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Laznicka T, Kizovsk\'fd M, Hrubanov\'e1 K, Je?ek J, Mrazova K, Obru?a S, Samek O, Krzy?\'e1nek V. Assembly for semi-correlation analysis of samples using cryogenic scanning electron microscopy and cryogenic Raman micro-spectroscopy. MEASUREMENT SCIENCE AND TECHNOLOGY, 36, 055903 (2025).\par \par Adhvaryu S, Kiskova J, Piknova M, Malinicova L, Beck T, Buchtikova I, Kourilova X, Kizovsk\'fd M, Samek O, Obru?a S, Pristas P. The characterization of halophilic polyhydroxyalkanoate-producing bacteria from brine in Solivar near Pre?ov (Slovakia). World Journal of Microbiology and Biotechnology, 41, 505 (2025).\par \par 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 Ghazalova M, Modlitbova P, Samek O, Rebro?ov\'e1 K, ?iler M, Je?ek J, Pil\'e1t Z. Surface-Enhanced Raman Spectroscopy for Adenine Detection in Five Selected Bacterial Strains Under Stress Conditions. SENSORS, 25, 4629 (2025).\par \par Lee KSoo, Landry Z, Athar A, Alcolombri U, Ayutthaya PPramoj Na, Berry D, de Bettignies P, Cheng J-X, Csucs G, Cui L, Deckert V, Dieing T, Dionne J, Doskocil O, D'Souza G, Garcia-Timermans C, Gierlinger N, Goda K, Hatzenpichler R, Henshaw RJ, Huang WE, Iermak I, Ivleva NP, Kneipp J, Kubryk P, Kuesel K, Lee TKwon, Lee SSik, Ma B, Martinez-Perez C, Matousek P, Meckenstock RU, Min W, Mojzes P, Mueller O, Kumar N, Nielsen PHalkjaer, Notingher I, Palatinszky M, Pereira FC, Pezzotti G, Pil\'e1t Z, Plesinger F, Popp J, Probst AJ, Riva A, Saleh AAE, Samek O, Sapers HM, Schubert OT, Stubbusch AKM, Tadesse LF, Taylor GT, Wagner M, Wang J, Yin H, Yue Y, Zenobi R, Zini J, Sarkans U, Stocker R. MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data. NATURE MICROBIOLOGY, 9, (2024).\par \par Khan A, Qadeer A, Wajid A, Ullah Q, Rahman SUr, Ullah K, Safi SZaman, Ticha L, Skalickova S, Chilala P, Bernatov\'e1 S, Samek O, Horky P. Microplastics in animal nutrition: Occurrence, spread, and hazard in animals. JOURNAL OF AGRICULTURE AND FOOD RESEARCH, 17, 101258 (2024).\par \par Siems K, Runzheimer K, Rebro?ov\'e1 K, Etzbach L, Auerhammer A, Rehm A, Schwengers O, ?iler M, Samek O, R??i?ka F, Moeller R. Identification of staphyloxanthin and derivates in yellow-pigmented Staphylococcus capitis subsp. capitis. Frontiers in Microbiology, 14, (2023).\par \par Bene?ov\'e1 M, Bernatov\'e1 S, Mika F, Pokorn\'e1 Z, Je?ek J, ?iler M, Samek O, R??i?ka F, Rebro?ov\'e1 K, Zem\'e1nek P, Pil\'e1t Z. SERS-Tags: Selective Immobilization and Detection of Bacteria by Strain-Specific Antibodies and Surface-Enhanced Raman Scattering. Biosensors, 13, 182 (2023).\par \par Rebro?ov\'e1 K, Samek O, Kizovsk\'fd M, Bernatov\'e1 S, Hol\'e1 V, R??i?ka F. Raman Spectroscopy-A Novel Method for Identification and Characterization of Microbes on a Single-Cell Level in Clinical Settings. FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY, 12, 866463 (2022).\par \par Samek O, Bernatov\'e1 S, Dohnal F. The potential of SERS as an AST methodology in clinical settings. NANOPHOTONICS, 10, 2537-2561 (2021).\par \par Kizovsk\'fd M, Pil\'e1t Z, Mylenko M, Hrouzek P, Kuta J, Skoup\'fd R, Krzy?\'e1nek V, Hrubanov\'e1 K, Adamczyk O, Je?ek J, Bernatov\'e1 S, Klementov\'e1 T, Gjevik A, ?iler M, Samek O, Zem\'e1nek P. Raman Microspectroscopic Analysis of Selenium Bioaccumulation by Green Alga Chlorella vulgaris. Biosensors, 11, 115 (2021).\par \par N?mcov\'e1 A, Gonov\'e1 D, Samek O, Sipiczki M, Breierov\'e1 E, M\'e1rov\'e1 I. The Use of Raman Spectroscopy to Monitor Metabolic Changes in Stressed Metschnikowia sp. Yeasts. Microorganisms, 9, 277 (2021).\par \par N?mcov\'e1 A, Szotkowski M, Samek O, Cag\'e1?ov\'e1 L, Sipiczki M, M\'e1rov\'e1 I. Use of Waste Substrates for the Lipid Production by Yeasts of the Genus Metschnikowia?Screening Study. Microorganisms, 9, 2295 (2021).\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. Identification of ability to form biofilm in Candida parapsilosis and Staphylococcus epidermidis by Raman spectroscopy. Future Microbiology, 14, 509-517 (2019).\par \par Bernatov\'e1 S, Donato MGrazia, Je?ek J, Pil\'e1t Z, Samek O, Magazzu A, Marag\'f2 OM, Zem\'e1nek P, Gucciardi PG. Wavelength-Dependent Optical Force Aggregation of Gold Nanorods for SERS in a Microfluidic Chip. J. Phys. Chem. C, 123, 5608-5615 (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 }