J. O'Connor

inSequio: A Programmable 3D CAD Application for Designing DNA Nanostructures

inSequio is a programmable 3D CAD tool for DNA nanostructure design that combines manual and programmatic editing, enhancing precision, scalability, and efficiency in DNA nanotechnology.

Deep neural network automated segmentation of cellular structures in volume electron microscopy

This paper introduces ASEM, a deep learning pipeline for automated segmentation of cellular structures in electron microscopy, demonstrating its effectiveness in identifying various organelles and membrane structures.

Insight into the evolutionary assemblage of cranial kinesis from a Cretaceous bird

This study reconstructs the skull of an Early Cretaceous bird to understand the evolutionary development of cranial kinesis in early avialans.

Increasing computational protein design literacy through cohort-based learning for undergraduate students

This paper describes a remote cohort-based curriculum for undergraduate students to learn computational protein design, enhancing their research skills and connecting them with the lab.

Sinking a giant: quantitative macroevolutionary comparative methods debunk qualitative assumptions

The paper responds to criticisms of their subaqueous foraging inferences for spinosaurids, showing that additional analyses do not alter their original conclusions.

Zones of Cellular Damage Around Pulsed-Laser Wounds

This study maps wound-induced cellular damage around laser wounds in Drosophila pupae, finding linear relationships between damage radii and wound size.

A new method based on the von Mises-Fisher distribution shows that a minority of liver-localized CD8 T cells display hard-to-detect attraction to Plasmodium-infected hepatocytes

The paper introduces a method using the von Mises-Fisher distribution to analyze T cell attraction to Plasmodium-infected hepatocytes, finding that most liver-localized CD8 T cells search randomly while a minority show weak attraction.

Liver environment-imposed constraints diversify movement strategies of liver-localized CD8 T cells

This study quantifies movement patterns of liver-localized CD8 T cells in mice, showing they perform correlated random walks and Levy flights influenced by liver structure and physiology.

Reply to Li et al. "Is Oculudentavis a bird or even archosaur?"

The paper responds to a claim that Oculudentavis khaungraae is a squamate, arguing that the evidence is inconclusive and the specimen remains enigmatic.

The Biogeography of coelurosaurian theropods and its impact on their evolutionary history

This study quantitatively analyzes coelurosaurian biogeography using evolutionary trees and biogeographic models, finding support for vicariance and dispersal events during the Mesozoic era.

Epigenetic analysis identifies factors driving racial disparity in prostate cancer

The paper analyzes epigenetic differences between African American and Caucasian prostate cancer patients to identify factors contributing to racial disparities in disease aggressiveness and outcomes.