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  • Sorg, G., Danowski, K., Korenkova, V., Rusnakova, V., Kueffner, R., Zimmer, R., Meyer, H. H. D., Kliem, H. 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, 2013. ISSN 1751-7311.
  • Bustin, S. A., Benes, V., Garson, J., Hellemans, J., Huggett, J., Kubista, M., Mueller, R., Nolan, T., Pfaffl, M. W., Shipley, G., Wittwer, C. T., Schjerling, P., Day, P. J., Abreu, M., Aguado, B., Beaulieu, J. F., Beckers, A., Bogaert, S., Browne, J. A., Carrasco-Ramiro, F., Ceelen, L., Ciborowski, K., Cornillie, P., Coulon, S., Cuypers, A., De Brouwer, S., De Ceuninck, L., De Craene, J., De Naeyer, H., De Spiegelaere, W., Deckers, K., Dheedene, A., Durinck, K., Ferreira-Teixeira, M., Fieuw, A., Gallup, J. M., Gonzalo-Flores, S., Goossens, K., Heindryckx, F., Herring, E., Hoenicka, H., Icardi, L., Jaggi, R., Javad, F., Karampelias, M., Kibenge, F., Kibenge, M., Kumps, C., Lambertz, I., Lammens, T., Markey, A., Messiaen, P., Mets, E., Morais, S., Mudarra-Rubio, A., Nakiwala, J., Nelis, H., Olsvik, P. A., Perez-Novo, C., Plusquin, M., Remans, T., Rihani, A., Rodrigues-Santos, P., Rondou, P., Sanders, R., Schmidt-Bleek, K., Skovgaard, K., Smeets, K., Tabera, L., Toegel, S., Van Acker, T., Van den Broeck, W., Van der Meulen, J., Van Gele, M., Van Peer, G., Van Poucke, M., Van Roy, N., Vergult, S., Wauman, J., Tshuikina-Wiklander, M., Willems, E., Zaccara, S., Zeka, F., Vandesompele, J. The need for transparency and good practices in the qPCR literature. Nature Methods, 10: 1063–1067, 2013. ISSN 1548-7091.
  • Svec, D., Andersson, D., Pekny M., Sjoback, R., Kubista, M., Stahlberg, A. Direct cell lysis for single-cell gene expression profiling. Front. Oncol, 3(274): 1-11, 2013.
  • Svec, D., Rusnakova, V., Korenkova, V., Kubista, M. Dye-based High-Throughput qPCR in Microfluidic Platform BioMark. In PCR Technology, Nolan, T. (ed.). CRC Press Inc., 323-339, 2013. ISBN 9781439848050.
  • Butenko, O., Benesova, J., Mikesova, M., Honsa, P., Dzamba, D., Kriska, J., Rusnakova, V., Kubista, M., Anderova, M. The fate of mdach1-expressing cells in the dorsal part of the lateral ventricles following focal cerebral ischemia. GLIA, 61(1): 207, 2013. ISSN 0894-1491.
  • Huggett, J. F., Foy, C. A., Benes, V., Emslie, K., Garson, J. A., Haynes, R., Hellemans, J., Kubista, M., Mueller, R. D., Nolan, T., Pfaffl, M. W., Shipley, G. L., Vandesompele, J., Bustin, S. A. The digital MIQE guidelines: Minimum Information for Publication of Quantitative Digital PCR Experiments. Clinical Chemistry, 59(6): 892-902, 2013. ISSN 0009-9147.
  • Stahlberg, A, Rusnakova, V, Kubista, M. The added value of single-cell gene expression profiling. Brief Funct Genomics, 12(2): 81-89, 2013. ISSN 2041-2649.
  • Stahlberg, A., Rusnakova, V., Forootan, A., Anderova, M., Kubista, M. RT-qPCR work-flow for single-cell data analysis. Methods, 59(1): 80-88, 2013, ISSN 1046-2023.
