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Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis

Angel E. Dago , Alexander Schug , Andrea Procaccini , James A. Hoch , Martin Weigt , et al.
Proceedings of the National Academy of Sciences of the United States of America, 2012, 109 (26), pp.E1733-E1742. ⟨10.1073/pnas.1201301109⟩
Article dans une revue hal-01528442v1

An evolution-based model for designing chorismate mutase enzymes

William Russ , Matteo Figliuzzi , Christian Stocker , Pierre Barrat-Charlaix , Michael Socolich , et al.
Science, 2020, 369 (6502), pp.440-445. ⟨10.1126/science.aba3304⟩
Article dans une revue hal-04028834v1

Approximation schemes for the dynamics of diluted spin models: the Ising ferromagnet on a Bethe lattice

Guilhem Semerjian , Martin Weigt
Journal of Physics A: Mathematical and Theoretical, 2004, 37, pp.5525
Article dans une revue hal-00117088v1
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Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis

Guido Uguzzoni , Shalini John Lovis , Francesco Oteri , Alexander Schug , Hendrik Szurmant , et al.
Proceedings of the National Academy of Sciences of the United States of America, 2017, 114 (13), pp.E2662 - E2671. ⟨10.1073/pnas.1615068114⟩
Article dans une revue hal-01566982v1

Simultaneous identification of specifically interacting paralogs and interprotein contacts by direct coupling analysis.

Thomas Gueudré , Carlo Baldassi , Marco Zamparo , Martin Weigt , Andrea Pagnani
Proceedings of the National Academy of Sciences of the United States of America, 2016, 113 (43), pp.12186-12191. ⟨10.1073/pnas.1607570113⟩
Article dans une revue hal-01567010v1
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Toward Inferring Potts Models for Phylogenetically Correlated Sequence Data

Edwin Rodriguez Horta , Pierre Barrat-Charlaix , Martin Weigt
Entropy, 2019, 21 (11), pp.1090. ⟨10.3390/e21111090⟩
Article dans une revue hal-02430765v1

A ferromagnet with a glass transition

Silvio Franz , Marc Mézard , Federico Ricci-Tersenghi , Martin Weigt , Riccardo Zecchina
EPL - Europhysics Letters, 2001, 55, pp.465
Article dans une revue hal-00002405v1

Direct Coupling Analysis for Protein Contact Prediction

Faruck Morcos , Terence Hwa , Jose N. Onuchic , Martin Weigt
Kihara, D. Protein Structure Prediction, 1137, Humana Press, pp.55-70, 2014, Methods in Molecular Biology, 978-1-4939-0366-5; 978-1-4939-0365-8. ⟨10.1007/978-1-4939-0366-5_5⟩
Chapitre d'ouvrage hal-01528529v1

Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1

Matteo Figliuzzi , Hervé Jacquier , Alexander Schug , Oliver Tenaillon , Martin Weigt
Molecular Biology and Evolution, 2015, 33 (1), pp.268-280. ⟨10.1093/molbev/msv211⟩
Article dans une revue hal-01284957v1

Structures of a dimodular nonribosomal peptide synthetase reveal conformational flexibility

Janice Reimer , Maximilian Eivaskhani , Ingrid Harb , Alba Guarné , Martin Weigt , et al.
Science, 2019, 366 (6466), ⟨10.1126/science.aaw4388⟩
Article dans une revue hal-04028848v1

Mutator genomes decay, despite sustained fitness gains, in a long-term experiment with bacteria

Alejandro Couce , Larissa Viraphong Caudwell , Christoph Feinauer , Thomas Hindré , Jean-Paul Feugeas , et al.
Proceedings of the National Academy of Sciences of the United States of America, 2017, 114 (43), pp.E9026 - E9035. ⟨10.1073/pnas.1705887114⟩
Article dans une revue hal-01653591v1
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Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon

Christoph Feinauer , Hendrik Szurmant , Martin Weigt , Andrea Pagnani
PLoS ONE, 2016, 11 (2), pp.e0149166. ⟨10.1371/journal.pone.0149166⟩
Article dans une revue hal-01294651v1
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Phylogenetic correlations can suffice to infer protein partners from sequences

Guillaume Marmier , Martin Weigt , Anne-Florence Bitbol
PLoS Computational Biology, 2019, 15 (10), pp.e1007179. ⟨10.1371/journal.pcbi.1007179⟩
Article dans une revue hal-02347705v1

Dissecting the Specificity of Protein-Protein Interaction in Bacterial Two-Component Signaling: Orphans and Crosstalks

Andrea Procaccini , Bryan Lunt , Hendrik Szurmant , Terence Hwa , Martin Weigt , et al.
PLoS ONE, 2011, 6 (5), ⟨10.1371/journal.pone.0019729⟩
Article dans une revue hal-01588986v1

Machine-learning-assisted Monte Carlo fails at sampling computationally hard problems

