I am an Assistant Professor between the Forschungszentrum Jülich and the Université catholique de Louvain since Sept 2016. More about my (new) group here.
The aim of my research is (i) to understand how various signals that carry information are interacting and being conveyed and integrated at the plant level and (ii) to amplify discrete physiological knowledge into functional plant processes. All of that using Functional Structural Plant Models.
I develop image analysis and phenotyping tools to help researchers in their scientific workflow. And when I am not implementing image analysis tools, I often play with plant models.
An overview of my research vision can be found in this presentation.
Tools we develop and database we curated, both in the lab or with close collaborators.
Together with researchers from INRIA, CPIB, Juelich, Vienna and Louvain, we created the Root System Markup Language (RSML) that has been designed to alleviate two major bottlenecks: (i) to enable portability of root architecture data between different software tools in an easy and interoperable manner allowing seamless collaborative work, and (ii) to provide a standard format upon which to base central repositories which will soon arise following the expanding worldwide root phenotyping effort. External Diffusion post
SmartRoot is a semi-automated image analysis software which streamlines the quantification of root growth and architecture for complex root systems. The software combines a vectorial representation of root objects with a powerful tracing algorithm which accommodates to a wide range of image source and quality. The software supports a sampling-based analysis of root system images, in which detailed information is collected on a limited number of roots selected by the user according to specific research requirements.
The Plant Image Analysis website is an online, manually curated, database referencing more than 130 plant image analysis software solutions. The website presents each software in a uniform and concise manner enabling users to identify the available solutions for their experimental needs. The website also enables user feedback, evaluations and new software submissions. The aim of such a toolbox is to help users to find solutions, and to provide developers a way to exchange and communicate about their work.
PRIMAL stands for a Pipeline of Root Image analysis using MAchine Learning. In short, the pipeline use Machine Learning techniques (Random Forest), to streamline the image analysis of large root dataset. PRIMAL needs only a subset of the data to be analysed manually, instead of the full dataset. That subset is then used to train the algorithm behind PRIMAL the predict the parameters of interest, based on automatically acquired descriptors.
The focus of CRootBox is the simulation of different types of root architecture, and to provide a generic interface for coupling with arbitrary soil/environmental models, e.g., in order to determine the impact of specific root architectures on function.
archiDART is an R package that was developed for the automated analysis of plant root system architectures from Root System Markup Language (RSML) files. The package enable the extraction of morphological (length, diameters), dynamic (growth rates, tropisms) and topological (Fitter indices, persistent homology) traits.
The aim of this figshare profile is to collect in one place illustrations and pictures of plants, roots, shoots, inflorescences, … The ultimate goal is to be a resource for the plant science community.
The transition to flowering is an essential step of the plant life cycle that is tightly controlled by both endogenous and environmental cues. Its regulation is extremely complex and involves hundreds of genes that are part of highly interconnected pathways. We are currently building a new web-based interactive resource organized around a curated database of the flowering time genes, FLOR-ID. This project is a collaboration with Fred Bouché. Article about the database here (in french) and here (Flowering Highlights).
I have the great chance to give lectures at the University of Louvain, in the Faculty of bioscience engineering. I also give seminars and workshop on random topics.
Teaching project that aims a gathering plant models to teach plant biology. Models should be usable online and based on sound biology.
Lecture on soil-root interactions given a the University of Louvain, to master students of the bio-engeneering faculty. Covering, among other, hydrotropisms, branching, hydropatterning, retention curves and many other cool topics.
Lecture on the modelisation of biological systems. Not a classical lecture, but project driven. Students are asked to learn about a model of their choice and use it to do some basic simulations. We also ask them to go on Twitter to learn to communicate about complex biological issues (in this case modelling). In 2017, the course lead to a blog post on Botany One.
Hands on on ImageJ. How to make some basic image analysis. Introduction to macros.
How to make a good scientific figure. How the better convey the important information. How not to get lost in graphic junk.
How to valorise all your research products. Very usefull for Early Career Researchers.
Some random stuff I did and maintain just for fun...
Website referencing fun plant gene names
Shiny app to create bingo table for scientific conference (plant science and others)
I have the great chance to have awesome colleagues in my team. Go check them out!
Xiaoran’s previous experiences are based on studying his major, Viticulture and Enology, with modeling and web applications. He obtained his B.E. in Northwest A&F University and M.Sc. in Erasmus Vinifera Programme. His interest is to develop a mechanistic model that traces carbon and water movement in maize by explicit coupling of xylem and phloem fluxes.
Adrien is a PhD student @UCLouvain, deeply interest “in silico” plants and ways to grow a more suistanable kind of agriculture
I did reviews for:
Plant Physiology, New Phytologist, GigaScience, PLoS One, Journal of Experimental Botany, Plant and Soil, Functional Plant Biology, Plant Methods, Annals of Botany, Microscopy and Microanalysis, Plant Signaling and Behavior, Journal of Hydrology, Journal of Visualized Experiments.
Program commity member
I love playing around with web technologies and build websites for various reasons. In addition to this one I designed these ones:
The PI describes in a self-sufficient manner his expertise even though it lacks significant papers as last author
CV is highly focused on methodologies [this was in the "Applicant weaknesses" section]
Important papers with the applicant as last author are lacking, so he needs to gain in independence.
The applicants don't appear to have any high impact papers that have been well cited. Their papers seem to report incremental advances rather than novel new ideas.
The applicants [...] are relatively inexperienced. Consequently, although they publish regularly [...], their publications have attracted few citations
This is a worthy topic that deserves attention, however the authors fall short in their attempt.
(this paper is) neither research nor science
(this paper is) not rocket science
(his research is) solid, but neither excellent nor innovative