eCOLOGY PUBLICATIONS:
Zooplankton feeding behaviour and survival to toxic and non-toxic cyanobacteria during the seasonal bloom progression of a eutrophic lake
Pinelopi Ntetsika, Salomé Stauffer, Stefanie Eyring, Marta Reyes, Xuejian Wang, Elisabeth M.-L. Janssen, Francesco Pomati
Harmful Algae (2025): 103045: https://doi.org/10.1016/j.hal.2025.103045
Biodiversity forecasting in natural plankton communities reveals temperature and biotic interactions as key predictors
Ewa Merz, Francesco Pomati, Serguei Saavedra, Luis J. Gilarranz
Proc. R. Soc. B. (2025): 292: https://doi.org/10.1098/rspb.2024.2895
Also available from (bioRxiv): https://doi.org/10.1101/2024.10.10.617676
Inferring coexistence likelihood in changing environments from ecological time series
Phuong L. Nguyen, Francesco Pomati, Rudolf P. Rohr
PNAS (2025): 122 (28): https://doi.org/10.1073/pnas.2417905122
Biotic interactions shape the realised niche of toxic cyanobacteria
Pinelopi Ntetsika, Stefanie Eyring, Ewa Merz, Marta Reyes, Benno Kaech, Stephan Munch, Stuart Dennis, Marco Baity Jesi, Francesco Pomati
bioRxiv (2025): 2025-04: https://doi.org/10.1101/2025.04.16.649070
Distinct phytoplankton size classes respond differently to biotic and abiotic factors
Stefanie Eyring, Ewa Merz, Marta Reyes, Pinelopi Ntetsika, Stuart Dennis, Peter D.F. Isles, Sreenath Kyathanahally, Marco Baity-Jesi, Sze-Wing To, Agostino Merico, Francesco Pomati
ISME Communications (2025): https://doi.org/10.1093/ismeco/ycae148
Also available from (bioRxiv): https://doi.org/10.1101/2024.02.23.581723
Inferring intrinsic population growth rates and per capita interactions from ecological time-series
Phuong L. Nguyen, Francesco Pomati, Rudolf P. Rohr
bioRxiv (2024): 2024-05: https://doi.org/10.1101/2024.05.07.592896
Laboratory application of the Aquascope approach of automated imaging and classification for long-term plankton monitoring & Planktonmonitoring: automatisierte Bildgebung. Chancen und Herausforderungen bei der Laboranwendung
Stefanie Merkli, Marta Reyes, Francesco Pomati
bioRxiv (2024): 2024-02: https://doi.org/10.1101/2024.02.23.581739
Aqua & Gas (2024): 104(9), 72-76: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:33321
Disruption of ecological networks in lakes by climate change and nutrient fluctuations
Ewa Merz, Erik Saberski, Luis J Gilarranz, Peter DF Isles, George Sugihara, Christine Berger, Francesco Pomati
Nature Climate Change (2023): 1-8: https://doi.org/10.48550/arXiv.2203.01726
Lake temperature and nutrient levels interact to reorganize ecological networks
Ewa Merz, Francesco Pomati
Nature Climate Change (2023): https://doi.org/10.48550/arXiv.2203.01726
aquascope CALIBRATION PUBLICATION:
Underwater dual-magnification imaging for automated lake plankton monitoring
Ewa Merz, Thea Kozakiewicz, Marta Reyes, Christian Ebi, Peter Isles, Marco Baity-Jesi, Paul Roberts, Jules S. Jaffe, Stuart R. Dennis, Thomas Hardeman, Nelson Stevens, Tom Lorimer, Francesco Pomati
Water Research 203 (2021): 117524: https://doi.org/10.1016/j.watres.2021.117524
Also available from (arxiv): https://doi.org/10.48550/arXiv.2104.06686
MACHINE LEARNING PUBLICATIONS:
Producing Plankton Classifiers that are Robust to Dataset Shift
Cheng Chen, Sreenath Kyathanahally, Marta Reyes, Stefanie Merkli, Ewa Merz, Emanuele Francazi, Marvin Hoege, Francesco Pomati, Marco Baity-Jesi
Limnology and Oceanography: Methods (2024): https://doi.org/10.1002/lom3.10659
Also available from (arXiv): https://doi.org/10.48550/arXiv.2401.14256
Ensembles of data-efficient vision transformers as a new paradigm for automated classification in ecology & Author Correction: Ensembles of data-efficient vision transformers as a new paradigm for automated classification in ecology
Sreenath P. Kyathanahally, Thomas Hardeman, Marta Reyes, Ewa Merz, Thea Bulas, Philipp Brun, Francesco Pomati, Marco Baity-Jesi
Scientific Reports (2022): 12, 18590: https://doi.org/10.1038/s41598-022-21910-0
Scientific Reports (2023): 13, 6243: https://doi.org/10.1038/s41598-023-32258-4
Also available from (arXiv): https://doi.org/10.48550/arXiv.2203.01726
Deep Learning Classification of Lake Zooplankton
Sreenath P. Kyathanahally, Thomas Hardeman, Ewa Merz, Thea Bulas, Marta Reyes, Peter Isles, Francesco Pomati, Marco Baity-Jesi
Frontiers in microbiology (2021): 3226: https://doi.org/10.3389/fmicb.2021.746297.
Also available from (arXiv): https://doi.org/10.48550/arXiv.2108.05258
DATA PUBLICATIONS:
Five years of high-frequency data of phytoplankton, zooplankton and limnology from a temperate eutrophic lake
Stefanie Eyring, Marta Reyes, Ewa Merz, Marco Baity-Jesi, Pinelopi Ntesika, Christian Ebi, Stuart Dennis, Francesco Pomati
Scientific Data (2025): 12, 653: https://doi.org/10.1038/s41597-025-04988-9
Available from (bioRxiv): https://doi.org/10.1101/2025.03.20.644357
Aquascope: Raw data, images and classifications – May 2018 to June 2023
Stuart R. Dennis, Ewa Merz, Marta Reyes, Stefanie Merkli, Marco Baity-Jesi, Sreenath Kyathanahally, Christian Ebi, Thomas Hardeman, Thea Bulas, Pinelopi Ntesika, Peter Isles, Tom Lorimer, Francesco Pomati
Eawag Research Data Institutional Collection (2023): https://doi.org/10.25678/000C2G
Greifensee meteo-CTD-chemistry data 2018 – 2023
Stefanie Merkli, Marta Reyes, Christian Ebi, Stuart Dennis, Francesco Pomati
Eawag Research Data Institutional Collection (2023): https://doi.org/10.25678/000C8P
AQUASCOPE 