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Publications

Dequeker C, Mohseni-Behbahani Y, David L, Laine E, Carbone A. From complete cross-docking to partners identification and binding sites predictions. PLOS Computational Biology. (In Press).
Rodriguez-Rivas J, Croce G, Muscat M, Weigt M. Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes. Proceedings of the National Academy of Sciences. 119, (2022).
Bisardi M, Rodriguez-Rivas J, Zamponi F, Weigt M. Modeling Sequence-Space Exploration and Emergence of Epistatic Signals in Protein Evolution. Molecular Biology and Evolution. (2021).
Trinquier J, Uguzzoni G, Pagnani A, Zamponi F, Weigt M. Efficient generative modeling of protein sequences using simple autoregressive models. Nature Communications. 12(1), pp.5800 (2021).
Muntoni AP, Pagnani A, Weigt M, Zamponi F. adabmDCA: adaptive Boltzmann machine learning for biological sequences. BMC Bioinformatics. 22(1), pp.528 (2021).
Delaveau T, Thiebaut A, Benchouaia M, Merhej J, Devaux F. Yap5 Competes With Hap4 for the Regulation of Iron Homeostasis Genes in the Human Pathogen. Front Cell Infect Microbiol. 11, pp.731988 (2021).
Martin H, Doumic M, Teixeira MTeresa, Xu Z. Telomere shortening causes distinct cell division regimes during replicative senescence in Saccharomyces cerevisiae. Cell Biosci. 11(1), pp.180 (2021).
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, Mohseni-Behbahani Y. Vanishing boosted weights: a consistent algorithm to learn interpretable rules. Pattern Recognition Letters. (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).
Rodriguez-Horta E, Lage A, Weigt M, Barrat-Charlaix P. Global multivariate model learning from hierarchically correlated data. J. Stat. Mech. (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).
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)
Barrat-Charlaix P, Muntoni AP, 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).
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).

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