Edwin Rodriguez Horta, former PhD student in co-supervision between the University of Havana and the LCQB, receives a research price of the Academy of Sciences of Cuba for his thesis work.
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Predicting species-specific mutation effects is a major challenge in genetics. Using diverged sequences, we learn protein sequence landscapes, which predict tolerated mutations in a species like E. coli and capture interactions between mutations.
See our article in Nature Communications.
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Towards predicting new mutations in SARS-CoV-2: in the very early stages of an emerging viral outbreak, can we predict new mutations in the proteins of the virus which might lead to its future variants? The "Statistical Genomics and Biological Physics" team proposes a computational approach based on a single viral genome infecting humans and pre-existing viral genomes infecting other species.
For more information see:
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A global study of 60 cities' microbes finds each has a signature microbial fingerprint. The project provides a great way to communicate about the invisible world of commensal microorganisms. Members at the LCQB, L3 and M1 Sorbonne’s students involved in our Bioinformatics courses and colleagues from other Sorbonne departments contributed to the collect of the samples for the Paris area. The article just appeared in Cell.
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The team "Statistical Genomics and Biological Physics" has obtained financial support by the Faculty of Sciences and Engineering of Sorbonne Université, to develop sequence-data driven models of evolutionary landscapes and selective constraints acting in the Covid-19 causing virus SARS-CoV-2. The projects aims at finding signatures of selection in the rapidly increasing number of available
genomes, and to interpret them in terms of protein structure, function and protein-protein interactions inside coronaviruses and with the host (e.g. the famous interaction of the viral spike protein with the human ACE2 receptor).
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Nonribosomal peptide synthetases (NRPSs) are microbial megaenzymes that make a wide variety of small-molecule products, including many that are clinically used as antitumors, antibiotics, or immunosuppressants. Peptide synthesis proceeds with assembly-line logic, where each station on the NRPS assembly line is a multidomain unit called a module. While the function of single modules is well studied, much less is known how they work together. Researchers from the Schmeing lab at McGill University have resolved several dimodular NRPS structures, which show coordinated interactions between modules, and large conformational changes between catalytically relevant states. Martin Weigt from the “Statstical Genomics and Biological Physics” team has performed complementary coevolutionary analyses using the direct coupling analysis (DCA), which confirm the biological relevance and evolutionary conservation of the observed inter-modular interactions. DCA analysis has also allowed to suggest mutations in a module-swapped chimeric NRPS protein, which significantly increased the activity of the protein, a result of direct relevance toward the longstanding goal of NRPS bioengineering for production of new-to-nature bioactive small molecules.
Link to article in Science
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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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Plasmobase is a unique database designed for the comparative study of 11 Plasmodium genomes. Plasmobase proposes new domain architectures as well as new domain families that have never been reported before for these genomes. It allows for an easy comparison among architectures within Plasmodium species and with other species, described in UniProt. Joint work of J.Bernardes and A.Carbone.
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