J. Yates

Repeat modules and N-linked glycans define structure and antigenicity of a critical enterotoxigenic E. coli adhesin

This study identifies key structural and glycosylation features of EtpA, an ETEC adhesin, and shows how antibodies target different epitopes to influence immune responses and pathogen-host interactions.

Effect of shipping on the microbiome of donor mice used to reconstitute germ-free recipients

The paper investigates how shipping affects the gut microbiome of donor mice and shows that shipping-induced changes are transmitted to germ-free recipients, though supplier-origin effects remain more prominent.

Open Iris - An Open Source Framework for Video-Based Eye-Tracking Research and Development

OpenIris provides an open-source framework for video-based eye-tracking with customizable plugins and high frame rates, addressing limitations in commercial solutions.

Comparative host-pathogen dynamics of Snake Fungal Disease in sympatric species of water snakes (Nerodia)

The paper surveys Ophidiomyces ophiodiicola prevalence in sympatric water snake species in Texas and finds higher infection rates in adults and the rare Brazos water snake.

Targeting cellular DNA damage responses in cancer: An in vitro-calibrated agent-based model simulating monolayer and spheroid treatment responses to ATR-inhibiting drugs

This paper develops an agent-based model calibrated with in vitro data to simulate cancer cell responses to ATR-inhibiting drugs in monolayers and spheroids, and compares its predictions to in vivo xenograft data.

A confirmation bias in perceptual decision-making due to hierarchical approximate inference

This paper explains perceptual decision-making biases using a hierarchical approximate inference model, showing how temporal bias changes with stimulus statistics in a visual discrimination task.

A spatially resolved mechanistic growth law for cancer drug development.

The paper presents a mechanistic tumor growth model for drug development that predicts spatial cell subpopulation distributions and integrates with existing pre-clinical workflows.

Platypus: an open-access software for integrating lymphocyte single-cell immune repertoires with transcriptomes

Platypus integrates single-cell immune repertoires with transcriptomes to analyze lymphocyte features and transcriptional profiles in convalescent COVID-19 patients.

Endpoint and Epitope-specific Antibody Responses as Correlates of Vaccine-mediated Protection of Mice against Ricin Toxin

This paper develops a multivariate model using antibody endpoint titers and epitope-specific inhibition values to predict vaccine-mediated protection against ricin toxin in mice.