in English
Plant Biophysics Project


Esa Tyystjärvi
e-mail esatyy [at]
phone: +358 50 438 2766 (office) +358 40 511 3503 (mobile)


Esa Tyystjärvi, PhD, Project Leader
Taras Antal, PhD, research fellow
Arto Soitamo, PhD, post-doc
Sergey Khorobrykh, PhD, pos-doc
Dimitar Valev, MSc, PhD student
Heta Mattila, M.Sc, PhD student
Suvi Ojanen, DI,  PhD student
Vesa Havurinne, PhD student
Pooneh Sotoudehnia, PhD student
Tinja Pitkämäki, Researcher
Mikko Antinluoma, student, research assistant
Olli Virtanen, student, research assistant
Iiris Kuusisto, student, research assistant
Telma Kuuslampi, student, research assistant
Past members
Susanne Rantamäki, PhD
Päivi Sarvikas, PhD
Eija Terävä, PhD
Mika Keränen, PhD
Marja Hakala-Yatkin, PhD
Sujata Mishra, PhD
Anna Polishchkuk, PhD
Lauri Mukkala, researcher
Kaija Porkka, researcher

Photosystem II is an enzyme complex used by plants and cyanobacteria to convert the energy of light to chemical form and to produce oxygen. Although light is the driving force of photosynthesis, light also damages the photosynthetic machinery. The damaging reaction is called photoinhibition and Photosystem II is its target. Plants need to continuously repair the damage caused by photoinhibition by degradation and synthesis of the D1 protein of Photosystem II. Both visible and ultraviolet light cause photoinhibition.


The main research topic of the project is photoinhibition of Photosystem II. Our group was the first to propose that photoinhibition starts with light absorption of the manganese ions of the oxygen evolving complex of Photosystem II. The hypothesis is known as the manganese mechanism of photoinhibition. The action spectrum of photoinhibition and release of manganese from Photosystem II during illumination support the manganese hypothesis. Phenomena related to photoinhibition can also be seen in other manganese complexes.
In addition to photoinhibition, we study energy and electron transfer reactions in Photosystem II. We are particularly interested in charge recombination reactions. We also develop a method for automatic identification of plants using chlorophyll fluorescence.


We do mainly basic research. Understanding Photosystem II is necessary for bioenergy production because splitting of water with sunlight is a goal of research on both artificial photosynthesis and bioenergy research that aims at developing biological processes.
Our work with chlorophyll fluorescence can be used for automatic identification of plants in precision farming.


Hakkila K, Valev D, Antal T, Tyystjärvi E, Tyystjärvi T (2018) Group 2 sigma factors are central regulators of oxidative stress acclimation in cyanobacteria. Plant & Cell Physiology, in press.
Havurinne V, Mattila H, Antinluoma M, Tyystjärvi E (2018) Unresolved quenching mechanisms may invalidate multiple turnover saturating pulse analyses of photosynthetic electron transfer in microalgae. Physiologia Plantarum, in press.
Antonacci A, Lambreva M, Margonelli A, Sobolev A,  Pastorelli S, Bertalan I, Johanningmeier U, Sobolev V, Samish I, Edelman M, Havurinne V, Tyystjärvi E, Giardi M, Mattoo AK, Rea G (2018) Photosystem-II D1 protein mutants of Chlamydomonas reinhardtii in relation to metabolic rewiring and remodelling of H-bond network at QB-site. Scientific Reports 8: 14745.
Koskinen S, Hakkila K, Kurkela J, Tyystjärvi E, Tyystjärvi T (2018) Inactivation of group 2 σ factors upregulates production of transcription and translation machineries in the cyanobacterium Synechocystis sp. PCC 6803. Scientific Reports 8: 10305. DOI:10.1038/S41598-018-28736-9.
Koskela MM, Brünje A, Ivanauskaite A, Grabsztunowicz M, Lassowskat I, Neumann U, Dinh TV, Sindlinger J, Schwartzer D, Wirtz M, Tyystjärvi E, Finkemeier I, Mulo P (2018) Chloroplast acetyltransferase NSI is required for state transitions in Arabidopsis thaliana. Plant Cell 30: 1695-1709.
Khorobrykh S, Tyystjärvi E (2018) Plastoquinol generates and scavenges reactive oxygen species in organic solvent:  potential relevance for thylakoids. Biochimica et Biophysica Acta - Bioenergetics 1859: 1119-1131​.
