Institute of Biological and Chemical Systems - Biological Information Processing

Selected Publications


  1. A stochastic oscillator model simulates the entrainment of vertebrate cellular clocks by light.
    Kumpošt, V.; Vallone, D.; Gondi, S. B.; Foulkes, N. S.; Mikut, R.; Hilbert, L.
    2021. Scientific reports, 11 (1), Art.-Nr.: 14497. doi:10.1038/s41598-021-93913-2
  2. Long photoperiod impairs learning in male but not female medaka.
    López-Olmeda, J. F.; Zhao, H.; Reischl, M.; Pylatiuk, C.; Lucon-Xiccato, T.; Loosli, F.; Foulkes, N. S.
    2021. iScience, 102784. doi:10.1016/j.isci.2021.102784
  3. Regulation of ddb2 expression in blind cavefish and zebrafish reveals plasticity in the control of sunlight-induced DNA damage repair.
    Zhao, H.; Li, H.; Du, J.; Di Mauro, G.; Lungu-Mitea, S.; Geyer, N.; Vallone, D.; Bertolucci, C.; Foulkes, N. S.
    2021. PLoS Genetics, 17 (2), Art.-Nr. e1009356. doi:10.1371/JOURNAL.PGEN.1009356
  4. Finding Nemo’s clock reveals switch from nocturnal to diurnal activity.
    Schalm, G.; Bruns, K.; Drachenberg, N.; Geyer, N.; Foulkes, N. S.; Bertolucci, C.; Gerlach, G.
    2021. Scientific Reports, 11 (1), Art.-Nr.: 6801. doi:10.1038/s41598-021-86244-9
  5. Remembering Paolo: A tribute to Paolo Sassone-Corsi.
    Foulkes, N. S.; Eckel-Mahan, K.; Cermakian, N.
    2020. Journal of pineal research, 69 (4), Art.Nr. e12692. doi:10.1111/jpi.12692
  6. Development of Open-Field Behaviour in the Medaka, Oryzias latipes.
    Lucon-Xiccato, T.; Conti, F.; Loosli, F.; Foulkes, N. S.; Bertolucci, C.
    2020. Biology, 9 (11), Article: 389. doi:10.3390/biology9110389
  7. YB-1 recruitment to stress granules in zebrafish cells reveals a differential adaptive response to stress.
    Guarino, A. M.; Mauro, G. D.; Ruggiero, G.; Geyer, N.; Delicato, A.; Foulkes, N. S.; Vallone, D.; Calabrò, V.
    2019. Scientific reports, 9 (1), Article no: 9059. doi:10.1038/s41598-019-45468-6
  8. Differential circadian and light-driven rhythmicity of clock gene expression and behaviour in the turbot, Scophthalmus maximus.
    Ceinos, R. M.; Chivite, M.; López-Patiño, M. A.; Naderi, F.; Soengas, J. L.; Foulkes, N. S.; Míguez, J. M.
    2019. PLOS ONE, 14 (7), e0219153. doi:10.1371/journal.pone.0219153
  9. Evolution Shapes the Gene Expression Response to Oxidative Stress.
    Siauciunaite, R.; Foulkes, N. S.; Calabrò, V.; Vallone, D.
    2019. International journal of molecular sciences, 20 (12), Art.Nr.: 3040. doi:10.3390/ijms20123040
  10. DIY Automated Feeding and Motion Recording System for the Analysis of Fish behaviour.
    Pylatiuk, C.; Zhao, H.; Gursky, E.; Reischl, M.; Peravali, R.; Foulkes, N.; Loosli, F.
    2019. SLAS technology, 24 (4), 394–398. doi:10.1177/2472630319841412
  11. Modulation of DNA Repair Systems in Blind Cavefish during Evolution in Constant Darkness.
    Zhao, H.; Di Mauro, G.; Lungu-Mitea, S.; Negrini, P.; Guarino, A. M.; Frigato, E.; Braunbeck, T.; Ma, H.; Lamparter, T.; Vallone, D.; Bertolucci, C.; Foulkes, N. S.
