Profile

Bioinformatics engineer with four years of experience working with experimental researchers on single-cell, spatial, and other sequencing projects. I develop practical and reproducible analysis strategies for complex or non-standard datasets and translate biological questions into interpretable results. My experience includes spatial transcriptomics, joint analysis of gene expression and chromatin accessibility, single-cell DNA sequencing, and gene-regulatory analysis. I am particularly interested in linking cell behaviour and spatial context to molecular states in tumour and immune cells.

jordan.bioinfo@gmail.com · LinkedIn · GitHub

Education

National Chung Hsing University

M.S. in Entomology, Department of Entomology · September 2019 – October 2021 · Taichung, Taiwan

Thesis: Anthropogenic activities, microplastics in deposit-feeders (Diptera: Chironomidae) in urban river and Chironomidae community structure.

National Taiwan University

B.S. in Entomology, Department of Entomology · September 2014 – January 2019 · Taipei, Taiwan

Pontifícia Universidade Católica do Rio de Janeiro

Exchange Student, International Program · Fall 2017, one semester · Rio de Janeiro, Brazil

Academic average: 9/10.

Research & Work Experience

Taiwan Genomic Industry Alliance Inc.

Bioinformatics Engineer · June 2024 – Present · Hsinchu, Taiwan

Improving the reliability of high-resolution spatial transcriptomics

  • Identified sparsity and noise in small Visium HD regions (8 µm) as barriers to reliable quality control.
  • Developed barcode-based and coordinate-based deconvolution to evaluate quality at a broader spatial scale and transfer quality decisions to the original high-resolution tissue map.
  • Implemented the R package visiumHDResDeconv, the company’s first reusable Visium HD workflow.

Standardized analysis platform for RNA-seq, scRNA-seq, and Visium HD

  • Built an internal platform for standardized quality control, analysis, and reporting of routine omics projects.
  • Created user-facing workflows that allow colleagues without programming experience to run reproducible analyses with consistent outputs.

Optimizing sample-index assignment and sequencing yield

  • Automated detection of duplicated or overly similar sample indexes, replacing manual comparisons and reducing assignment risk.
  • Determined the maximum safe mismatch allowance for each sequencing lane to improve read assignment without compromising sample separation.
  • Reduced manual index review time by approximately 98% and increased usable sequencing yield by approximately 2%, minimizing avoidable re-sequencing costs.

Standardizing RNA-seq deliverables and client communication

  • Created the company’s first RNA-seq deliverables guideline, covering analyses, figures, tables, and reports.
  • Translated technical workflows into client-facing documentation that explains service scope and expected outputs.

Tailored analysis strategies for complex RNA-seq experiments

  • Developed hypothesis-driven strategies for multi-condition and repeated-measures experiments, accounting for within-individual variation and batch effects.
  • Used pathway-level scoring to assess the consistency and distinguishability of biological signals across samples.

Bioinformatics Core Lab, ICOB, Academia Sinica

IT Specialist · January 2024 – May 2024
Research Assistant · May 2022 – January 2024 · Taipei, Taiwan

Single-cell multi-omics analysis of mouse lung development

  • Analyzed same-cell gene expression and chromatin accessibility across developmental stages of the mouse lung.
  • Used public references and RNA velocity to support cell annotation and investigation of cellular transitions.
  • Compared transcription-factor activity across cell types and developmental stages through gene-regulatory analysis.

Single-cell DNA-seq QC of chromosome segregation for asynthetic fission

  • Developed quality-control approaches for non-standard Mission Bio single-cell DNA sequencing of zebrafish tissue.
  • Customized pipelines and scoring strategies to translate noisy DNA variants into chromosome-arm patterns and assess reproducibility of chromosome segregation.
  • Worked with the principal investigator to align biological questions with the limits of the experimental data.
  • Built an interactive R Shiny dashboard to inspect individual cells, chromosomes, and quality-control results.

Chromatin profiling and epigenomics workflow

  • Standardized a CUT&RUN workflow to compare chromatin signals between control and knockout samples.

Exploratory cross-species cell-type mapping

  • Established a SAMap workflow to explore transcriptomic relationships across four metazoan species.

Insect Ecology Laboratory, Department of Entomology, National Chung Hsing University

Research Assistant · October 2021 – May 2022
Graduate Student Researcher · July 2019 – October 2021 · Taichung, Taiwan

Seasonal drivers of microplastic accumulation in urban river invertebrates

  • Investigated insect microplastic accumulation across seasons and locations in an urban river.
  • Combined field sampling with watershed land-use and wastewater mapping to distinguish seasonal and anthropogenic influences.
  • Published the work as first author in Journal of Hazardous Materials.

Evolutionary differences in microplastic ingestion

  • Investigated how evolutionary history and ecological traits explain differences in microplastic ingestion among related insect species.
  • Integrated taxonomy, traits, microplastic characteristics, and phylogenetic analysis.
  • Published the work in Journal of Hazardous Materials Advances, with Chun-Ting Lin and Jhih-Rong Liao contributing equally.

Research program initiation and grant development

  • Independently initiated the laboratory’s microplastics research direction, including core hypotheses and the study framework for my master’s research.
  • Led scientific conceptualization and proposal drafting for a submission to Taiwan’s National Science and Technology Council.
  • This research direction later formed the basis of two funded General Research Projects awarded to the laboratory’s principal investigator in 2023 and 2025, with a combined budget of NTD 2.43 million.