Temporary free link: Khorobrykh and Tyystjärvi 2018
Mattila H, Valev D, Havurinne V, Khorobrykh S, Virtanen O, Antinluoma M, Mishra KB, Tyystjärvi E (2018) Degradation of chlorophylls and synthesis of flavonols during autumn senescence - The story told by individual leaves. AoB Plants 10: ply028.​
Havurinne V, Tyystjärvi E (2017) Action spectrum of photoinhibition in the diatom Phaeodactylum tricornutum. Plant and Cell Physiology 58: 2217-2225.doi: 10.1093/pcp/pcx156​
Ojanen S, Tyystjärvi E, Holmberg H, Kouhia M, Ahtila P (2017) Can bacterial biofiltration be replaced by autotrophic organisms in recirculating fresh water aquaculture? Aquaculture International, in press.   (Epub 2017 Feb 18); open link:
Soitamo S, Havurinne V, Tyystjärvi E (2017) Photoinhibition in marine picocyanobacteria. Physiologia Plantarum 161: 97-108 (http:///
Koski T-M, Lindstedt C, Klemola T, Troscianko J, Mäntylä E, Tyystjärvi E, Stevens M, Helander M, Laaksonen T (2017) Insect herbivory may cause changes in the visual properties of leaves and affect the camouflage of herbivores to avian predators. Behavioral Ecology and Sociobiology 71: 97. DOI 10.1007/S00265-017-2326-0.
Sarvikas P, Suorsa M, Rintamäki E, Vapaavuori E, Aro E-M, Tyystjärvi E (text); Lepistö A, Sarvikas P (figs.); Sarvikas P (ed.) (2017) Fotosynteesi. 304 pages., ISBN 9789515680891. BoD, Helsinki. Facebook. Video. E-book​.
Ojanen S, Tyystjärvi E, Jokinen K (2017) Utilization of microalgae in industrial symbiosis, focus on Finland. Natural resources and bioeconomy studies 33/2017. Natural Resources Institute Finland.
Rantamäki S, Meriluoto J, Spoof L, Puputti E-M, Tyystjärvi T, Tyystjärvi E (2016) Oxygen produced by cyanobacteria in simulated Archaean conditions partly oxidizes and ferrous iron but mostly escapes - conclusion about early evolution. Photosynthesis Research, 130(1): 103-111.   (Epub 2016 Feb 19).
Antal T, Kurkela J, Parikainen M, Kårlund A, Hakkila K, Tyystjärvi E and Tyystjärvi T: Roles of group 2 sigma factors in acclimation of the cyanobacterium Synechocystis sp. PCC 6803 to nitrogen deficiency. Plant and Cell Physiology  57(6): 1309-1318.  Free article   (Epub 2016 Apr 19).
Antal TK, Kukarskikh GP, Volgusheva AA, Krendeleva TE, Tyystjärvi E, Rubin AB: Hydrogen photoproduction by immobilized S-deprived Chlamydomonas reinhardtii: effect of light intensity and spectrum, and initial medium pH. Algal Research 17: 38-45.   (Epub 2016 May 3).
Lama AD, Kim J, Martiskainen O, Klemola T, Niemelä P, Salminen J-P, Tyystjärvi E, Vuorisalo J (2016) Impacts of simulated drought stress and artificial damage on concentrations of flavonoids in Jatropha curcas (L.), a biofuel shrub. Journal of Plant Research 129(6):1141-1150.   (Epub 2016 Jul 14).
Mattila H, Khorobrykh S, Havurinne V, Tyystjärvi E (2015) Reactive oxygen species: Reactions and detection from photosynthetic tissues. Journal of Photochemistry and Photobiology B: Biology 152: 176-214.   (Epub 2015 Oct 9).
Wondraczec L, Tyystjärvi E, Méndez-Ramos J, Müller FA, Zhang O (2015) Shifting the Sun: Solar spectral conversion and extrinsic sensitization in natural and artificial photosynthesis. Advanced Science 2: 1500218.   (Epub 2015 Dec 2).
Pahikkala T, Kari K, Mattila H, Lepistö A, Teuhola J, Nevalainen OS, Tyystjärvi E (2015) Classification of plant species from images of overlapping leaves. Computers and Electronics in Agriculture 118: 186-192.   (Epub 2015 Sep 20).
