In silico proof of principle of machine learning-based antibody design at unconstrained scale

Machine Learning for Biologics: Opportunities for Protein Engineering, Developability, and Formulation

(2021) Harini Narayanan et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Antibody design using LSTM based deep generative model from phage display library for affinity maturation

(2021) Koichiro Saka et al.   Scientific Reports

Low-N protein engineering with data-efficient deep learning

(2021) Surojit Biswas et al.   NATURE METHODS

Animal Immunization, in Vitro Display Technologies, and Machine Learning for Antibody Discovery

(2021) Andreas H. Laustsen et al.   TRENDS IN BIOTECHNOLOGY

Applications of Machine and Deep Learning in Adaptive Immunity

(2021) Margarita Pertseva et al.   Annual Review of Chemical and Biomolecular Engineering

Protein design and variant prediction using autoregressive generative models

(2021) Jung-Eun Shin et al.   Nature Communications

A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding

(2021) Rahmad Akbar et al.   Cell Reports

Optimization of therapeutic antibodies by predicting antigen specificity from antibody sequence via deep learning

(2021) Derek M. Mason et al.   Nature Biomedical Engineering

The challenges with developing therapeutic monoclonal antibodies for pandemic application

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Differentiable biology: using deep learning for biophysics-based and data-driven modeling of molecular mechanisms

(2021) Mohammed AlQuraishi et al.   NATURE METHODS

Factors of Influence for Transfer Learning Across Diverse Appearance Domains and Task Types

(2021) Thomas Mensink et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Learning Context-aware Structural Representations to Predict Antigen and Antibody Binding Interfaces

(2020) Srivamshi Pittala et al.   BIOINFORMATICS

immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking

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Improved Prediction of MHC II Antigen Presentation through Integration and Motif Deconvolution of Mass Spectrometry MHC Eluted Ligand Data

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A human monoclonal antibody blocking SARS-CoV-2 infection

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Research and Development on Therapeutic Agents and Vaccines for COVID-19 and Related Human Coronavirus Diseases

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Immune Literacy: Reading, Writing, and Editing Adaptive Immunity

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Five computational developability guidelines for therapeutic antibody profiling

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Validation strategies for target prediction methods

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Induction of broadly neutralizing antibodies in Germinal Centre simulations

(2018) Philippe A Robert et al.   CURRENT OPINION IN BIOTECHNOLOGY

Computational design of antibodies

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High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis

(2018) Derek M Mason et al.   NUCLEIC ACIDS RESEARCH

Fréchet ChemNet Distance: A Metric for Generative Models for Molecules in Drug Discovery

(2018) Kristina Preuer et al.   Journal of Chemical Information and Modeling

Observed Antibody Space: A Resource for Data Mining Next-Generation Sequencing of Antibody Repertoires

(2018) Aleksandr Kovaltsuk et al.   JOURNAL OF IMMUNOLOGY

The impact of imbalanced training data on machine learning for author name disambiguation

(2018) Jinseok Kim et al.   SCIENTOMETRICS

Learning the High-Dimensional Immunogenomic Features That Predict Public and Private Antibody Repertoires

(2017) Victor Greiff et al.   JOURNAL OF IMMUNOLOGY

Next generation antibody drugs: pursuit of the 'high-hanging fruit'

(2017) Paul J. Carter et al.   NATURE REVIEWS DRUG DISCOVERY

Systems Analysis Reveals High Genetic and Antigen-Driven Predetermination of Antibody Repertoires throughout B Cell Development

(2017) Victor Greiff et al.   Cell Reports

The influence of the negative-positive ratio and screening database size on the performance of machine learning-based virtual screening

(2017) Rafał Kurczab et al.   PLoS One

An R package for statistical provenance analysis

(2016) Pieter Vermeesch et al.   SEDIMENTARY GEOLOGY

A Public Database of Memory and Naive B-Cell Receptor Sequences

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Biopython: freely available Python tools for computational molecular biology and bioinformatics

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