PreciGen Lab · National Taiwan University

Genes – Gut – Food – Environment

One Connected Story of Health.

We integrate genomics, microbiome research, artificial intelligence, and environmental exposure data to understand disease risk and advance precision health.

What we study

Genomic risk and causality

GWAS, PheWAS, TWAS, Mendelian randomization and polygenic risk scores, with a focus on East Asian and Taiwanese populations.

Cancer genomics and AI

Deep-learning and language models that predict cancer and disease outcomes, strengthen screening, prognosis and survival modelling, and detect food fraud.

Microbiome, diet and environment

16S and shotgun metagenomics linking the gut microbiome to health, and to food safety and authentication.

Population health and infection

Host and pathogen genomics for infection, sepsis outcomes, aging and longevity.

Statistical genetics and risk modelling

Disease association studies, new gene–gene interaction methods, and clinically oriented polygenic risk score models.

Publications

Genetic determinants of kidney function in 297,355 individuals from Taiwan and Japan. Chen et al. Nature Communications, 2024.
An epigenetic clock for chronological age estimation in East Asian populations. Lu, Kuo, Chattopadhyay*, Lu*. NAR Genomics and Bioinformatics, 2026.
Age-stratified genomic analyses reveal population-specific genetic determinants of exceptional longevity in Taiwan. Hsieh et al. GeroScience, 2026.
Population-specific genetic-risk scores enable improved prediction of mortality within 28 days of sepsis onset. Hsieh et al. Journal of Intensive Care, 2025.
Twnbiome: a public database of the healthy Taiwanese gut microbiome. Chattopadhyay et al. BMC Bioinformatics, 2023.
Multi-ethnic Imputation System (MI-System): a genotype imputation server for high-dimensional data. Chattopadhyay et al. Journal of Biomedical Informatics, 2023.

* corresponding author. The six above are highlights; the full list of 47 peer-reviewed articles is below.

