Francois Keck

Quantitative Ecology, Freshwater Biology & Data Science ·

My name is François Keck, I am a community ecologist interested in using large datasets and computational methods to investigate ecological questions in the field of limnology. Broadly, my research activities are focussed on the links between environmental variation and community dynamics in freshwater organisms, with a particular focus on diatoms. A significant part of my work also involves developing ideas, methods and scientific principles to support environmental monitoring and management. Over the years, I have developed a broad spectrum of skills and expertise in data science including statistics, data mining and modelling to extract valuable knowledge and insights from ecological data. My interest for scientific programming and data visualization led me to develop and maintain several R packages.


[33] Meta-analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment

Keck, F., Blackman, R. C., Bossart, R., Brantschen, J., Couton, M., Hürlemann, S., Kirschner, D., Locher, N., Zhang, H., Altermatt, F. (2022). Molecular Ecology, 31(6), 1820-1835.

[32] Paleoreconstructions of ciliate communities reveal long-term ecological changes in temperate lakes

Barouillet, C., Vasselon, V., Keck, F., Millet, L., Etienne, D., Galop, D., Rius, D., Domaizon, I. (2022). Scientific Reports, 12(1), 7899.

[31] A triad of kicknet sampling, eDNA metabarcoding, and predictive modeling to assess richness of mayflies, stoneflies and caddisflies in rivers

Keck, F., Hürlemann, S., Locher, N., Stamm, C., Deiner, K., Altermatt, F. (2022). Metabarcoding and Metagenomics, 6, e79351.

[30] Co-occurrence, ecological profiles and geographical distribution based on unique molecular identifiers of the common freshwater diatoms Fragilaria and Ulnaria

Kahlert, M., Maaria Karjalainen, S., Keck, F., Kelly, M., Ramon, M., Rimet, F., Schneider, S., Tapolczai, K., Zimmermann, J. (2022). Ecological Indicators, 141, 109114.

[29] Management of DNA reference libraries for barcoding and metabarcoding studies with the R package refdb

Keck, F., Altermatt, F. (2022). Molecular Ecology Resources.

[28] Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses

Keck, F., Couton, M., Altermatt, F. (2022). Molecular Ecology Resources.

[27] The potential of exact sequence variants (ESVs) to interpret and assess the impact of agricultural pressure on stream diatom assemblages revealed by DNA metabarcoding

Tapolczai, K., Selmeczy, G. B., Szabó, B., B-Béres, V., Keck, F., Bouchez, A., Rimet, F., Padisák, J. (2021). Ecological Indicators, 122, 107322.

[26] DNA metabarcoding reveals differences in distribution patterns and ecological preferences among genetic variants within some key freshwater diatom species

Pérez-Burillo, J., Trobajo, R., Leira, M., Keck, F., Rimet, F., Sigró, J., Mann, D. G. (2021). Science of The Total Environment, 798, 149029.

[25] Assessing the response of micro-eukaryotic diversity to the Great Acceleration using lake sedimentary DNA

Keck, F., Millet, L., Debroas, D., Etienne, D., Galop, D., Rius, D., Domaizon, I. (2020). Nature Communications, 11(1), 3831.

[24] Handling biological sequences in R with the bioseq package

Keck, F. (2020). Methods in Ecology and Evolution, 11(12), 1728-1732.

[23] Key Questions for Next-Generation Biomonitoring

Makiola, A., Compson, Z. G., Baird, D. J., Barnes, M. A., Boerlijst, S. P., Bouchez, A., Brennan, G., Bush, A., Canard, E., Cordier, T., Creer, S., Curry, R. A., David, P., Dumbrell, A. J., Gravel, D., Hajibabaei, M., Hayden, B., van der Hoorn, B., Jarne, P., Jones, J. I., Karimi, B., Keck, F., Kelly, M., Knot, I. E., Krol, L., Massol, F., Monk, W. A., Murphy, J., Pawlowski, J., Poisot, T., Porter, T. M., Randall, K. C., Ransome, E., Ravigné, V., Raybould, A., Robin, S., Schrama, M., Schatz, B., Tamaddoni-Nezhad, A., Trimbos, K. B., Vacher, C., Vasselon, V., Wood, S., Woodward, G., Bohan, D. A. (2020). Frontiers in Environmental Science, 7.

[22] Biodiversity patterns of Arctic diatom assemblages in lakes and streams: Current reference conditions and historical context for biomonitoring

Kahlert, M., Rühland, K. M., Lavoie, I., Keck, F., Saulnier‐Talbot, E., Bogan, D., Brua, R. B., Campeau, S., Christoffersen, K. S., Culp, J. M., Karjalainen, S. M., Lento, J., Schneider, S. C., Shaftel, R., Smol, J. P. (2020). Freshwater Biology.

[21] Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap

Cordier, T., Alonso‐Sáez, L., Apothéloz‐Perret‐Gentil, L., Aylagas, E., Bohan, D. A., Bouchez, A., Chariton, A., Creer, S., Frühe, L., Keck, F., Keeley, N., Laroche, O., Leese, F., Pochon, X., Stoeck, T., Pawlowski, J., Lanzén, A. (2020). Molecular Ecology.

[20] Ecological correlates of riverine diatom and macroinvertebrate alpha and beta diversity across Arctic Fennoscandia

Brittain, J. E., Heino, J., Friberg, N., Aroviita, J., Kahlert, M., Karjalainen, S.-M., Keck, F., Lento, J., Liljaniemi, P., Mykrä, H., Schneider, S. C., Ylikörkkö, J. (2020). Freshwater Biology.

