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Found 12 papers, 7 papers with code
H-Packer: Holographic Rotationally Equivariant Convolutional Neural Network for Protein Side-Chain Packing
Accurately modeling protein 3D structure is essential for the design of functional proteins.
Variability in the local and global composition of human T-cell receptor repertoires during thymic development across cell types and individuals
The adaptive immune response relies on T cells that combine phenotypic specialization with diversity of T cell receptors (TCRs) to recognize a wide range of pathogens.
Learning the shape of protein micro-environments with a holographic convolutional neural network
Proteins play a central role in biology from immune recognition to brain activity.
Holographic-(V)AE: an end-to-end SO(3)-Equivariant (Variational) Autoencoder in Fourier Space
Group-equivariant neural networks have emerged as a data-efficient approach to solve classification and regression tasks, while respecting the relevant symmetries of the data.
Design of an optimal combination therapy with broadly neutralizing antibodies to suppress HIV-1
Lastly, we show that a cocktail of three bNAbs is necessary to suppress the chances of viral escape below 1%, and we predict the optimal composition of such a bNAb cocktail.
MINIMALIST: Mutual INformatIon Maximization for Amortized Likelihood Inference from Sampled Trajectories
One class of methods uses data simulated with different parameters to infer models of the likelihood-to-evidence ratio, or equivalently the posterior function.
Deep generative selection models of T and B cell receptor repertoires with soNNia
Additionally to these functional roles, T and B-cell lymphocytes rely on the diversity of their receptor chains to recognize different pathogens.
Dynamics of B-cell repertoires and emergence of cross-reactive responses in COVID-19 patients with different disease severity
Using single-cell sequencing, we verified reactivity of BCRs shared among individuals to SARS-CoV-2 epitopes.
Optimal evolutionary decision-making to store immune memory
The adaptive immune system provides a diverse set of molecules that can mount specific responses against a multitude of pathogens.
SOS: Online probability estimation and generation of T and B cell receptors
Recent advances in modelling VDJ recombination and subsequent selection of T and B cell receptors provide useful tools to analyze and compare immune repertoires across time, individuals, and tissues.
Optimal evolutionary control for artificial selection on molecular phenotypes
Controlling an evolving population is an important task in modern molecular genetics, including directed evolution for improving the activity of molecules and enzymes, in breeding experiments in animals and in plants, and in devising public health strategies to suppress evolving pathogens.
On generative models of T-cell receptor sequences
T-cell receptors (TCR) are key proteins of the adaptive immune system, generated randomly in each individual, whose diversity underlies our ability to recognize infections and malignancies.
Quantitative Methods
