In the midst of the COVID19 pandemic and in order to adapt ventilation in class, I have built a WiFi connected CO₂ sensor that allows real time [CO₂] monitoring in the rooms where I teach. The sensor is adapted from the plans offered by the Boîte à Formes 3D printing company. Students and myself…
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With 25 years experience lecturing bioinformatics at university, I have progressively turned most of my teaching into hands-on problem solving using real world research datasets. To support such a challenging approach to large student cohorts, I have developed a bioinformatics specific online e-learning environment called the Annotathon. In a flipped classroom setting, trainees are…
Research interests Computational biology / bioinformatics : environmental genomics (especially metagenomes and metabarcodes), high throughput sequence analysis, plankton biology and ecology, virology (large DNA viruses, coronaviruses). Grants and Research Contracts Invited Associate Professor, Kyoto University (Japan, May-Jul 2015)French ANR / Investement of the Future contract OCEANOMICS (ANR-11-BTBR-0008, 425.000€, 2012-2019)European Union FP7 contract MicroB3 (FP7-OCEAN-2011…
As a participant of the Tara Oceans pan-oceanic marine plankton exploration campaign, I strive to make the resulting genomics data available to the research community. Because of the sheer volume of the resulting genomics datasets (Tara Ocean is over 60 terabases and growing), transforming such data into knowledge is difficult for biologists without high…
The diversity of giant double stranded viruses in the sea is extremely high, but they are notoriously difficult to observe and cultivate. In collaboration with my colleagues from Kyoto University, I developped a bioinformatics workflow to design a set of primers that target all known members of the megaviridae. The workflow, named UjiLity after…
