Direct coupling analysis (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Direct coupling analysis" in English language version.

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48nih.gov

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28doi.org

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19harvard.edu

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10arxiv.org

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6worldcat.org

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5semanticscholar.org

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1sciencedirect.com

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arxiv.org

Morcos, F.; Pagnani, A.; Lunt, B.; Bertolino, A.; Marks, D. S.; Sander, C.; Zecchina, R.; Onuchic, J. N.; Hwa, T.; Weigt, M. (21 November 2011). "Direct-coupling analysis of residue coevolution captures native contacts across many protein families". Proceedings of the National Academy of Sciences. 108 (49): E1293–E1301. arXiv:1110.5223. Bibcode:2011PNAS..108E1293M. doi:10.1073/pnas.1111471108. PMC 3241805. PMID 22106262.
Ekeberg, Magnus; Lövkvist, Cecilia; Lan, Yueheng; Weigt, Martin; Aurell, Erik (11 January 2013). "Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models". Physical Review E. 87 (1): 012707. arXiv:1211.1281. Bibcode:2013PhRvE..87a2707E. doi:10.1103/PhysRevE.87.012707. PMID 23410359. S2CID 27772365.
Ekeberg, Magnus; Hartonen, Tuomo; Aurell, Erik (2014-11-01). "Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences". Journal of Computational Physics. 276: 341–356. arXiv:1401.4832. Bibcode:2014JCoPh.276..341E. doi:10.1016/j.jcp.2014.07.024. ISSN 0021-9991. S2CID 15635703.
De Leonardis, Eleonora; Lutz, Benjamin; Ratz, Sebastian; Cocco, Simona; Monasson, Rémi; Schug, Alexander; Weigt, Martin (29 September 2015). "Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction". Nucleic Acids Research. 43 (21): 10444–55. arXiv:1510.03351. doi:10.1093/nar/gkv932. PMC 4666395. PMID 26420827.
Feinauer, Christoph; Szurmant, Hendrik; Weigt, Martin; Pagnani, Andrea; Keskin, Ozlem (16 February 2016). "Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon". PLOS ONE. 11 (2): e0149166. arXiv:1512.05420. Bibcode:2016PLoSO..1149166F. doi:10.1371/journal.pone.0149166. PMC 4755613. PMID 26882169.
Uguzzoni, Guido; John Lovis, Shalini; Oteri, Francesco; Schug, Alexander; Szurmant, Hendrik; Weigt, Martin (2017-03-28). "Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis". Proceedings of the National Academy of Sciences. 114 (13): E2662–E2671. arXiv:1703.01246. Bibcode:2017PNAS..114E2662U. doi:10.1073/pnas.1615068114. ISSN 0027-8424. PMC 5380090. PMID 28289198.
Rodriguez-Rivas, Juan; Croce, Giancarlo; Muscat, Maureen; Weigt, Martin (2022-01-25). "Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes". Proceedings of the National Academy of Sciences. 119 (4). arXiv:2112.10093. Bibcode:2022PNAS..11913118R. doi:10.1073/pnas.2113118119. ISSN 0027-8424. PMC 8795541. PMID 35022216.
Feinauer, Christoph; Skwark, Marcin J.; Pagnani, Andrea; Aurell, Erik (9 October 2014). "Improving Contact Prediction along Three Dimensions". PLOS Computational Biology. 10 (10): e1003847. arXiv:1403.0379. Bibcode:2014PLSCB..10E3847F. doi:10.1371/journal.pcbi.1003847. PMC 4191875. PMID 25299132.
Baldassi, Carlo; Zamparo, Marco; Feinauer, Christoph; Procaccini, Andrea; Zecchina, Riccardo; Weigt, Martin; Pagnani, Andrea (24 March 2014). "Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners". PLOS ONE. 9 (3): e92721. arXiv:1404.1240. Bibcode:2014PLoSO...992721B. doi:10.1371/journal.pone.0092721. PMC 3963956. PMID 24663061.
Weigt, M.; White, R. A.; Szurmant, H.; Hoch, J. A.; Hwa, T. (30 December 2008). "Identification of direct residue contacts in protein-protein interaction by message passing". Proceedings of the National Academy of Sciences. 106 (1): 67–72. arXiv:0901.1248. Bibcode:2009PNAS..106...67W. doi:10.1073/pnas.0805923106. PMC 2629192. PMID 19116270.

