnova, B. Bendlova, M. Kunesova and V. Hainer (2013). "Association of obesity susceptibility gene variants with metabolic syndrome and related traits in 1,443 Czech adolescents." Folia Biol (Praha) 59(3): 123-133.

  • Flachsova, M., R. Sindelka and M. Kubista (2013). "Single blastomere expression profiling of Xenopus laevis embryos of 8 to 32-cells reveals developmental asymmetry." Scientific Reports 3.

  • Huggett, J. F., C. A. Foy, V. Benes, K. Emslie, J. A. Garson, R. Haynes, J. Hellemans, M. Kubista, R. D. M. T. Nolan, M. W. Pfaffl, M. W. Pfaffl, G. L. Shipley, J. Vandesompele, C. T. Wittwer and S. A. Bustin (2013). "The Digital MIQE Guidelines: Minimum Information for Publication of Quantitative Digital PCR Experiments." Clinical Chemistry 59(6): 892-902.

  • Malentacchi, F., M. Pazzagli, L. Simi, C. Orlando, R. Wyrich, C. C. Hartmann, P. Verderio, S. Pizzamiglio, C. M. Ciniselli, A. Tichopad, M. Kubista and S. Gelmini (2013). "SPIDIA-DNA: An External Quality Assessment for the pre-analytical phase of blood samples used for DNA-based analyses." Clinica Chimica Acta 424: 274-286.

  • Pazzagli, M., F. Malentacchi, L. Simi, C. Orlando, R. Wyrich, K. Gunther, C. C. Hartmann, P. Verderio, S. Pizzamiglio, C. M. Ciniselli, A. Tichopad, M. Kubista and S. Gelmini (2013). "SPIDIA-RNA: First external quality assessment for the pre-analytical phase of blood samples used for RNA based analyses." Methods 59(1): 20-31.

  • Polakova Vymetalkova, V., L. Vannucci, V. Korenkova, P. Prochazka, J. Slyskova, L. Vodickova, V. Rusnakova, L. Bielik, M. Burocziova, P. Rossmann and P. Vodicka (2013). "Evaluation of tumor suppressor gene expressions and aberrant methylation in the colon of cancer-induced rats: a pilot study." Mol Biol Rep 40(10): 5921-5929.

  • Rusnakova, V., P. Honsa, D. Dzamba, A. Stahlberg, M. Kubista and M. Anderova (2013). "Heterogeneity of Astrocytes: From Development to Injury - Single Cell Gene Expression." Plos One 8(8).

  • Sorg, D., K. Danowski, V. Korenkova, V. Rusnakova, R. Kuffner, R. Zimmer, H. H. Meyer and H. Kliem (2013). "Microfluidic high-throughput RT-qPCR measurements of the immune response of primary bovine mammary epithelial cells cultured from milk to mastitis pathogens." Animal 7(5): 799-805.

  • Stahlberg, A., V. Rusnakova, A. Forootan, M. Anderova and M. Kubista (2013). "RT-qPCR work-flow for single-cell data analysis." Methods 59(1): 80-88.

  • Stahlberg, A., V. Rusnakova and M. Kubista (2013). "The added value of single-cell gene expression profiling." Briefings in Functional Genomics 12(2): 81-89.

  • Svec, D., D. Andersson, M. Pekny, R. Sjoback, M. Kubista and A. Stahlberg (2013). "Direct cell lysis for single-cell gene expression profiling." Front Oncol 3: 274.

  • Svec, D., V. Rusnakova, V. Korenkova and M. Kubista (2013). "Dye-Based High-Throughput qPCR in Microfluidic Platform BioMark (TM)." Pcr Technology: Current Innovations, 3rd Edition: 323-337.

  • Virant-Klun, I., T. Skutella, M. Kubista, A. Vogler, J. Sinkovec and H. Meden-Vrtovec (2013). "Expression of Pluripotency and Oocyte-Related Genes in Single Putative Stem Cells from Human Adult Ovarian Surface Epithelium Cultured In Vitro in the Presence of Follicular Fluid." Biomed Research International.

2012

  • Bar, T., M. Kubista and A. Tichopad (2012). "Validation of kinetics similarity in qPCR." Nucleic Acids Research 40(4): 1395-1406.

