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Vejrosta J, Cabalov\'e1 S, Plichta T, ?er\'fd M, Ma?ka T, Samek O, Zem\'e1nek P. Preparation and pilot experiments on microfluidic chip with surface acoustic waves, 23rd Slovak-Czech-Polish Optical Conference on Wave and Quantum Aspects of Contemporary Optics, (Pudi? D, Jandura D, Lettrichov\'e1 Ied.), 2025, International Society for Optics and Photonics.\par \par Meixner K, Daffert C, Dalnodar D, Mrazova K, Hrubanov\'e1 K, Krzyzanek V, Nebes\'e1?ov\'e1 J, Samek O, Sedrlova Z, Slaninov\'e1 E, Sedl\'e1?ek P, Obru?a S, Fritz I. Glycogen, poly(3-hydroxybutyrate) and pigment accumulation in three Synechocystis strains when exposed to a stepwise increasing salt stress. JOURNAL OF APPLIED PHYCOLOGY, 34, 1227-1241 (2022).\par \par Bernatov\'e1 S, Rebro?ov\'e1 K, Pil\'e1t Z, ?er\'fd M, Gjevik A, Samek O, Je?ek J, ?iler M, Kizovsk\'fd M, Klementov\'e1 T, Hol\'e1 V, R??i?ka F, Zem\'e1nek P. Rapid detection of antibiotic sensitivity of Staphylococcus aureus by Raman tweezers. Eur. Phys. J. Plus, 136, 233 (2021).\par \par Pavlokov\'e1 S, Mu?el\'edk J, Sabadkov\'e1 D, Bernatov\'e1 S, Samek O, Neumann D, Franc A. The effects of the treatment conditions on the dissolution profile of ethylcellulose coated pellets. Europ. J. of Pharmaceutical Sci., 132, 86-95 (2019).\par \par Sedl\'e1?ek P, Slaninov\'e1 E, Enev V, Koller M, Nebes\'e1?ov\'e1 J, M\'e1rov\'e1 I, Hrubanov\'e1 K, Krzy?\'e1nek V, Samek O, Obru?a S. What keeps polyhydroxyalkanoates in bacterial cells amorphous? A derivation from stress exposure experiments. Appl. Microbiol. Biotech., 103, 1905-1917 (2019).\par \par Proch\'e1zka D, Mazura M, Samek O, Rebro?ov\'e1 K, Po?\'edzka P, Klus J, Proch\'e1zkov\'e1 P, Novotn\'fd J, Novotn\'fd K, Kaiser J. Combination of laser-induced breakdown spectroscopy and Raman spectroscopy for multivariate classification of bacteria. Spec. Acta Part B, 139, 6-12 (2018).\par \par Pil\'e1t Z, Kizovsk\'fd M, Je?ek J, Kr\'e1tk\'fd S, Sobota J, ?iler M, Samek O, Bury?ka T, Va?\'e1?ek P, Damborsk\'fd J, Prokop Z, Zem\'e1nek P. Detection of chloroalkanes by surface-enhanced raman spectroscopy in microfluidic chips. Sensors, 18, 3212 (2018).\par \par Pil\'e1t Z, Bernatov\'e1 S, Je?ek J, Kirchhoff J, Tannert A, Neugebauer U, Samek O, Zem\'e1nek P. Microfluidic Cultivation and Laser Tweezers Raman Spectroscopy of E-coli under Antibiotic Stress. Sensors, 18, 1623 (2018).\par \par Hrubanov\'e1 K, Krzy?\'e1nek V, Nebes\'e1?ov\'e1 J, R??i?ka F, Pil\'e1t Z, Samek O. Monitoring Candida parapsilosis and Staphylococcus epidermidis Biofilms by a Combination of Scanning Electron Microscopy and Raman Spectroscopy. Sensors, 18, 4089 (2018).\par \par Rebro?ov\'e1 K, ?iler M, Samek O, R??i?ka F, Bernatov\'e1 S, Je?ek J, Zem\'e1nek P, Hol\'e1 V. Differentiation between Staphylococcus aureus and Staphylococcus epidermidis strains using Raman spectroscopy. Future Microbiology, 12, 10 (2017).