doi.org

Morcos, F.; Pagnani, A.; Lunt, B.; Bertolino, A.; Marks, D. S.; Sander, C.; Zecchina, R.; Onuchic, J. N.; Hwa, T.; Weigt, M. (21 November 2011). "Direct-coupling analysis of residue coevolution captures native contacts across many protein families". Proceedings of the National Academy of Sciences. 108 (49): E1293–E1301. arXiv:1110.5223. Bibcode:2011PNAS..108E1293M. doi:10.1073/pnas.1111471108. PMC 3241805. PMID 22106262.
Kamisetty, H.; Ovchinnikov, S.; Baker, D. (5 September 2013). "Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era". Proceedings of the National Academy of Sciences. 110 (39): 15674–15679. Bibcode:2013PNAS..11015674K. doi:10.1073/pnas.1314045110. PMC 3785744. PMID 24009338.
Ekeberg, Magnus; Lövkvist, Cecilia; Lan, Yueheng; Weigt, Martin; Aurell, Erik (11 January 2013). "Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models". Physical Review E. 87 (1): 012707. arXiv:1211.1281. Bibcode:2013PhRvE..87a2707E. doi:10.1103/PhysRevE.87.012707. PMID 23410359. S2CID 27772365.
Marks, Debora S.; Colwell, Lucy J.; Sheridan, Robert; Hopf, Thomas A.; Pagnani, Andrea; Zecchina, Riccardo; Sander, Chris; Sali, Andrej (7 December 2011). "Protein 3D Structure Computed from Evolutionary Sequence Variation". PLOS ONE. 6 (12): e28766. Bibcode:2011PLoSO...628766M. doi:10.1371/journal.pone.0028766. PMC 3233603. PMID 22163331.
Ekeberg, Magnus; Hartonen, Tuomo; Aurell, Erik (2014-11-01). "Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences". Journal of Computational Physics. 276: 341–356. arXiv:1401.4832. Bibcode:2014JCoPh.276..341E. doi:10.1016/j.jcp.2014.07.024. ISSN 0021-9991. S2CID 15635703.
De Leonardis, Eleonora; Lutz, Benjamin; Ratz, Sebastian; Cocco, Simona; Monasson, Rémi; Schug, Alexander; Weigt, Martin (29 September 2015). "Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction". Nucleic Acids Research. 43 (21): 10444–55. arXiv:1510.03351. doi:10.1093/nar/gkv932. PMC 4666395. PMID 26420827.
Weinreb, Caleb; Riesselman, Adam J.; Ingraham, John B.; Gross, Torsten; Sander, Chris; Marks, Debora S. (May 2016). "3D RNA and Functional Interactions from Evolutionary Couplings". Cell. 165 (4): 963–975. doi:10.1016/j.cell.2016.03.030. PMC 5024353. PMID 27087444.
Ovchinnikov, Sergey; Kamisetty, Hetunandan; Baker, David (1 May 2014). "Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information". eLife. 3: e02030. doi:10.7554/eLife.02030. PMC 4034769. PMID 24842992.
Feinauer, Christoph; Szurmant, Hendrik; Weigt, Martin; Pagnani, Andrea; Keskin, Ozlem (16 February 2016). "Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon". PLOS ONE. 11 (2): e0149166. arXiv:1512.05420. Bibcode:2016PLoSO..1149166F. doi:10.1371/journal.pone.0149166. PMC 4755613. PMID 26882169.
dos Santos, R.N.; Morcos, F.; Jana, B.; Andricopulo, A.D.; Onuchic, J.N. (4 September 2015). "Dimeric interactions and complex formation using direct coevolutionary couplings". Scientific Reports. 5: 13652. Bibcode:2015NatSR...513652D. doi:10.1038/srep13652. PMC 4559900. PMID 26338201.
Uguzzoni, Guido; John Lovis, Shalini; Oteri, Francesco; Schug, Alexander; Szurmant, Hendrik; Weigt, Martin (2017-03-28). "Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis". Proceedings of the National Academy of Sciences. 114 (13): E2662–E2671. arXiv:1703.01246. Bibcode:2017PNAS..114E2662U. doi:10.1073/pnas.1615068114. ISSN 0027-8424. PMC 5380090. PMID 28289198.
Croce, Giancarlo; Gueudré, Thomas; Cuevas, Maria Virginia Ruiz; Keidel, Victoria; Figliuzzi, Matteo; Szurmant, Hendrik; Weigt, Martin (2019-10-21). "A multi-scale coevolutionary approach to predict interactions between protein domains". PLOS Computational Biology. 15 (10): e1006891. Bibcode:2019PLSCB..15E6891C. doi:10.1371/journal.pcbi.1006891. ISSN 1553-7358. PMC 6822775. PMID 31634362.
Ferguson, Andrew L.; Mann, Jaclyn K.; Omarjee, Saleha; Ndung'u, Thumbi; Walker, Bruce D.; Chakraborty, Arup K. (March 2013). "Translating HIV Sequences into Quantitative Fitness Landscapes Predicts Viral Vulnerabilities for Rational Immunogen Design". Immunity. 38 (3): 606–617. doi:10.1016/j.immuni.2012.11.022. PMC 3728823. PMID 23521886.
Figliuzzi, Matteo; Jacquier, Hervé; Schug, Alexander; Tenaillon, Oliver; Weigt, Martin (January 2016). "Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1". Molecular Biology and Evolution. 33 (1): 268–280. doi:10.1093/molbev/msv211. PMC 4693977. PMID 26446903.
