Curriculum Vitae

Person Identification

• doc. Mgr. Zdeněk Farka, Ph.D.
  born December 26, 1989 in Brno, Czech Republic

Workplace

• Department of Biochemistry
  Faculty of Science
  Masaryk University
  Kamenice 5
  625 00 Brno

Employment Position

• Associate Professor

Education and Academic Qualifications

• 2022: Habilitation (Assoc. Prof.) in Biochemistry, Masaryk University
  Thesis: Advanced lmmunochemical Biosensors and Assays: From Label-Free to Single-Molecule Detection
• 2014–2017: Ph.D. in Structural Biology, Masaryk University
  Thesis: Bioelectronic interfaces studied with scanning probe microscopy
• 2012–2014: Mgr. (M.Sc.) in Analytical Biochemistry (with honors), Masaryk University
  Thesis: Interaction of antibodies with microbial cells studied using biosensors
• 2009–2012: Bc. (B.Sc.) in Biochemistry (with honors), Masaryk University
  Thesis: Interaction of antibodies with Bacillus atrophaeus studied using biosensors

Professional Experience

• 2022–present: Associate Professor
  Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
• 2020–2022: Assistant Professor
  Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
• 2018–2020: Senior Researcher
  CEITEC MU, Masaryk University, Brno, Czech Republic
• 2017: Research Specialist
  CEITEC MU, Masaryk University, Brno, Czech Republic
• 2011–2016: Seven Work agreements in total length of 29 months
  CEITEC MU and Faculty of Science, Masaryk University, Brno, Czech Republic

Teaching Activities

• Supervision of Students:
  Dissertation theses (Ph.D.): 1× supervisor (1 active), 2× consultant (2 active), 3× reviewer
  Master’s degree theses (Mgr.): 4× supervisor (3 graduates, 1 active), 5× consultant (4 graduates, 1 active), 10× reviewer
  Bachelor’s degree theses (Bc.): 12× supervisor (7 graduates, 5 active), 2× consultant (2 graduates), 7× reviewer
• Awards of Supervised Students:
  2023: D. Sklenárová, First prize in Karel Štulík Award, Czech Republic
  2022: E. Macháčová, First prize in Karel Štulík Award, Czech Republic
  2022: D. Sklenárová, Honorable Mention in Dr. Tasilo Prnka Prize, NANOCON 2022, Brno, Czech Republic
  2021: E. Macháčová, Dean’s Award, Faculty of Science, Masaryk University, Brno, Czech Republic
• Teaching:
  C3002 Nanobiotechnology
  C3190 Biochemistry I - seminar C3600 Biochemistry – laboratory course
  C4200 Biochemistry II - seminar
  C4220 Biochemistry – laboratory course
  C5850 Introduction to Biophysical Chemistry
  C5855 Methods in Biophysical Chemistry
  C5856 Methods in Biophysical Chemistry – seminar
  C6200 Biochemical Methods
  C9320 Methods of biochemical research
  

Scientific and Research Projects

• 2021–2024: GAČR Standard (Co-investigator)
  Photon-upconversion labeling for microfluidic single-molecule immunoassays of protein biomarkers; 7,360,000 CZK
• 2019–2021: MŠMT INTER-ACTION Bavaria (Principal Investigator)
  Sensitive bioanalytical tools for the surveillance of honey bee diseases; 1,200,000 CZK
• 2017–2019: TAČR ZETA (Principal Investigator)
  Immunoassay for rapid diagnostics of European foulbrood; 2,700,000 CZK
• 2018: COST, Short-Term Scientific Mission (Principal Investigator)
  Enhancing properties of upconversion-linked immunoassays by reducing non-specific binding; 2,000 €
• 2018: COST, Short-Term Scientific Mission (Principal Investigator)
  Magnetic microspheres for enhancing the sensitivity of upconversion-linked immunoassays; 2,000 €
• 2017: TAČR GAMA, Proof-of-Concept subproject via CTT MU (Principal Investigator)
  Point-of-care immunosensor for detection of pathogenic bacteria in food; 670,000 CZK
• 2016: COST, Short-Term Scientific Mission (Principal Investigator)
  Electrophoretic purification of photon-upconversion nanomaterials for upconversion microscopy; 2,400 €