Lambreva MD, Lavecchia T, Tyystjärvi E, Antal TK, Orlanducci S, Margonelli A, Rea G (2015) Potential of carbon nanotubes in algal biotechnology. Photosynthesis Research,125(3): 451-471.   (Epub 2015 Jun 26).
Antal TK, Krendeleva TE, Tyystjärvi E (2015) Multiple regulatory mechanisms in the chloroplast of green algae: relation to hydrogen production. Photosynthesis Research, 125(3): 357-381.   (Epub 2015 May 19).
Konert G, Rahikainen M, Trotta A, Durian G, Salojärvi J, Khorobrykh S, Tyystjärvi E, Kangasjärvi S (2015) Subunits B’γ and B’ζ of protein phosphatase 2A regulate photo-oxidative stress responses and growth in Arabidopsis thaliana. Plant, Cell & Environment, in press.   (Epub 2015 May 27).
Nath*, K.; Najafpour*, MM.; Voloshin*, RA.; Balaghi*, SE.; Tyystjärvi, E.; Timilsina*, R.; Eaton-Rye*, JJ.; Tomo*, T.; Nam*, HG.; Nishihara*, H.; Ramakrishna*, S.; Shen*, JR. & Allakhverdiev*, SI. (2015) Photobiological hydrogen production and artificial photosynthesis for clean energy: From bio to nanotechnologies. - Photosynthesis Research 126(2): 237-247.   (Epub Apr 22). 
Khorobrykh SA, Karonen M, Tyystjärvi E (2015) Experimental evidence suggesting that H2O2 is produced within the thylakoid membrane in a reaction between plastoquinol and singlet oxygen. FEBS Letters, 589(6): 779-786.
Ojanen S, Tyystjärvi E, Holmberg H, Ahtila P (2015) Porous membrane as a means of gas and nutrient exchange in a tubular photobioreactor. Journal of Applied Phycology 27: 1169-1175
Martinez*, DE.; Borniego*, ML.; Battchikova, N.; Aro, EM.; Tyystjärvi, E. & Guiamét, JJ. 2014:  SASP, a Senescence-Associated Subtilisin Protease, is involved in reproductive development and determination of silique number in Arabidopsis. - JOURNAL OF EXPERIMENTAL BOTANY 66(1): 161-174.   Free article   (Epub 2014 Nov 4).
Antal TK, Matorin DN, Kukarshkikh GP, Lambreva MD, Tyystjärvi E, Krendeleva TE, Tsygankov AA,  Rubin AB (2014) Pathways of hydrogen photoproduction by immobilized Chlamydomonas reinhardtii cells deprived of sulfur. International Journal of Hydrogen Energy 39: 18194-18203
Gunnelius, L.; Hakkila, K.: Kurkela, J.; Wada*, H.; Tyystjärvi, E. & Tyystjärvi, T. 2014:  The omega subunit of the RNA polymerase core directs transcription efficiency in cyanobacteria. - NUCLEIC ACIDS RESEARCH 42(7): 4606-4614.    Free article
Hakkila, K.; Antal, T.; Rehman*, AU.; Kurkela, J.; Wada*, H.; Vass*, I.; Tyystjärvi, E. & Tyystjärvi, T. 2014:  Oxidative stress and photoinhibition can be separated in the cyanobacterium Synechocystis sp. PCC 6803. - BIOCHIMICA ET BIOPHYSICA ACTA - BIOENERGETICS 1837(2): 217-225.
Karonen, M.; Mattila, H.; Huang, P.; Mamedov, F.; Styring, S. & Tyystjärvi, E. 2014:  A tandem mass spectrometric method for singlet oxygen measurement. - PHOTOCHEMISTRY AND PHOTOBIOLOGY 90(5): 965-971.
Porcar-Castell, A.; Tyystjärvi, E.; Atherton, J.; van der Tol, C.; Flexas, J.; Pfündel, EE.; Moreno, J.; Frankenberg, C. & Berry, JA. 2014:  Linking chlorophyll a fluorescence to photosynthesis for remote sensing applications: mechanisms and challenges. - JOURNAL OF EXPERIMENTAL BOTANY 65(15): 4065-4095.   Free article 
Antal TK, Kovalenko IB, Rubin AB, Tyystjärvi E (2013)  Photosynthesis-related quantities for education and modeling. Photosynthesis Research 117: 1-30.
