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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).
Shirogane Y, Rousseau E, Voznica J, Xiao Y, Su W, Catching A, Whitfield ZJ, Rouzine IM, Bianco S, Andino R. Experimental and mathematical insights on the interactions between poliovirus and a defective interfering genome. bioRxiv. (2021).
Sokolovska N, Behbahani YMohseni. Vanishing boosted weights: a consistent algorithm to learn interpretable rules. Pattern Recognition Letters. (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)
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).
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).
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).

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