References
Pierre Barrat-Charlaix, Anna Paola Muntoni, Kai Shimagaki, Martin Weigt, and Francesco Zamponi. Sparse generative modeling via parameter reduction of boltzmann machines: application to protein-sequence families. Physical Review E, 104(2):024407, 2021. URL: https://link.aps.org/doi/10.1103/PhysRevE.104.024407, doi:10.1103/PhysRevE.104.024407.
Francesco Calvanese, Camille N Lambert, Philippe Nghe, Francesco Zamponi, and Martin Weigt. Towards parsimonious generative modeling of RNA families. Nucleic Acids Research, 52(10):5465–5477, 2024. URL: https://doi.org/10.1093/nar/gkae289, doi:10.1093/nar/gkae289.
Magnus Ekeberg, Cecilia Lövkvist, Yueheng Lan, Martin Weigt, and Erik Aurell. Improved contact prediction in proteins: using pseudolikelihoods to infer potts models. Physical Review E, 87(1):012707, 2013. URL: https://link.aps.org/doi/10.1103/PhysRevE.87.012707, doi:10.1103/PhysRevE.87.012707.
Christoph Feinauer, Marcin J. Skwark, Andrea Pagnani, and Erik Aurell. Improving contact prediction along three dimensions. PLOS Computational Biology, 10(10):e1003847, 2014. URL: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003847, doi:10.1371/journal.pcbi.1003847.
Matteo Figliuzzi, Pierre Barrat-Charlaix, and Martin Weigt. How pairwise coevolutionary models capture the collective residue variability in proteins? Molecular Biology and Evolution, 35(4):1018–1027, 2018. URL: https://doi.org/10.1093/molbev/msy007, doi:10.1093/molbev/msy007.
Thomas A. Hopf, John B. Ingraham, Frank J. Poelwijk, Charlotta P. I. Schärfe, Michael Springer, Chris Sander, and Debora S. Marks. Mutation effects predicted from sequence co-variation. Nature Biotechnology, 35(2):128–135, 2017. URL: https://www.nature.com/articles/nbt.3769, doi:10.1038/nbt.3769.
Anna Paola Muntoni, Andrea Pagnani, Martin Weigt, and Francesco Zamponi. adabmDCA: adaptive boltzmann machine learning for biological sequences. BMC Bioinformatics, 22(1):528, 2021. URL: https://doi.org/10.1186/s12859-021-04441-9, doi:10.1186/s12859-021-04441-9.
W R Pearson and D J Lipman. Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences of the United States of America, 85(8):2444–2448, 1988. URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC280013/.