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Global Change Research Institute, CAS

Ing. Jan Červený, Ph.D.


Position: Head of Research Division, Head of Department

Branch: Department of Adaptive Biotechnologies

Branch: Department of Smart Biotechnologies

Workplace: ÚVGZ AV ČR, v. v. i.Drásov 470Drásov664 24


Phone: +420 775 171 968

Research Focus

cybernetics; process optimizationsystems biology; experimental biology; artificial intelligence; machine learning; biological rhythms; microalgal biotechnology; development of bio-applications;  microalgae selection/breeding; mathematical modeling; cybernetics

  • Development of methods for characterization and effective optimization of production and adaptive properties of photosynthetic microorganisms
  • Development of reference experimental platform for validation experiments
  • Development and design of technological solutions and bio-applications for viable microalgal biotechnologies
  • Development of a computational platform for predictive (in silico) experiments (,
  • Mathematical modeling and identification of oscillatory mechanisms of algae and cyanobacteria under a wide range of controlled environmental conditions
  • High-throughput fluorescence microscopic single-cell level analyses of photosynthetic cultures
  • Sorting of mixed populations and selection of subpopulations with “on-demand” properties
  • Application of controlled selective pressure (breeding) on different types of photosynthetic microorganisms for both increased adaptivity to unnatural conditions and production capacity


  • 2011: Ph.D. degree in Technical Cybernetics the study field Control and Systems Engineering, Czech Technical University in Prague (topic Mathematical models in algal biotechnologies, supervisor prof. P. Zítek)
  • 2004: M.Sc. degree in Process Control and Automation at Department of Process Instrumentation and Control, Czech Technical University in Prague.


  • 2015 onward: Head of Research Domain, Domain of Adaptative and Innovative Techniques, Global Change Research Institute CAS, Drásov
  • 2013 onward: Head of Department, Department of Adaptive Biotechnologies, Global Change Research Centre CAS, Drásov
  • 2010 – 2013: Group Leader, Laboratory of Physiology and Biotechnology, Institute of Systems Biology and Ecology CAS, Nové Hrady
  • 2009 – 2012: R&D and Scientific Advisor, Photon Systems Instruments, spol. s r.o., Drásov
  • 2005 – 2010: Junior Research Scientist, Institute of Systems Biology and Ecology CAS, Nové Hrady
  • 2004 – 2007: Research and Lecture Assistant, Department of Instrumentation and Control Engineering, Czech Technical University in Prague, Prague
  • 2002 – 2007: Junior Research Scientist, Centre of Applied Cybernetics, Prague


Doctorate Degree received with honors (cum laude)

Nominated as a Full Member in Sigma Xi – The Scientific Research Honor Society

Important research visits and fellowships

  • 2019 (3 months): Honorary Appointment Fellow at Climate Change Cluster, University of Technology Sydney, Sydney, Australia (Prof. Peter Ralph)
  • 2010 (7 months): Research Associate at Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, USA (Prof. Sabeeha S. Merchant)
  • 2008 (1 month): Visiting Scientist at Department of Biology, Washington University in St. Louis, St. Louis, USA (Prof. Himadri B. Pakrasi)


Member of Institue board, Global Change Researh Institute CAS

Member of Director’s board, Global Change Researh Institute CAS

MathWorks Advisory Board Member

Member of CzechGlobe-HRS4R/HR Excellence in Research Award board

Member of Steering committee, ESFRI Center for Systems Biology – C4Sys

Member of Review board, Nature Communications

Member of Review board, Mayo Clinic: Digital Health

Member of Review board, PLOS ONE

Member of Review board, Engineering in Life Sciences journal

Member of Review board, Bioresource Technology

Member of Review board, Plant and Cell Physiology journal

Member of Review board, Algal Research

Member of Review board, Photosynthetica

Member of Review board, Journal of Advanced Research

Member of Review board, BioProtocols

Member of Society for Experimental Biology

Science Mentor for young reviewers of Frontiers for Young Minds

Brief scientometrics

Statistics (GS [WoS]):

Publications: 87 [51] 
Sum of the Times Cited
: 1701 [871]

h-index: 23 [16]


Journal papers:

– leading, corresponding or supervising author:

Monitoring fitness and productivity in cyanobacteria batch cultures

Zavřel T, Schoffman H, Lukeš M, Fedorko J, Keren N, Červený J

2021. Algal Research 56: 102328

Accumulation of cyanobacterial oxadiazine nocuolin A is enhanced by temperature shift during cultivation and is promoted by bacterial co-habitants in the culture
Chmelík D, Hrouzek P, Fedorko J, Vu DL, Urajová P, Mareš J, Červený J
2019. Algal Research 44: 101673

Towards a quantitative assessment of inorganic carbon cycling in photosynthetic microorganisms
Müller S, Zavřel T, Červený J
2019. Eng Life Sci 19(12): 955-967 

Quantitative insights into the cyanobacterial cell economy
Zavřel T, Faizi M, Loureiro C, Poschmann G, Stühler K, Sinetova M, Zorina A, Steuer R, Červený J
2019. Elife 8: e4250

Spectrophotometric determination of phycobiliprotein content in cyanobacterium Synechocystis
Zavřel T, Chmelík D, Sinetova MA, Červený J
2018. Journal of Visualized Experiments 139: 1–9

Phenotypic characterization of Synechocystis sp. PCC 6803 substrains reveals differences in sensitivity to abiotic stress
Zavřel T, Očenášová P, Červený J
2017PLOS ONE 12(12): 1-21