  • Pazzagli, M., Malentacchi, F., Simi, L., Wyrich, R., Guenther, K., Hartmann, C., Verderio, P., Pizzamiglio, S., Ciniselli, C. M., Tichopad, A., Kubista, M., Gelmini, S. SPIDIA-RNA: First external quality assessment for the pre-analytical phase of blood samples used for RNA based analyses. Methods, 59(1): 20-31, 2013. ISSN 1046-2023.
  • Stahlberg, A., Kubista, M. Unrevealing biological secrets by single cell expression profilig. Drug Discovery World Summer, 2013.
  • Andersson, D., Wilhelmsson, U., Nilsson, M., Kubista, M., Stahlberg, A., Pekna, M., Pekny, M. Plasticity response in the contralesional hemisphere after subtle neurotrauma: gene expression profiling after partial deafferentation of the hippocampus. PLoS ONE, 8(7): e706992013, 2013. ISSN 1932-6203.
  • Flachsova, M., Sindelka, R., Kubista, M. Single blastomere expression profiling of Xenopus laevis embryos of 8 to 32-cells reveals developmental asymmetry. Scientific Reports, 3: 2278, 2013. ISSN: 2045-2322.
  • Virant-Klun, I., Skutella, T., Kubista, M., Vogler A., Sinkovec, J., Meden-Vrtovec, H. 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, 861460, 2013. ISSN: 2314-6133.
  • Rusnakova, V., Honsa, P., Dzamba, D., Stahlberg A., Kubista, M., Anderova, M. Heterogeneity of Astrocytes: From Development to Injury – Single Cell Gene Expression. PLoS ONE 8(8): e69734, 2013. ISSN 1932-6203.
  • Malentacchi, F., Pazzagli, M., Simi, L., Orlando, C., Wyrich, R., Hartmann, C. C., Verderio, P., Pizzamiglio, S., Ciniselli, C. M., Tichopad, A., Kubista, M., Gelmini, S. 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, 2013. ISSN 0009-8981.
  • Dusatkova, L., Zamrazilova, H., Sedlackova, B., Vcelak, J., Hlavaty, P., Aldhoon Hainerova, I., Korenkova, V., Bradnova, O., Bendlova, B., Kunesova, M., Hainer, V. Association of obesity susceptibility gene variants with metabolic syndrome and related traits in 1,443 czech adolescents. Folia Biologica 59: 123-133, 2013. ISSN 0015-5500.
  • Polakova Vymetalkova, V., Vannucci, L., Korenkova, V., Prochazka, P., Slyskova, J., Vodickova, L., Rusnakova, V., Bielik, L., Burocziova, M., Rossmann, P., Vodicka, P. Evaluation of tumor suppressor gene expressions and aberrant methylation in the colon of cancer-induced rats: a pilot study. Molecular Biology Reports, 40(10): 5921-5929, 2013. doi: 10.1007/s11033-013-2699-8. ISSN 0301-4851.


  • Bar, T., Kubista, M., Tichopad, A. Validation of kinetics similarity in qPCR. Nucleic Acids Research, 40: 1395-1406, 2012. ISSN 0305-1048. 
  • Benesova, J., Rusnakova, V., Honsa, P., Pivonkova, H., Dzamba, D., Kubista, M., Anderova, M. Distinct expression/function of potassium and chloride channels contributes to the diverse volume regulation in cortical astrocytes of GFAP/EGFP mice. PLoS ONE, 7: e29725, 2012. ISSN 1932-6203. 
  • Bibova, I., Linhartova, I., Stanek, O., Rusnakova, V., Kubista, M., Suchanek, M., Vasakova, M., Sebo, P. Detection of immune cell response to M. tuberculosis-specific antigens by quantitative polymerase chain reaction. Diagnostic Microbiology and Infectious Disease, 72: 68-78, 2012. ISSN 0732-8893. 