Asti, Lorenzo; Uguzzoni, Guido; Marcatili, Paolo; Pagnani, Andrea; Ofran, Yanay (13 April 2016). "Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity". PLOS Computational Biology. 12 (4): e1004870. Bibcode:2016PLSCB..12E4870A. doi:10.1371/journal.pcbi.1004870. PMC 4830580. PMID 27074145.
Russ, William P.; Figliuzzi, Matteo; Stocker, Christian; Barrat-Charlaix, Pierre; Socolich, Michael; Kast, Peter; Hilvert, Donald; Monasson, Remi; Cocco, Simona; Weigt, Martin; Ranganathan, Rama (2020-07-24). "An evolution-based model for designing chorismate mutase enzymes". Science. 369 (6502): 440–445. Bibcode:2020Sci...369..440R. doi:10.1126/science.aba3304. ISSN 0036-8075. PMID 32703877. S2CID 220714458.
Rodriguez-Rivas, Juan; Croce, Giancarlo; Muscat, Maureen; Weigt, Martin (2022-01-25). "Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes". Proceedings of the National Academy of Sciences. 119 (4). arXiv:2112.10093. Bibcode:2022PNAS..11913118R. doi:10.1073/pnas.2113118119. ISSN 0027-8424. PMC 8795541. PMID 35022216.
Vigué, Lucile; Croce, Giancarlo; Petitjean, Marie; Ruppé, Etienne; Tenaillon, Olivier; Weigt, Martin (2022-07-12). "Deciphering polymorphism in 61,157 Escherichia coli genomes via epistatic sequence landscapes". Nature Communications. 13 (1): 4030. Bibcode:2022NatCo..13.4030V. doi:10.1038/s41467-022-31643-3. ISSN 2041-1723. PMC 9276797. PMID 35821377.
Feinauer, Christoph; Skwark, Marcin J.; Pagnani, Andrea; Aurell, Erik (9 October 2014). "Improving Contact Prediction along Three Dimensions". PLOS Computational Biology. 10 (10): e1003847. arXiv:1403.0379. Bibcode:2014PLSCB..10E3847F. doi:10.1371/journal.pcbi.1003847. PMC 4191875. PMID 25299132.
Baldassi, Carlo; Zamparo, Marco; Feinauer, Christoph; Procaccini, Andrea; Zecchina, Riccardo; Weigt, Martin; Pagnani, Andrea (24 March 2014). "Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners". PLOS ONE. 9 (3): e92721. arXiv:1404.1240. Bibcode:2014PLoSO...992721B. doi:10.1371/journal.pone.0092721. PMC 3963956. PMID 24663061.
Stein, Richard R.; Marks, Debora S.; Sander, Chris; Chen, Shi-Jie (30 July 2015). "Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models". PLOS Computational Biology. 11 (7): e1004182. Bibcode:2015PLSCB..11E4182S. doi:10.1371/journal.pcbi.1004182. PMC 4520494. PMID 26225866.
Burger, Lukas; van Nimwegen, Erik; Bourne, Philip E. (1 January 2010). "Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments". PLOS Computational Biology. 6 (1): e1000633. Bibcode:2010PLSCB...6E0633B. doi:10.1371/journal.pcbi.1000633. PMC 2793430. PMID 20052271.
Weigt, M.; White, R. A.; Szurmant, H.; Hoch, J. A.; Hwa, T. (30 December 2008). "Identification of direct residue contacts in protein-protein interaction by message passing". Proceedings of the National Academy of Sciences. 106 (1): 67–72. arXiv:0901.1248. Bibcode:2009PNAS..106...67W. doi:10.1073/pnas.0805923106. PMC 2629192. PMID 19116270.
Barton, J. P.; De Leonardis, E.; Coucke, A.; Cocco, S. (21 June 2016). "ACE: adaptive cluster expansion for maximum entropy graphical model inference". Bioinformatics. 32 (20): 3089–3097. doi:10.1093/bioinformatics/btw328. PMID 27329863.
Göbel, Ulrike; Sander, Chris; Schneider, Reinhard; Valencia, Alfonso (April 1994). "Correlated mutations and residue contacts in proteins". Proteins: Structure, Function, and Genetics. 18 (4): 309–317. doi:10.1002/prot.340180402. PMID 8208723. S2CID 14978727.
Dunn, S.D.; Wahl, L.M.; Gloor, G.B. (5 December 2007). "Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction". Bioinformatics. 24 (3): 333–340. doi:10.1093/bioinformatics/btm604. PMID 18057019.
Schug, A.; Weigt, M.; Onuchic, J. N.; Hwa, T.; Szurmant, H. (17 December 2009). "High-resolution protein complexes from integrating genomic information with molecular simulation". Proceedings of the National Academy of Sciences. 106 (52): 22124–22129. Bibcode:2009PNAS..10622124S. doi:10.1073/pnas.0912100106. PMC 2799721. PMID 20018738.
Jarmolinska, Aleksandra I.; Zhou, Qin; Sulkowska, Joanna I.; Morcos, Faruck (11 January 2019). "DCA-MOL: A PyMOL Plugin To Analyze Direct Evolutionary Couplings". Journal of Chemical Information and Modeling. 59 (2): 625–629. doi:10.1021/acs.jcim.8b00690. PMID 30632747. S2CID 58634008.

