Jason P. Gleghorn

Protify benchmarks protein language models across tasks and evaluation settings, revealing task dependence and homology leakage in model performance.

This study shows that blocking lymphocyte entry into lymph nodes increases intracellular drug concentration for some antiretroviral drugs, but not others, due to changes in extracellular fluid volume.

This study investigates VPS34 activation in pulmonary arterial vascular smooth muscle cells in pulmonary hypertension, finding it drives proliferation and fibrotic remodeling, and shows SAR405 inhibition reduces disease progression.

The paper shows that protein language models can exploit taxonomic information rather than true interaction features in PPI datasets, leading to inflated performance.

BEADS provides a semi-automated image analysis pipeline for 3D fibrin angiogenesis assays, enabling co-culture and directionality analysis with improved efficiency and accuracy.

This paper introduces a modular flow chamber that independently controls substrate stiffness and fluid shear stress to study their combined effects on cell behavior.

This paper develops a high-fidelity 3D reconstruction pipeline for murine lymph nodes, enabling accurate modeling of drug transport and immune cell dynamics.

This paper presents a confocal-compatible workflow for 3D anatomical reconstruction of murine lymph nodes using vibratome sectioning and immunostaining.

This paper introduces a modular, reusable, and perfusion-ready microphysiological system to simplify organ-on-chip technology for broader use.

This paper develops a microphysiologic model of the cervical epithelium that replicates microbial, immunologic, and pathogenic features of STIs caused by Chlamydia and Neisseria.

This study uses lipid nanoparticles to deliver cytokine mRNA to placental cells, inducing anti-inflammatory responses and revealing dose-dependent polarization of macrophages.

This paper develops a method to create serially perfusable multiscale capillary beds in vitro for studying vascular biology and integration into organoid and organ-on-a-chip models.

The paper uses photocrosslinking to alter tissue stiffness in embryonic lungs and shows it inhibits epithelial budding morphogenesis.

The paper introduces Annotation Vocabulary to enhance protein embeddings using structured ontologies, demonstrating its effectiveness through various downstream tasks and generative models.

The paper develops a cell culture insert model with hydrogels to study transplacental transport by incorporating stromal properties.

This paper develops a microphysiological system to spatially pattern ECM composition and stromal cells in a 3D microchannel, demonstrating spatial control of cell interactions and signaling gradients.

This paper introduces cdsBERT, a protein language model trained on codon sequences, which outperforms amino acid-based models in enzyme prediction and reveals codon usage patterns in embeddings.

This paper demonstrates that large language models can predict protein-protein interactions with high accuracy using synthetic data and fine-tuned models.

This paper develops a computational method to infer intercellular gene regulatory networks between different cell types using fluorescence reporter data and validates it through in silico case studies.