    2018. Current biology, 28 (20), 3229–3243.e4. doi:10.1016/j.cub.2018.08.039
  12. Evolution shapes the responsiveness of the D-box enhancer element to light and reactive oxygen species in vertebrates.
    Pagano, C.; Siauciunaite, R.; Idda, M. L.; Ruggiero, G.; Ceinos, R. M.; Pagano, M.; Frigato, E.; Bertolucci, C.; Foulkes, N. S.; Vallone, D.
    2018. Scientific reports, 8 (1), Art.-Nr.:13180 /1–17. doi:10.1038/s41598-018-31570-8
  13. Interactions between the circadian clock and TGF-β signaling pathway in zebrafish.
    Sloin, H. E.; Ruggiero, G.; Rubinstein, A.; Smadja Storz, S.; Foulkes, N. S.; Gothilf, Y.
    2018. PLoS one, 13 (6), e0199777. doi:10.1371/journal.pone.0199777
  14. Mutations in blind cavefish target the light-regulated circadian clock gene, period 2.
    Ceinos, R. M.; Frigato, E.; Pagano, C.; Fröhlich, N.; Negrini, P.; Cavallari, N.; Vallone, D.; Fuselli, S.; Bertolucci, C.; Foulkes, N. S.
    2018. Scientific reports, 8 (1), Art.Nr.: 8754. doi:10.1038/s41598-018-27080-2
  15. The fish circadian timing system: The illuminating case of light-responsive peripheral clocks.
    Pagano, C.; Ceinos, R. M.; Vallone, D.; Foulkes, N. S.
    2017. Biological Timekeeping: Clocks, Rhythms and Behaviour. Ed. V. Kumar, 177–192, Springer India. doi:10.1007/978-81-322-3688-7_7
  16. Instrument design and protocol for the study of light controlled processes in aquatic organisms, and its application to examine the effect of infrared light on zebrafish.
    Dekens, M. P. S.; Foulkes, N. S.; Tessmar-Raible, K.
    2017. PLoS one, 12 (2), Art. Nr. e0172038. doi:10.1371/journal.pone.0172038
  17. Genetically Blocking the Zebrafish Pineal Clock Affects Circadian Behavior.
    Ben-Moshe Livne, Z.; Alon, S.; Vallone, D.; Bayleyen, Y.; Tovin, A.; Shainer, I.; Nisembaum, L. G.; Aviram, I.; Smadja-Storz, S.; Fuentes, M.; Falcón, J.; Eisenberg, E.; Klein, D. C.; Burgess, H. A.; Foulkes, N. S.; Gothilf, Y.
    2016. PLoS Genetics, 12 (11), e1006445. doi:10.1371/journal.pgen.1006445
  18. Relaxed selective constraints drove functional modifications in peripheral photoreception of the cavefish P. andruzzii and provide insight into the time of cave colonization.
    Calderoni, L.; Rota-Stabelli, O.; Frigato, E.; Panziera, A.; Kirchner, S.; Foulkes, N. S.; Kruckenhauser, L.; Bertolucci, C.; Fuselli, S.
    2016. Heredity, 117 (5), 383–392. doi:10.1038/hdy.2016.59
  19. Studying the Evolution of the Vertebrate Circadian Clock: The Power of Fish as Comparative Models.
    Foulkes, N., S.; Whitmore, D.; Vallone, D.; Bertolucci, C.
    2016. Genetics, Genomics and Phenomics of Fish. Ed. N.S. Foulkes, 1–30, Academic Press. doi:10.1016/bs.adgen.2016.05.002
  20. Cavefish eye loss in response to an early block in retinal differentiation progression.
    Stemmer, M.; Schuhmacher, L. N.; Foulkes, N. S.; Bertolucci, C.; Wittbrodt, J.
    2015. Development <Cambridge>, 142, 743–752. doi:10.1242/dev.114629
  21. Functional development of the circadian clock in the zebrafish pineal gland.
    Ben-Moshe, Z.; Foulkes, N. S.; Gothilf, Y.