Academical Stays

• 2020: Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, Germany (PD Dr. Hans-Heiner Gorris), 2 months
• 2019: COBRA laboratory - Organic and Bioorganic Chemistry, Reactivity and Analysis, University of Rouen, France (prof. Niko Hildebrandt), 1 month
• 2019: Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, Germany (PD Dr. Hans-Heiner Gorris), 2 months
• 2018: Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, Germany (PD Dr. Hans-Heiner Gorris), 3 months
• 2016: Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, Germany (PD Dr. Hans-Heiner Gorris), 3 months
• 2015: Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, Germany (PD Dr. Hans-Heiner Gorris), 1 month
• 2014: Research group Proteomics, CEITEC MU, Czech Republic (doc. RNDr. Zbyněk Zdráhal, Dr.), 2 months
• 2012: Department of Bioanalytical Instrumentation, Institute of Analytical Chemistry of the CAS, Czech Republic (Ing. František Foret, CSc.), 1 month

University Activities

• 2023–present: Member of Biochemistry program board, Faculty of Science, Masaryk University

Non-university Activities

• Early Career Advisory Board member in Analysis & Sensing
• Guest editor in Monatshefte für Chemie
• Reviewer in:
  ACS: ACS Applied Materials & Interfaces, ACS Applied Nano Materials, ACS Sensors, Analytical Chemistry, Langmuir
  Elsevier: Analytica Chimica Acta, Bioelectrochemistry, Biosensors and Bioelectronics, Biosystems Engineering, Environmental Pollution, Optics and Laser Technology, Sensors and Actuators: B Chemical
  Future Science Group: Nanomedicine
  MDPI: Applied Sciences, Biosensors, Foods, Molecules, Nanomaterials, Sensors, Toxins
  RSC: Lab on a Chip, Nanoscale
  Springer Nature: Analytical and Bioanalytical Chemistry, Chemical Papers, Monatshefte für Chemie, Nature Communications, Scientific Reports
  Wiley: Advanced Materials, Advanced Science, Angewandte Chemie International Edition, Electroanalysis
• Evaluation of grant proposals:
  GAMU at Masaryk University
  IGA at Brno University of Technology
  START at Charles University
• Lecturer of Certified courses of Origin for Czech Republic (DataScript s.r.o.) and MP-SPR (Chromspec spol. s r.o.)

Awards

• 2022: Rector's Award for Outstanding Research Results Achieved by Young Scientists under 35, Masaryk University, Brno, Czech Republic
• 2022: MUNI Scientist Award for Outstanding Research Results, Masaryk University, Brno, Czech Republic
• 2021: First prize in Materials Science for Life section, Interdisciplinary Meeting of Young Life Scientists, Czech Republic
• 2019: Small Bronze Medal of MU, Masaryk University, Brno, Czech Republic
• 2019: Honorable Mention in Dr. Tasilo Prnka Prize, NANOCON 2019, Brno, Czech Republic
• 2018: First prize in Jean-Marie Lehn Prize for Chemistry, Solvay and Embassy of France in the Czech Republic
• 2018: Second prize in Shimadzu Award for young chemists and biologists, 70. Congress of the Czech and Slovak Chemical Societies
• 2017: Dean’s Award, Faculty of Science, Masaryk University, Brno, Czech Republic
• 2017: CEITEC MU Award for extraordinary scientific contribution for the scientists under the age of 35, Masaryk University, Brno, Czech Republic
• 2017: Honorable Mention in Dr. Tasilo Prnka Prize, NANOCON 2017, Brno, Czech Republic
• 2016: Best Poster Prize in Symposium 02, 67th Annual Meeting of the International Society of Electrochemistry, The Hague, Netherlands
• 2016: First prize in Biomaterials section, Interdisciplinary Meeting of Young Biologists, Biochemists and Chemists, Milovy, Czech Republic
• 2016: First prize in Young scientists’ section, XVI. Workshop of Physical Chemists and Electrochemists, Brno, Czech Republic
• 2014: Rector’s Award for the Best Students in Master’s Programmes, Masaryk University, Brno, Czech Republic
• 2014: First prize in Young scientists’ section, XIV. Workshop of Physical Chemists and Electrochemists, Brno, Czech Republic
• 2013: Dean’s Award, Faculty of Science, Masaryk University, Brno, Czech Republic
• 2012: First prize in Young scientists’ section, XII. Workshop of Physical Chemists and Electrochemists, Brno, Czech Republic

