Laznicka T, Kizovský M, Hrubanová K, Je?ek J, Mrazova K, Obru?a S, Samek O, Krzy?ánek 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).

Vejrosta J, Cabalová S, Plichta T, ?erý M, Ma?ka T, Samek O, Zemánek 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, Lettrichová Ied.), 2025, International Society for Optics and Photonics.

Ghazalova M, Modlitbova P, Samek O, Rebro?ová K, ?iler M, Je?ek J, Pilát Z. Surface-Enhanced Raman Spectroscopy for Adenine Detection in Five Selected Bacterial Strains Under Stress Conditions. SENSORS, 25, 4629 (2025).

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, Pilát 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).

Khan A, Qadeer A, Wajid A, Ullah Q, Rahman SUr, Ullah K, Safi SZaman, Ticha L, Skalickova S, Chilala P, Bernatová S, Samek O, Horky P. Microplastics in animal nutrition: Occurrence, spread, and hazard in animals. JOURNAL OF AGRICULTURE AND FOOD RESEARCH, 17, 101258 (2024).

Siems K, Runzheimer K, Rebro?ová 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).

Bene?ová M, Bernatová S, Mika F, Pokorná Z, Je?ek J, ?iler M, Samek O, R??i?ka F, Rebro?ová K, Zemánek P, Pilát Z. SERS-Tags: Selective Immobilization and Detection of Bacteria by Strain-Specific Antibodies and Surface-Enhanced Raman Scattering. Biosensors, 13, 182 (2023).

Rebro?ová K, Samek O, Kizovský M, Bernatová S, Holá 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).

Samek O, Bernatová S, Dohnal F. The potential of SERS as an AST methodology in clinical settings. NANOPHOTONICS, 10, 2537-2561 (2021).

Kizovský M, Pilát Z, Mylenko M, Hrouzek P, Kuta J, Skoupý R, Krzy?ánek V, Hrubanová K, Adamczyk O, Je?ek J, Bernatová S, Klementová T, Gjevik A, ?iler M, Samek O, Zemánek P. Raman Microspectroscopic Analysis of Selenium Bioaccumulation by Green Alga Chlorella vulgaris. Biosensors, 11, 115 (2021).

N?mcová A, Gonová D, Samek O, Sipiczki M, Breierová E, Márová I. The Use of Raman Spectroscopy to Monitor Metabolic Changes in Stressed Metschnikowia sp. Yeasts. Microorganisms, 9, 277 (2021).

N?mcová A, Szotkowski M, Samek O, Cagá?ová L, Sipiczki M, Márová I. Use of Waste Substrates for the Lipid Production by Yeasts of the Genus Metschnikowia?Screening Study. Microorganisms, 9, 2295 (2021).

Rebro?ová K, ?iler M, Samek O, R??i?ka F, Bernatová S, Je?ek J, Zemánek P, Holá V. Identification of ability to form biofilm in Candida parapsilosis and Staphylococcus epidermidis by Raman spectroscopy. Future Microbiology, 14, 509-517 (2019).

Bernatová S, Donato MGrazia, Je?ek J, Pilát Z, Samek O, Magazzu A, Maragò OM, Zemánek 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).

Sedlá?ek P, Slaninová E, Enev V, Koller M, Nebesá?ová J, Márová I, Hrubanová K, Krzy?ánek 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).

Procházka D, Mazura M, Samek O, Rebro?ová K, Po?ízka P, Klus J, Procházková P, Novotný J, Novotný 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).

Pilát Z, Kizovský M, Je?ek J, Krátký S, Sobota J, ?iler M, Samek O, Bury?ka T, Va?á?ek P, Damborský J, Prokop Z, Zemánek P. Detection of chloroalkanes by surface-enhanced raman spectroscopy in microfluidic chips. Sensors, 18, 3212 (2018).

Pilát Z, Bernatová S, Je?ek J, Kirchhoff J, Tannert A, Neugebauer U, Samek O, Zemánek P. Microfluidic Cultivation and Laser Tweezers Raman Spectroscopy of E-coli under Antibiotic Stress. Sensors, 18, 1623 (2018).

Hrubanová K, Krzy?ánek V, Nebesá?ová J, R??i?ka F, Pilát Z, Samek O. Monitoring Candida parapsilosis and Staphylococcus epidermidis Biofilms by a Combination of Scanning Electron Microscopy and Raman Spectroscopy. Sensors, 18, 4089 (2018).

Rebro?ová K, ?iler M, Samek O, R??i?ka F, Bernatová S, Je?ek J, Zemánek P, Holá V. Differentiation between Staphylococcus aureus and Staphylococcus epidermidis strains using Raman spectroscopy. Future Microbiology, 12, 10 (2017).

Hrubanová K, Krzy?ánek V, Samek O, Skoupý R, ?iler M, Je?ek J, Obru?a S, Zemánek P. Morphological and Production Changes in Planktonic and Biofilm Cells Monitored Using SEM and Raman Spectroscopy. Microscopy and Microanalysis, 23, S1 (2017).

Obru?a S, Sedlá?ek P, Mravec F, Krzy?ánek V, Nebesá?ová J, Samek O, Ku?era D, Bene?ová P, Hrubanová K, Milerová M, Márová 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).