  • Guenther, K., Malentacchi, F., Verderio, P., Pizzamiglio, S., Ciniselli, Ch. M., Tichopad, A., Kubista, M., Wyrich, R., Pazzagli, M., Gelmini, S. Implementation of a proficiency testing for the assessment of the preanalytical phase of blood samples used for RNA based analysis. Clinica Chimica Acta, 413: 779-786, 2012. ISSN 0009-8981. 
  • Laurell, H., Iacovoni, J., Abot, A., Svec, D., Maoret, J.-J., Arnal, J.-F., Kubista, M. Correction of RT-qPCR data for genomic DNA-derived signals with ValidPrime. Nucleic Acids Research, 40: 1-10, 2012. ISSN 0305-1048. 
  • Stimpfel, M., Skutella, T., Kubista, M., Malicev, E., Conrad, S., Virant-Klun, I. Potential Stemness of Frozen-Thawed Testicular Biopsies without Sperm in Infertile Men Included into the In Vitro Fertilization Programme. Journal of Biomedicine and Biotechnology, 291038: 1-15, 2012. ISSN 1110-7243. 
  • Slyskova, J., Korenkova, V., Collins, A. R., Prochazka, P., Vodickova, L., Svec, J., Lipska, L., Levy, M., Schneiderova, M., Liska, V., Holubec, L., Kumar, R., Soucek, P., Naccarati, A., Vodicka, P. Functional, Genetic, and Epigenetic Aspects of Base and Nucleotide Excision Repair in Colorectal Carcinoma. Clinical Cancer Research, 18:5878-5887, 2012. ISSN 1078-0432.
  • Sorg, D., Danowski, K., Korenkova, V., Rusnakova, V., Küffner, R., Zimmer, R., Meyer, H. H., Kliem, H. Microfluidic high-throughput RTqPCR measurements of the immune response of primary bovine mammary epithelial cells cultured from milk to mastitis pathogens. Animal, 7(5): 799-805, 2012. ISSN 1751-7311.
  • Ahmadi, S., Deligeorgiev, T. G., Vasilev, A., Kubista, M. The dimerization study of some cationic monomethine cyanine dyes by chemometrics method. Russian Journal of Physical Chemistry, 86(13): 1974-1981, 2012. ISSN 0036-0244.
  • Kubista, M. Q & A. European Pharmaceutical Review, 17(5): 57, 2012.
  • Kubista, M., Tichopad, A. Setting the bar. European Pharmaceutical Review, 17(5): 53-56, 2012.
  • Kubista, M. I See the Light! And I See It Again and Again! Clinical Chemistry, 58(11): 1505-1506, 2012. ISSN 0009-9147.
  • Guertler, P., Brandl, C., Meyer, H. H. D., Tichopad, A. Feeding genetically modified maize (MON810) to dairy cows: comparison of gene expression pattern of markers for apoptosis, inflammation and cell cycle. Journal fur Verbraucherschutz und Lebensmittelsicherheit-Journal of Consumer Protection and Food Safety, 7(3):195-202, 2012. ISSN 1661-5751.
  • Butenko, O., Dzamba, D., Benesova, J., Honsa, P., Benfenati, V., Rusnakova, V., Ferroni, S., Anderova, M. The Increased Activity of TRPV4 Channel in the Astrocytes of the Adult Rat Hippocampus after Cerebral Hypoxia/Ischemia. PLoS ONE, 7(6): e39959, 2012. ISSN 1932-6203.
  • Brevik, A., Lindeman, B., Rusnakova, V., Olsen, A. K., Brunborg, G., Duale, N. Paternal benzo[a]pyrene exposure affects gene expression in the early developing mouse embryo. Toxicological Sciences, 129(1), 2012. ISSN 1096-6080.
  • Kubista, M., Rusnakova, V., Svec, D., Sjogreen, B., Tichopad, A. Genex: Data Analysis Software. Quantitative Real-Time PCR in Applied Microbiology, 63-84, 2012. ISBN 978-1-908230-01-0.
