Several members of LCQB co-authored « Meet-U: educating through research immersion », which appeared in PLOS Computational Biology on 03/15/2018. Meet-U is a new educational initiative that aims to train students for collaborative work in computational biology and to bridge the gap between education and research. Meet-U mimics the setup of collaborative research projects and takes advantage of the most popular tools for collaborative work and of cloud computing. Students are grouped in teams of 4–5 people and have to realize a project from A to Z that answers a challenging question in biology. In this paper, we report on our experience with Meet-U in two French universities with master’s students in bioinformatics and modeling, and with protein–protein docking as the subject of the course.
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In the framework of their cooperation, IFOM (Milan) and CQB (Paris) have set up a scientific rotation program specifically targeted to PhD students.
Students can spend three months in a host group on a scientific topic, with the goal of exploring new approaches and contexts,and acquiring new skills.
Here you can find general rules and how to apply.
Here you can find a list of currently posted projects ( you can also apply spontaneously outside of posted projects).
Contact: phd-rotation@ifom.eu
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"A protein coevolution method uncovers critical features of the Hepatitis C Virus fusion mechanism" appeared in PLoS Pathogens, from A.Carbone team. This work sheds light on important structural features of the HCV fusion mechanism and contributes to advance our functional understanding of this process. This study also provides an important proof of concept that coevolution can be employed to explore viral protein mediated-processes, and can guide the development of innovative translational strategies against challenging human-tropic viruses.
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Alessandra Carbone and Elodie Laine are organizing the "UPMC Young Researchers' Meeting: Modeling Complex Biological Systems".
The talks on current work in computational biology at UPMC will be given by PhD students and Postdocs working at UPMC labs. It will be an opportunity to listen at ongoing research and learn what is done in close by departments.
The up to date program is available here
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F.Nadalin and A.Carbone published CIPS, a new computational method for scoring protein docking decoys based on a combination of residue-residue contact preferences and interface compositional bias. CIPS outperforms state-of-the-art methods on screening protein-protein docking models and improves the ranking on 28 CAPRI targets. The drastic reduction of candidate solutions produced by thousands of proteins docked against each other makes large-scale docking accessible to analysis.
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We highlight our new database Plasmobase to the community working in malaria with a new blog appeared in malariaworld.org.
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Eleonora De Lazzari* published her findings on scaling laws for gene families. A striking quantitative invariant in evolutionary genomics is the scaling with genome size of the number of proteins sharing a specific function. E.D.L. showed that such scaling laws exist systematically at the level of single evolutionary families. This provides a novel view of the links between evolutionary expansion of protein families and gene functions.This work was performed in collaboration with J Grilli (U. Chicago) and S Maslov (U. Illinois).
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