Prospective mapping of viral mutations that escape antibodies used to treat COVID-19

Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

(2020) Daniel Wrapp et al.   SCIENCE

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

(2020) Alexandra C. Walls et al.   CELL

A human neutralizing antibody targets the receptor binding site of SARS-CoV-2

(2020) Rui Shi et al.   NATURE

Structural basis of receptor recognition by SARS-CoV-2

(2020) Jian Shang et al.   NATURE

Protocol and Reagents for Pseudotyping Lentiviral Particles with SARS-CoV-2 Spike Protein for Neutralization Assays

(2020) Katharine H. D. Crawford et al.   Viruses-Basel

Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding

(2020) Tyler N. Starr et al.   CELL

Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies

(2020) Alina Baum et al.   SCIENCE

Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail

(2020) Johanna Hansen et al.   SCIENCE

Fruitful neutralizing antibody pipeline brings hope to defeat SARS-Cov-2

(2020) Alex Renn et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Suptavumab for the Prevention of Medically Attended Respiratory Syncytial Virus Infection in Preterm Infants

(2020) Eric A F Simões et al.   CLINICAL INFECTIOUS DISEASES

Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease

(2020) Tian-hao Zhang et al.   PLoS Genetics

Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition

(2020) Allison J. Greaney et al.   Cell Host & Microbe

Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host

(2020) Bina Choi et al.   NEW ENGLAND JOURNAL OF MEDICINE

OUP accepted manuscript

(2018)   BIOINFORMATICS

Inferring the shape of global epistasis

(2018) Jakub Otwinowski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Parallel evolution of influenza across multiple spatiotemporal scales

(2017) Katherine S Xue et al.   eLife

More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1

(2016) Alison F Feder et al.   eLife

Viraemia suppressed in HIV-1-infected humans by broadly neutralizing antibody 3BNC117

(2015) Marina Caskey et al.   NATURE

Emergence of Ebola Virus Escape Variants in Infected Nonhuman Primates Treated with the MB-003 Antibody Cocktail

(2015) Jeffrey R. Kugelman et al.   Cell Reports

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Stability-mediated epistasis constrains the evolution of an influenza protein

(2013) Lizhi Ian Gong et al.   eLife

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Permissive Secondary Mutations Enable the Evolution of Influenza Oseltamivir Resistance

(2010) J. D. Bloom et al.   SCIENCE