    2014. BioMed Research International, 2014, 235781. doi:10.1155/2014/235781
  22. The light-induced transcriptome of the zebrafish pineal gland reveals complex regulation of the circadian clockwork by light.
    Ben-Moshe, Z.; Alon, S.; Mracek, P.; Faigenbloom, L.; Tovin, A.; Vatine, G. D.; Eisenberg, E.; Foulkes, N. S.; Gothilf, Y.
    2014. Nucleic Acids Research, 42 (6), 3750–3767. doi:10.1093/nar/gkt1359
  23. Effect of lighting conditions on zebrafish growth and development.
    Villamizar, N.; Vera, L. M.; Foulkes, N. S.; Sanchez-Vazquez, F. J.
    2014. Zebrafish, 11, 173–181. doi:10.1089/zeb.2013.0926
  24. Developmental stage-specific regulation of the circadian Clock by Temperature in Zebrafish.
    Lahiri, K.; Froehlich, N.; Heyd, A.; Foulkes, N. S.; Vallone, D.
    2014. BioMed Research International, 2014, 930308. doi:10.1155/2014/930308
  25. Differential maturation of rhythmic clock gene expression during early development in medaka (Oryzias latipes).
    Cuesta, I. H.; Lahiri, K.; Lopez-Olmeda, J. F.; Loosli, F.; Foulkes, N. S.; Vallone, D.
    2014. Chronobiology international, 31 (4), 468–478. doi:10.3109/07420528.2013.856316
  26. ERK Signaling Regulates Light-Induced Gene Expression via D-Box Enhancers in a Differential, Wavelength-Dependent Manner.
    Mracek, P.; Pagano, C.; Fröhlich, N.; Idda, M. L.; Cuesta, I. H.; Lopez-Olmeda, J. F.; Sánchez-Vázquez, F. J.; Daniela Vallone, D.; Foulkes, N. S.
    2013. PLoS one, 8 (6), Art.Nr. e67858. doi:10.1371/journal.pone.0067858
  27. Circadian clocks, rhythmic synaptic plasticity and the sleep-wake cycle in zebrafish.
    Elbaz, I.; Foulkes, N. S.; Gothilf, Y.; Appelbaum, L.
    2013. Frontiers in neural circuits, 7, 9. doi:10.3389/fncir.2013.00009
  28. Casein kinase 1δ activity: a key element in the zebrafish cricadian timing system.
    Smadja-Storz, S.; Tovin, A.; Mracek, P.; Alon, S.; Foulkes, N. S.; Gothilf, Y.
    2013. PLoS One, 8, e54189/1–10. doi:10.1371/journal.pone.0054189
  29. Report of the second European Zebrafish principal investigator meeting in Karlsruhe, Germany, March 21-24, 2012.
    Cavodeassi, F.; Del Bene, F.; Fürthauer, M.; Grabner, C.; Herzog, W.; Lehtonen, S.; Linker, C.; Mercader, N.; Mikut, R.; Norton, W.; Strähle, U.; Tiso, N.; Foulkes, N. S.
    2013. Zebrafish, 10 (1), 119–123. doi:10.1089/zeb.2012.0829
  30. Circadian Timing of Injury-Induced Cell Proliferation in Zebrafish.
    Idda, M. L.; Kage, E.; Lopez-Olmeda, J. F.; Mracek, P.; Foulkes, N. S.; Vallone, D.
    2012. PLoS one, 7 (3), Art.Nr. e34203. doi:10.1371/journal.pone.0034203
  31. Systematic identification of rhythmic genes reveals camk1gb as a new element in the circadian clockwork.
    Tovin, A.; Alon, S.; Ben-Moshe, Z.; Mracek, P.; Vatine, G.; Foulkes, N. S.; Jacob-Hirsch, J.; Rechavi, G.; Toyama, R.; Coon, S. L.; Klein, D. C.; Eisenberg, E.; Gothilf, Y.