Hakkila K, Antal T, Gunnelius L, Kurkela J, Matthijs HCP, Tyystjärvi E, Tyystjärvi T (2013) Group 2 sigma factor mutant sigCDE of the cyanobacterium Synechocystis sp. PCC 6803 reveals functionality of both carotenoids and flavodiiron proteins in photoprotection of Photosystem II. Plant & Cell Physiology 54: 1780-1790
Mattila H, Valli P, Pahikkala T, Teuhola J, Nevalainen J, Tyystjärvi E (2013) Comparison of chlorophyll fluorescence curves and texture analysis for automatic plant identification. Precision Agriculture 14: 621-636
Antal TK, Kukarskikh GP, Bulychev AA, Tyystjärvi E, Krendeleva T (2013) Antimycin A effect on the electron transport in chloroplasts of two Chlamydomonas reinhardtii strains. Planta 237: 1241-1250.
Tyystjärvi T, Huokko T, Rantamäki S, Tyystjärvi E (2013) Impact of different group 2 sigma factors on light use efficiency and high salt stress in the cyanobacterium Synechocystis sp. PCC 6803. Plos One 8: 463020. doi: 10.1371/journal.pone.0063020
Tyystjärvi E (2013) Photoinhibition of Photosystem II. International Review Of Cell and Molecular Biology 300: 243-303.
Antal T, Harju E, Pihlgren L, Lastusaari M, Tyystjärvi T, Hölsä J, Tyystjärvi E (2012) Use of near-infrared radiation for oxygenic photosynthesis via photon up-conversion. International Journal of Hydrogen Energy 37: 8859-8863
Campbell DA, Tyystjärvi E (2012) Parametrization of Photosystem II photoinhibition and repair. Biochimica et Biophysica Acta - Bioenergetics 1817: 258-265
Antal TK, Krendeleva TE, Pashchenko VZ, Rubin AB, Stensjo K, Tyystjärvi E, Ramakrishna S, Los DA, Carpentier R, Nishihara H, Allakhverdiev SI (2012) Photosynthetic hydrogen production: Mechanisms and approaches. In: Azbar N, Levin DB (editors) State of the Art and Progress in Production of Biohydrogen. Bentham Science Publishers, e-book. pp. 25-53.DOI: 10.2174/9781608052240120101
Rantamäki S, Tyystjärvi E (2011) Analysis of S2QA - charge recombination with the Arrhenius, Eyring and Marcus theories.Journal of Photochemistry and Photobiology B: Biology 104: 292-300
Hakala-Yatkin M, Sarvikas P, Paturi P, Mäntysaari M, Mattila H, Tyystjärvi T, Nedbal L, Tyystjärvi E (2011) Magnetic field protects plants against high light by slowing down production of singlet oxygen. Physiologia Plantarum 142: 26-34
Pollari, M.; Rantamäki, S.; Huokko, T.; Kårlund-Marttila, A.; Virjamo, V.; Tyystjärvi, E. & Tyystjärvi, T. (2011)  Effects of deficiency and overdose of group 2 Sigma factors in triple inactivation strains of Synechocystis sp. strain PCC 6803. - Journal of Bacteriology 193: 265-273.
Inoue, S., Ejima, K., Iwai, E., Hayashi, H., Appel, J., Tyystjärvi, E., Murata, N., Nishiyama, Y. (2011)  Protection by a-tocopherol of the repair of photosystem II during photoinhibition in Synechocystis sp. PCC 6803. - Biochimica et Biophysica Acta - Bioenergetics 1807: 236-241.
