The paper examines immune system changes in individuals recovering from SARS-CoV-2 infection up to 24 weeks post-infection, finding persistent immune and metabolic dysregulation linked to long COVID symptoms.

BMC Medicine · Jan 13, 2022Peer-reviewedGenetic & Genomic Medicine

Seeing the forest through the trees: Identifying functional interactions from Hi-C

Ning Liu, Wai Yee Low, Hamid Alinejad‐Rokny, Stephen Pederson, Timothy J. Sadlon, Simon Charles Barry, James Breen

This paper reviews methods for identifying functional interactions from Hi-C data by classifying approaches into three categories: domain discovery, statistical significance detection, and epigenomic integration.

Epigenetics & Chromatin · Aug 28, 2021Peer-reviewedBioinformatics

3DFAACTS-SNP: Using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of Type-1 Diabetes (T1D) risk

Ning Liu, Timothy J. Sadlon, Ying Y. Wong, Stephen Pederson, James Breen, Simon Charles Barry

This paper introduces 3DFAACTS-SNP, a workflow that identifies T1D risk variants with regulatory mechanisms using Treg-specific epigenomic data, finding 36 candidate SNPs and 51 target genes.

bioRxiv · Sep 4, 2020 · PreprintBioinformatics

Influence of fecal collection conditions and 16S rRNA gene sequencing protocols at two centers on human gut microbiota analysis

Jocelyn Sietsma Penington, Megan A. S. Penno, Katrina Ngui, Nadim J. Ajami, Alexandra J. Roth‐Schulze, Stephen Wilcox, Esther Bandala‐Sanchez, John M. Wentworth, Simon Charles Barry, Cheryl Y. Brown, Jennifer Couper, Joseph F. Petrosino, Anthony T. Papenfuss, Leonard C. Harrison, ENDIA Study Group*, , Peter Vuillermin

This study evaluates how fecal collection conditions and 16S rRNA sequencing protocols affect gut microbiome analysis across two centers, finding that center-specific differences outweigh collection method variations.

Scientific Reports · Mar 6, 2018Peer-reviewedBioinformatics