    2012. PLoS Genetics, 8, e1003116/1–11. doi:10.1371/journal.pgen.1003116
  32. Encephalic photoreception and phototactic response in the troglobiont Somalian blind cavefish Phreatichthys andruzzii.
    Tarttelin, E. E.; Frigato, E.; Bellingham, J.; di Rosa, V.; Berti, R.; Foulkes, N. S.; Lucas, R. J.; Bertolucci, C.
    2012. Journal of Experimental Biology, 215, 2898–2903. doi:10.1242/jeb.071084
  33. Regulation of per and cry genes reveals a central role for the D-box enhancer in light-dependent gene expression.
    Mracek, P.; Santoriello, C.; Idda, M. L.; Pagano, C.; Ben-Moshe, Z.; Gothilf, Y.; Vallone, D.; Foulkes, N. S.
    2012. PLoS One, 7, e51278/1–12. doi:10.1371/journal.pone.0051278
  34. Circadian clocks: lessons from fish.
    Idda, M. L.; Bertolucci, C.; Vallone, D.; Gothilf, Y.; Sanchez-Vazquez, F. J.; Foulkes, N. S.
    2012. The Neurobiology of Circadian Timing Amsterdam. Ed.: A. Kalsbeek, 41–57, Elsevier
  35. The Light Responsive Transcriptome of the Zebrafish: Function and Regulation.
    Weger, B. D.; Sahinbas, M.; Otto, G. W.; Mracek, P.; Armant, O.; Dolle, D.; Lahiri, K.; Vallone, D.; Ettwiller, L.; Geisler, R.; Foulkes, N. S.; Dickmeis, T.
    2011. PLoS One, 6 (2), e17080/1–15. doi:10.1371/journal.pone.0017080
  36. A blind circadian clock in cavefish reveals that opsins mediate peripheral clock photoreception.
    Cavallari, N.; Frigato, E.; Vallone, D.; Fröhlich, N.; Lopez-Olmeda, J. F.; Foa, A.; Berti, R.; Sanchez-Vazquez, F. J.; Bertolluci, C.; Foulkes, N. S.
    2011. PLoS biology, 9 (9), e1001142. doi:10.1371/journal.pbio.1001142
  37. It’s time to swim! Zebrafish and the circadian clock.
    Vatine, G.; Vallone, D.; Gothilf, Y.; Foulkes, N. S.
    2011. FEBS Letters, 585, 1485–1494. doi:10.1016/j.febslet.2011.04.007
  38. Glucocorticoids and circadian clock control of cell proliferation: At the interface between three dynamic systems.
    Dickmeis, T.; Foulkes, N. S.
    2011. Molecular and Cellular Endocrinology, 331, 11–22. doi:10.1016/j.mce.2010.09.001
  39. Multiple par and E4BP4 bZIP transcription factors in zebrafish: diverse spatial and temporal expression patterns.
    Ben-Moshe, Z.; Vatine, G.; Alon, S.; Tovin, A.; Mracek, P.; Foulkes, N. S.; Gothilf, Y.
    2010. Chronobiology International, 27, 1509–1531. doi:10.3109/07420528.2010.510229
  40. Cellular signaling and time: links between light, clocks and the cell cycle.
    Mracek, P.; Cavallari, N.; Lahiri, K.; Radeva, S.; Vallone, D.; Foulkes, N. S.
    2009. 26th Congress of the European Society of Comparative Biochemistry and Physiology, Innsbruck, A, September 6-9, 2009 Comparative Biochemistry and Physiology A, 154(2009) Suppl.1, (Abstract)
  41. Light directs zebrafish period2 expression via conserved D and E boxes.
    Vatine, G.; Vallone, D.; Appelbaum, L.; Mracek, P.; Ben-Moshe, Z.; Lahiri, K.; Gothilf, Y.; Foulkes, N. S.
    2009. Plos Biology, e1000223/1-18, 7. doi:10.1371/journal.pbio.1000223