  • Kubista, M. Drivers and Hurdles for qPCR. Genetic Engineering & Biotechnology News, 32(9): 24, 2012. ISSN 1935-472X.


  • Pazzagli, M., Malentacchi, F., Simi, L., Orlando, C., Wyrich, R., Gunther, K., Hartmann, C., Verderio, P., Pizzamiglio, S., Ciniselli, C. M., Tichopad, A., Kubista, M., Gelmini, S. Evidence-based quality guidelines for pre-analytical phase of blood samples. Clinical Chemistry and Laboratory Medicine, 49(1): 128, 2011. ISSN 1434-6621.
  • Brevik, A., Rusnakova, V., Duale, N., Slagsvold, H. H., Olsen, A.-K., Storeng, R., Kubista, M., Brunborg, G., Lindeman, B. Preconceptional paternal glycidamide exposure affects embryonic gene expression: Single embryo gene expression study following in vitro fertilization. Reproductive Toxicology, 32: 463-471, 2011. ISSN 0890-6238.
  • Bustin, A., Benes, V., Garson, J. A., Hellemans, J., Huggett, J., Kubista, M., Mueller, R., Nolan, T., Pfaffl , M. W., Shipley, G. L., Vandesompele, J., Wittwer, C. T. Primer Sequence Disclosure: A Clarification of the MIQE Guideline. Clinical Chemistry, 57: 919-921, 2011. ISSN 0009-9147.
  • Stahlberg, A., Kubista, M., Aman, P. Single-cell gene-expression profiling and its potential diagnostic application. Expert Review of Molecular Diagnostics, 11: 735-740, 2011. ISSN 1473-7159.
  • Kubista, M., Stahlberg, A. DNA diagnostics get digitased. Drug Discovery World, 2011.
  • Kubista, M., Tichopad, A. qPCR Round Table. International Drug Discovery 2011.
  • Gruber, H., Paul, V., Guertler, P., Spiekers, H., Tichopad, A., Meyer, H. H. D., Muller M. Fate of Cry1Ab Protein in Agricultural Systems under Slurry Management of Cows Fed Genetically Modified Maize (Zea mays L.) MON810: A Quantitative Assessment. J Agric Food Chem 2011.
  • Kubista, M., Rusnakova, V., Svec, D., Stahlberg, A. High throughput single cell expression profiling: Taking a closer look on biological response. Clinical Chemistry and Laboratory Medicine, 49(1): 118, 2011. ISSN 1434-6621.
  • Kubista, M., Strombom, L., Svec, D., Rusnakova, V., Stahlberg, A. High throughput single cell expression profiling: Taking a closer look on biological response. European Pharmaceutical Review, 16(2): 20-24, 2011.


  • Mikulova, V., Cabinakova, M., Pobudova, J., Tesarova, P., Pavlista, D., Kolostova, K., Kubista, M., Romzova, M., Zima, T. The role of disseminated tumor cells and circulating tumor cells in management of breast cancer patients. Tumor Biology, 31(1): 73, 2010. ISSN 1010-428.
  • Bergkvist, A., Rusnakova, V., Sindelka, R., Garda, J. M. A., Sjogreen, B., Lindh, D., Forootan, A., Kubista, M. Gene expression profiling – Clusters of possibilities. Methods, 50: 323-335, 2010. ISSN 1046-2023.
  • Bohuslavova, R., Kolar, F., Kuthanova, L., Neckar, J., Tichopad, A., Pavlinkova, G. Gene expression profiling of sex differences in HIF1-dependent adaptive cardiac responses to chronic hypoxia. Journal of Applied Physiology, 109: 1195-1202, 2010. ISSN 8750-7587.
