Biomedical subjects

Shawn Hoon

Publications and source records attributed to Shawn Hoon.

3 recordsLinked to original sources

PubMed2025

Impact of polymorphisms on gene expression and splicing in response to exercise and diet-induced weight loss in human skeletal muscle tissues.

Weight loss through exercise and diet reduces the risk of type 2 diabetes, but the genetic regulation of gene expression and splicing in response to weight loss remains unclear in humans. We collected clinical data and skeletal muscle biopsies from 54 overweight/obese Asian individuals before and after a 16-week lifestyle intervention, which resulted in an average of ∼10% weight loss, accompanied by an ∼30% increase in insulin-stimulated glucose uptake. Improvements were observed in 118 of 252 clinical traits and six blood lipids. Transcriptomic analysis of paired skeletal muscle biopsies identified 505 differentially expressed genes enriched in mitochondrial function and insulin sensitivity. Thousands of muscle-specific expression/splicing quantitative trait loci (e/sQTLs) were detected pre- and post-intervention, including hundreds of lifestyle-responsive e/sQTLs. Notably, approximately 4.2% of eQTLs and 7.3% of sQTLs showed Asian specificity. Joint analysis with genome-wide association study (GWAS) identified 16 putative metabolic risk genes. Our study reveals gene-by-lifestyle interactions and how lifestyle modulates gene regulation in skeletal muscle.

Humans↗

PubMed2003

Biopipe: a flexible framework for protocol-based bioinformatics analysis.

We identify several challenges facing bioinformatics analysis today. Firstly, to fulfill the promise of comparative studies, bioinformatics analysis will need to accommodate different sources of data residing in a federation of databases that, in turn, come in different formats and modes of accessibility. Secondly, the tsunami of data to be handled will require robust systems that enable bioinformatics analysis to be carried out in a parallel fashion. Thirdly, the ever-evolving state of bioinformatics presents new algorithms and paradigms in conducting analysis. This means that any bioinformatics framework must be flexible and generic enough to accommodate such changes. In addition, we identify the need for introducing an explicit protocol-based approach to bioinformatics analysis that will lend rigorousness to the analysis. This makes it easier for experimentation and replication of results by external parties. Biopipe is designed in an effort to meet these goals. It aims to allow researchers to focus on protocol design. At the same time, it is designed to work over a compute farm and thus provides high-throughput performance. A common exchange format that encapsulates the entire protocol in terms of the analysis modules, parameters, and data versions has been developed to provide a powerful way in which to distribute and reproduce results. This will enable researchers to discuss and interpret the data better as the once implicit assumptions are now explicitly defined within the Biopipe framework.

Amino Acid Sequence↗

PubMed2002

Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes.

The compact genome of Fugu rubripes has been sequenced to over 95% coverage, and more than 80% of the assembly is in multigene-sized scaffolds. In this 365-megabase vertebrate genome, repetitive DNA accounts for less than one-sixth of the sequence, and gene loci occupy about one-third of the genome. As with the human genome, gene loci are not evenly distributed, but are clustered into sparse and dense regions. Some "giant" genes were observed that had average coding sequence sizes but were spread over genomic lengths significantly larger than those of their human orthologs. Although three-quarters of predicted human proteins have a strong match to Fugu, approximately a quarter of the human proteins had highly diverged from or had no pufferfish homologs, highlighting the extent of protein evolution in the 450 million years since teleosts and mammals diverged. Conserved linkages between Fugu and human genes indicate the preservation of chromosomal segments from the common vertebrate ancestor, but with considerable scrambling of gene order.

Animals↗