Spatial omics
Visium HD resolution deconvolution
Transferred quality-control decisions from broader spatial scales back to high-resolution tissue maps.
- R
- Visium HD
- Spatial QC
- visiumHDResDeconv
About
Bioinformatics engineer with four years of experience collaborating with experimental researchers on single-cell, spatial, and other sequencing projects. I develop reproducible analysis strategies for complex or non-standard datasets and translate biological questions into interpretable results.
My work spans spatial transcriptomics, joint analysis of gene expression and chromatin accessibility, single-cell DNA sequencing, and gene-regulatory analysis. I am interested in linking cell behaviour and spatial context to molecular states in tumour and immune cells.
Research interests
- Genomics
- Transcriptomics
- Single-cell & Spatial Omics
Research
44 projectsProjects
Workflow engineering
RNA-seq and single-cell analysis platform
A web platform for analysis requests, reproducible pipelines, case tracking, and result delivery.
- FastAPI
- Vue.js
- Celery
- Snakemake
- R
- MySQL
Genomics
Sample-index collision detection
Automated index review and calculated safe mismatch allowances for demultiplexing.
- Python
- Demultiplexing
- Sequence comparison
- Input validation
Transcriptomics
PacBio Kinnex host–symbiont transcriptomics
A dual-reference Iso-Seq workflow separating host and symbiont isoforms for downstream expression analysis.
- PacBio Kinnex
- Iso-Seq
- Pigeon
- SQANTI3
- DTE
Transcriptomics
Repeated-measures RNA-seq analysis
Compared models that account for individual-level dependence and assessed sample-level pathway separation.
- RNA-seq
- limma
- duplicateCorrelation
- DREAM
- Gene-set scoring
Single-cell
10x Multiome RNA–ATAC workflows
Compared integration strategies for same-cell gene expression and chromatin accessibility.
- 10x Multiome
- Cell Ranger ARC
- Seurat
- SoupX
- RNA velocity
Genomics
WES/WGS annotation and containerized MOPline
Consolidated annotation workflows and isolated structural-variant callers with conflicting dependencies.
- WES/WGS
- MOPline
- Docker
- smoove
- SV/CNV
Transcriptomics
GO and KEGG enrichment for a non-model organism
Curated gene-level annotations and reproducible enrichment resources for Marchantia polymorpha.
- GO
- KEGG
- clusterProfiler
- MarpolBase
- R
Transcriptomics
Targeted expression patterns and lipid-gene correlations
Combined batch-aware contrasts, expression-pattern clustering, and targeted gene correlation analysis.
- DESeq2
- VST
- clusterProfiler
- pheatmap
- Pearson correlation
Web applications
Deploying an order application on Synology NAS
Containerized a client-facing application with separate staging and production environments.
- Docker Compose
- Synology NAS
- MariaDB
- Reverse proxy
- SSH
Web applications
Session timeouts with recoverable order drafts
Added automatic logout without discarding unfinished order forms.
- Session management
- Database design
- Draft recovery
Web applications
Order operations dashboard
Combined order activity, service health, and performance metrics in a MariaDB-backed dashboard.
- MariaDB
- Monitoring
- Data visualization
Teaching & talks2026
Bioinformatics engineering in the biomedical industry
Career talk for pharmacology students at National Yang Ming Chiao Tung University.
- Bioinformatics
- Pharmacology
- Science communication
Teaching & talks2024
Explaining an RNA-seq analysis service
Presented the RNA-seq workflow and interpretation of its outputs at Kaohsiung Chang Gung Memorial Hospital.
- RNA-seq
- MultiQC
- DESeq2
- GO/KEGG
- GSEA
Teaching & talks2024
Single-cell analysis in glioblastoma
Presented a published study to clinicians and researchers at the Single-Cell Forum.
- scRNA-seq
- Glioblastoma
- Tumour heterogeneity
Teaching & talks2024
Single-cell RNA-seq analysis workflow
An invited seminar on the decisions between raw sequencing data and biological interpretation.
- Cell Ranger
- Seurat
- CellBender
- SCTransform
Single-cell
Eight iterations of a single-cell DNA-seq pipeline
Documented evolving filtering criteria for a non-standard zebrafish sequencing experiment.
- scDNA-seq
- Mission Bio
- Zebrafish
- Quality control
Single-cell
SNP-consistency quality control
Used within-amplicon consistency to identify unreliable single-cell DNA measurements.
- scDNA-seq
- R
- Allele frequency
- Amplicon QC
Transcriptomics
Bulk RNA-seq pairwise comparisons
A DESeq2 workflow from count matrices to differential expression, enrichment, and visualizations.
- DESeq2
- R
- ORA
- GSEA
- VST
Transcriptomics
Testing interactions in bulk RNA-seq
Compared strain-by-treatment responses across full and subsetted experimental designs.
- DESeq2
- Interaction terms
- R
- Experimental design
Transcriptomics
Time-series RNA-seq and likelihood-ratio testing
Compared per-timepoint models with shared fits and analyzed treatment-by-time responses.
- DESeq2
- LRT
- Time series
- Clustering
Single-cell
Regulon analysis with pySCENIC
Inferred and visualized transcription-factor activity across cell types and conditions.
- pySCENIC
- Regulons
- R
- Seurat
- Heatmaps
Epigenomics
CUT&RUN analysis workflow
A chromatin-profiling workflow covering alignment, QC, peak calling, and signal comparison.
