Deep diversification of an AAV capsid protein by machine learning

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

De novo design of bioactive protein switches

(2019) Robert A. Langan et al.   NATURE

Machine-learning-guided directed evolution for protein engineering

(2019) Kevin K. Yang et al.   NATURE METHODS

Antibody Complementarity Determining Region Design Using High-Capacity Machine Learning

(2019) Ge Liu et al.   BIOINFORMATICS

Unified rational protein engineering with sequence-based deep representation learning

(2019) Ethan C. Alley et al.   NATURE METHODS

Comprehensive AAV capsid fitness landscape reveals a viral gene and enables machine-guided design

(2019) Pierce J. Ogden et al.   SCIENCE

Evolutionary constraints in fitness landscapes

(2018) Luca Ferretti et al.   HEREDITY

Gene therapy comes of age

(2018) Cynthia E. Dunbar et al.   SCIENCE

Efficacy and safety of voretigene neparvovec (AAV2-hRPE65v2) in patients with RPE65 -mediated inherited retinal dystrophy: a randomised, controlled, open-label, phase 3 trial

(2017) Stephen Russell et al.   LANCET

Evolution of a designed protein assembly encapsulating its own RNA genome

(2017) Gabriel L. Butterfield et al.   NATURE

Directing evolution: the next revolution in drug discovery?

(2017) Andrew M. Davis et al.   NATURE REVIEWS DRUG DISCOVERY

Single-Dose Gene-Replacement Therapy for Spinal Muscular Atrophy

(2017) Jerry R. Mendell et al.   NEW ENGLAND JOURNAL OF MEDICINE

Structure-guided evolution of antigenically distinct adeno-associated virus variants for immune evasion

(2017) Longping Victor Tse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Local fitness landscape of the green fluorescent protein

(2016) Karen S. Sarkisyan et al.   NATURE

Pydna: a simulation and documentation tool for DNA assembly strategies using python

(2015) Filipa Pereira et al.   BMC BIOINFORMATICS

Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models

(2014) Travis J Wheeler et al.   BMC BIOINFORMATICS

High thermodynamic stability of parametrically designed helical bundles

(2014) Po-Ssu Huang et al.   SCIENCE

Drawing a high-resolution functional map of adeno-associated virus capsid by massively parallel sequencing

(2014) Kei Adachi et al.   Nature Communications

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

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

A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function

(2012) C. L. Araya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

Worldwide Epidemiology of Neutralizing Antibodies to Adeno‐Associated Viruses

(2009) Roberto Calcedo et al.   JOURNAL OF INFECTIOUS DISEASES

In Vitro and In Vivo Gene Therapy Vector Evolution via Multispecies Interbreeding and Retargeting of Adeno-Associated Viruses

(2008) D. Grimm et al.   JOURNAL OF VIROLOGY