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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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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) |
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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. From principal component to direct coupling analysis of coevolution in proteins: low-eigenvalue modes are needed for structure prediction. PLoS Comput Biol. 9(8), pp.e1003176 (2013). |
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Ekeberg M, Lövkvist C, Lan Y, Weigt M, Aurell E. Improved contact prediction in proteins: using pseudolikelihoods to infer Potts models. Phys Rev E Stat Nonlin Soft Matter Phys. 87(1), pp.012707 (2013). |
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Molinelli EJ, Korkut A, Wang W, Miller ML, Gauthier NP, Jing X, Kaushik P, He Q, Mills G, Solit DB, Pratilas CA, Weigt M, Braunstein A, Pagnani A, Zecchina R, Sander C. Perturbation biology: inferring signaling networks in cellular systems. PLoS Comput Biol. 9(12), pp.e1003290 (2013). |
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Sułkowska JI, Morcos F, Weigt M, Hwa T, Onuchic JN. Genomics-aided structure prediction. Proc Natl Acad Sci U S A. 109(26), pp.10340-5 (2012). |
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Dago AE, Schug A, Procaccini A, Hoch JA, Weigt M, Szurmant H. Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis. Proc Natl Acad Sci U S A. 109(26), pp.E1733-42 (2012). |
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Procaccini A, Lunt B, Szurmant H, Hwa T, Weigt M. Dissecting the Specificity of Protein-Protein Interaction in Bacterial Two-Component Signaling: Orphans and Crosstalks. Rattray M (Eds.). PLoS One. 6, pp.e19729 (2011). |