harvard.edu

ui.adsabs.harvard.edu

Morcos, F.; Pagnani, A.; Lunt, B.; Bertolino, A.; Marks, D. S.; Sander, C.; Zecchina, R.; Onuchic, J. N.; Hwa, T.; Weigt, M. (21 November 2011). "Direct-coupling analysis of residue coevolution captures native contacts across many protein families". Proceedings of the National Academy of Sciences. 108 (49): E1293–E1301. arXiv:1110.5223. Bibcode:2011PNAS..108E1293M. doi:10.1073/pnas.1111471108. PMC 3241805. PMID 22106262.
Kamisetty, H.; Ovchinnikov, S.; Baker, D. (5 September 2013). "Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era". Proceedings of the National Academy of Sciences. 110 (39): 15674–15679. Bibcode:2013PNAS..11015674K. doi:10.1073/pnas.1314045110. PMC 3785744. PMID 24009338.
Ekeberg, Magnus; Lövkvist, Cecilia; Lan, Yueheng; Weigt, Martin; Aurell, Erik (11 January 2013). "Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models". Physical Review E. 87 (1): 012707. arXiv:1211.1281. Bibcode:2013PhRvE..87a2707E. doi:10.1103/PhysRevE.87.012707. PMID 23410359. S2CID 27772365.
Marks, Debora S.; Colwell, Lucy J.; Sheridan, Robert; Hopf, Thomas A.; Pagnani, Andrea; Zecchina, Riccardo; Sander, Chris; Sali, Andrej (7 December 2011). "Protein 3D Structure Computed from Evolutionary Sequence Variation". PLOS ONE. 6 (12): e28766. Bibcode:2011PLoSO...628766M. doi:10.1371/journal.pone.0028766. PMC 3233603. PMID 22163331.
Ekeberg, Magnus; Hartonen, Tuomo; Aurell, Erik (2014-11-01). "Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences". Journal of Computational Physics. 276: 341–356. arXiv:1401.4832. Bibcode:2014JCoPh.276..341E. doi:10.1016/j.jcp.2014.07.024. ISSN 0021-9991. S2CID 15635703.
Feinauer, Christoph; Szurmant, Hendrik; Weigt, Martin; Pagnani, Andrea; Keskin, Ozlem (16 February 2016). "Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon". PLOS ONE. 11 (2): e0149166. arXiv:1512.05420. Bibcode:2016PLoSO..1149166F. doi:10.1371/journal.pone.0149166. PMC 4755613. PMID 26882169.
dos Santos, R.N.; Morcos, F.; Jana, B.; Andricopulo, A.D.; Onuchic, J.N. (4 September 2015). "Dimeric interactions and complex formation using direct coevolutionary couplings". Scientific Reports. 5: 13652. Bibcode:2015NatSR...513652D. doi:10.1038/srep13652. PMC 4559900. PMID 26338201.
Uguzzoni, Guido; John Lovis, Shalini; Oteri, Francesco; Schug, Alexander; Szurmant, Hendrik; Weigt, Martin (2017-03-28). "Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis". Proceedings of the National Academy of Sciences. 114 (13): E2662–E2671. arXiv:1703.01246. Bibcode:2017PNAS..114E2662U. doi:10.1073/pnas.1615068114. ISSN 0027-8424. PMC 5380090. PMID 28289198.
Croce, Giancarlo; Gueudré, Thomas; Cuevas, Maria Virginia Ruiz; Keidel, Victoria; Figliuzzi, Matteo; Szurmant, Hendrik; Weigt, Martin (2019-10-21). "A multi-scale coevolutionary approach to predict interactions between protein domains". PLOS Computational Biology. 15 (10): e1006891. Bibcode:2019PLSCB..15E6891C. doi:10.1371/journal.pcbi.1006891. ISSN 1553-7358. PMC 6822775. PMID 31634362.
Asti, Lorenzo; Uguzzoni, Guido; Marcatili, Paolo; Pagnani, Andrea; Ofran, Yanay (13 April 2016). "Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity". PLOS Computational Biology. 12 (4): e1004870. Bibcode:2016PLSCB..12E4870A. doi:10.1371/journal.pcbi.1004870. PMC 4830580. PMID 27074145.
Russ, William P.; Figliuzzi, Matteo; Stocker, Christian; Barrat-Charlaix, Pierre; Socolich, Michael; Kast, Peter; Hilvert, Donald; Monasson, Remi; Cocco, Simona; Weigt, Martin; Ranganathan, Rama (2020-07-24). "An evolution-based model for designing chorismate mutase enzymes". Science. 369 (6502): 440–445. Bibcode:2020Sci...369..440R. doi:10.1126/science.aba3304. ISSN 0036-8075. PMID 32703877. S2CID 220714458.
Rodriguez-Rivas, Juan; Croce, Giancarlo; Muscat, Maureen; Weigt, Martin (2022-01-25). "Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes". Proceedings of the National Academy of Sciences. 119 (4). arXiv:2112.10093. Bibcode:2022PNAS..11913118R. doi:10.1073/pnas.2113118119. ISSN 0027-8424. PMC 8795541. PMID 35022216.
Vigué, Lucile; Croce, Giancarlo; Petitjean, Marie; Ruppé, Etienne; Tenaillon, Olivier; Weigt, Martin (2022-07-12). "Deciphering polymorphism in 61,157 Escherichia coli genomes via epistatic sequence landscapes". Nature Communications. 13 (1): 4030. Bibcode:2022NatCo..13.4030V. doi:10.1038/s41467-022-31643-3. ISSN 2041-1723. PMC 9276797. PMID 35821377.
Feinauer, Christoph; Skwark, Marcin J.; Pagnani, Andrea; Aurell, Erik (9 October 2014). "Improving Contact Prediction along Three Dimensions". PLOS Computational Biology. 10 (10): e1003847. arXiv:1403.0379. Bibcode:2014PLSCB..10E3847F. doi:10.1371/journal.pcbi.1003847. PMC 4191875. PMID 25299132.
Baldassi, Carlo; Zamparo, Marco; Feinauer, Christoph; Procaccini, Andrea; Zecchina, Riccardo; Weigt, Martin; Pagnani, Andrea (24 March 2014). "Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners". PLOS ONE. 9 (3): e92721. arXiv:1404.1240. Bibcode:2014PLoSO...992721B. doi:10.1371/journal.pone.0092721. PMC 3963956. PMID 24663061.
Stein, Richard R.; Marks, Debora S.; Sander, Chris; Chen, Shi-Jie (30 July 2015). "Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models". PLOS Computational Biology. 11 (7): e1004182. Bibcode:2015PLSCB..11E4182S. doi:10.1371/journal.pcbi.1004182. PMC 4520494. PMID 26225866.
Burger, Lukas; van Nimwegen, Erik; Bourne, Philip E. (1 January 2010). "Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments". PLOS Computational Biology. 6 (1): e1000633. Bibcode:2010PLSCB...6E0633B. doi:10.1371/journal.pcbi.1000633. PMC 2793430. PMID 20052271.
Weigt, M.; White, R. A.; Szurmant, H.; Hoch, J. A.; Hwa, T. (30 December 2008). "Identification of direct residue contacts in protein-protein interaction by message passing". Proceedings of the National Academy of Sciences. 106 (1): 67–72. arXiv:0901.1248. Bibcode:2009PNAS..106...67W. doi:10.1073/pnas.0805923106. PMC 2629192. PMID 19116270.
Schug, A.; Weigt, M.; Onuchic, J. N.; Hwa, T.; Szurmant, H. (17 December 2009). "High-resolution protein complexes from integrating genomic information with molecular simulation". Proceedings of the National Academy of Sciences. 106 (52): 22124–22129. Bibcode:2009PNAS..10622124S. doi:10.1073/pnas.0912100106. PMC 2799721. PMID 20018738.

