Sorbonne University

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Sorbonne University is a world-class research university, presenting the comprehensive disciplinary range of arts, humanities, social sciences, natural sciences, engineering and medicine. It is one of the leading French universities with more than 55,600 students. The Laboratory of Computational and Quantitative Biology (LCQB) is an interdisciplinary laboratory working at the interface between biology and quantitative sciences. It is built to promote a balanced interaction of theoretical and experimental approaches in biology and to foster the definition of new experimental questions, data analysis and modeling of biological phenomena. Our projects address questions on biological structures and processes through the gathering of experimental measures, the in-silico generation of new biological data that remain inaccessible to experiments today (modeling of biological systems), the development of statistical methods for data analysis, and the conception of original algorithms aimed at predictions. The lab is supported by the CNRS and Sorbonne University.

Dates
Between 6/17/24 and 7/31/24.

Funding
Up to $7,000.
Grant recipients will be required to submit a three-page report within two weeks after their return.Recipients for this internship must be enrolled at Stanford the quarter following the completion of the project for which they received funding. Thus, students who wish to pursue a fellowship the summer after their senior year may do so, but only if they apply for and receive permission from the University Registrar to enroll for a “graduation quarter” for the summer quarter. More information on graduation quarters can be found here.

Description
Metagenomics provides a huge inventory of species present in environments and of metabolic functions performed by environmental communities. It offers enormous potential for discoveries, as more than 99% of microbial species cannot be cultivated in the laboratory. It has given rise to several large-scale projects to characterize the microbial diversity of the oceans (e.g., GOS [1], Tara Oceans [2], Malaspina [3], OSD [4]), of microbes in symbiosis with humans [5], of the composition of soils [6], urban environments [7], or subjected to extreme conditions (eXtreme Microbiome Project). Each metagenomics experiment generates large amounts of raw data (on the order of several terabytes of sequence per sample), the processing of which presents several algorithmic and data analysis / learning challenges. The goal of this project will be to help ongoing work in the lab in the development of new computational approaches based on deep learning to reconstruct protein-protein interaction (PPI) networks for metagenomic samples starting from sequence reads and for holobionts that have been completely sequenced. The aim is to predict PPI networks that allow a community of microbes to perform metabolic functions or different species to live in symbiosis. Questions on the evolution of PPIs might be addressed with a comparison of PPIs through samples from different ecosystems.

Location
Paris, France.

Eligibility
Undergraduate students (Freshman/Sophomore/Junior/Senior).

Language requirement
English is spoken in the lab. French is helpful, but not required.

Prerequisites
This internship is open to undergraduate students at any level (Freshman to Senior level). The work will be adjusted depending on the background and the interest of the student. The internship topic is particularly well suited for students with a computer science, physics or mathematics background. Programming skills and deep learning are highly desired.

Application
Applicants should submit the following documents:

  • Application form
  • Itemized budget
  • Letter to be addressed to the France-Stanford Center Director describing your research interests and why you are applying for the position. Please explain the nature of your background and skills in computer science, physics or mathematics. Where and how did you acquire the relevant training? Are there particular courses you took, particular research projects you pursued, etc.? (1 page, ~ 800 words)
  • Recommendation letter from the applicant’s advisor, discussing the applicant and the merits of the proposed visit (1 page). Request this recommendation on your application form
  • Applicant’s resume (1 page)
  • Unofficial Stanford transcript

ContactIsabelle Collignon, francestanford [at] stanford.edu (francestanford[at]stanford[dot]edu)

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