Simone Ciarella , Jeanne Trinquier , Martin Weigt , Francesco Zamponi
Machine Learning: Science and Technology, 2023, 4 (1), pp.010501. ⟨10.1088/2632-2153/acbe91⟩
Article dans une revue hal-04028482v1

Cavity Approach to the Random Solid State

Xiaoming Mao , Paul M. Goldbart , Marc Mezard , Martin Weigt
Physical Review Letters, 2005, 95, pp.148302
Article dans une revue hal-00011184v1
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Perturbation Biology: Inferring Signaling Networks in Cellular Systems

Evan J. Molinelli , Anil Korkut , Weiqing Wang , Martin L. Miller , Nicholas P. Gauthier , et al.
PLoS Computational Biology, 2013, 9 (12), pp.e1003290. ⟨10.1371/journal.pcbi.1003290⟩
Article dans une revue hal-01527329v1
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A multi-scale coevolutionary approach to predict interactions between protein domains

Giancarlo Croce , Thomas Gueudré , Maria Virginia Ruiz Cuevas , Victoria Keidel , Matteo Figliuzzi , et al.
PLoS Computational Biology, 2019, 15 (10), pp.e1006891. ⟨10.1371/journal.pcbi.1006891⟩
Article dans une revue hal-02417872v1
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Improving landscape inference by integrating heterogeneous data in the inverse Ising problem

Pierre Barrat-Charlaix , Matteo Figliuzzi , Martin Weigt
Scientific Reports, 2016, 6, pp.37812. ⟨10.1038/srep37812⟩
Article dans une revue hal-01405150v1
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Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners

Carlo Baldassi , Marco Zamparo , Christoph Feinauer , Andrea Procaccini , Riccardo Zecchina , et al.
PLoS ONE, 2014, 9 (3), pp.e92721. ⟨10.1371/journal.pone.0092721⟩
Article dans une revue hal-01344551v1
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Deciphering polymorphism in 61,157 Escherichia coli genomes via epistatic sequence landscapes

Lucile Vigué , Giancarlo Croce , Marie Petitjean , Etienne Ruppé , Olivier Tenaillon , et al.
Nature Communications, 2022, 13 (1), pp.4030. ⟨10.1038/s41467-022-31643-3⟩
Article dans une revue hal-03721049v1
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From principal component to direct coupling analysis of coevolution in proteins: Low-eigenvalue modes are needed for structure prediction

Simona Cocco , Remi Monasson , Martin Weigt
PLoS Computational Biology, 2013, 9 (8), pp.e1003176. ⟨10.1371/journal.pcbi.1003176⟩
Article dans une revue hal-00764377v2
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Meet-U: educating through research immersion

Nika Abdollahi , Alexandre Albani , Eric Anthony , Agnes Baud , Mélissa Cardon , et al.
PLoS Computational Biology, 2018, 14 (3), pp.1-10. ⟨10.1371/journal.pcbi.1005992⟩
Article dans une revue hal-01722019v1

The evolution of the temporal program of genome replication

Nicolas Agier , Stéphane Delmas , Qing Zhang , Aubin Fleiss , Yan Jaszczyszyn , et al.
Nature Communications, 2018, 9 (1), pp.2199. ⟨10.1038/s41467-018-04628-4⟩
Article dans une revue hal-02175123v1

Inference of Hopfield-Potts patterns from covariation in protein families: calculation and statistical error bars

Simona Cocco , Rémi Monasson , Martin Weigt
Journal of Physics: Conference Series, 2013, 473, pp.012010 ⟨10.1088/1742-6596/473/1/012010⟩
Article dans une revue hal-01567856v1

Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes

Juan Rodriguez-Rivas , Giancarlo Croce , Maureen Muscat , Martin Weigt
Proceedings of the National Academy of Sciences of the United States of America, 2022, 119 (4), ⟨10.1073/pnas.2113118119⟩
Article dans une revue hal-03721064v1

Genetic covariance

Hendrik Szurmant , Martin Weigt
Brenner's Encyclopedia of Genetics, 2nd edition, 2013
Chapitre d'ouvrage hal-01567874v1

Integrating Genomic Information with Molecular Simulation to Understand Protein Complex- and Active Conformation Formation in Two-Component Signal Transduction

Alexander Schug , Martin Weigt , Hendrik Szurmant
Biophysical Journal, 2012, 102 (3, 1), pp.45A. ⟨10.1016/j.bpj.2011.11.279⟩
Article dans une revue hal-01528433v1

Genomics-aided structure prediction

Joanna I. Sulkowska , Faruck Morcos , Martin Weigt , Terence Hwa , Jose N. Onuchic
Proceedings of the National Academy of Sciences of the United States of America, 2012, 109 (26), pp.10340-10345. ⟨10.1073/pnas.1207864109⟩
Article dans une revue hal-01528443v1

Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins

Carlos Gandarilla-Pérez , Sergio Pinilla , Anne-Florence Bitbol , Martin Weigt
PLoS Computational Biology, 2023, 19 (3), pp.e1011010. ⟨10.1371/journal.pcbi.1011010⟩
Article dans une revue hal-04054471v1