nih.gov

pubmed.ncbi.nlm.nih.gov

Morcos, F.; Pagnani, A.; Lunt, B.; Bertolino, A.; Marks, D. S.; Sander, C.; Zecchina, R.; Onuchic, J. N.; Hwa, T.; Weigt, M. (21 November 2011). "Direct-coupling analysis of residue coevolution captures native contacts across many protein families". Proceedings of the National Academy of Sciences. 108 (49): E1293–E1301. arXiv:1110.5223. Bibcode:2011PNAS..108E1293M. doi:10.1073/pnas.1111471108. PMC 3241805. PMID 22106262.
Kamisetty, H.; Ovchinnikov, S.; Baker, D. (5 September 2013). "Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era". Proceedings of the National Academy of Sciences. 110 (39): 15674–15679. Bibcode:2013PNAS..11015674K. doi:10.1073/pnas.1314045110. PMC 3785744. PMID 24009338.
Ekeberg, Magnus; Lövkvist, Cecilia; Lan, Yueheng; Weigt, Martin; Aurell, Erik (11 January 2013). "Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models". Physical Review E. 87 (1): 012707. arXiv:1211.1281. Bibcode:2013PhRvE..87a2707E. doi:10.1103/PhysRevE.87.012707. PMID 23410359. S2CID 27772365.
Marks, Debora S.; Colwell, Lucy J.; Sheridan, Robert; Hopf, Thomas A.; Pagnani, Andrea; Zecchina, Riccardo; Sander, Chris; Sali, Andrej (7 December 2011). "Protein 3D Structure Computed from Evolutionary Sequence Variation". PLOS ONE. 6 (12): e28766. Bibcode:2011PLoSO...628766M. doi:10.1371/journal.pone.0028766. PMC 3233603. PMID 22163331.
De Leonardis, Eleonora; Lutz, Benjamin; Ratz, Sebastian; Cocco, Simona; Monasson, Rémi; Schug, Alexander; Weigt, Martin (29 September 2015). "Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction". Nucleic Acids Research. 43 (21): 10444–55. arXiv:1510.03351. doi:10.1093/nar/gkv932. PMC 4666395. PMID 26420827.
Weinreb, Caleb; Riesselman, Adam J.; Ingraham, John B.; Gross, Torsten; Sander, Chris; Marks, Debora S. (May 2016). "3D RNA and Functional Interactions from Evolutionary Couplings". Cell. 165 (4): 963–975. doi:10.1016/j.cell.2016.03.030. PMC 5024353. PMID 27087444.
Ovchinnikov, Sergey; Kamisetty, Hetunandan; Baker, David (1 May 2014). "Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information". eLife. 3: e02030. doi:10.7554/eLife.02030. PMC 4034769. PMID 24842992.
Feinauer, Christoph; Szurmant, Hendrik; Weigt, Martin; Pagnani, Andrea; Keskin, Ozlem (16 February 2016). "Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon". PLOS ONE. 11 (2): e0149166. arXiv:1512.05420. Bibcode:2016PLoSO..1149166F. doi:10.1371/journal.pone.0149166. PMC 4755613. PMID 26882169.
dos Santos, R.N.; Morcos, F.; Jana, B.; Andricopulo, A.D.; Onuchic, J.N. (4 September 2015). "Dimeric interactions and complex formation using direct coevolutionary couplings". Scientific Reports. 5: 13652. Bibcode:2015NatSR...513652D. doi:10.1038/srep13652. PMC 4559900. PMID 26338201.
Uguzzoni, Guido; John Lovis, Shalini; Oteri, Francesco; Schug, Alexander; Szurmant, Hendrik; Weigt, Martin (2017-03-28). "Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis". Proceedings of the National Academy of Sciences. 114 (13): E2662–E2671. arXiv:1703.01246. Bibcode:2017PNAS..114E2662U. doi:10.1073/pnas.1615068114. ISSN 0027-8424. PMC 5380090. PMID 28289198.
Croce, Giancarlo; Gueudré, Thomas; Cuevas, Maria Virginia Ruiz; Keidel, Victoria; Figliuzzi, Matteo; Szurmant, Hendrik; Weigt, Martin (2019-10-21). "A multi-scale coevolutionary approach to predict interactions between protein domains". PLOS Computational Biology. 15 (10): e1006891. Bibcode:2019PLSCB..15E6891C. doi:10.1371/journal.pcbi.1006891. ISSN 1553-7358. PMC 6822775. PMID 31634362.
Ferguson, Andrew L.; Mann, Jaclyn K.; Omarjee, Saleha; Ndung'u, Thumbi; Walker, Bruce D.; Chakraborty, Arup K. (March 2013). "Translating HIV Sequences into Quantitative Fitness Landscapes Predicts Viral Vulnerabilities for Rational Immunogen Design". Immunity. 38 (3): 606–617. doi:10.1016/j.immuni.2012.11.022. PMC 3728823. PMID 23521886.
Figliuzzi, Matteo; Jacquier, Hervé; Schug, Alexander; Tenaillon, Oliver; Weigt, Martin (January 2016). "Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1". Molecular Biology and Evolution. 33 (1): 268–280. doi:10.1093/molbev/msv211. PMC 4693977. PMID 26446903.
