I. R. Humphreys

Generalized Biomolecular Modeling and Design with RoseTTAFold All-Atom

This paper introduces RFAA and RFdiffusionAA, models that can predict and design complex biomolecular assemblies including proteins, nucleic acids, small molecules, and covalent modifications.

Genetic manipulation of candidate phyla radiation bacteria provides functional insights into microbial dark matter

The paper genetically manipulates Saccharibacteria from the CPR to study their role in epibiotic growth and develops bioinformatic resources for their analysis.

Structures of core eukaryotic protein complexes

The paper uses coevolution analysis and deep learning to model core eukaryotic protein complexes in yeast, identifying 104 new assemblies and structurally characterizing 608 previously unknown complexes.

ADNKA overcomes SARS-CoV2-mediated NK cell inhibition through non-spike antibodies

This study identifies ADNKA as a mechanism by which SARS-CoV-2-infected cells evade NK cell inhibition, showing that non-spike antibodies drive sustained NK activation and cytokine production.

Optimal CD8+ T-cell memory formation following subcutaneous cytomegalovirus infection requires virus replication but not early dendritic cell responses

Interspecies comparative metagenomics reveals correlated gut microbiome functional capacities among vertebrates

This study compares gut metagenomes across 10 vertebrate species to identify conserved and variable microbial functional pathways, showing general similarity to human gut microbiomes but with notable differences in disease-related pathways.

An integrated gene catalog of the zebrafish gut microbiome reveals significant homology with mammalian microbiomes

The paper constructs a zebrafish gut microbiome gene catalog, showing significant homology with human and mouse microbiomes despite taxonomic differences.