  • Benesova, J., V. Rusnakova, P. Honsa, H. Pivonkova, D. Dzamba, M. Kubista and M. Anderova (2012). "Distinct Expression/Function of Potassium and Chloride Channels Contributes to the Diverse Volume Regulation in Cortical Astrocytes of GFAP/EGFP Mice." Plos One 7(1).

  • Bibova, I., I. Linhartova, O. Stanek, V. Rusnakova, M. Kubista, M. Suchanek, M. Vasakova and P. Sebo (2012). "Detection of immune cell response to M. tuberculosis-specific antigens by quantitative polymerase chain reaction." Diagnostic Microbiology and Infectious Disease 72(1): 68-78.

  • Gunther, K., F. Malentacchi, P. Verderio, S. Pizzamiglio, C. M. Ciniselli, A. Tichopad, M. Kubista, R. Wyrich, M. Pazzagli and S. Gelmini (2012). "Implementation of a proficiency testing for the assessment of the preanalytical phase of blood samples used for RNA based analysis." Clinica Chimica Acta 413(7-8): 779-786.

  • Kubista, M. (2012). "I See the Light! And I See It Again and Again!" Clinical Chemistry 58(11): 1505-1506.

  • Kubista, M., V. Rusnakova, D. Svec, B. Sjogreen and A. Tichopad (2012). "GenEx: Data Analysis Software." Quantitative Real-Time Pcr in Applied Microbiology: 63-84.

  • Kubista, M. (2012). "Drivers and Hurdles for qPCR." Genetic Engineering & Biotechnology News 32(9): 24-+.

  • Laurell, H., J. S. Iacovoni, A. Abot, D. Svec, J. J. Maoret, J. F. Arnal and M. Kubista (2012). "Correction of RT-qPCR data for genomic DNA-derived signals with ValidPrime." Nucleic Acids Research 40(7).

  • Slyskova, J., V. Korenkova, A. R. Collins, P. Prochazka, L. Vodickova, J. Svec, L. Lipska, M. Levy, M. Schneiderova, V. Liska, L. Holubec, R. Kumar, P. Soucek, A. Naccarati and P. Vodicka (2012). "Functional, genetic, and epigenetic aspects of base and nucleotide excision repair in colorectal carcinomas." Clin Cancer Res 18(21): 5878-5887.

  • Stimpfel, M., T. Skutella, M. Kubista, E. Malicev, S. Conrad and I. Virant-Klun (2012). "Potential Stemness of Frozen-Thawed Testicular Biopsies without Sperm in Infertile Men Included into the In Vitro Fertilization Programme." Journal of Biomedicine and Biotechnology.

2011

  • Brevik, A., V. Rusnakova, N. Duale, H. H. Slagsvold, A. K. Olsen, R. Storeng, M. Kubista, G. Brunborg and B. Lindeman (2011). "Preconceptional paternal glycidamide exposure affects embryonic gene expression: Single embryo gene expression study following in vitro fertilization." Reproductive Toxicology 32(4): 463-471.

  • Bustin, S. A., V. Benes, J. A. Garson, J. Hellemans, J. Huggett, M. Kubista, R. Mueller, T. Nolan, M. W. Pfaffl, G. L. Shipley, J. Vandesompele and C. T. Wittwer (2011). "Primer Sequence Disclosure: A Clarification of the MIQE Guidelines." Clinical Chemistry 57(6): 919-921.

  • Pazzagli, M., F. Malentacchi, L. Simi, C. Orlando, R. Wyrich, K. Gunther, C. Hartmann, P. Verderio, S. Pizzamiglio, C. M. Ciniselli, A. Tichopad, M. Kubista and S. Gelmini (2011). "Evidence-Based Quality Guidelines for the Pre-Analytical Phase of Blood Samples." Clinical Chemistry and Laboratory Medicine 49: S128-S128.

  • Stahlberg, A., D. Andersson, J. Aurelius, M. Faiz, M. Pekna, M. Kubista and M. Pekny (2011). "Defining cell populations with single-cell gene expression profiling: correlations and identification of astrocyte subpopulations." Nucleic Acids Research 39(4).

  • Stahlberg, A., M. Kubista and P. Aman (2011). "Single-cell gene-expression profiling and its potential diagnostic applications." Expert Review of Molecular Diagnostics 11(7): 735-740.

2010

  • Bergkvist, A., V. Rusnakova, R. Sindelka, J. M. A. Garda, B. Sjogreen, D. Lindh, A. Forootan and M. Kubista (2010). "Gene expression profiling - Clusters of possibilities." Methods 50(4): 323-335.