Asti, Lorenzo; Uguzzoni, Guido; Marcatili, Paolo; Pagnani, Andrea; Ofran, Yanay (13 April 2016). "Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity". PLOS Computational Biology. 12 (4): e1004870. Bibcode:2016PLSCB..12E4870A. doi:10.1371/journal.pcbi.1004870. PMC 4830580. PMID 27074145.
Russ, William P.; Figliuzzi, Matteo; Stocker, Christian; Barrat-Charlaix, Pierre; Socolich, Michael; Kast, Peter; Hilvert, Donald; Monasson, Remi; Cocco, Simona; Weigt, Martin; Ranganathan, Rama (2020-07-24). "An evolution-based model for designing chorismate mutase enzymes". Science. 369 (6502): 440–445. Bibcode:2020Sci...369..440R. doi:10.1126/science.aba3304. ISSN 0036-8075. PMID 32703877. S2CID 220714458.
Rodriguez-Rivas, Juan; Croce, Giancarlo; Muscat, Maureen; Weigt, Martin (2022-01-25). "Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes". Proceedings of the National Academy of Sciences. 119 (4). arXiv:2112.10093. Bibcode:2022PNAS..11913118R. doi:10.1073/pnas.2113118119. ISSN 0027-8424. PMC 8795541. PMID 35022216.
Vigué, Lucile; Croce, Giancarlo; Petitjean, Marie; Ruppé, Etienne; Tenaillon, Olivier; Weigt, Martin (2022-07-12). "Deciphering polymorphism in 61,157 Escherichia coli genomes via epistatic sequence landscapes". Nature Communications. 13 (1): 4030. Bibcode:2022NatCo..13.4030V. doi:10.1038/s41467-022-31643-3. ISSN 2041-1723. PMC 9276797. PMID 35821377.
Feinauer, Christoph; Skwark, Marcin J.; Pagnani, Andrea; Aurell, Erik (9 October 2014). "Improving Contact Prediction along Three Dimensions". PLOS Computational Biology. 10 (10): e1003847. arXiv:1403.0379. Bibcode:2014PLSCB..10E3847F. doi:10.1371/journal.pcbi.1003847. PMC 4191875. PMID 25299132.
Baldassi, Carlo; Zamparo, Marco; Feinauer, Christoph; Procaccini, Andrea; Zecchina, Riccardo; Weigt, Martin; Pagnani, Andrea (24 March 2014). "Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners". PLOS ONE. 9 (3): e92721. arXiv:1404.1240. Bibcode:2014PLoSO...992721B. doi:10.1371/journal.pone.0092721. PMC 3963956. PMID 24663061.
Stein, Richard R.; Marks, Debora S.; Sander, Chris; Chen, Shi-Jie (30 July 2015). "Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models". PLOS Computational Biology. 11 (7): e1004182. Bibcode:2015PLSCB..11E4182S. doi:10.1371/journal.pcbi.1004182. PMC 4520494. PMID 26225866.
Burger, Lukas; van Nimwegen, Erik; Bourne, Philip E. (1 January 2010). "Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments". PLOS Computational Biology. 6 (1): e1000633. Bibcode:2010PLSCB...6E0633B. doi:10.1371/journal.pcbi.1000633. PMC 2793430. PMID 20052271.
Weigt, M.; White, R. A.; Szurmant, H.; Hoch, J. A.; Hwa, T. (30 December 2008). "Identification of direct residue contacts in protein-protein interaction by message passing". Proceedings of the National Academy of Sciences. 106 (1): 67–72. arXiv:0901.1248. Bibcode:2009PNAS..106...67W. doi:10.1073/pnas.0805923106. PMC 2629192. PMID 19116270.
Barton, J. P.; De Leonardis, E.; Coucke, A.; Cocco, S. (21 June 2016). "ACE: adaptive cluster expansion for maximum entropy graphical model inference". Bioinformatics. 32 (20): 3089–3097. doi:10.1093/bioinformatics/btw328. PMID 27329863.
Göbel, Ulrike; Sander, Chris; Schneider, Reinhard; Valencia, Alfonso (April 1994). "Correlated mutations and residue contacts in proteins". Proteins: Structure, Function, and Genetics. 18 (4): 309–317. doi:10.1002/prot.340180402. PMID 8208723. S2CID 14978727.
Dunn, S.D.; Wahl, L.M.; Gloor, G.B. (5 December 2007). "Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction". Bioinformatics. 24 (3): 333–340. doi:10.1093/bioinformatics/btm604. PMID 18057019.
Schug, A.; Weigt, M.; Onuchic, J. N.; Hwa, T.; Szurmant, H. (17 December 2009). "High-resolution protein complexes from integrating genomic information with molecular simulation". Proceedings of the National Academy of Sciences. 106 (52): 22124–22129. Bibcode:2009PNAS..10622124S. doi:10.1073/pnas.0912100106. PMC 2799721. PMID 20018738.
Jarmolinska, Aleksandra I.; Zhou, Qin; Sulkowska, Joanna I.; Morcos, Faruck (11 January 2019). "DCA-MOL: A PyMOL Plugin To Analyze Direct Evolutionary Couplings". Journal of Chemical Information and Modeling. 59 (2): 625–629. doi:10.1021/acs.jcim.8b00690. PMID 30632747. S2CID 58634008.