Hakala-Yatkin, M., Tyystjärvi, E. (2011) Inhibition of Photosystem II by the singlet oxygen sensor compounds TEMP and TEMPD. - Biochimica et Biophysica Acta - Bioenergetics 1807: 243-250
Hideg E, Déak Z, Hakala-Yatkin M, Karonen M, Rutherford AW, Tyystjärvi E, Vass I, Krieger-Liszkay A (2011) Pure forms of the singlet oxygen sensors TEMP and TEMPD do not inhibit Photosystem II. - Biochim Biophys Acta - Bioenergetics 1807: 1658-1661
Tyystjärvi, E., Nørremark, M., Mattila, H., Keränen, M., Hakala-Yatkin, M., Ottosen, C.-O., Rosenqvist, E. (2011) Automatic identification of crop and weed species with chlorophyll fluorescence induction curves. - Precision Agriculture 12: 546-563
Gylle, M., Rantamäki, S., Ekelund, NGA., Tyystjärvi, E. (2011)  Fluorescence emission spectra of marine and brackish water ecotypes of Fucus vesiculosus and F. radicans sp. nov. (Phaeophyceae) reveal differences in light harvesting apparatus. -Journal of Phycology 47: 98-105
Hakala-Yatkin, M., Mäntysaari, M., Mattila, H., Tyystjärvi, E. (2010) Contributions of visible and ultraviolet parts of sunlight to photoinhibition. - Plant & Cell Physiology 51: 1745-1753 
Antal, T., Mattila, H., Hakala-Yatkin, M., Tyystjärvi, T., Tyystjärvi, E. (2010)  Acclimation of photosynthesis to nitrogen deficiency in Phaseolus vulgaris. - Planta 232:887-898
Codrea, MC., Hakala-Yatkin, M., Kårlund-Marttila, A., Nedbal, L., Aittokallio, T., Nevalainen, OS., Tyystjärvi, E. (2010)  Mahalanobis distance screening of Arabidopsis mutants with chlorophyll fluorescence. -  Photosynthesis Research 105:273-283
Sarvikas, P., Hakala-Yatkin, M., Dönmez, S., Tyystjärvi, E. (2010)  Short flashes and continuous light have similar photoinhibitory efficiency in intact leaves. - Journal of Experimental Botany 61:4239-4247.
Sarvikas P, Tyystjärvi T, Tyystjärvi E (2010) Kinetics of prolonged photoinhibition revisited: Photoinhibited Photosystem II centres do not protect the active ones against loss of oxygen evolution. Photosynthesis Research 103:7-17
Gunnelius L, Tuominen I, Rantamäki S, Pollari M, Ruotsalainen V, Tyystjärvi E, Tyystjärvi T (2010) SigC sigma factor is involved in acclimation to low inorganic carbon at high temperature in Synechocystis sp. PCC 6803. Microbiology 156: 220-229
Antal T, Lo W, Armstrong WH, Tyystjärvi E (2009)  Illumination with ultraviolet or visible light induces chemical changes in the water-soluble manganese complex, [Mn4O6(bpea)4]Br4. - Photochemistry and Photobiology 85: 663-668 (DOI: 10.1111 / j.1751-1097.2008.00502.x)
Tyystjärvi E, Rantamäki S, Tyystjärvi J (2009) Connectivity of photosystem II is the physical basis of retrapping in photosynthetic thermoluminescence. - Biophysical Journal 96: 3735-3743 ( doi:10.1016/j.bpj.2009.02.014)
Antal T, Sarvikas P, Tyystjärvi E (2009) Two-electron reactions S2QB ->S0QB and S3QB->S1QB are involved in deactivation of higher S states of Photosystem II. - Biophysical Journal 96: 4672-4680 (doi:10.1016/j.bpj.2009.03.007)
Keränen M, Aro E-M, Nevalainen O, Tyystjärvi E (2009) Toxic and non-toxic Nodularia strains can be distinguished from each other and from eukaryotic algae with chlorophyll fluorescence fingerprinting. - Harmful Algae 8: 817-822doi:10.1016/j.hal.2007.12.023  
Pollari M, Ruotsalainen V, Rantamäki S, Tyystjärvi E, Tyystjärvi T (2009) Simultaneous inactivation of sigma factors B and D interferes with light acclimation of the cyanobacterium Synechocystis sp. PCC 6803. Journal of Bacteriology 12: 3992-4001(doi:10.1128/JB.00132-09)
Tyystjärvi E (2009) Do environmental effects of herbicide-resistant GM plants differ from effects of other herbicide-resistant plants? The Open Ethics Journal 3: 93-96 (doi: 10.2174/1874761200903030093)
Tyystjärvi E (2008) Photoinhibition of Photosystem II and photodamage of the oxygen evolving manganese cluster. Coordination Chemistry Reviews 252: 361-376
Tuominen I, Pollari M, Aguirre von Wobeser E, Tyystjärvi E, Ibelings BW, Matthijs HCP, Tyystjärvi T (2008) Sigma factor SigC is required for heat acclimation of the cyanobacterium Synechocystis sp. strain PCC 6803. FEBS Lett. 582: 346-350
M. Pollari, L. Gunnelius, I. Tuominen, V.  Ruotsalainen, E. Tyystjärvi, T. Salminen, T. Tyystjärvi (2008) Characterization of single and double inactivation strains reveals new physiological roles for group 2 sigma factors in the cyanobacterium Synechocystis sp.  PCC 6803. Plant  Physiology 147: 1994-2005
Tyystjärvi E, Hakala M, Tyystjärvi T (2008) Photoinhibitory efficiency of saturating laser pulses depends on pulse energy. In: JF Allen, E Gantt, JH Golbeck, B Osmond (eds) Photosynthesis. Energy from the Sun: 14th International Congress on Photosynthesis. Springer. pp. 1587-1590. ISBN: 978-1-4020-6707-5
Järvenpää S, Lundberg-Niinistö C, Spoof L, Sjövall O, Tyystjärvi E, Meriluoto J (2007) Effects of microcystins on broccoli and mustard, and analysis of accumulated toxin by liquid chromatography-mass spectrometry. Toxicon 49: 865-874
Sarvikas P, Hakala M, Pätsikkä E, Tyystjärvi T, Tyystjärvi E (2006) Action spectrum of photoinhibition in leaves of wild type and npq1-2 and npq4-1 mutants ofArabidopsis thaliana. Plant and Cell Physiology 47: 391-400
Hakala M, Rantamäki S, Puputti E-M, Tyystjärvi T, Tyystjärvi E (2006) Photoinhibition of manganese enzymes ? insights into the mechanism of Photosystem II photoinhibition. Journal of Experimental Botany 57: 1809-1816.