Rebro?ová K, ?iler M, Samek O, R??i?ka F, Bernatová S, Holá V, Je?ek J, Zemánek P, Sokolová J, Petrá? P. Rapid identification of staphylococci by Raman spectroscopy. Sci. Rep., 7, 14846 (2017).

Mravec F, Obru?a S, Krzy?ánek V, Sedlá?ek P, Hrubanová K, Samek O, Ku?era D, Bene?ová P, Nebesá?ová J. Accumulation of PHA granules in Cupriavidus necator as seen by confocal fluorescence microscopy. FEMS Microbiology Letters, 363, 10 (2016).

Obru?a S, Sedlá?ek P, Krzy?ánek V, Mravec F, Hrubanová K, Samek O, Ku?era D, Bene?ová P, Márová I. Accumulation of Poly(3-hydroxybutyrate) Helps Bacterial Cells to Survive Freezing. PLoS ONE, 11, e0157778 (2016).

Obru?a S, Sedlá?ek P, Mravec F, Samek O, Márová 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).

Hrubanová K, Samek O, Haroniková A, Bernatová S, Zemánek P, Márová I, Krzy?ánek V. Morphological and Production Changes in Stressed Red Yeasts Monitored Using SEM and Raman Spectroscopy. Microscopy and Microanalysis, 22, S3 (2016).

Samek O, Obru?a S, ?iler M, Sedlá?ek P, Bene?ová P, Ku?era D, Márová I, Je?ek J, Bernatová S, Zemánek P. Quantitative Raman Spectroscopy Analysis of Polyhydroxyalkanoates Produced by Cupriavidus necator H16. Sensors, 16, 1808 (2016).

Krzy?ánek V, Hrubanová K, Samek O, Obru?a S, Márová I, Bernatová S, ?iler M, Zemánek P. Cryo-SEM and Raman Spectroscopy Study of the Involvement of Polyhydroxyalkanoates in Stress Response of Bacteria. Microscopy and Microanalysis, 21, 183-184 (2015).

Samek O, Bernatová S, Je?ek J, ?iler M, ?erý M, Krzy?ánek V, Hrubanová K, Zemánek P, Holá V, R??i?ka F. Identification of individual biofilm-forming bacterial cells using Raman tweezers. J. Biomed. Opt., 20, (2015).

Mlynariková K, Samek O, Bernatová S, R??i?ka F, Je?ek J, Haroniková A, ?iler M, Zemánek P, Holá V. Influence of Culture Media on Microbial Fingerprints Using Raman Spectroscopy. Sensors, 15, 29635-29647 (2015).

Hrubanová K, Bernatová S, Samek O, ?erý M, Zemánek P, Nebesá?ová J, R??i?ka F, Krzy?ánek V. Monitoring of Multilayered Bacterial Biofilm Morphology by Cryo-SEM for Raman Spectroscopy Measurements. Microscopy and Microanalysis, 21, 187-188 (2015).

Samek O, Haroniková A, Va?kovicová N, Hrubanová K, Je?ek J, Márová I, Krzy?ánek V, Zemánek 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).

Burdiková Z, Svindrych Z, Hickey C, Wilkinson MG, Auty MAE, Samek O, Bernatová S, Krzy?ánek 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).

Po?ízka P, Procházková P, Procházka D, Sládková L, Novotný J, Petrilak M, Brada M, Samek O, Pilát Z, Zemánek P, Adam V, Kizek R, Novotný J, Kaiser J. Algal Biomass Analysis by Laser-Based Analytical Techniques?A Review. Sensors, 14, 17725-17752 (2014).

Samek O, Mlynariková K, Bernatová S, Je?ek J, Krzy?ánek V, ?iler M, Zemánek P, R??i?ka F, Holá V, Mahelová M. Candida parapsilosis Biofilm Identification by RamanSpectroscopy. Int. J. Mol. Sci., 15, 23924-23935 (2014).

Bernatová S, Samek O, Pilát Z, ?erý M, Je?ek J, Jákl P, ?iler M, Krzy?ánek V, Zemánek P, Holá V, Dvo?á?ková M, R??i?ka F. Following the mechanisms of bacteriostatic versus bacericidal action using Raman spectroscopy. Molecules, 18, 13188-13199 (2013).

Po?ízka P, Procházka D, Pilát Z, Kraj?arová L, Kaiser J, Malina R, Novotný J, Zemánek P, Je?ek J, ?erý M, Bernatová S, Krzy?ánek V, Dobranská K, Novotný K, Trtílek 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).

Pilát Z, Bernatová S, Je?ek J, ?erý M, Samek O, Zemánek P, Nedbal L, Trtílek M. Raman microspectroscopy of algal lipid bodies: beta-carotene quantification. J. Appl. Phycol., 24, 541-546 (2012).

Samek O, Zemánek P, Joná? A, Telle HH. Characterization of oil-producing microalgae using Raman spectroscopy. Laser Phys. Lett., 8, 701?709 (2011).

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).

Samek O, Joná? A, Pilát Z, Zemánek P, Nedbal L, T?íska J, Kotas P, Trtílek M. Raman Microspectroscopy of Individual Algal Cells: Sensing Unsaturation of Storage Lipids in vivo. Sensors, 10, 8635?8651 (2010).