\par \par Hrubanov\'e1 K, Krzy?\'e1nek V, Samek O, Skoup\'fd R, ?iler M, Je?ek J, Obru?a S, Zem\'e1nek P. Morphological and Production Changes in Planktonic and Biofilm Cells Monitored Using SEM and Raman Spectroscopy. Microscopy and Microanalysis, 23, S1 (2017).\par \par Obru?a S, Sedl\'e1?ek P, Mravec F, Krzy?\'e1nek V, Nebes\'e1?ov\'e1 J, Samek O, Ku?era D, Bene?ov\'e1 P, Hrubanov\'e1 K, Milerov\'e1 M, M\'e1rov\'e1 I. The presence of PHB granules in cytoplasm protects non-halophilic bacterial cells against the harmful impact of hypertonic environments. New Biotechnol., 39, 10 (2017).\par \par Rebro?ov\'e1 K, ?iler M, Samek O, R??i?ka F, Bernatov\'e1 S, Hol\'e1 V, Je?ek J, Zem\'e1nek P, Sokolov\'e1 J, Petr\'e1? P. Rapid identification of staphylococci by Raman spectroscopy. Sci. Rep., 7, 14846 (2017).\par \par Mravec F, Obru?a S, Krzy?\'e1nek V, Sedl\'e1?ek P, Hrubanov\'e1 K, Samek O, Ku?era D, Bene?ov\'e1 P, Nebes\'e1?ov\'e1 J. Accumulation of PHA granules in Cupriavidus necator as seen by confocal fluorescence microscopy. FEMS Microbiology Letters, 363, 10 (2016).\par \par Obru?a S, Sedl\'e1?ek P, Krzy?\'e1nek V, Mravec F, Hrubanov\'e1 K, Samek O, Ku?era D, Bene?ov\'e1 P, M\'e1rov\'e1 I. Accumulation of Poly(3-hydroxybutyrate) Helps Bacterial Cells to Survive Freezing. PLoS ONE, 11, e0157778 (2016).\par \par Obru?a S, Sedl\'e1?ek P, Mravec F, Samek O, M\'e1rov\'e1 I. Evaluation of 3-hydroxybutyrate as an enzyme-protective agent against heating and oxidative damage and its potential role in stress response of poly(3-hydroxybutyrate) accumulating cells. Appl Microbiol Biotechnol, 100, 1365-1376 (2016).\par \par Hrubanov\'e1 K, Samek O, Haronikov\'e1 A, Bernatov\'e1 S, Zem\'e1nek P, M\'e1rov\'e1 I, Krzy?\'e1nek V. Morphological and Production Changes in Stressed Red Yeasts Monitored Using SEM and Raman Spectroscopy. Microscopy and Microanalysis, 22, S3 (2016).\par \par Samek O, Obru?a S, ?iler M, Sedl\'e1?ek P, Bene?ov\'e1 P, Ku?era D, M\'e1rov\'e1 I, Je?ek J, Bernatov\'e1 S, Zem\'e1nek P. Quantitative Raman Spectroscopy Analysis of Polyhydroxyalkanoates Produced by Cupriavidus necator H16. Sensors, 16, 1808 (2016).\par \par Krzy?\'e1nek V, Hrubanov\'e1 K, Samek O, Obru?a S, M\'e1rov\'e1 I, Bernatov\'e1 S, ?iler M, Zem\'e1nek P. Cryo-SEM and Raman Spectroscopy Study of the Involvement of Polyhydroxyalkanoates in Stress Response of Bacteria. Microscopy and Microanalysis, 21, 183-184 (2015).\par \par Samek O, Bernatov\'e1 S, Je?ek J, ?iler M, ?er\'fd M, Krzy?\'e1nek V, Hrubanov\'e1 K, Zem\'e1nek P, Hol\'e1 V, R??i?ka F. Identification of individual biofilm-forming bacterial cells using Raman tweezers. J. Biomed. Opt., 20, (2015).\par \par Mlynarikov\'e1 K, Samek O, Bernatov\'e1 S, R??i?ka F, Je?ek J, Haronikov\'e1 A, ?iler M, Zem\'e1nek P, Hol\'e1 V. Influence of Culture Media on Microbial Fingerprints Using Raman Spectroscopy. Sensors, 15, 29635-29647 (2015).