Výsledky vyhľadávania - "Bravi, Barbara"

Development and use of machine learning algorithms in vaccine target selection Autor Bravi, Barbara

“…Computer-aided discovery of vaccine targets has become a cornerstone of rational vaccine design. In this article, I discuss how Machine Learning (ML) can…”
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Neoantigen quality predicts immunoediting in survivors of pancreatic cancer Autor Łuksza, Marta, Sethna, Zachary M., Rojas, Luis A., Lihm, Jayon, Bravi, Barbara, Elhanati, Yuval, Soares, Kevin, Amisaki, Masataka, Dobrin, Anton, Hoyos, David, Guasp, Pablo, Zebboudj, Abderezak, Yu, Rebecca, Chandra, Adrienne Kaya, Waters, Theresa, Odgerel, Zagaa, Leung, Joanne, Kappagantula, Rajya, Makohon-Moore, Alvin, Johns, Amber, Gill, Anthony, Gigoux, Mathieu, Wolchok, Jedd, Merghoub, Taha, Sadelain, Michel, Patterson, Erin, Monasson, Remi, Mora, Thierry, Walczak, Aleksandra M., Cocco, Simona, Iacobuzio-Donahue, Christine, Greenbaum, Benjamin D., Balachandran, Vinod P.

“…Cancer immunoediting 1 is a hallmark of cancer 2 that predicts that lymphocytes kill more immunogenic cancer cells to cause less immunogenic clones to dominate…”
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Direct coupling analysis of epistasis in allosteric materials Autor Bravi, Barbara, Ravasio, Riccardo, Brito, Carolina, Wyart, Matthieu

“…In allosteric proteins, the binding of a ligand modifies function at a distant active site. Such allosteric pathways can be used as target for drug design,…”
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A transfer-learning approach to predict antigen immunogenicity and T-cell receptor specificity Autor Bravi, Barbara, Di Gioacchino, Andrea, Fernandez-de-Cossio-Diaz, Jorge, Walczak, Aleksandra M, Mora, Thierry, Cocco, Simona, Monasson, Rémi

“…Antigen immunogenicity and the specificity of binding of T-cell receptors to antigens are key properties underlying effective immune responses. Here we propose…”
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Probing T-cell response by sequence-based probabilistic modeling Autor Bravi, Barbara, Balachandran, Vinod P., Greenbaum, Benjamin D., Walczak, Aleksandra M., Mora, Thierry, Monasson, Rémi, Cocco, Simona

“…With the increasing ability to use high-throughput next-generation sequencing to quantify the diversity of the human T cell receptor (TCR) repertoire, the…”
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Benchmarking solutions to the T-cell receptor epitope prediction problem: IMMREP22 workshop report Autor Meysman, Pieter, Barton, Justin, Bravi, Barbara, Cohen-Lavi, Liel, Karnaukhov, Vadim, Lilleskov, Elias, Montemurro, Alessandro, Nielsen, Morten, Mora, Thierry, Pereira, Paul, Postovskaya, Anna, Martínez, María Rodríguez, Fernandez-de-Cossio-Diaz, Jorge, Vujkovic, Alexandra, Walczak, Aleksandra M., Weber, Anna, Yin, Rose, Eugster, Anne, Sharma, Virag

“…Many different solutions to predicting the cognate epitope target of a T-cell receptor (TCR) have been proposed. However several questions on the advantages…”
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ANTIPASTI: Interpretable prediction of antibody binding affinity exploiting normal modes and deep learning Autor Michalewicz, Kevin, Barahona, Mauricio, Bravi, Barbara

“…The high binding affinity of antibodies toward their cognate targets is key to eliciting effective immune responses, as well as to the use of antibodies as…”
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The unbearable lightness of restricted Boltzmann machines: Theoretical insights and biological applications Autor di Sarra, Giovanni, Bravi, Barbara, Roudi, Yasser

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Systematic model reduction captures the dynamics of extrinsic noise in biochemical subnetworks Autor Bravi, Barbara, Rubin, Katy J, Sollich, Peter

“…We consider the general problem of describing the dynamics of subnetworks of larger biochemical reaction networks, e.g., protein interaction networks involving…”
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RBM-MHC: A Semi-Supervised Machine-Learning Method for Sample-Specific Prediction of Antigen Presentation by HLA-I Alleles Autor Bravi, Barbara, Tubiana, Jérôme, Cocco, Simona, Monasson, Rémi, Mora, Thierry, Walczak, Aleksandra M

“…The recent increase of immunopeptidomics data, obtained by mass spectrometry or binding assays, opens up possibilities for investigating endogenous antigen…”
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Path integral approaches to subnetwork description and inference Autor Bravi, Barbara

“…Path integral formalism is a powerful tool borrowed from theoretical physics to build dynamical descriptions, yet its potential is largely unexplored in the…”
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Responses to auxin signals: an operating principle for dynamical sensitivity yet high resilience Autor Grigolon, S., Bravi, B., Martin, O. C.

“…Plants depend on the signalling of the phytohormone auxin for their development and for responding to environmental perturbations. The associated biomolecular…”
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Computational design of target-specific linear peptide binders with TransformerBeta Autor Zhao, Haowen, Aprile, Francesco A, Bravi, Barbara

“…The computational prediction and design of peptide binders targeting specific linear epitopes is crucial in biological and biomedical research, yet it remains…”
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ANTIPASTI: interpretable prediction of antibody binding affinity exploiting Normal Modes and Deep Learning Autor Michalewicz, Kevin, Barahona, Mauricio, Bravi, Barbara

“…The high binding affinity of antibodies towards their cognate targets is key to eliciting effective immune responses, as well as to the use of antibodies as…”
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Statistical physics approaches to subnetwork dynamics in biochemical systems Autor Bravi, Barbara, Sollich, Peter

“…We apply a Gaussian variational approximation to model reduction in large biochemical networks of unary and binary reactions. We focus on a small subset of…”
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Critical scaling in hidden state inference for linear Langevin dynamics Autor Bravi, Barbara, Sollich, Peter

“…We consider the problem of inferring the dynamics of unknown (i.e. hidden) nodes from a set of observed trajectories and study analytically the average…”
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Systematic model reduction captures the dynamics of extrinsic noise in biochemical subnetworks Autor Bravi, Barbara, Rubin, Katy J, Sollich, Peter

“…We consider the general problem of describing the dynamics of subnetworks of larger biochemical reaction networks, e.g. protein interaction networks involving…”
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Inference for dynamics of continuous variables: the Extended Plefka Expansion with hidden nodes Autor Bravi, Barbara, Sollich, Peter

“…We consider the problem of a subnetwork of observed nodes embedded into a larger bulk of unknown (i.e. hidden) nodes, where the aim is to infer these hidden…”
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Wavelet-Based Density Estimation for Persistent Homology Autor Häberle, Konstantin, Bravi, Barbara, Monod, Anthea

“…Persistent homology is a central methodology in topological data analysis that has been successfully implemented in many fields and is becoming increasingly…”
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ANTIPASTI: interpretable prediction of antibody binding affinity exploiting Normal Modes and Deep Learning Autor Michalewicz, Kevin, Barahona, Mauricio, Bravi, Barbara

“…The high binding affinity of antibodies towards their cognate targets is key to eliciting effective immune responses, as well as to the use of antibodies as…”
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