Research & Computational Work

Production workflows, analytical frameworks, and peer-reviewed publications.

Pipelines & Analysis Workflows

Single-Cell & Single-Nuclear RNA-Seq Framework

Standardized bioinformatic processing workflow for core facility clients of 10x Genomics data, covering the Cell Ranger pipeline, including alignment and quantification, ambient RNA removal, doublet/multiplet detection, quality control, filtering, clustering, and automated cell-type annotation.

Tech: RNA-seq • Single-Cell • Cell Ranger • CellBender • DoubletFinder • Seurat • SingleR • R • Python • HPC / SLURM • Snakemake

Bulk RNA-Seq Processing and Quantification Workflow

Scalable Snakemake workflow for transcriptomics data transcript- and gene-level profiling, as well as QC statistics at various stages of the workflow.

Tech: RNA-seq • STAR • Salmon • DESeq2 • R • Python • HPC / SLURM • Snakemake

Automated Reporting & Visualization Framework

Automated report generation using outputs from the above RNA-Seq workflows to visualize key findings such as clustering patterns, cell-type annotations, and differentially expressed genes. Built with Quarto to deliver presentation-ready visualizations and interactive tables.

Tech: HTML Report Generation • Quarto • Data Visualization • Multi-Omics

Microbiome Amplicon Sequence Processing Workflow

Scalable microbiome amplicon sequence processing workflow for 16S rRNA and ITS amplicon sequencing data, including quality control, denoising, taxonomic assignment, and phylogeny reconstruction.

Tech: Microbiome Amplicon Sequencing • DADA2 • MAFFT • Phyloseq • R • HPC / SLURM • Snakemake

Selected Publications

BMX-001, a clinically relevant radioprotector, can reverse radiation-induced fibrosis when given three weeks after radiation, in part, by restoring methylation

Molly S Myers, Elizabeth A Kosmacek, Chia Sin Liew, et al.

Redox Biology (2026)

Analyzed bisulfite and RNA-seq data to characterize epigenetic and transcriptomic changes associated with BMX-001's ability to reverse radiation-induced fibrosis; generated manuscript figures and contributed to writing.

View Article / DOI ↗

Challenges and opportunities: computational biology and the future of agriculture

Joao Carlos Gomes-Neto, Alexandra Crook, …, Chia-Sin Liew, et al.

Bioinformatics Advances (2026)

Contributed perspective on agricultural genetics, genomics, and epigenetics—focusing on the importance of quality genomes, annotations and associated databases, bioinformatics tools, and training the next generation of scientists.

View Article / DOI ↗

Dietary dipeptide γ-glutamyl valine (γ-ev) activates AMPK and improves glucose homeostasis in db/db mice

Bikram Upadhyaya, Chia-Sin Liew, Jean-Jack M. Riethoven, et al.

The Journal of Nutritional Biochemistry (2025)

Led the analysis of RNA-seq data to identify differentially expressed genes and pathways associated with diabetes and fatty acid metabolism in the liver and the jejunum.

View Article / DOI ↗

Genome structure and evolutionary history of frankincense producing Boswellia sacra

Abdul Latif Khan, Ahmed Al-Harrasi, …, Chia-Sin Liew, et al.

iScience (2022)

Assembled the first genome in the genus Boswellia using short- and long-read sequencing data, and performed genome annotation for downstream comparative genomics and evolutionary analyses.

View Article / DOI ↗

Porcine Reproductive and Respiratory Syndrome Virus Infection Upregulates Negative Immune Regulators and T-Cell Exhaustion Markers

Jayeshbhai Chaudhari, Chia-Sin Liew, Jean-Jack M. Riethoven, et al.

Journal of Virology (2021)

Led the analysis of RNA-seq data to understand the host immune response to Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) infection, and identified upregulation of negative immune regulators and T-cell exhaustion markers.