ncbi.nlm.nih.gov

Morcos, F.; Pagnani, A.; Lunt, B.; Bertolino, A.; Marks, D. S.; Sander, C.; Zecchina, R.; Onuchic, J. N.; Hwa, T.; Weigt, M. (21 November 2011). "Direct-coupling analysis of residue coevolution captures native contacts across many protein families". Proceedings of the National Academy of Sciences. 108 (49): E1293–E1301. arXiv:1110.5223. Bibcode:2011PNAS..108E1293M. doi:10.1073/pnas.1111471108. PMC 3241805. PMID 22106262.
Kamisetty, H.; Ovchinnikov, S.; Baker, D. (5 September 2013). "Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era". Proceedings of the National Academy of Sciences. 110 (39): 15674–15679. Bibcode:2013PNAS..11015674K. doi:10.1073/pnas.1314045110. PMC 3785744. PMID 24009338.
Marks, Debora S.; Colwell, Lucy J.; Sheridan, Robert; Hopf, Thomas A.; Pagnani, Andrea; Zecchina, Riccardo; Sander, Chris; Sali, Andrej (7 December 2011). "Protein 3D Structure Computed from Evolutionary Sequence Variation". PLOS ONE. 6 (12): e28766. Bibcode:2011PLoSO...628766M. doi:10.1371/journal.pone.0028766. PMC 3233603. PMID 22163331.
De Leonardis, Eleonora; Lutz, Benjamin; Ratz, Sebastian; Cocco, Simona; Monasson, Rémi; Schug, Alexander; Weigt, Martin (29 September 2015). "Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction". Nucleic Acids Research. 43 (21): 10444–55. arXiv:1510.03351. doi:10.1093/nar/gkv932. PMC 4666395. PMID 26420827.
Weinreb, Caleb; Riesselman, Adam J.; Ingraham, John B.; Gross, Torsten; Sander, Chris; Marks, Debora S. (May 2016). "3D RNA and Functional Interactions from Evolutionary Couplings". Cell. 165 (4): 963–975. doi:10.1016/j.cell.2016.03.030. PMC 5024353. PMID 27087444.
Ovchinnikov, Sergey; Kamisetty, Hetunandan; Baker, David (1 May 2014). "Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information". eLife. 3: e02030. doi:10.7554/eLife.02030. PMC 4034769. PMID 24842992.
Feinauer, Christoph; Szurmant, Hendrik; Weigt, Martin; Pagnani, Andrea; Keskin, Ozlem (16 February 2016). "Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon". PLOS ONE. 11 (2): e0149166. arXiv:1512.05420. Bibcode:2016PLoSO..1149166F. doi:10.1371/journal.pone.0149166. PMC 4755613. PMID 26882169.
dos Santos, R.N.; Morcos, F.; Jana, B.; Andricopulo, A.D.; Onuchic, J.N. (4 September 2015). "Dimeric interactions and complex formation using direct coevolutionary couplings". Scientific Reports. 5: 13652. Bibcode:2015NatSR...513652D. doi:10.1038/srep13652. PMC 4559900. PMID 26338201.
Uguzzoni, Guido; John Lovis, Shalini; Oteri, Francesco; Schug, Alexander; Szurmant, Hendrik; Weigt, Martin (2017-03-28). "Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis". Proceedings of the National Academy of Sciences. 114 (13): E2662–E2671. arXiv:1703.01246. Bibcode:2017PNAS..114E2662U. doi:10.1073/pnas.1615068114. ISSN 0027-8424. PMC 5380090. PMID 28289198.
Croce, Giancarlo; Gueudré, Thomas; Cuevas, Maria Virginia Ruiz; Keidel, Victoria; Figliuzzi, Matteo; Szurmant, Hendrik; Weigt, Martin (2019-10-21). "A multi-scale coevolutionary approach to predict interactions between protein domains". PLOS Computational Biology. 15 (10): e1006891. Bibcode:2019PLSCB..15E6891C. doi:10.1371/journal.pcbi.1006891. ISSN 1553-7358. PMC 6822775. PMID 31634362.
Ferguson, Andrew L.; Mann, Jaclyn K.; Omarjee, Saleha; Ndung'u, Thumbi; Walker, Bruce D.; Chakraborty, Arup K. (March 2013). "Translating HIV Sequences into Quantitative Fitness Landscapes Predicts Viral Vulnerabilities for Rational Immunogen Design". Immunity. 38 (3): 606–617. doi:10.1016/j.immuni.2012.11.022. PMC 3728823. PMID 23521886.
Figliuzzi, Matteo; Jacquier, Hervé; Schug, Alexander; Tenaillon, Oliver; Weigt, Martin (January 2016). "Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1". Molecular Biology and Evolution. 33 (1): 268–280. doi:10.1093/molbev/msv211. PMC 4693977. PMID 26446903.
Asti, Lorenzo; Uguzzoni, Guido; Marcatili, Paolo; Pagnani, Andrea; Ofran, Yanay (13 April 2016). "Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity". PLOS Computational Biology. 12 (4): e1004870. Bibcode:2016PLSCB..12E4870A. doi:10.1371/journal.pcbi.1004870. PMC 4830580. PMID 27074145.
Rodriguez-Rivas, Juan; Croce, Giancarlo; Muscat, Maureen; Weigt, Martin (2022-01-25). "Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes". Proceedings of the National Academy of Sciences. 119 (4). arXiv:2112.10093. Bibcode:2022PNAS..11913118R. doi:10.1073/pnas.2113118119. ISSN 0027-8424. PMC 8795541. PMID 35022216.
Vigué, Lucile; Croce, Giancarlo; Petitjean, Marie; Ruppé, Etienne; Tenaillon, Olivier; Weigt, Martin (2022-07-12). "Deciphering polymorphism in 61,157 Escherichia coli genomes via epistatic sequence landscapes". Nature Communications. 13 (1): 4030. Bibcode:2022NatCo..13.4030V. doi:10.1038/s41467-022-31643-3. ISSN 2041-1723. PMC 9276797. PMID 35821377.
Feinauer, Christoph; Skwark, Marcin J.; Pagnani, Andrea; Aurell, Erik (9 October 2014). "Improving Contact Prediction along Three Dimensions". PLOS Computational Biology. 10 (10): e1003847. arXiv:1403.0379. Bibcode:2014PLSCB..10E3847F. doi:10.1371/journal.pcbi.1003847. PMC 4191875. PMID 25299132.
Baldassi, Carlo; Zamparo, Marco; Feinauer, Christoph; Procaccini, Andrea; Zecchina, Riccardo; Weigt, Martin; Pagnani, Andrea (24 March 2014). "Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners". PLOS ONE. 9 (3): e92721. arXiv:1404.1240. Bibcode:2014PLoSO...992721B. doi:10.1371/journal.pone.0092721. PMC 3963956. PMID 24663061.
Stein, Richard R.; Marks, Debora S.; Sander, Chris; Chen, Shi-Jie (30 July 2015). "Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models". PLOS Computational Biology. 11 (7): e1004182. Bibcode:2015PLSCB..11E4182S. doi:10.1371/journal.pcbi.1004182. PMC 4520494. PMID 26225866.
Burger, Lukas; van Nimwegen, Erik; Bourne, Philip E. (1 January 2010). "Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments". PLOS Computational Biology. 6 (1): e1000633. Bibcode:2010PLSCB...6E0633B. doi:10.1371/journal.pcbi.1000633. PMC 2793430. PMID 20052271.
Weigt, M.; White, R. A.; Szurmant, H.; Hoch, J. A.; Hwa, T. (30 December 2008). "Identification of direct residue contacts in protein-protein interaction by message passing". Proceedings of the National Academy of Sciences. 106 (1): 67–72. arXiv:0901.1248. Bibcode:2009PNAS..106...67W. doi:10.1073/pnas.0805923106. PMC 2629192. PMID 19116270.
Schug, A.; Weigt, M.; Onuchic, J. N.; Hwa, T.; Szurmant, H. (17 December 2009). "High-resolution protein complexes from integrating genomic information with molecular simulation". Proceedings of the National Academy of Sciences. 106 (52): 22124–22129. Bibcode:2009PNAS..10622124S. doi:10.1073/pnas.0912100106. PMC 2799721. PMID 20018738.