  • Coll, A., Nadal, A., Collado, R., Capellades, G., Kubista, M., Messeguer, J., Pla, M. Natural variation explains most transcriptomic changes among maize plants of MON810 and comparable non-GM varieties subjected to two N-fertilization farming practice. Plant Molecular Biology, 73: 349-362, 2010. ISSN 0167-4412.
  • Kitchen, R. R., Kubista, M., Tichopad, A. Statistical aspects of quantitative real-time PCR experiment design. Methods, 50: 231-236, 2010. ISSN 1046-2023.
  • Kozubenko, N., Turnovcova, K., Kapcalova, M., Butenko, O., Anderova, M., Rusnakova, V., Kubista, M., Hampl, A., Jendelova, P., Sykova, E. Analysis of In Vitro and In Vivo Characteristics of Human Embryonic Stem Cell-Derived Neural Precursor. Cell Transplantation, 19: 471-486, 2010. ISSN 0963-6897.
  • Sindelka, R., Sidova, M., Svec, D., Kubista, M. Spatial expression profiles in the Xenopus laevis oocytes measured with qPCR tomography. Methods, 51: 87-91, 2010. ISSN 1046-2023.
  • Tichopad, A., Bar, T., Pecen, L., Kitchen, R. R., Kubista, M., Pfaffl , M. W. Quality control for quantitative PCR based on amplification compatibility test. Methods, 50: 308-312, 2010. ISSN 1046-2023.
  • Zanvit, P., Tichopad, A., Havlickova, M., Novotna, O., Jirkovska, M., Kolostova, K., Cechova, D., Julak, J., Sterzl, I., Prokesova, L. 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. Immunology Letters, 134: 26-34, 2010. ISSN 0165-2478.
  •  Veiga, M. I., Ferreira, P. E., Schmidt, B. A., Ribacke, U., Bjorkman, A., Tichopad, A., Gil, J. P. Antimalarial Exposure Delays Plasmodium falciparum Intra-Erythrocytic Cycle and Drives Drug Transporter Genes Expression. PLoS ONE, 5(8): e12408, 2010. ISSN 1932-6203.
  • Stahlberg, A., Andersson, D., Aurelius, J., Faiz, M., Pekna, M., Kubista, M., Pekny, M., Defining cell populations with single-cell gene expression profiling: correlations and identification of astrocyte subpopulations. Nucleic Acids Research, 39(4): 1-12, 2010. ISSN 0305-1048.
  • Kolostova, K., Pinterova, D., Tesarova, P., Bobek, V., Mikulova, V., Kubecova, M., Brychta, M., Rusnakova, V., Bauer, S. K., Kubista, M. Gene expression profiling in circulation cells (CTCS) of breast carcinoma patients. Annals of Oncology, 21(4): 49-50, 2010.
  • Stofkova, A., Zelezna, B., Romzova, M., Ulicna, O., Kiss, A., Skurlova, M., Jurcovicova, J. Effect of feeding status on adjuvant arthritis severity, cachexia, and insulin sensitivity in male Lewis rats. Mediators of Inflammation, Article No.: 398026, 2010. ISSN 0962-9351.
  • Kubista, M. Real-time PCR: Where we are and where are we heading. Drug Discovery World Spring 2010.
  • Ctrnacta, V., Fritzler, J. M., Surinova, M., Hrdy, I., Zhu, G., Stejskal, F. Efficacy of S-adenosylhomocysteine hydrolase inhibitors, D-eritadenine and (S)-DHPA, against the growth of Cryptosporidium parvum in vitro. Experimental Parasitology, 126(2): 113-116, 2010. ISSN:0014-4894.


  • Bustin, A., Benes, V., Garson, J. A., Hellemans, J., Huggett, J., Kubista, M., Mueller, R., Nolan, T., Pfaffl , M. V., Shipley, G. L., Vandesompele, J., Wittver, C. T. The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR. Experiment Clinical Chemistry, 55: 611-622, 2009. ISSN 0009-9147.