Industry–academic ecological research workshop

  • Collaborated with Bayer on field insect diversity in Prophet Rice® fields and demonstrated sample-processing methods to industry participants.

Laboratory of Insect Microbiology, Department of Entomology, National Taiwan University

Undergraduate Student Researcher · September 2014 – January 2019 · Taipei, Taiwan

Publications

Published

  1. Chun-Ting Lin, Jhih-Rong Liao, Yu-Cheng Wu, Mei-Hwa Kuo, Ming-Chih Chiu, and Vincent H. Resh. 2026. Evolutionary legacy can shape microplastic ingestion in riverine chironomid insects. Journal of Hazardous Materials Advances, 24, 101583. Chun-Ting Lin and Jhih-Rong Liao contributed equally.
  2. Chun-Ting Lin, Ming-Chih Chiu, and Mei-Hwa Kuo. 2023. Seasonality can override the effects of anthropogenic activities on microplastic presence in invertebrate deposit feeders in an urban river system. Journal of Hazardous Materials, 443, Part B.
  3. Chun-Ting Lin, Ming-Chih Chiu, and Mei-Hwa Kuo. 2022. A Mini-Review of Strategies for Quantifying Anthropogenic Activities in Microplastic Studies in Aquatic Environments. Polymers, 14(1), 198.
  4. Chun-Ting Lin, Ming-Chih Chiu, and Mei-Hwa Kuo. 2021. Effects of anthropogenic activities on microplastics in deposit-feeders (Diptera: Chironomidae) in an urban river of Taiwan. Scientific Reports, 11, 400.
  5. Matan Shelomi and Chun-Ting Lin. 2021. Mosquito and bacterial diversity in Phytotelmata in northern Taiwan. International Journal of Tropical Insect Science, 41, 969–978.

Presentations

  • Bioinformatics Engineering in the Biomedical Industry. Career talk, Institute of Pharmacology, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan. May 20, 2026.
  • TGIA RNA-seq Pipeline. Presentation on the analysis workflow and interpretation of RNA-seq outputs, Kaohsiung Chang Gung Memorial Hospital. October 2, 2024.
  • Introduction of Single-Cell Analysis: A Different Perspective in Glioblastoma. Invited presentation, Single-Cell Forum, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan. September 30, 2024.
  • Single-cell RNA-seq Analysis Workflow. Invited seminar, Department of Life Science, National Taiwan University, Taipei, Taiwan. June 19, 2024.
  • Industrial Area Predicts Microplastics in Midge Larvae (Diptera: Chironomidae) in a River Basin of Central Taiwan. Poster, 40th Annual Meeting of the Taiwan Entomological Society, Taiwan. October 2019. Best Scientific Poster Award.

Honors & Awards

  • Publication Scholarship, National Chung Hsing University — 2021.
  • Best Scientific Poster Award, Taiwan Entomological Society — 2019.
  • One-Year Entrance Scholarship, National Chung Hsing University — 2019.
  • Finalist, Taiwan English Debate Open, Taiwan Debate Open — 2017.
  • Top 10, World Schools Debating Championship, Taiwan Wenzao English Debate Workshop — 2016.

Certifications & Workshops

  • Docker Training, 5xRuby Training Group — 2025.
  • 10x Genomics Spatial Workshop: Integration of single-cell RNA-seq data with Visium/Xenium data, Academia Sinica — November 2023.
  • BROAD Institute @ Taiwan GATK International Education and Training, National Center for High-Performance Computing and the Broad Institute — November 2023.
  • Nanopore RNA-seq Practical Workshop, Taipei Bioinformatics Omnibus Facebook Society — November 2023.
  • Workshop on Single-Cell RNA Sequencing Data Analysis Related to Cancer Research, National Health Research Institutes — 2023.
  • PacBio HiFi Workshop, NGS High Throughput Genomics Core and PacBio — 2023.
  • TaiBIF Biodiversity Data Publication and Application Workshop and Volunteer Training, Taiwan Biodiversity Information Facility — December 2022.
  • High-Throughput Data Bioinformatics Analysis Workshop: A Case Study on Single-Cell RNA Sequencing Analysis, National Health Research Institutes — September 2022.

Teaching

Teaching Assistant, Comparative Transcriptomics Workshop · December 2023

Prepared and supported practical material on transcription-factor prediction, DESeq2 pairwise comparisons, likelihood-ratio testing, and student questions. Teaching records.

Technical Skills

Programming & reproducibility: R, Python, Bash/Linux, command-line tools, Git, Docker, conda, R packages, and reproducible workflow development.

Single-cell & multimodal analysis: scRNA-seq, 10x Multiome RNA–ATAC, scDNA-seq, RNA velocity, cell annotation, differential expression, and gene-regulatory analysis.

Spatial transcriptomics: Visium HD, spatial quality control, normalization, spatial domain analysis, tissue visualization, and cell–cell communication.

Genomics & epigenomics: bulk RNA-seq, CUT&RUN, WGS/WES annotation, structural variant analysis, and long-read transcriptomics.

Interpretation & communication: pathway analysis, R Shiny, one-to-one consultation with experimental researchers, presentations, and workshop teaching.

Selected tools: Cell Ranger, Seurat, CellBender, SCTransform, DESeq2, pySCENIC, BANKSY, and CellChat.