View Article / DOI ↗

Taxonomic realignment of Senecio glaucophyllus (Asteraceae; Senecioneae) necessitates a new name for a widespread New Zealand species

Chia-Sin Liew, Shannel P. Courtney, Peter J. de Lange, et al.

New Zealand Journal of Botany (2021)

Reclassified a New Zealand Senecio species as Senecio matatini using phylogenetic analyses of nuclear and plastid DNA sequences alongside random forest analysis of morphological data.

View Article / DOI ↗

All Publications

Understanding Rice Responses to the Combination of Bacterial Panicle Blight and High Night Temperatures

Sapana Ghimire, Shilu Dahal, Chia-Sin Liew, et al. • Rice (2026)

BMX-001 acts as a selective chemoradioprotector in rectal cancer

Molly S Myers, Elizabeth A Kosmacek, Chia Sin Liew, et al. • Redox Biochem Chem. (2026)

BMX-001, a clinically relevant radioprotector, can reverse radiation-induced fibrosis when given three weeks after radiation, in part, by restoring methylation

Molly S Myers, Elizabeth A Kosmacek, Chia Sin Liew, et al. • Redox Biology (2026)

Show full publication list ▼

Challenges and opportunities: computational biology and the future of agriculture

Joao Carlos Gomes-Neto, Alexandra Crook, …, Chia-Sin Liew, et al. • Bioinformatics Advances (2026)

Dietary dipeptide γ-glutamyl valine (γ-ev) activates AMPK and improves glucose homeostasis in db/db mice

Bikram Upadhyaya, Chia-Sin Liew, Jean-Jack M. Riethoven, et al. • The Journal of Nutritional Biochemistry (2025)

Genome structure and evolutionary history of frankincense producing Boswellia sacra

Abdul Latif Khan, Ahmed Al-Harrasi, …, Chia-Sin Liew, et al. • iScience (2022)

The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms

Kimberly Walker, Divya Kalra, …, Chia-Sin Liew, et al. • F1000Research (2022)

Senecio pokohinuensis (Asteraceae), a new combination for an endemic species of Mokohinau Islands, Hauraki Gulf (Tikapa Moana o Hauraki), northern Te Ika a Maui/North Island, Aotearoa/New Zealand

Peter James de Lange, Pieter B. Pelser, Chia-Sin Liew, et al. • Ukrainian Botanical Journal (2022)

Porcine Reproductive and Respiratory Syndrome Virus Infection Upregulates Negative Immune Regulators and T-Cell Exhaustion Markers

Jayeshbhai Chaudhari, Chia-Sin Liew, Jean-Jack M. Riethoven, et al. • Journal of Virology (2021)

Taxonomic realignment of Senecio glaucophyllus (Asteraceae; Senecioneae) necessitates a new name for a widespread New Zealand species

Chia-Sin Liew, Shannel P. Courtney, Peter J. de Lange, et al. • New Zealand Journal of Botany (2021)

Host Transcriptional Response to Persistent Infection with a Live-Attenuated Porcine Reproductive and Respiratory Syndrome Virus Strain

Jayeshbhai Chaudhari, Chia-Sin Liew, Aspen M Workman, et al. • Viruses (2020)

The delimitation and evolutionary history of the Australasian Lautusoid group of Senecio (Asteraceae; Senecioneae)

Chia-Sin Liew, Andrew E. Memory, Daniel Ortiz-Barrientos, et al. • Taxon (2018)

Senecio esperensis (Asteraceae: Senecioneae)—a new combination for the L’Esperance Rock groundsel, Kermadec Islands

Peter J. de Lange, Chia Sin Liew, Jeremy R Rolfe, et al. • New Zealand Journal of Botany (2015)

Senecio australis Willd. (Asteraceae: Senecioneae) – a new and uncommon addition to the indigenous vascular flora of New Zealand

Peter J. de Lange, Jeremy R Rolfe, Chia-Sin Liew, et al. • New Zealand Journal of Botany (2014)