  • Masova, A., Sindelka, R., Kubista, M., Kindl, J., Jiracek, J. Gene Expression Responses in Larvae of the Fleshfly Sarcophaga bullata after Immune Stimulation. Folia Biologica, 55: 98-106, 2009. ISSN 0015-5500.
  • Tichopad, A., Kitchen, R., Riedmaier, I., Becker, Ch., Ståhlberg, A., Kubista, M. Design and Optimization of Reverse-Transcription Quantitative PCR. Experiment Clinical Chemistry, 55:1816-1823, 2009. ISSN 0009-9147.
  • Pfaffl, M. V., Vandesompele, J., Kubista, M. Data Analysis Software: Chapter 5 in Real-Time PCR: Current Technology and Applications. Caister Academic Press, editor: Logan, J., Edwards, K., Saunders, N., 2009. ISBN 978-1-904455-39-4.
  • Kubista, M. Intracellular Gene Expression Profiles Revealed with Real-time PCR Tomography. Research Spotlight:Gene Expression, 2009.
  • Kubista, M. What future holds for real-time PCR. European Pharmaceutical Reviews Industry Focus, 2009.
  • Pytelkova, J., Hubert, J., Lepsik, M., Sobotnik, J., Sindelka, R., Krizkova, I., Horn, M., Mares, M. Digestive alpha-amylases of the flour moth Ephestia kuehniella - adaptation to alkaline environment and plant inhibitors. FEBS Journal, 276 (13): 3531-3546, 2009. doi: 10.1111/j.1742-4658.2009.07074.x. ISSN 1742-464X.


  • Niazi, A., Yazdanipour, A., Ghasemi, J., Amini, A., Bozorgzad, S., Kubista, M. Spectrophotometric investigation of the Acidity constants of fluorescein in various water-organic solvent media. Chemical Engineering Communications, 195: 1257-1268, 2008. ISSN 0098-6445.
  • Stahlberg, A., Elbing, K., Andrade-Garda, J. M., Sjögreen, B., Forootan, A., Kubista, M. Multiway real-time PCR gene expression profiling in yeast. Saccharomyces cerevisiae reveals altered transcriptional response of ADH-genes to glucose stimuli. B M C Genomics, 9: 1-41, 2008. ISSN 1471-2164.
  • Sindelka, R., Jonak, J., Hands, R., Bustin, A., Kubista, M. Intracellular expression profiles measured by real-time PCR tomography in the Xenopus laevis oocyte. Nucleic Acids Research, 36: 387-392, 2008. ISSN 0305-1048. 
  • Kubista, M., Eliasson, J., Lennerls, M., Andersson, S., Sjöback, R. What is needed to measure a difference with real-time PCR? Eppendorf BioNews Application Notes, 2008.
  • Kubista, M. Emerging real-time PCR applications. Drug Discovery World Summer, 2008.
  • Pinzani, P., Lind, K., Malentacchi, F., Nesi, G., Salvianti, F., Villari, D., Kubista, M., Pazzagli, M., Orlando, C. 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, 2008. ISSN 0046-8177.
  • Bergkvist, A., Forootan, A., Zoric, N., Strombom, L., Sjoback, R., Kubista, M. Choosing a normalization strategy for RT-PCR. Genetic Engineering & Biotechnology News, 28(13):26-9, 2008. ISSN 1935-472X.
  • Li, L., Lundkvist, A., Andersson, D., Wilhelmsson, U., Nagai, N., Pardo, A. C., Nodin, C., Stahlberg, A., Aprico, K., Larsson, K., Yabe, T., Moons, L., Fotheringham, A., Davies, I., Carmeliet, P., Schwartz, J. P., Pekna, M., Kubista, M., Blomstrand, F., Maragakis, N., Nilsson, M., Pekny, M. Protective role of reactive astrocytes in brain ischemia. Journal of Cerebral Blood Flow and Metabolism, 28(3):468-481, 2008. ISSN 0271-678X.