\par \par Hrubanov\'e1 K, Bernatov\'e1 S, Samek O, ?er\'fd M, Zem\'e1nek P, Nebes\'e1?ov\'e1 J, R??i?ka F, Krzy?\'e1nek V. Monitoring of Multilayered Bacterial Biofilm Morphology by Cryo-SEM for Raman Spectroscopy Measurements. Microscopy and Microanalysis, 21, 187-188 (2015).\par \par Burdikov\'e1 Z, Svindrych Z, Hickey C, Wilkinson MG, Auty MAE, Samek O, Bernatov\'e1 S, Krzy?\'e1nek V, Periasamy A, Sheehan JJ. SEM and Raman Spectroscopy Applied to Biomass Analysis for Application in the Field of Biofuels and Food Industry. Dairy Sci. Technol., 95, 687-700 (2015).\par \par Samek O, Haronikov\'e1 A, Va?kovicov\'e1 N, Hrubanov\'e1 K, Je?ek J, M\'e1rov\'e1 I, Krzy?\'e1nek V, Zem\'e1nek P. SEM and Raman Spectroscopy Applied to Biomass Analysis for Application in the Field of Biofuels and Food Industry. Microscopy and Microanalysis, 21, 1775-1776 (2015).\par \par Po?\'edzka P, Proch\'e1zkov\'e1 P, Proch\'e1zka D, Sl\'e1dkov\'e1 L, Novotn\'fd J, Petrilak M, Brada M, Samek O, Pil\'e1t Z, Zem\'e1nek P, Adam V, Kizek R, Novotn\'fd J, Kaiser J. Algal Biomass Analysis by Laser-Based Analytical Techniques?A Review. Sensors, 14, 17725-17752 (2014).\par \par Samek O, Mlynarikov\'e1 K, Bernatov\'e1 S, Je?ek J, Krzy?\'e1nek V, ?iler M, Zem\'e1nek P, R??i?ka F, Hol\'e1 V, Mahelov\'e1 M. Candida parapsilosis Biofilm Identification by RamanSpectroscopy. Int. J. Mol. Sci., 15, 23924-23935 (2014).\par \par Bernatov\'e1 S, Samek O, Pil\'e1t Z, ?er\'fd M, Je?ek J, J\'e1kl P, ?iler M, Krzy?\'e1nek V, Zem\'e1nek P, Hol\'e1 V, Dvo?\'e1?kov\'e1 M, R??i?ka F. Following the mechanisms of bacteriostatic versus bacericidal action using Raman spectroscopy. Molecules, 18, 13188-13199 (2013).\par \par Po?\'edzka P, Proch\'e1zka D, Pil\'e1t Z, Kraj?arov\'e1 L, Kaiser J, Malina R, Novotn\'fd J, Zem\'e1nek P, Je?ek J, ?er\'fd M, Bernatov\'e1 S, Krzy?\'e1nek V, Dobransk\'e1 K, Novotn\'fd K, Trt\'edlek M, Samek O. Application of laser-induced breakdown spectroscopy to the analysis ofalgal biomass for industrial biotechnology. Spectrochim. Acta B, 74-75, 169-176 (2012).\par \par Pil\'e1t Z, Bernatov\'e1 S, Je?ek J, ?er\'fd M, Samek O, Zem\'e1nek P, Nedbal L, Trt\'edlek M. Raman microspectroscopy of algal lipid bodies: beta-carotene quantification. J. Appl. Phycol., 24, 541-546 (2012).\par \par Samek O, Zem\'e1nek P, Jon\'e1? A, Telle HH. Characterization of oil-producing microalgae using Raman spectroscopy. Laser Phys. Lett., 8, 701?709 (2011).\par \par Samek O, Al-Marashi JFM, Telle HH. The potential of Raman spectroscopy for the identification of biofilm formation by Staphylococcusepidermidis. Laser Phys. Lett., 7, 378?383 (2010).\par \par Samek O, Jon\'e1? A, Pil\'e1t Z, Zem\'e1nek P, Nedbal L, T?\'edska J, Kotas P, Trt\'edlek M. Raman Microspectroscopy of Individual Algal Cells: Sensing Unsaturation of Storage Lipids in vivo. Sensors, 10, 8635?8651 (2010).\par \par }