  • Bohuslavova, R., F. Kolar, L. Kuthanova, J. Neckar, A. Tichopad and G. Pavlinkova (2010). "Gene expression profiling of sex differences in HIF1-dependent adaptive cardiac responses to chronic hypoxia." J Appl Physiol (1985) 109(4): 1195-1202.

  • Coll, A., A. Nadal, R. Collado, G. Capellades, M. Kubista, J. Messeguer and M. Pla (2010). "Natural variation explains most transcriptomic changes among maize plants of MON810 and comparable non-GM varieties subjected to two N-fertilization farming practices." Plant Molecular Biology 73(3): 349-362.

  • Kitchen, R. R., M. Kubista and A. Tichopad (2010). "Statistical aspects of quantitative real-time PCR experiment design." Methods 50(4): 231-236.

  • Kolostova, K., D. Pinterova, P. Tesarova, V. Bobek, V. Mikulova, M. Kubecova, M. Brychta, V. Rusnakova, S. Kasimir-Bauer and M. Kubista (2010). "Gene Expression Profiling in Circulating Cells (Ctcs) of Breast Carcinoma Patients." Annals of Oncology 21: 49-50.

  • Kozubenko, N., K. Turnovcova, M. Kapcalova, O. Butenko, M. Anderova, V. Rusnakova, M. Kubista, A. Hampl, P. Jendelova and E. Sykova (2010). "Analysis of In Vitro and In Vivo Characteristics of Human Embryonic Stem Cell-Derived Neural Precursors." Cell Transplantation 19(4): 471-486.

  • Mikulova, V., M. Cabinakova, J. Pobudova, P. Tesarova, D. Pavlista, K. Kolostova, M. Kubista, M. Romzova and T. Zima (2010). "The Role of Disseminated Tumor Cells and Circulating Tumor Cells in Management of Breast Cancer Patients." Tumor Biology 31: S73-S73.

  • Sindelka, R., M. Sidova, D. Svec and M. Kubista (2010). "Spatial expression profiles in the Xenopus laevis oocytes measured with qPCR tomography." Methods 51(1): 87-91.

  • Tichopad, A., T. Bar, L. Pecen, R. R. Kitchen, M. Kubista and M. W. Pfaffl (2010). "Quality control for quantitative PCR based on amplification compatibility test." Methods 50(4): 308-312.

  • Zanvit, P., A. Tichopad, M. Havlickova, O. Novotna, M. Jirkovska, K. Kolostova, D. Cechova, J. Julak, I. Sterzl and L. Prokesova (2010). "Adjuvant effect of Bacillus firmus on the expression of cytokines and toll-like receptors in mouse nasopharynx-associated lymphoid tissue (NALT) after intranasal immunization with inactivated influenza virus type A." Immunol Lett 134(1): 26-34.

2009

  • Bustin, S. A., V. Benes, J. A. Garson, J. Hellemans, J. Huggett, M. Kubista, R. Mueller, T. Nolan, M. W. Pfaffl, G. L. Shipley, J. Vandesompele and C. T. Wittwer (2009). "The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments." Clinical Chemistry 55(4): 611-622.

  • Masova, A., R. Sindelka, M. Kubista, J. Kindl and J. Jiracek (2009). "Gene expression responses in larvae of the fleshfly Sarcophaga bullata after immune stimulation." Folia Biol (Praha) 55(3): 98-106.

  • Pytelkova, J., J. Hubert, M. Lepsik, J. Sobotnik, R. Sindelka, I. Krizkova, M. Horn and M. Mares (2009). "Digestive alpha-amylases of the flour moth Ephestia kuehniella--adaptation to alkaline environment and plant inhibitors." FEBS J 276(13): 3531-3546.

  • Tichopad, A., R. Kitchen, I. Riedmaier, C. Becker, A. Stahlberg and M. Kubista (2009). "Design and Optimization of Reverse-Transcription Quantitative PCR Experiments." Clinical Chemistry 55(10): 1816-1823.

2008

  • Pinzani, P., K. Lind, F. Malentacchi, G. Nesi, F. Salvianti, D. Villari, M. Kubista, M. Pazzagli and C. Orlando (2008). "Prostate-specific antigen mRNA and protein levels in laser microdissected cells of human prostate measured by real-time reverse transcriptase-quantitative polymerase chain reaction and immuno-quantitative polymerase chain reaction." Human Pathology 39(10): 1474-1482.