Selected Publications

• FARKA, Zdeněk, Julian BRANDMEIER, Matthias Jürgen MICKERT, Matěj PASTUCHA, Karel LACINA, Petr SKLÁDAL, Tero SOUKKA and Hans-Heiner GORRIS. Nanoparticle-Based Bioaffinity Assays: From the Research Laboratory to the Market. Advanced Materials. Weinheim: Wiley-VCH, 2024, vol. 36, No 3, p. 1-23. ISSN 0935-9648. Available from: https://dx.doi.org/10.1002/adma.202307653. URL info
• MÁČALA, Jakub, Ekaterina MAKHNEVA, Antonín HLAVÁČEK, Martin KOPECKÝ, Hans-Heiner GORRIS, Petr SKLÁDAL and Zdeněk FARKA. Upconversion Nanoparticle-Based Dot-Blot Immunoassay for Quantitative Biomarker Detection. Analytical Chemistry. Washington, DC: American Chemical Society, 2024, vol. 96, No 25, p. 10237-10245. ISSN 0003-2700. Available from: https://dx.doi.org/10.1021/acs.analchem.4c00837. URL info
• SKLENÁROVÁ, Dorota, Antonín HLAVÁČEK, Jana KŘIVÁNKOVÁ, Julian BRANDMEIER, Julie WEISOVÁ, Michal ŘIHÁČEK, Hans-Heiner GORRIS, Petr SKLÁDAL and Zdeněk FARKA. Single-molecule microfluidic assay for prostate-specific antigen based on magnetic beads and upconversion nanoparticles. Lab on a Chip. Royal Society of Chemistry, 2024, vol. 24, 24 Jun 2024, p. 3536-3545. ISSN 1473-0197. Available from: https://dx.doi.org/10.1039/D4LC00346B. URL info
• HLAVÁČEK, Antonín, Zdeněk FARKA, Matthias Jürgen MICKERT, Uliana KOSTIV, Julian BRANDMEIER, Daniel HORÁK, Petr SKLÁDAL, František FORET and Hans-Heiner GORRIS. Bioconjugates of photon-upconversion nanoparticles for cancer biomarker detection and imaging. Nature Protocols. Springer Nature, 2022, vol. 17, April 2022, p. 1028-1072, 47 pp. ISSN 1754-2189. Available from: https://dx.doi.org/10.1038/s41596-021-00670-7. URL info
• MAKHNEVA, Ekaterina, Dorota SKLENÁROVÁ, Julian BRANDMEIER, Antonín HLAVÁČEK, Hans-Heiner GORRIS, Petr SKLÁDAL and Zdeněk FARKA. Influence of Label and Solid Support on the Performance of Heterogeneous Immunoassays. Analytical Chemistry. Washington, DC: American Chemical Society, 2022, vol. 94, No 47, p. 16376-16383. ISSN 0003-2700. Available from: https://dx.doi.org/10.1021/acs.analchem.2c03543. URL info
• OBOŘILOVÁ, Radka, Hana ŠIMEČKOVÁ, Matěj PASTUCHA, Šimon KLIMOVIČ, Ivana VÍŠOVÁ, Jan PŘIBYL, Hana VAISOCHEROVÁ-LÍSALOVÁ, Roman PANTŮČEK, Petr SKLÁDAL, Ivana MAŠLAŇOVÁ and Zdeněk FARKA. Atomic force microscopy and surface plasmon resonance for real-time single-cell monitoring of bacteriophage-mediated lysis of bacteria. Nanoscale. Cambridge: Royal Society of Chemistry, 2021, vol. 13, No 31, p. 13538-13549. ISSN 2040-3364. Available from: https://dx.doi.org/10.1039/D1NR02921E. URL info
