Search Results - "Feinauer, Christoph"

Inverse statistical physics of protein sequences: a key issues review by Cocco, Simona, Feinauer, Christoph, Figliuzzi, Matteo, Monasson, Rémi, Weigt, Martin

“…In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their…”
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Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon by Feinauer, Christoph, Szurmant, Hendrik, Weigt, Martin, Pagnani, Andrea

“…Interaction between proteins is a fundamental mechanism that underlies virtually all biological processes. Many important interactions are conserved across a…”
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Interpretable pairwise distillations for generative protein sequence models by Feinauer, Christoph, Meynard-Piganeau, Barthelemy, Lucibello, Carlo

“…Many different types of generative models for protein sequences have been proposed in literature. Their uses include the prediction of mutational effects,…”
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Fast and accurate multivariate Gaussian modeling of protein families: predicting residue contacts and protein-interaction partners by Baldassi, Carlo, Zamparo, Marco, Feinauer, Christoph, Procaccini, Andrea, Zecchina, Riccardo, Weigt, Martin, Pagnani, Andrea

“…In the course of evolution, proteins show a remarkable conservation of their three-dimensional structure and their biological function, leading to strong…”
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Improving contact prediction along three dimensions by Feinauer, Christoph, Skwark, Marcin J, Pagnani, Andrea, Aurell, Erik

“…Correlation patterns in multiple sequence alignments of homologous proteins can be exploited to infer information on the three-dimensional structure of their…”
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The twin peaks of learning neural networks by Demyanenko, Elizaveta, Feinauer, Christoph, Malatesta, Enrico M, Saglietti, Luca

“…Recent works demonstrated the existence of a double-descent phenomenon for the generalization error of neural networks, where highly overparameterized models…”
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Generating interacting protein sequences using domain-to-domain translation by Meynard-Piganeau, Barthelemy, Fabbri, Caterina, Weigt, Martin, Pagnani, Andrea, Feinauer, Christoph

“…Abstract Motivation Being able to artificially design novel proteins of desired function is pivotal in many biological and biomedical applications. Generative…”
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TULIP — a Transformer based Unsupervised Language model for Interacting Peptides and T-cell receptors that generalizes to unseen epitopes by Meynard-Piganeau, Barthelemy, Feinauer, Christoph, Weigt, Martin, Walczak, Aleksandra, Mora, Thierry

“…The accurate prediction of binding between T-cell receptors (TCR) and their cognate epitopes is key to understanding the adaptive immune response and…”
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Zinc Finger Proteins and the 3D Organization of Chromosomes by Feinauer, Christoph J., Hofmann, Andreas, Goldt, Sebastian, Liu, Lei, Máté, Gabriell, Heermann, Dieter W.

“…Zinc finger domains are one of the most common structural motifs in eukaryotic cells, which employ the motif in some of their most important proteins…”
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TULIP: A transformer-based unsupervised language model for interacting peptides and T cell receptors that generalizes to unseen epitopes by Meynard-Piganeau, Barthelemy, Feinauer, Christoph, Weigt, Martin, Walczak, Aleksandra M, Mora, Thierry

“…The accurate prediction of binding between T cell receptors (TCR) and their cognate epitopes is key to understanding the adaptive immune response and…”
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Mutator genomes decay, despite sustained fitness gains, in a long-term experiment with bacteria by Couce, Alejandro, Caudwell, Larissa Viraphong, Feinauer, Christoph, Hindré, Thomas, Feugeas, Jean-Paul, Weigt, Martin, Lenski, Richard E., Schneider, Dominique, Tenaillon, Olivier

“…Understanding the extreme variation among bacterial genomes remains an unsolved challenge in evolutionary biology, despite long-standing debate about the…”
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Improving Contact Prediction along Three Dimensions: e1003847 by Feinauer, Christoph, Skwark, Marcin J, Pagnani, Andrea, Aurell, Erik

“…Correlation patterns in multiple sequence alignments of homologous proteins can be exploited to infer information on the three-dimensional structure of their…”
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Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon: e0149166 by Feinauer, Christoph, Szurmant, Hendrik, Weigt, Martin, Pagnani, Andrea

“…Interaction between proteins is a fundamental mechanism that underlies virtually all biological processes. Many important interactions are conserved across a…”
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Reconstruction of Pairwise Interactions using Energy-Based Models by Feinauer, Christoph, Lucibello, Carlo

“…Pairwise models like the Ising model or the generalized Potts model have found many successful applications in fields like physics, biology, and economics…”
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Uncovering sequence diversity from a known protein structure by Silva, Luca Alessandro, Meynard-Piganeau, Barthelemy, Lucibello, Carlo, Feinauer, Christoph

“…We present InvMSAFold, a method for generating a diverse set of protein sequences that fold into a single structure. For a given structure, InvMSAFold defines…”
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The Mean Dimension of Neural Networks -- What causes the interaction effects? by Hahn, Roman, Feinauer, Christoph, Borgonovo, Emanuele

“…Owen and Hoyt recently showed that the effective dimension offers key structural information about the input-output mapping underlying an artificial neural…”
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The twin peaks of learning neural networks by Demyanenko, Elizaveta, Feinauer, Christoph, Malatesta, Enrico M, Saglietti, Luca

“…Recent works demonstrated the existence of a double-descent phenomenon for the generalization error of neural networks, where highly overparameterized models…”
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Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners: e92721 by Baldassi, Carlo, Zamparo, Marco, Feinauer, Christoph, Procaccini, Andrea, Zecchina, Riccardo, Weigt, Martin, Pagnani, Andrea

“…In the course of evolution, proteins show a remarkable conservation of their three-dimensional structure and their biological function, leading to strong…”
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Context-Aware Prediction of Pathogenicity of Missense Mutations Involved in Human Disease by Feinauer, Christoph, Weigt, Martin

“…Amino-acid substitutions are implicated in a wide range of human diseases, many of which are lethal. Distinguishing such mutations from polymorphisms without…”
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Deep Networks on Toroids: Removing Symmetries Reveals the Structure of Flat Regions in the Landscape Geometry by Pittorino, Fabrizio, Ferraro, Antonio, Perugini, Gabriele, Feinauer, Christoph, Baldassi, Carlo, Zecchina, Riccardo

“…We systematize the approach to the investigation of deep neural network landscapes by basing it on the geometry of the space of implemented functions rather…”
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