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Hannezo E, Coucke A, Joanny J-F. Interplay of migratory and division forces as a generic mechanism for stem cell patterns. Phys. Rev. E. 93, pp.022405 (2016). |
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Gueudré T, Baldassi C, Zamparo M, Weigt M, Pagnani A. Simultaneous identification of specifically interacting paralogs and inter-protein contacts by Direct-Coupling Analysis. Proc. Natl. Acad. Sci. 113(43), pp.12186-12191 (2016). |
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Feinauer C, Szurmant H, Weigt M, Pagnani A. Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon. PLoS ONE. 11, pp.1-18 (2016). |
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Bernardes JS, Zaverucha G, Vaquero C, Carbone A*. Improvement in protein domain identification is reached by breaking consensus, with the agreement of many profiles and domain co-occurrence. PLoS Computational Biology. 12(7), (2016). |
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Fortunato AE, Jaubert M, Enomoto G, Bouly J-P, Raniello R, Thaler M, Malviya S, Bernardes JS, Rappaport F, Gentili B, Huysman MJJ, Carbone A*, Bowler C, Riberà d'Alcalà M, Ikeuchi M, Falciatore A. Diatom Phytochromes Reveal the Existence of Far-Red-Light-Based Sensing in the Ocean. The Plant Cell. 28(3), pp.616 - 628 (2016). |
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De Leonardis E, Lutz B, Ratz S, Cocco S, Monasson R, Schug A, Weigt M. Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction. Nucleic Acids Res. 43(21), pp.10444-10455 (2015). |
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Figliuzzi M, Jacquier H, Schug A, Tenaillon O, Weigt M. Coevolutionary landscape inference and the context-dependence of mutations in beta-lactamase TEM-1. Mol Biol Evol. 33(1), pp.268-280 (2015). |
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Bernardes JS, Vieira FRJ, Zaverucha G, Carbone A*. A multi-objective optimization approach accurately resolves protein domain architectures. Bioinformatics. (2015). |
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Figliuzzi M, De Martino A, Marinari E. RNA-Based Regulation: Dynamics and Response to Perturbations of Competing RNAs. Biophysical Journal. 107(4), pp.1011-1022 (2015). |
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Bernardes JS, Vieira F, Costa L, Zaverucha G. Evaluation and improvements of clustering algorithms for detecting remote homologous protein families. BMC Bioinformatics. 16(1), pp.34 (2015). |
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Baldassi C, Zamparo M, Feinauer C, Procaccini A, Zecchina R, Weigt M, Pagnani A. Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners. Hamacher K (Eds.). PLoS ONE. 9, pp.e92721 (2014). |
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Morcos F, Hwa T, Onuchic JN, Weigt M Direct Coupling Analysis for Protein Contact Prediction. in Methods in Molecular Biology, Protein Structure Prediction. 1137, Springer New York. pp. 55-70 (2014) |
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Bernardes JS, Pedreira CE. A Review of Protein Function Prediction Under Machine Learning Perspective. (2013). |
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Szurmant H, Weigt M Genetic covariance. in Brenner's Encyclopedia of Genetics, 2nd edition. (2013) |
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Cocco S, Monasson R, Weigt M Inference of Hopfield-Potts patterns from covariation in protein families: calculation and statistical error bars. in Journal of Physics: Conference Series. 473, IOP Publishing. p. 012010 (2013) |
