A. M. Phillips

Protein sequence landscapes are not so simple: on reference-free versus reference-based inference

The paper shows that reference-free analysis is equivalent to reference-based methods, leading to identical landscapes but different interpretations of epistasis.

Five inhibitory receptors display distinct vesicular distributions in T cells

The paper characterizes the subcellular distributions of five inhibitory receptors in T cells and finds they are distinct, with CTLA-4 preferentially associating with lysosomal-derived vesicles.

Hierarchical sequence-affinity landscapes shape the evolution of breadth in an anti-influenza receptor binding site antibody

This study characterizes the hierarchical epistasis between heavy and light chain mutations in an anti-influenza bnAb, showing how such interactions shape the evolution of broad antigen affinity.

The landscape of antibody binding affinity in SARS-CoV-2 Omicron BA.1 evolution

The paper maps how mutations in the SARS-CoV-2 Omicron BA.1 RBD affect antibody binding affinity through systematic analysis of 32,768 genotypes against four monoclonal antibodies.

Compensatory epistasis maintains ACE2 affinity in SARS-CoV-2 Omicron BA.1

This study identifies compensatory epistasis in SARS-CoV-2 Omicron BA.1 that maintains ACE2 affinity despite antibody-escape mutations.

MAVS mediates a protective immune response in the brain to Rift Valley fever virus

This study shows that MAVS is critical for microglial antiviral responses in the brain during RVFV infection, reducing viral burden and mortality.

Development of Potent and Effective Synthetic SARS-CoV-2 Neutralizing Nanobodies

This paper identifies and characterizes potent SARS-CoV-2 neutralizing nanobodies that block viral entry and show efficacy in vivo.

Dynamics and variability in the pleiotropic effects of adaptation in laboratory budding yeast populations

The paper studies how pleiotropic effects of adaptation in yeast change over time and vary across environments, finding increasing variability and overlapping contributions of chance and contingency.

Binding affinity landscapes constrain the evolution of broadly neutralizing anti-influenza antibodies

This study measures binding affinity landscapes of two influenza bnAbs to understand their evolutionary pathways and how they acquire breadth.

Molecular and cell biological analysis of SwrB in Bacillus subtilis

This study investigates SwrB's role in Bacillus subtilis flagellar type III secretion, showing it acts sub-stoichiometrically and transiently, with specific residues critical for its function.

The Host Cell's Endoplasmic Reticulum Proteostasis Network Profoundly Shapes the Protein Sequence Space Accessible to HIV Envelope

This study shows that upregulating the host ER proteostasis network via the UPR reduces mutational tolerance of HIV Env, with some regions becoming more tolerant, suggesting host proteostasis influences HIV adaptation.

The Genetic Basis of Differential Autodiploidization in Evolving Yeast Populations

This study identifies SSD1 gene variants as the genetic determinant of differential autodiploidization rates in yeast strains.

Phenotypic and molecular evolution across 10,000 generations in laboratory budding yeast populations

This study tracks phenotypic and molecular evolution in 205 yeast populations over 10,000 generations, revealing patterns of declining adaptability, mutation accumulation, and genetic parallelism.