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Publications

Trinquier J, Uguzzoni G, Pagnani A, Zamponi F, Weigt M. Efficient generative modeling of protein sequences using simple autoregressive models. Nature Comm. (In Press).
Agier N, Fleiss A, Delmas S, Fischer G A Versatile Protocol to Generate Translocations in Yeast Genomes Using CRISPR/Cas9. in Methods Mol Biol. 2196, pp. 181-198 (2021)
Le Moigne T, Gurrieri L, Crozet P, Marchand CH, Zaffagnini M, Sparla F, Lemaire SD, Henri J. Crystal structure of chloroplastic thioredoxin z defines a type-specific target recognition. The Plant Journal. 107, pp.434-447 (2021).
Rodriguez-Horta E, Lage A, Weigt M, Barrat-Charlaix P. Global multivariate model learning from hierarchically correlated data. J. Stat. Mech. (2021).
Pérez-Pérez MEsther, Lemaire SD, Crespo JL. The ATG4 protease integrates redox and stress signals to regulate autophagy. Journal of Experimental Botany. 72, pp.3340-3351 (2021).
Barrat-Charlaix P, Muntoni APaola, Shimagaki K, Weigt M, Zamponi F. Sparse generative modeling via parameter reduction of Boltzmann machines: Application to protein-sequence families. Phys. Rev. E. 104, pp.024407 (2021).
Roret T, Zhang B, Moseler A, Dhalleine T, Gao X-H, Couturier J, Lemaire SD, Didierjean C, Johnson MK, Rouhier N. Atypical Iron-Sulfur Cluster Binding, Redox Activity and Structural Properties of Chlamydomonas reinhardtii Glutaredoxin 2. Antioxidants. 10, pp.803 (2021).
Rodriguez-Horta E, Weigt M. On the effect of phylogenetic correlations in coevolution-based contact prediction in proteins. PLOS Computational Biology. 17, pp.1-17 (2021).
Droghetti R, Agier N, Fischer G, Gherardi M, Cosentino Lagomarsino M. An evolutionary model identifies the main evolutionary biases for the evolution of genome-replication profiles. Elife. 10, (2021).
Chen R, Droux M, Goyer A, Hirel B, Hodges M, Issakidis-Bourguet E, Jacquot J-P, De Lamotte F, Lemaire SD, Lemaire-Chamley M, Miginiac-Maslow M, Sugiyama T, Suzuki A, Vidal J Chapter Three - Scientific contributions of Pierre Gadal and his lab—A tribute to Pierre Gadal (1938–2019). in Past, Current and Future Topics. 100, Academic Press. pp. 41-127 (2021)
Laine E, Eismann S, Elofsson A, Grudinin S. Protein sequence-to-structure learning: Is this the end(-to-end revolution)?. Proteins: Structure, Function, and Bioinformatics. (2021).
Colas C, Laine E. Targeting Solute Carrier Transporters through Functional Mapping. Trends Pharmacol Sci. 42(1), pp.3-6 (2021).
Zea DJavier, Laskina S, Baudin A, Richard H, Laine E. Assessing conservation of alternative splicing with evolutionary splicing graphs. Genome Res. 31(8), pp.1462-1473 (2021).
Roux P, Salort D, Xu Z. Adaptation to DNA damage as a bet-hedging mechanism in a fluctuating environment. R Soc Open Sci. 8(8), pp.210460 (2021).
Pérez-Vargas J§, Teppa E§, Amirache F, Boson B, R de Oliveira R, Combet C, Böckmann A, Fusil F, Freitas N, Carbone A*, Cosset FL*. A fusion peptide in preS1 and the human protein-disulfide isomerase ERp57 are involved in HBV membrane fusion process. eLife. (2021).

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