James Taylor

This study identifies conserved and species-specific cis-regulatory elements in human and mouse blood cells using integrative epigenomic analysis and clustering.

The paper investigates the spatiotemporal development of M and L cones in the human retina, finding that retinoic acid signaling promotes M cone fate early in development.

The paper highlights the importance of open data and analytics in responding to public health emergencies, using COVID-19 genomic data to demonstrate the effectiveness of community-driven software tools and infrastructure.

The paper integrates epigenomic and transcriptomic data from mouse hematopoiesis to identify regulatory elements and their dynamics across cell types.

This study uses direct RNA sequencing to characterize the full-length transcriptome of C. elegans, identifying novel splice and 3UTR isoforms and providing a public dataset.

The paper integrates GATA transcription factors and epigenomes in mouse hematopoietic cells using IDEAS to map regulatory landscapes and identify candidate cis-regulatory elements.

The paper introduces Structural Motif (StruM), a DNA representation method that complements sequence-based PWMs for transcription factor binding site analysis.

The paper develops a secure method for accessing distributed biomedical datasets across cloud platforms using OpenID Connect and OAuth2 integrated with Galaxy.

The paper evaluates reproducibility and quality measures for Hi-C data using real and simulated datasets, showing that specialized methods outperform simple correlation analysis.

The paper shows that the B-compartment self-organizes early in the cell cycle before associating with the nuclear lamina.

The paper identifies TADs as button loci that facilitate homologous chromosome pairing and cell-type-specific interchromosomal gene regulation in Drosophila.

The paper shows thyroid hormone signaling controls the temporal switch between S and L/M cone fates in human retinal organoids.

This study shows that lamins maintain TAD-TAD interactions and regulate chromatin domain interactions, which are correlated with transcription changes in mouse ES cells.

The paper presents technologies that make computational reproducibility practical by integrating package management, containerization, and workflow systems.

The paper identifies a genetic variant that alters the stochastic expression of a transcription factor in Drosophila, affecting photoreceptor cell fate and color preference.

QuASAR assesses Hi-C data quality by detecting noise, estimating sequencing returns, and measuring replicate agreement across resolutions.

This study uses chromosome conformation paints to show that LADs form compact regions at the nuclear lamina and are linked to B compartments, with some regions interacting with the A compartment.

The paper describes a hybrid platform integrating predefined workflows with ad hoc analytics to simplify and reproduce the raw data-to-publication process in biomedical research.

The paper compares regulatory sequences between human and mouse to show how regulatory elements are conserved, repurposed, and exapted across species.