• FARKA, Zdeněk, Matthias Jürgen MICKERT, Zuzana MIKUŠOVÁ, Antonín HLAVÁČEK, Pavla BOUCHALOVÁ, Wenshu XU, Pavel BOUCHAL, Petr SKLÁDAL and Hans-Heiner GORRIS. Surface design of photon-upconversion nanoparticles for high-contrast immunocytochemistry. Nanoscale. Cambridge: Royal Society of Chemistry, 2020, vol. 12, No 15, p. 8303-8313. ISSN 2040-3364. Available from: https://dx.doi.org/10.1039/C9NR10568A. URL info
• FARKA, Zdeněk, Matthias Jürgen MICKERT, Matěj PASTUCHA, Zuzana MIKUŠOVÁ, Petr SKLÁDAL and Hans-Heiner GORRIS. Advances in Optical Single-Molecule Detection: En Route to Supersensitive Bioaffinity Assays. Angewandte Chemie International Edition. Weinheim: Wiley-VCH, 2020, vol. 59, No 27, p. 10746-10773. ISSN 1433-7851. Available from: https://dx.doi.org/10.1002/anie.201913924. URL info
• POLÁCHOVÁ, Veronika, Matěj PASTUCHA, Zuzana MIKUŠOVÁ, Matthias Jürgen MICKERT, Antonín HLAVÁČEK, Hans-Heiner GORRIS, Petr SKLÁDAL and Zdeněk FARKA. Click-conjugated photon-upconversion nanoparticles in an immunoassay for honeybee pathogen Melissococcus plutonius. Nanoscale. Cambridge: Royal Society of Chemistry, 2019, vol. 11, No 17, p. 8343-8351. ISSN 2040-3364. Available from: https://dx.doi.org/10.1039/C9NR01246J. URL info
• FARKA, Zdeněk, Veronika ČUNDERLOVÁ, Veronika HORÁČKOVÁ, Matěj PASTUCHA, Zuzana MIKUŠOVÁ, Antonín HLAVÁČEK and Petr SKLÁDAL. Prussian Blue Nanoparticles as a Catalytic Label in a Sandwich Nanozyme-Linked Immunosorbent Assay. Analytical Chemistry. Washington, DC: American Chemical Society, 2018, vol. 90, No 3, p. 2348-2354. ISSN 0003-2700. Available from: https://dx.doi.org/10.1021/acs.analchem.7b04883. URL info
• FARKA, Zdeněk, Tomáš JUŘÍK, David KOVÁŘ, Libuše TRNKOVÁ and Petr SKLÁDAL. Nanoparticle-Based Immunochemical Biosensors and Assays: Recent Advances and Challenges. Chemical Reviews. Washington, D.C., USA: American Chemical Society, 2017, vol. 117, No 15, p. 9973-10042. ISSN 0009-2665. Available from: https://dx.doi.org/10.1021/acs.chemrev.7b00037. URL info
• FARKA, Zdeněk, Matthias J. MICKERT, Antonín HLAVÁČEK, Petr SKLÁDAL and Hans H. GORRIS. Single Molecule Upconversion-Linked Immunosorbent Assay with Extended Dynamic Range for the Sensitive Detection of Diagnostic Biomarkers. Analytical Chemistry. Washington, DC: American Chemical Society, 2017, vol. 89, No 21, p. 11825-11830. ISSN 0003-2700. Available from: https://dx.doi.org/10.1021/acs.analchem.7b03542. URL info
• FARKA, Zdeněk, Tomáš JUŘÍK, Matěj PASTUCHA and Petr SKLÁDAL. Enzymatic Precipitation Enhanced Surface Plasmon Resonance Immunosensor for the Detection of Salmonella in Powdered Milk. Analytical Chemistry. Washington, DC: American Chemical Society, 2016, vol. 88, No 23, p. 11830-11836. ISSN 0003-2700. Available from: https://dx.doi.org/10.1021/acs.analchem.6b03511. URL info

2023/07/03