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

The Molecular Mechanisms That Underlie the Immune Biology of Anti-drug Antibody Formation Following Treatment With Monoclonal Antibodies

(2020) Anna Vaisman-Mentesh et al.   Frontiers in Immunology

Large-scale network analysis reveals the sequence space architecture of antibody repertoires

(2019) Enkelejda Miho et al.   Nature Communications

Net charge of antibody complementarity-determining regions is a key predictor of specificity

(2019) Lilia A Rabia et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Five computational developability guidelines for therapeutic antibody profiling

(2019) Matthew I. J. Raybould et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering a HER2-specific antibody–drug conjugate to increase lysosomal delivery and therapeutic efficacy

(2019) Jeffrey C. Kang et al.   NATURE BIOTECHNOLOGY

Machine learning-assisted directed protein evolution with combinatorial libraries

(2019) Zachary Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Logomaker: beautiful sequence logos in Python

(2019) Ammar Tareen et al.   BIOINFORMATICS

Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning

(2019) P. Gainza et al.   NATURE METHODS

NGL viewer: web-based molecular graphics for large complexes

(2018) Alexander S Rose et al.   BIOINFORMATICS

Improved methods for predicting peptide binding affinity to MHC class II molecules

(2018) Kamilla Kjaergaard Jensen et al.   IMMUNOLOGY

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

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

Deep learning in biomedicine

(2018) Michael Wainberg et al.   NATURE BIOTECHNOLOGY

Deep generative models of genetic variation capture the effects of mutations

(2018) Adam J. Riesselman et al.   NATURE METHODS

In vitro and in silico assessment of the developability of a designed monoclonal antibody library

(2018) Adriana-Michelle Wolf Pérez et al.   mAbs

Deep learning using tumor HLA peptide mass spectrometry datasets improves neoantigen identification

(2018) Brendan Bulik-Sullivan et al.   NATURE BIOTECHNOLOGY

Avidity-based binding to HER2 results in selective killing of HER2-overexpressing cells by anti-HER2/CD3

(2018) Dionysos Slaga et al.   Science Translational Medicine

Deep learning of the regulatory grammar of yeast 5′ untranslated regions from 500,000 random sequences

(2017) Josh T. Cuperus et al.   GENOME RESEARCH

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

(2017) Victor Greiff et al.   JOURNAL OF IMMUNOLOGY

Antidrug Antibodies in Patients Treated with Alirocumab

(2017) Eli M. Roth et al.   NEW ENGLAND JOURNAL OF MEDICINE

Biophysical properties of the clinical-stage antibody landscape

(2017) Tushar Jain et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization

(2017) Claire N. Bedbrook et al.   PLoS Computational Biology

Optimal classifier for imbalanced data using Matthews Correlation Coefficient metric

(2017) Sabri Boughorbel et al.   PLoS One

Molecular basis of high viscosity in concentrated antibody solutions: Strategies for high concentration drug product development

(2016) Dheeraj S. Tomar et al.   mAbs

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

Antidrug Antibody Formation in Oncology: Clinical Relevance and Challenges

(2016) Emilie M.J. van Brummelen et al.   ONCOLOGIST

Immunogenomic engineering of a plug-and-(dis)play hybridoma platform

(2016) Mark Pogson et al.   Nature Communications

The CamSol Method of Rational Design of Protein Mutants with Enhanced Solubility

(2015) Pietro Sormanni et al.   JOURNAL OF MOLECULAR BIOLOGY

Deep learning

(2015) Yann LeCun et al.   NATURE

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

MiXCR: software for comprehensive adaptive immunity profiling

(2015) Dmitriy A Bolotin et al.   NATURE METHODS

Methods for the directed evolution of proteins

(2015) Michael S. Packer et al.   NATURE REVIEWS GENETICS

Effective Optimization of Antibody Affinity by Phage Display Integrated with High-Throughput DNA Synthesis and Sequencing Technologies

(2015) Dongmei Hu et al.   PLoS One

Augmented Binary Substitution: Single-pass CDR germ-lining and stabilization of therapeutic antibodies

(2015) Sue Townsend et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development of a semi-automated high throughput transient transfection system

(2014) Aaron B. Bos et al.   JOURNAL OF BIOTECHNOLOGY

Comprehensive Evaluation and Optimization of Amplicon Library Preparation Methods for High-Throughput Antibody Sequencing

(2014) Ulrike Menzel et al.   PLoS One

In silico selection of therapeutic antibodies for development: Viscosity, clearance, and chemical stability

(2014) Vikas K. Sharma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Innovation by homologous recombination

(2013) Devin L Trudeau et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Navigating the protein fitness landscape with Gaussian processes

(2013) P. A. Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing

(2012) Timothy A Whitehead et al.   NATURE BIOTECHNOLOGY

Functional classification of class II human leukocyte antigen (HLA) molecules reveals seven different supertypes and a surprising degree of repertoire sharing across supertypes

(2011) Jason Greenbaum et al.   IMMUNOGENETICS

Antibody recycling by engineered pH-dependent antigen binding improves the duration of antigen neutralization

(2010) Tomoyuki Igawa et al.   NATURE BIOTECHNOLOGY

High-resolution mapping of protein sequence-function relationships

(2010) Douglas M Fowler et al.   NATURE METHODS

How to improve R&D productivity: the pharmaceutical industry's grand challenge

(2010) Steven M. Paul et al.   NATURE REVIEWS DRUG DISCOVERY

A systematic analysis of performance measures for classification tasks

(2009) Marina Sokolova et al.   INFORMATION PROCESSING & MANAGEMENT