Tuominen I, Pollari M, Tyystjärvi E, Tyystjärvi T (2006) High temperature responses in the cyanobacterium Synechocystis sp. PCC6803 are mediated by the sigB sigma factor. FEBS Letters 580: 319-323
Hakala, M., Tuominen, I., Keränen, M., Tyystjärvi, T., Tyystjärvi, E. (2005) Evidence for the role of the oxygen-evolving manganese complex in photoinhibition of Photosystem II. - Biochimica et Biophysica Acta - Bioenergetics 1706:68-80
Tyystjärvi, E., Hakala, M., Sarvikas, P. (2005) Mathematical Modelling of the Light Response Curve of Photoinhibition of Photosystem II. Photosynthesis Research 84: 21-27
Breitholtz, H-L, Srivastava R., Tyystjärvi, E., Rintamäki, E. (2005) LHCII protein phosphorylation in leaves of Arabidopsis thaliana mutants deficient in non-photochemical quenching. Photosynthesis Research 84: 217-223
M. C. Codrea, T. Aittokallio, M. Keränen, E. Tyystjärvi, O. S. Nevalainen (2005) On the robustness of fluorescence fingerprinting of plants. In  Hamza MH (ed) Proceedings of the IASTED International Conference on Artificial Intelligence and Applications, February 14-16, 2005, Innsbruck, Austria. pp. 400-405. ACTA Press, Zurich.
Nedbal L, Matous K, B?ezina V, Trtílek M, Hakala M, Tyystjärvi E, Barón M (2005) Forced oscillations - a new way to extract information from chlorophyll fluorescence transients of mutants, stressed plants, and of plants in a dynamic environment.In: van der Est A and Bruce D (eds) Photosynthesis: Fundamental Aspects to Global Perspectives. Int Soc Photosynthesis, CD-ROM.
E. Tyystjärvi (2004) Phototoxicity. In Noodén, L. D. (ed.) Plant Cell Death Processes (Academic Press, San Diego), pp. 271-283
E. Tyystjärvi and I. Vass (2004) Light Emission as a Probe of Charge Separation and Recombination in the Photosynthetic Apparatus: Relation of Prompt Fluorescence to Delayed Light Emission and Thermoluminescence. In Papageorgiou, G. C. and Govindjee (eds) Chlorophyll a Fluorescence: A Signature of Photosynthesis. Series: Advances in Photosynthesis and Respiration, Vol. 19. Kluwer Academic Publishers, Dordrecht, ISBN 14020-3217-X, pp. 363-388
E. Tyystjärvi (2004) Fotosynteesin varhaishistoria. Luonnon Tutkija 1-2: 30-39
Codrea MC, Nevalainen, O.S., Tyystjärvi E, Vandeven M, Valcke, R. (2004) Classifying apples by the means of fluorescence imaging. International Journal of Pattern Recognition and Artificial Intelligence 18: 157-174
Codrea MC, Aittokallio T, Keränen M, Tyystjärvi E, Nevalainen OS (2004) Genetic algorithms-based feature learning method; an application to fluorescence fingerprinting. Lecture Notes in Computer Science 2936: 371-383
Keränen M, Aro E-M, Tyystjärvi E and Nevalainen O (2003) Automatic plant identification with chlorophyll fluorescence fingerprinting. Precision Agriculture 4: 53-67
Tuominen I, Tyystjärvi E, Tyystjärvi T (2003) Expression of primary sigma factor (PSF) and PSF-like sigma factors in the cyanobacterium Synechocystis sp. strain PCC 6803. Journal of Bacteriology 185: 1116-1119
Codrea MC, Aittokallio T, Keränen M, Tyystjärvi E, Nevalainen OS (2003) Feature learning with a genetic algorithm for fluorescence fingerprinting of plant species. Pattern Recognition Letters 24: 2663-2673
