Lonnie R. Welch

The paper compares super-enhancer networks in embryonic stem cells and dopaminergic neurons, revealing their structural differences and functional roles in transcriptional regulation.

The paper introduces multiplex-GAM, a ligation-free method for genome-wide chromatin contact mapping, showing it detects different strong contacts compared to Hi-C, particularly involving active genomic regions.

The paper examines 3D genome structures in mouse blastocyst cells to identify lineage-specific chromatin organization differences between epiblast and primitive endoderm cells.

The paper identifies 15 cis-regulatory motifs controlling pollen-specific expression of HRGP genes in Arabidopsis thaliana using RNA-seq and promoter analysis.

The paper develops a motif prediction pipeline to identify regulatory motifs in Brugia malayi, focusing on those involved in the L3-L4 molt stage.

The paper investigates cell-type specific 3D chromatin structures in the brain using immunoGAM, finding TAD melting, neuron-specific contacts, and compartmentalization patterns related to gene expression and neurodegenerative diseases.

The paper introduces a single-cell analysis of Genome Architecture Mapping (GAM) data, revealing intercellular heterogeneity in 3D chromatin topology and developing a geometric model for nuclear structure.

The paper identifies core bioinformatics competencies needed for undergraduate life sciences education based on a national survey and syllabus analysis.

This study identifies barriers to integrating bioinformatics into undergraduate life sciences education through a survey of faculty, highlighting lack of training as the most common issue.