H. K. Haddox

Deep mutational scanning reveals functional constraints and antigenic variability of Lassa virus glycoprotein complex

Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin

The paper maps how HA mutations affect neutralization by serum from different age groups, showing age-dependent antigenic effects and implications for viral evolution.

Small-molecule binding and sensing with a designed protein family

This paper designs a protein family that binds and senses small molecules using deep learning and physics-based methods, achieving nanomolar sensitivity for cortisol.

De Novo Design of Immunoglobulin-like Domains

This paper introduces design rules for immunoglobulin-like domains and demonstrates the de novo creation of stable, functional scaffolds with improved biophysical properties.

Large-scale design and refinement of stable proteins using sequence-only models

The paper presents two neural network models for predicting and generating stable proteins based on amino acid sequences, showing improved stability in both expert-designed and model-generated proteins.

Complete functional mapping of infection- and vaccine-elicited antibodies against the fusion peptide of HIV

The paper maps functional epitopes of antibodies targeting HIV Env fusion peptide by analyzing mutations affecting neutralization, revealing differences between vaccine- and infection-elicited antibodies.

Mapping mutational effects along the evolutionary landscape of HIV envelope

The paper quantifies how amino-acid mutations affect HIV Env protein fitness across two diverged viral strains, finding most sites have conserved preferences but some show shifted mutational tolerance.

Comprehensive mapping of HIV-1 escape from a broadly neutralizing antibody

This study maps HIV-1 escape mutations from a broadly neutralizing antibody by quantifying the effect of all single amino-acid mutations on viral sensitivity.