  • Stahlberg, A., K. Elbing, J. M. Andrade-Garda, B. Sjogreen, A. Forootan and M. Kubista (2008). "Multiway real-time PCR gene expression profiling in yeast Saccharomyces cerevisiae reveals altered transcriptional response of ADH-genes to glucose stimuli." Bmc Genomics 9.

GAČR: GA20-23836S Sturgeon as a unique model for evolutionary transition from holoblastic to meroblastic cleavage pattern, and for endoderm development in vertebrates. 2020-2022

MAg: Globalization, modern technologies and climate change provide both new opportunities and hazards for salmonid breeding management. 2021-2025.

MŠMT (Project ALEXANDER): EJPRD19-256, Kubista, Valihrach: The astrocyte nanofilament system in Alexander disease – from molecules to function, uncovering new leads for therapy. 2020-2022.

GAČR: GA20-05770S, Kubista: The role of glial TRPV4 channels in brain edema formation and post-ischemic regeneration. 2020-2022.

GAČR: GA19-11313S, Kubista: Interspecies comparison of RNA localization within oocytes to elucidate regulation of early development and asymetric cell division. 2019-2021.

GAČR: GA19-02046S, Valihrach: Glial cells - the key players in the progression of amyotrophic lateral sclerosis. 2019-2021.

GAČR: GA18-21942S, Kubista: MicroRNA in central nervous system injury: potential roles and therapeutic implications. 2018-2020.

GAČR: GJ18-24753Y, Švec: Properties of horizontal mitochondrial transfer in cancer. 2018-2020.

GAČR: GA17-24441S, Kubista: Molecular mechanisms of proliferation during tumor progression and wound healing studied by profiling on single cell level. 2017-2019.

GAČR: GA17-0403, 4S, Kubista: Principal signaling pathways regulating NG2 glia proliferation and differentiation following brain injuries. 2017-2019.

GAČR: GA16-07500S, Kubista: Distribution of biomolecules studied on single cell and subcellular levels in Xenopus early stages to reveal mechanisms of asymmetric cell division. 2016-2018.

GAČR: GA16-10214S, Valihrach: Age-related changes in brain diffusivity, extracellular matrix composition and glial physiology - impact on pathogenesis of ischemia. 2016-2018.

GAČR: GA15-08239S, Korenková: The diagnostic and prognostic role of microRNA signature in rectal cancer. 2015-2017.

MŠMT: LH15074, Kubista: Elucidating the mechanism of asymmetric cell division using Xenopus oocytes as model system. 2015-2017.

GAČR: GA13-02154S, Kubista: Gene expression profiling and functional characterization of glial cell subpopulations following ischemic brain injury. 2013-2016.

MŠMT: LK21305, Šindelka: NO signaling during early embryogenesis and regeneration. 2013-2015.

GAČR: GAP304/12/1585, Korenková: Molecular DNA repair characteristics in colorectal tumor tissue. 2012-2015.

MŠMT (program OP VK): CZ.1.07/2.3.00/30.0045, Bařinka, Nováková, Kubista, Valihrach, Hejnalová: Biotechnological expert in structural biology and gene expression. 2012-2015.

MŠMT: ME10052, Kubista: Cellular Expression Signatures in Idiopathic Pulmonary Fibrosis. 2010-2012.

GAČR: GAP303/10/1338, Cell volume regulation in glial cells during brain ischemia/reperfusion. 2010-2012.

MŠMT (FP7): HEALTH-F5-2008-222916, Kubista: Standardisation and improvement of generic pre-analytical tools and procedures for in vitro diagnostics. 2009-2012.

MZ: NS9976, Gene expression profiling in cancer circulating cells (CTCs) in breast carcinoma patients - a tool for early metastasis detection and therapy individualisation. 2009-2011.

AVČR: IAA500970904, Kubista: MicroRNA expression during early development of Xenopus laevis and mRNA degradation. 2009-2011.

GAČR: GA301/09/1752, Kubista: Formation of spatiotemporal molecular gradients in early development of Xenopus laevis. 2009-2011.

AVČR: IAA500520809, Kubista: Mechanisms of embryonic stem cells early differentiation. 2008-2010.