M. C. Codrea, T. Aittokallio, M. Keränen, E. Tyystjärvi, O. S. Nevalainen (2003) Genetic algorithms-based feature learning method; an application to fluorescence fingerprinting. EA03 - In Proceedings of the 6th International Conference on Artificial Evolution (Eds P. Liardet, P. Collet, C. Fonlupt, E. Lutton & M. Schoenauer), Université de Provence, France, October 27-30 2003. pp. 327-339
Codrea, M., Aittokallio, T., Keränen, M., Tyystjärvi, E. & Nevalainen, O. (2003) Using genetics algorithms to optimize the features for fluorescence fingerprinting of plant species. In Tietojenkäsittelytieteen päivät 2003 (Eds. Ari Korhonen & Jorma Tarhio), pp. 26-28. Helsinki University of Technology. Department of Computer Science and Engineering. Laboratory of Information Processing Science. TKO-A39/03, Yliopistopaino, Helsinki 2003.
Guiamét, J.J.,  Tyystjärvi, E., Tyystjärvi, T., John, I., Kairavuo, M.,   Pichersky, E. and  Noodén, L. D. (2002) Photoinhibition and loss of photosystem II center proteins during senescence of soybean leaves.  Enhancement of photoinhibition by the stay-green mutation cytG. Physiologia Plantarum 115: 468-478
Tyystjärvi, T., Tuominen, I., Herranen, M., Aro, E-M. and Tyystjärvi, E. (2002) Action spectrum of psbA gene transcription is similar to that of photoinhibition in Synechocystis sp. PCC 6803. FEBS Letters 516: 167-171
Pätsikkä, E., Kairavuo, M., ?er?en, F., Aro, E.-M. and Tyystjärvi, E. (2002) Excess copper predisposes photosystem II to photoinhibition in vivo by outcompeting iron and causing decrease in leaf chlorophyll. Plant Physiology 129: 1-9.
Hiriart, J. B., Lehto, K., Tyystjärvi, E., Junttila, T. and Aro, E.-M. (2002) Suppression of a key enzyme of chlorophyll biosynthesis using virus-induced gene silencing. Plant Molecular Biology 50: 213-224
M. Codrea, E. Tyystjärvi, M. VandeVen, R. Valcke, O. Nevalainen (2002) Using fluorescence images in classification of apples. 2nd IASTED International Conference Visualization, Imaging and Image Processing (VIIP 2002) September 9-12, 2002 Malaga, Spain
Pätsikkä E., Aro E-M. and Tyystjärvi E. (2001) Mechanism of copper-enhanced photoinhibition in thylakoid membranes. Physiologia Plantarum 113: 142-150
Baena-González, E., Gray, J., Tyystjärvi, E., Aro, E-M. and Mäenpää, P. (2001) Abnormal regulation of photosynthetic electron transport in a chloroplast ycf9 deletion mutant. Journal or Biological Chemistry 276: 20795-20802
Tyystjärvi, E, Kairavuo, M. , Pätsikkä, E., Keränen, M., Khriachtchev, L., Tuominen, I., Guiamet, J. J. and Tyystjärvi, T. (2001) The quantum yield of photoinhibition is the same in flash light and under continuous illumination - implications for the mechanism. In 'PS2001 Proceedings: 12th International Congress on Photosynthesis.' (CSIRO Publishing Company; Melbourne, Australia). CD-ROM
Baena-González, E., Gray, J. C., Tyystjärvi, E., Battchikova, N., Mäenpää, P. and Aro, E.-M. (2001) The ORF62 protein of the thylakoid membrane is involved in regulation of photosynthetic electron transport. In 'PS2001 Proceedings: 12th International Congress on Photosynthesis.' (CSIRO Publishing Company; Melbourne, Australia). CD-ROM