- CUT&RUN
- Bowtie2
- SEACR
- R
- Chromatin profiling
Genomics
extract_isoform: preparing representative protein sequences
Linked FASTA and GFF/GTF records and selected representative isoforms for comparative analysis.
- FASTA
- GFF/GTF
- AGAT
- Bash
- OrthoFinder
Genomics
Predicting transcription factors in non-model organisms
Compared domain-based predictions with sequence-similarity evidence from reference transcription factors.
- AnimalTFDB
- DIAMOND
- Protein FASTA
- Annotation
Genomics
Mapping peptide and nucleotide FASTA identifiers
Combined reciprocal and one-way best hits to reconcile sequence identifiers within a species.
- MMseqs2
- Reciprocal best hits
- FASTA
- Bash
Analysis tools
R Shiny application for GSEA
An interactive GSEA application with a recorded workflow diagram and source archive.
- R Shiny
- GSEA
- RNA-seq
Analysis tools
Exploring hierarchical clustering in R Shiny
An interactive tool for comparing clustering approaches in single-cell DNA analysis.
- R Shiny
- Hierarchical clustering
- Heatmaps
- scDNA-seq
Analysis tools
Column-wise out-of-range ratios
Compared allele-frequency tails across SNPs to flag unusual distribution patterns.
- R
- Allele frequency
- Quality control
- Visualization
Analysis tools
VST heatmaps and expression-pattern clustering
A reusable R function linking gene heatmaps with time-series expression profiles.
- R
- pheatmap
- ggplot2
- VST
- Time series
Single-cell
Bootstrapping single-cell discrepancy
Estimated average pairwise differences in chromosome-arm patterns with vectorized, parallel computation.
- Python
- Bootstrap
- Parallel computing
- scDNA-seq
Analysis tools
DotplotNN
A customized dot-plot function with example usage and a recorded output figure.
- R
- Seurat
- Dot plots
- Visualization
Visualization
Over-representation analysis visualization
A recorded enrichment figure for selected C5 terms.
- ORA
- Gene sets
- Enrichment
Genomics
Comparative synteny with OrthoFinder and RIdeogram
Prepared orthology, gene-coordinate, and karyotype files for cross-species visualization.
- OrthoFinder
- RIdeogram
- Synteny
- GFF/GTF
Single-cell
Chromosome-arm co-occurrence for scDNA-seq QC
Normalized arm-pair frequencies to identify unreliable amplicons in zebrafish blood-cell data.
- scDNA-seq
- R
- Conditional frequency
- Quality control
Visualization
From chromosome-arm heatmaps to bar plots
Summarized cell-level arm states as distributions and compared selected arms across datasets.
- R
- ggplot2
- Reshaping
- scDNA-seq
Visualization
Phylogenetic tree visualization
A preserved cladogram output from a phylogenetic analysis record.
- Phylogenetics
- Cladogram
Teaching & talks2023
Comparative transcriptomics workshop
Teaching-assistant work covering sequencing analysis, differential expression, and comparative genomics.
- RNA-seq
- DESeq2
- OrthoFinder
- Linux
- R
Teaching & talks2023
Workshop: transcription-factor prediction
Demonstrated a staged annotation strategy using single-copy orthologues and best hits.
- OrthoFinder
- DIAMOND
- AnimalTFDB
- Orthology
Teaching & talks2023
Workshop: DESeq2 likelihood-ratio test
A teaching workflow for treatment-by-time effects and temporal expression patterns.
- DESeq2
- LRT
- R
- Time series
Teaching & talks2023
Workshop: DESeq2 pairwise comparisons
A worked example of count filtering, model construction, differential expression, and plotting.
- DESeq2
- VST
- R
- Differential expression
Teaching & talks2023
Workshop: understanding DESeq2
Explained normalization, dispersion estimates, and variance-stabilizing transformation.
- DESeq2
- VST
- Normalization
- Dispersion
Analysis tools
Reverse search with a decision tree
Enumerated integers that reach zero after a fixed number of rule-based operations.
- Python
- Decision trees
- Enumeration
Analysis tools
A simple sequence-matching exercise
Implemented an ungapped query-to-reference comparison as a programming exercise.
- Python
- Sequence matching
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Publications
Evolutionary legacy can shape microplastic ingestion in riverine chironomid insects (opens in a new tab)
Chun-Ting Lin, Jhih-Rong Liao, Yu-Cheng Wu, Mei-Hwa Kuo, Ming-Chih Chiu, and Vincent H. Resh
Journal of Hazardous Materials Advances, 24, 101583 · 2026
Seasonality can override the effects of anthropogenic activities on microplastic presence in invertebrate deposit feeders in an urban river system (opens in a new tab)
Chun-Ting Lin, Ming-Chih Chiu, and Mei-Hwa Kuo
Journal of Hazardous Materials, 443, Part B · 2023
A Mini-Review of Strategies for Quantifying Anthropogenic Activities in Microplastic Studies in Aquatic Environments (opens in a new tab)
Chun-Ting Lin, Ming-Chih Chiu, and Mei-Hwa Kuo
Polymers, 14(1), 198 · 2022
Mosquito and bacterial diversity in Phytotelmata in northern Taiwan (opens in a new tab)
Matan Shelomi and Chun-Ting Lin
International Journal of Tropical Insect Science, 41, 969–978 · 2021
Effects of anthropogenic activities on microplastics in deposit-feeders (Diptera: Chironomidae) in an urban river of Taiwan (opens in a new tab)
Chun-Ting Lin, Ming-Chih Chiu, and Mei-Hwa Kuo
Scientific Reports, 11, 400 · 2021
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