Matthew J. O’Meara

A High-Content Pseudotime Framework for Morphological Profiling of Dengue Virus Inhibitors from a Drug-Repurposing Library

This study identifies four DENV inhibitors from a drug library using high-content screening and a pseudotime model to map drug mechanisms onto viral life cycle stages.

Assessing the Generalizability of Machine Learning and Physics-Based Methods with DNA-Encoded Libraries

The paper evaluates ML and physics-based methods for predicting protein-ligand binding using DNA-encoded libraries, finding that no single method consistently generalizes to out-of-distribution chemical space.

A pooled image-based CRISPR screen identifies EAF1 as a T. gondii modulator of ESCRT subversion.

The paper identifies EAF1 as a Toxoplasma gondii effector that modulates ESCRT subversion using a pooled image-based CRISPR screening framework called spaCR.

HSP-1-Specific Nanobodies Alter Chaperone Function in vitro and in vivo

This study develops two nanobodies that specifically target HSP-1, reducing its ATPase activity and protein folding capacity both in vitro and in vivo.

Phenotypic Screening Coupled with AI-Driven Target Deconvolution Identifies α-Terthienyl as a Dual DPP-IV/HSD17β13 Modulator with Efficacy in a Mouse Model of MASLD

Predicting the Structural Impact of Human Alternative Splicing

The paper predicts the structural impact of human alternative splicing using AlphaFold2 on over 11,000 isoforms and identifies structural changes across multiple metrics.

Deep homology and design of proteasome chaperone proteins in Candida auris

The paper uses structural similarity to identify and design proteasome chaperone proteins in Candida auris, showing conservation of function despite sequence divergence.

AMP-activated protein kinase (AMPK) is essential for tendon homeostasis and prevents premature senescence and ectopic calcification

This study shows AMPK1 is essential for tendon health, preventing senescence and calcification through metabolic regulation and ECM remodeling.

LUMIC: Latent diffUsion for Multiplexed Images of Cells

LUMIC generates high-quality cell images using diffusion models and self-supervised learning, outperforming existing methods across cell lines and treatments.

CryptoCEN: A Co-Expression Network for Cryptococcus neoformans reveals novel proteins involved in DNA damage repair

CryptoCEN, a co-expression network for Cryptococcus neoformans, identifies 13 novel DNA damage repair genes with 100% predictive accuracy.

Prioritizing virtual screening with interpretable interaction fingerprints

The paper introduces LUNA, a toolkit that generates interpretable interaction fingerprints for protein-ligand interactions to improve machine learning-based virtual screening.

Valproic Acid-Induced Changes of 4D Nuclear Morphology in Astrocyte Cells

This study quantifies 4D nuclear morphology changes in human astrocytes treated with valproic acid, showing significant size and shape differences by day 7.

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing

Affinity-purification mass spectrometry of 26 SARS-CoV-2 proteins in HEK293T cells yields 332 high-confidence host interactions and 67 druggable human proteins with known compounds.