D. Griffith

Dissecting Mechanisms of Ligand Binding and Conformational Changes in the Glutamine-Binding Protein

This study investigates the ligand binding mechanism of GlnBP in E. coli, finding that conformational changes and ligand binding are correlated, and that the induced-fit mechanism is more consistent with the data than conformational selection.

Labelizer: systematic selection of protein residues for covalent fluorophore labeling

Labelizer systematically selects protein residues for covalent fluorophore labeling using a naive Bayes classifier and provides a tool and webserver for this purpose.

Direct prediction of intrinsically disordered protein conformational properties from sequence

This paper develops ALBATROSS, a deep learning model that predicts ensemble conformational properties of intrinsically disordered proteins from sequence, enabling proteome-wide analysis.

Physiological responses to drought stress and recovery reflect differences in leaf function and anatomy among grass lineages

This study compares drought responses across 12 grass species, finding lineage-specific physiological and anatomical strategies affecting drought tolerance and recovery.

The kinetic landscape of human transcription factors

This study develops CRISPRburst to measure how 92 human transcription factors affect transcriptional bursting kinetics and identifies kinetic signatures that classify TFs and predict their regulatory roles.

Hypoxia shapes the immune landscape in lung injury promoting inflammation persistence

This study shows hypoxia suppresses type I interferon signaling in ALI, leading to monocytopenia and unchecked inflammation, which can be mitigated by CSF1 administration.

Ex vivo and in vivo evidence that cigarette smoke-exposed T regulatory cells impair host immunity against Mycobacterium tuberculosis

This study shows that cigarette smoke-exposed T regulatory cells impair macrophage control of Mycobacterium tuberculosis infection in vitro and in vivo.

A Marmoset Model for Mycobacterium avium Complex Pulmonary Disease

This study infects marmosets with M. intracellulare to model M. avium complex pulmonary disease, showing infection, immune response, and radiographic changes similar to human disease.

The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA

This study investigates the SARS-CoV-2 nucleocapsid protein's dynamics, disorder, and RNA phase separation using single-molecule spectroscopy and simulations, revealing its multivalent RNA binding properties and phase separation behavior.

Lineage Functional Types (LFTs): Characterizing functional diversity to enhance the representation of ecological behavior in Earth System Models

The paper develops lineage-based functional types (LFTs) to improve Earth System Models by incorporating phylogenetic relatedness and trait variation in grasses.

Functional diversification enabled grassy biomes to fill global climate space

The paper maps global grassy biomes and identifies key traits and lineages driving their distribution across climates.