sciencedirect.com

Ekeberg, Magnus; Hartonen, Tuomo; Aurell, Erik (2014-11-01). "Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences". Journal of Computational Physics. 276: 341–356. arXiv:1401.4832. Bibcode:2014JCoPh.276..341E. doi:10.1016/j.jcp.2014.07.024. ISSN 0021-9991. S2CID 15635703.

sciencemag.org

Russ, William P.; Figliuzzi, Matteo; Stocker, Christian; Barrat-Charlaix, Pierre; Socolich, Michael; Kast, Peter; Hilvert, Donald; Monasson, Remi; Cocco, Simona; Weigt, Martin; Ranganathan, Rama (2020-07-24). "An evolution-based model for designing chorismate mutase enzymes". Science. 369 (6502): 440–445. Bibcode:2020Sci...369..440R. doi:10.1126/science.aba3304. ISSN 0036-8075. PMID 32703877. S2CID 220714458.

semanticscholar.org

api.semanticscholar.org

Ekeberg, Magnus; Lövkvist, Cecilia; Lan, Yueheng; Weigt, Martin; Aurell, Erik (11 January 2013). "Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models". Physical Review E. 87 (1): 012707. arXiv:1211.1281. Bibcode:2013PhRvE..87a2707E. doi:10.1103/PhysRevE.87.012707. PMID 23410359. S2CID 27772365.
Ekeberg, Magnus; Hartonen, Tuomo; Aurell, Erik (2014-11-01). "Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences". Journal of Computational Physics. 276: 341–356. arXiv:1401.4832. Bibcode:2014JCoPh.276..341E. doi:10.1016/j.jcp.2014.07.024. ISSN 0021-9991. S2CID 15635703.
Russ, William P.; Figliuzzi, Matteo; Stocker, Christian; Barrat-Charlaix, Pierre; Socolich, Michael; Kast, Peter; Hilvert, Donald; Monasson, Remi; Cocco, Simona; Weigt, Martin; Ranganathan, Rama (2020-07-24). "An evolution-based model for designing chorismate mutase enzymes". Science. 369 (6502): 440–445. Bibcode:2020Sci...369..440R. doi:10.1126/science.aba3304. ISSN 0036-8075. PMID 32703877. S2CID 220714458.
Göbel, Ulrike; Sander, Chris; Schneider, Reinhard; Valencia, Alfonso (April 1994). "Correlated mutations and residue contacts in proteins". Proteins: Structure, Function, and Genetics. 18 (4): 309–317. doi:10.1002/prot.340180402. PMID 8208723. S2CID 14978727.
Jarmolinska, Aleksandra I.; Zhou, Qin; Sulkowska, Joanna I.; Morcos, Faruck (11 January 2019). "DCA-MOL: A PyMOL Plugin To Analyze Direct Evolutionary Couplings". Journal of Chemical Information and Modeling. 59 (2): 625–629. doi:10.1021/acs.jcim.8b00690. PMID 30632747. S2CID 58634008.

worldcat.org

search.worldcat.org

Ekeberg, Magnus; Hartonen, Tuomo; Aurell, Erik (2014-11-01). "Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences". Journal of Computational Physics. 276: 341–356. arXiv:1401.4832. Bibcode:2014JCoPh.276..341E. doi:10.1016/j.jcp.2014.07.024. ISSN 0021-9991. S2CID 15635703.
Uguzzoni, Guido; John Lovis, Shalini; Oteri, Francesco; Schug, Alexander; Szurmant, Hendrik; Weigt, Martin (2017-03-28). "Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis". Proceedings of the National Academy of Sciences. 114 (13): E2662–E2671. arXiv:1703.01246. Bibcode:2017PNAS..114E2662U. doi:10.1073/pnas.1615068114. ISSN 0027-8424. PMC 5380090. PMID 28289198.
Croce, Giancarlo; Gueudré, Thomas; Cuevas, Maria Virginia Ruiz; Keidel, Victoria; Figliuzzi, Matteo; Szurmant, Hendrik; Weigt, Martin (2019-10-21). "A multi-scale coevolutionary approach to predict interactions between protein domains". PLOS Computational Biology. 15 (10): e1006891. Bibcode:2019PLSCB..15E6891C. doi:10.1371/journal.pcbi.1006891. ISSN 1553-7358. PMC 6822775. PMID 31634362.
Russ, William P.; Figliuzzi, Matteo; Stocker, Christian; Barrat-Charlaix, Pierre; Socolich, Michael; Kast, Peter; Hilvert, Donald; Monasson, Remi; Cocco, Simona; Weigt, Martin; Ranganathan, Rama (2020-07-24). "An evolution-based model for designing chorismate mutase enzymes". Science. 369 (6502): 440–445. Bibcode:2020Sci...369..440R. doi:10.1126/science.aba3304. ISSN 0036-8075. PMID 32703877. S2CID 220714458.
Rodriguez-Rivas, Juan; Croce, Giancarlo; Muscat, Maureen; Weigt, Martin (2022-01-25). "Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes". Proceedings of the National Academy of Sciences. 119 (4). arXiv:2112.10093. Bibcode:2022PNAS..11913118R. doi:10.1073/pnas.2113118119. ISSN 0027-8424. PMC 8795541. PMID 35022216.
Vigué, Lucile; Croce, Giancarlo; Petitjean, Marie; Ruppé, Etienne; Tenaillon, Olivier; Weigt, Martin (2022-07-12). "Deciphering polymorphism in 61,157 Escherichia coli genomes via epistatic sequence landscapes". Nature Communications. 13 (1): 4030. Bibcode:2022NatCo..13.4030V. doi:10.1038/s41467-022-31643-3. ISSN 2041-1723. PMC 9276797. PMID 35821377.