Sophie de Buyl

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Research interests

My education is in Theoretical and Mathematical Physics. During my last postdoc at Harvard University, I changed research field by joining Erin O'Shea lab and worked on biological rhythms. My interests include all biological systems which can benefit from a mathematical approach from genetic regulations to ecosystems. I find great motivation in identifying general principles in biological systems.

Dynamical models of microbial communities: We aim at building dynamical models for human-associated microbial communities. We are interested in mechanisms leading to community structure and in predicting responses to perturbations, such as antibiotic treatments.

./embryo.jpg Cell fate decision in embryonic development: We work in collaboration with the lab of H. Yasuo to study the embryonic development of ascidians which are model organisms for vertebrate development. How do cells take decision about their fate? What are the molecular mechanisms underlying this decision? To answer those questions and understand reproducibility in the process, we are focusing on neural induction in early embryonic development. More recently, we started working on information theory in embryogenesis.

./microbial_factory.jpg Engineering genetic circuits for synthetic biology: In the long run, we aim at designing microbial factories for biofuel production in collaboration with Eveline Peeters. In the short run, we aim at developmenting biosensor modules to optimize production pathway performance in E. Coli, the most studied prokaryotic organism.

Team members

PhD students: Rossana Bettoni (joint PhD with G. Dupont at ULB) and Amber Bernauw (Joint PhD, main advisor E. Peeters at VUB).

Alumni

Lana Descheemaeker 2020 Modeling Biological Networks - From single gene systems to large microbial communities

Nathaniel Mon Père (joint Phd with T. Lenaert ULB) Statistical biophysics of hematopoiesis and growing cell populations .

Master students : L. Tuijnder and Z. Heyvaert -- Bachelor students : R. Dubois, A. Markavian, E. Vrijsen

IB2

I am the VUB director of the Interuniversity Institute of Bioinformatics in Brussels link since March 2020.

Publications

Cell geometry, signal dampening and a bimodal transcriptional response underlie spatial precision of an embryonic induction, Géraldine Williaume*, Sophie de Buyl*, Cathy Sirour*, Nicolas Haupaix, Rossana Bettoni, Kaoru Imai, Yutaka Satou, Geneviève Dupont**, Clare Hudson**, Hitoyoshi Yasuo**, 2020 (accepted for publication in Developmental Cell)

Heavy-tailed abundance distributions from stochastic Lotka-Volterra models, Lana Descheemaeker, Jacopo Grilli and Sophie de Buyl, PRE 2021 link code.

Stochastic logistic models reproduce experimental time series of microbial communities, Lana Descheemaeker and Sophie de Buyl, eLife 2020 link code.

Non-monotonic auto-regulation in single gene circuits, Lana Descheemaeker, Eveline Peeters, Sophie de Buyl, PLOS One 2019 code.

Signatures of ecological processes in microbial community time series, Karoline Faust, Franziska Bauchinger, Béatrice Laroche, Sophie de Buyl, Leo Lahti, Alex D Washburne, Didier Gonze, Stefanie Widder, Microbiome 2018 link.

Bistability in a system of two species interacting through mutualism as well as competition: Chemostat vs. Lotka-Volterra equations, Stefan Vet, Sophie de Buyl, Karoline Faust, Jan Danckaert, Didier Gonze, Lendert Gelens, PLOS One link.

Robust Circadian Oscillations in Growing Cyanobacteria Require Transcriptional Feedback, Shu-Wen Teng, Shankar Mukherji, Jeffrey R. Moffitt, Sophie de Buyl, Erin K. O'Shea, Science 340, 737 (2013) link.

All my physics publications can be found on inSPIRES - * and ** mean equal contribution.

Bachelor and Master thesis topics

Contact me for more details, for a not updated version of possibilities see:

link

Teaching

Nonlinear dynamics and chaos slides and exercises (not updated! see canvas).

Quantitative cell biology (see canvas).

Computational Physics (see canvas and github).

Data processing and representation in Life Science (see canvas).

Education

Work experience

Outreach

I am a founding member and co-organizer of Science&Cocktails Brussels

webmaster Pierre de Buyl