Mechanisms of high temperature resistance of Synechocystis sp. PCC 6803: an impact of histidine kinase 34
Červený J, Sinetova MA, Zavřel T, Los DA
2015. Life 5(1): 676-699

Characterization of a model cyanobacterium Synechocystis sp. PCC 6803 autotrophic growth in a flat-panel photobioreactor
Zavřel T, Sinetová MA, Búzová D, Literáková P, Červený J
2015. Eng Life Sci 15: 122 – 132

Ultradian metabolic rhythm in the diazotrophic cyanobacterium Cyanothece sp. ATCC 51142
Červený J, Sinetova MA, Valledor L, Sherman LA, Nedbal L
2013. Proc Natl Acad Sci USA 110: 13210-13215

On the dynamics and constraints of batch culture growth of the cyanobacterium Cyanothece sp. ATCC 51142
Sinetova MA, Červený J, Zavřel T, Nedbal L
2012. J Biotechnol 162: 148-155

E-photosynthesis: Web-based platform for modeling of complex photosynthetic processes
Šafránek D, Červený J, Klement M, Pospíšilová J, Brim L, Lazár D, Nedbal L
2011. Biosystems 103: 115-124

Metabolic rhythms of the cyanobacterium Cyanothece sp. ATCC 51142 correlate with modeled dynamics of circadian clock
Červený J, Nedbal L
2009. J Biol Rhythms 24: 295-303.

Photobioreactor for cultivation and real-time, in-situ measurement of O2 and CO2 exchange rates, growth dynamics, and of chlorophyll fluorescence emission of photoautotrophic microorganisms
Červený J, Šetlíš I, Trtíšek M, Nedbal L
2009. Eng Life Sci 9: 247-253.

– selected co-authoring:

SBML Level 3: An Extensible Format for the Exchange and Reuse of Biological Models.
Keating, SM, et al.

2020. Molecular Systems Biology 16: e9110

Advancement of the cultivation and upscaling of photoautotrophic suspension cultures using Chenopodium rubrum as a case study.
Segečová A, Červený J, Roitsch T
2018. Plant Cell, Tissue and Organ Culture (PCTOC) 135(1): 37-51

A model of optimal protein allocation during phototrophic growth
Faizi M, Zavřel T, Loureiro C, Červený J, Steuer R
2018. Biosystems 
166: 26–36

Effect of carbon limitation on photosynthetic electron transport in Nannochloropsis oculata
Zavřel T, Szabó M, Tamburic B, Evenhuis C, Kuzhiumparambil U, Literáková P, Červený J, Ralph PJ
2018. J Photochem Photobiol B 181: 31–43

A quantitative evaluation of ethylene production in the recombinant cyanobacterium Synechocystis sp. PCC 6803 harboring the ethylene-forming enzyme by membrane inlet mass spectrometry
Zavřel T, Knoop H, Steuer R, Jones PR, Červený J, Trtílek M
2016. Bioresour Technol 202: 142-151

Experimental validation of a nonequilibrium model of CO2 fluxes between gas, liquid medium, and algae in a flat-panel photobioreactor
Nedbal L, Červený J, Keren N, Kaplan A
2010. J Ind Microbiol Biotechnol 37: 1319-26

Book chapters

Influence of Circadian Clocks on Optimal Regime of Central C-N Metabolism of Cyanobacteria.
Červený J, Šalagovič J, Muzika F, Šafránek D, Schreiber I
2019. In Cyanobacteria: From Basic Science to Applications, pp. 193–206 

Microalgal adaptive biotechnologies for sustainable future.
Červený J, Zavřel T, Chmelík D, Búzová D, Fedorko J, Literáková P, Sukačová K, Segečová A, Roitsch T
2016. In Global Change & Ecosystems, Volume 2: Adaptation to global changepp. 148-160 A Web-Based Platform for Systems Biology of Cyanobacteria.
Troják M, Šafránek D, Hrabec J, Šalagovič J, Romanovská F, Červený J
2016. In Computational Methods in Systems Biology, pp. 316–322

Oscillators for modelling circadian rhythms in cyanobacteria growth
Fišer J, Červený J, Zítek P
2010. In Modelling, Simulation and Optimization – Focus on Applications, Cakaj S, ed, pp 105-119, In-Tech, Vukovar, Croatia.

Scaling and integration of kinetic models of photosynthesis: Towards comprehensive E-photosynthesis
Nedbal L, Červený J, Schmidt H
2009. In Photosynthesis in silico: Understanding Complexity from Molecules to Ecosystems, Laisk A, Nedbal L, Govindjee, eds, pp 17-29, Springer Netherlands, Dordrecht.

Other imporatant publications

Circulating histone signature of human lean metabolic-associated fatty liver disease (MAFLD)
Búzová D, et al.
2020. Clinical Epigenetics 12: 126

Biochemical Space: A Framework for Systemic Annotation of Biological Models
Klement M, Děd T, Šafránek D, Červený J, Müller S, Steuer R
2014. Electron Notes Theor Comput Sci 306: 31-44

A Comprehensive Web-based Platform For Domain-Specific Biological Models
Klement M, Šafránek D, Děd T, Pejznoch A, Nedbal L, Steuer R, Červený J, Müller S
2013. Electron Notes Theor Comput Sci 299: 61-67

E-photosynthesis: a comprehensive modeling approach to understand chlorophyll fluorescence transients and other complex dynamic features of photosynthesis in fluctuating light.
Nedbal L, Červený J, Rascher U, Schmidt H
2007. Photosynth Res 93(1-3): 223-234