[19] Community phylogenetic structure reveals the imprint of dispersal-related dynamics and environmental filtering by nutrient availability in freshwater diatoms

Keck, F., Kahlert, M. (2019). Scientific Reports, 9(1), 1-8.

[18] Benthic Diatom Communities in an Alpine River Impacted by Waste Water Treatment Effluents as Revealed Using DNA Metabarcoding

Chonova, T., Kurmayer, R., Rimet, F., Labanowski, J., Vasselon, V., Keck, F., Illmer, P., Bouchez, A. (2019). Frontiers in Microbiology, 10.

[17] Molecular versus morphological data for benthic diatoms biomonitoring in Northern Europe freshwater and consequences for ecological status

Bailet, B., Bouchez, A., Franc, A., Frigerio, J.-M., Keck, F., Karjalainen, S.-M., Rimet, F., Schneider, S., Kahlert, M. (2019). Metabarcoding and Metagenomics, 3, e34002.

[16] Connecting the morphological and molecular species concepts to facilitate species identification within the genus Fragilaria (Bacillariophyta)

Kahlert, M., Kelly, M. G., Mann, D. G., Rimet, F., Sato, S., Bouchez, A., Keck, F. (2019). Journal of Phycology.

[15] Diatom DNA Metabarcoding for Biomonitoring: Strategies to Avoid Major Taxonomical and Bioinformatical Biases Limiting Molecular Indices Capacities

Tapolczai, K., Keck, F., Bouchez, A., Rimet, F., Kahlert, M., Vasselon, V. (2019). Frontiers in Ecology and Evolution, 7.

[14] Disentangling the processes driving the biogeography of freshwater diatoms: A multiscale approach

Keck, F., Franc, A., Kahlert, M. (2018). Journal of Biogeography, 45(7), 1582-1592.

[13] Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units’ ecological profiles

Keck, F., Vasselon, V., Rimet, F., Bouchez, A., Kahlert, M. (2018). Molecular Ecology Resources, 18(6), 1299-1309.

[12] The potential of High-Throughput Sequencing (HTS) of natural samples as a source of primary taxonomic information for reference libraries of diatom barcodes

Rimet, F., Abarca, N., Bouchez, A., Kusber, W.-H., Jahn, R., Kahlert, M., Keck, F., Kelly, M. G., Mann, D. G., Piuz, A., Trobajo, R., Tapolczai, K., Vasselon, V., Zimmermann, J. (2018). Fottea, 18(1), 37-54.

[11] River biofilm community changes related to pharmaceutical loads emitted by a wastewater treatment plant

Chonova, T., Labanowski, J., Cournoyer, B., Chardon, C., Keck, F., Laurent, É., Mondamert, L., Vasselon, V., Wiest, L., Bouchez, A. (2018). Environmental Science and Pollution Research, 25(10), 9254-9264.

[10] Freshwater biomonitoring in the Information Age

Keck, F., Vasselon, V., Tapolczai, K., Rimet, F., Bouchez, A. (2017). Frontiers in Ecology and the Environment, 15(5), 266–274.

[9] Can we predict diatoms herbicide sensitivities with phylogeny? Influence of intraspecific and interspecific variability

Esteves, S. M., Keck, F., Almeida, S. F. P., Figueira, E., Bouchez, A., Rimet, F. (2017). Ecotoxicology, 26(8), 1065-1077.

[8] Phylogenetic signal in diatom ecology: Perspectives for aquatic ecosystems biomonitoring

Keck, F., Rimet, F., Franc, A., Bouchez, A. (2016). Ecological Applications, 26(3), 861–872.

[7] Linking phylogenetic similarity and pollution sensitivity to develop ecological assessment methods: a test with river diatoms

Keck, F., Bouchez, A., Franc, A., Rimet, F. (2016). Journal of Applied Ecology, 53(3), 856–864.

[6] phylosignal: an R package to measure, test, and explore the phylogenetic signal

Keck, F., Rimet, F., Bouchez, A., Franc, A. (2016). Ecology and Evolution, 6(9), 2774–2780.

[5] Separate treatment of hospital and urban wastewaters: A real scale comparison of effluents and their effect on microbial communities

Chonova, T., Keck, F., Labanowski, J., Montuelle, B., Rimet, F., Bouchez, A. (2016). Science of The Total Environment, 542, 965-975.

[4] R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring

Rimet, F., Chaumeil, P., Keck, F., Kermarrec, L., Vasselon, V., Kahlert, M., Franc, A., Bouchez, A. (2016). Database, 2016, baw016.

[3] Linking Diatom Sensitivity to Herbicides to Phylogeny: A Step Forward for Biomonitoring?

Larras, F., Keck, F., Montuelle, B., Rimet, F., Bouchez, A. (2014). Environmental Science & Technology, 48(3), 1921-1930.

[2] Can we predict nutrient limitation in streams and rivers?

Keck, F., Lepori, F. (2012). Freshwater Biology, 57(7), 1410–1421.

[1] Effects of Atmospheric Nitrogen Deposition on Remote Freshwater Ecosystems

Lepori, F., Keck, F. (2012). AMBIO: A Journal of the Human Environment, 41(3), 235-246.



A reference database manager for R

Keck, F., 2021.


A toolbox for manipulating biological sequences in R

Keck, F., 2020.


Access the diat.barcode database with R

Keck, F., 2019.


Exploring the phylogenetic signal in continuous traits

Keck, F., 2016.


Maucha diagrams with R

Tapolczai, K., Keck, F., 2015.


Interactive maps with R and Leaflet

Keck, F., 2014.


I blog on my personal website mainly about my activity as a R programmer. This blog allows me to publish my side projects and helps me stay in touch with the R community.

Curriculum vitæ

You can view my CV online or download a pdf version.