Show all 47 publications
  1. Impact of surgical approach on post-esophagectomy muscle wasting: a secondary analysis of a prospective randomized controlled trial. International Journal of Surgery, 2026.
  2. Comparative analysis of multiple polygenic risk scores for predicting breast cancer. Journal of Epidemiology and Global Health, 2026.
  3. A causal association between alkaline phosphatase and natural-cause mortality: a Mendelian randomization study in East Asians and Europeans. Biomedicine, 2026.
  4. An epigenetic clock for chronological age estimation in East Asian populations. NAR Genomics and Bioinformatics, 2026.
  5. Age-stratified genomic analyses reveal population-specific genetic determinants of exceptional longevity in Taiwan. GeroScience, 2026.
  6. A methodological framework for analyzing and differentiating daily physical activity across groups using digital biomarkers from the frequency domain. Mathematics, 2025.
  7. Integrated genomic approaches to elucidate the genetic basis of Brugada syndrome in Taiwanese patients. Bioinformatics and Biology Insights, 2025.
  8. Population-specific genetic-risk scores enable improved prediction of mortality within 28 days of sepsis onset: a retrospective Taiwanese cohort study. Journal of Intensive Care, 2025.
  9. Predicting survival outcomes for patients with ovarian cancer using national cancer registry data from Taiwan. Women’s Health Reports, 2025.
  10. Discovery and prioritization of genetic determinants of kidney function in 297,355 individuals from Taiwan and Japan. Nature Communications, 2024.
  11. Cross-population enhancement of PrediXcan predictions with a gnomAD-based East Asian reference framework. Briefings in Bioinformatics, 2024.
  12. Utilizing the National Early Warning Score 2 (NEWS2) to confirm the impact of emergency department management in sepsis patients. International Journal of Emergency Medicine, 2024.
  13. Population-based prognostic models for head and neck cancers using national cancer registry data from Taiwan. Journal of Epidemiology and Global Health, 2024.
  14. Twnbiome: a public database of the healthy Taiwanese gut microbiome. BMC Bioinformatics, 2023.
  15. Utilizing multimodal approach to identify candidate pathways and biomarkers and predicting frailty syndrome in individuals from UK Biobank. GeroScience, 2023.
  16. Multi-ethnic Imputation System (MI-System): a genotype imputation server for high-dimensional data. Journal of Biomedical Informatics, 2023.
  17. The largest genome-wide association study for breast cancer in Taiwanese Han population. Breast Cancer Research and Treatment, 2023.
  18. Effect of end-stage kidney disease on the return of spontaneous circulation in Taiwanese adults with out-of-hospital cardiac arrest. Scientific Reports, 2023.
  19. Exploring the genetic correlation of cardiovascular diseases and mood disorders in the UK Biobank. Epidemiology and Psychiatric Sciences, 2023.
  20. CLIN_SKAT: an R package to conduct association analysis using functionally relevant variants. BMC Bioinformatics, 2022.
  21. End-stage renal disease patients undergoing hemodialysis have higher possibility of return of spontaneous circulation during out-of-hospital cardiac arrest and non-inferior short-term survival. Journal of Clinical Medicine, 2022.
  22. Uremic toxin-producing Bacteroides species prevail in the gut microbiota of Taiwanese CKD patients. Frontiers in Cellular and Infection Microbiology, 2022.
  23. Joint classifier of type and index mutation on lung cancer DNA using sequential labeling model. IEEE Access, 2022.
  24. High-performance deep learning pipeline predicts individuals in mixtures of DNA using sequencing data. Briefings in Bioinformatics, 2021.
  25. CNVIntegrate: the first multi-ethnic database for identifying copy number variations associated with cancer. Database, 2021.
  26. Transcript annotation tool (TransAT): an R package for retrieving annotations for transcript-specific genetic variants. BMC Bioinformatics, 2021.
  27. Elucidation of a causal relationship between platelet count and hypertension: a bidirectional Mendelian randomization study. Frontiers in Cardiovascular Medicine, 2021.
  28. Identification of prognostic factors for stage-III pancreatic ductal adenocarcinoma patients. Annals of Surgical Oncology, 2021.
  29. Robust prediction models for colon cancer in Asian patients. Annals of Surgical Oncology, 2021.
  30. Develop and apply electrocardiography-based risk score to identify community-based elderly individuals at high risk of mortality. Frontiers in Cardiovascular Medicine, 2021.
  31. Rare variants: data types and analysis strategies. Annals of Translational Medicine, 2021.
  32. Predicting colon cancer-specific survival for the Asian population using national cancer registry data from Taiwan. Annals of Surgical Oncology, 2021.
  33. Distinct survival outcomes in subgroups of stage III pancreatic cancer patients using the Taiwan Cancer Registry and the SEER registry. Annals of Surgical Oncology, 2021.
  34. Differential whole-genome doubling and homologous recombination deficiencies across breast cancer subtypes from the Taiwanese population. Communications Biology, 2021.
  35. Evolutionary trajectories and genomic divergence in localized breast cancers after ipsilateral breast tumor recurrence. Cancers, 2021.
  36. Targeting the gut microbiome for non-communicable diseases: present and future. Annals of Translational Medicine, 2021.
  37. Development of a gene-based prediction model for recurrence of colorectal cancer using an ensemble learning algorithm. Frontiers in Oncology, 2021.
  38. Overcoming the challenges of imputation of rare variants in a Taiwanese cohort. Translational Cancer Research, 2020.
  39. Leveraging well-annotated databases for deep learning in biomedical research. Translational Cancer Research, 2020.
  40. Validation and disease risk assessment of previously reported genome-wide genetic variants associated with Brugada syndrome: SADS-TW BrS Registry. Circulation: Genomic and Precision Medicine, 2020.
  41. Gene-gene interaction: the curse of dimensionality. Annals of Translational Medicine, 2019.
  42. VariED: the first integrated database of gene annotation and expression profiles for variants related to human diseases. Database, 2019.
  43. Role of artificial intelligence in integrated analysis of multi-omics and imaging data in cancer research. Translational Cancer Research, 2019.
  44. Whole-genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant. GigaScience, 2018.
  45. A non-threshold region-specific method for detecting rare variants in complex diseases. PLOS One, 2017.
  46. Using propensity score adjustment method in genetic association studies. Computational Biology and Chemistry, 2016.
  47. Summarizing techniques that combine three non-parametric scores to detect disease-associated 2-way SNP-SNP interactions. Gene, 2014.

Tools and databases

  • MI-SystemOnline genotype imputation server for high-dimensional data
  • TwnbiomePublic database of the healthy Taiwanese gut microbiome
  • CNVIntegrateMulti-ethnic database of copy number variations in cancer
  • VariEDGene annotation and expression profiles for disease variants
  • CLIN_SKATR package for association analysis with functionally relevant variants
  • TransATR package for transcript-specific variant annotation

Principal investigator

Portrait of Amrita Chattopadhyay

Amrita Chattopadhyay, Ph.D.

Assistant Professor, Global Health Program, Institute of Food Safety and Health, National Taiwan University. Amrita is a bioinformatician and statistical geneticist with over 15 years of experience in genomics, multi-omics and predictive modeling. Her long-term goal is to connect precision medicine, precision food safety and population health.

She holds a Ph.D. in Bioinformatics from the TIGP program at Academia Sinica and National Yang Ming University, and an M.S. in Statistics from Calcutta University. She received the 20th National Innovation Award in 2023, serves on the editorial board of BMC Bioinformatics, and is an Associate Editor of the European Journal of Medical Research.

Teaching: R programming for public health data, biostatistics, meta-analysis, GWAS and polygenic risk scores, and machine learning, all in English.

Recent talks

  • AACR Annual Meeting, San Diego, April 2026Matched-normal-free tumor mutation burden estimation in colorectal cancer
  • Taiwan Digestive Disease Week, September 2025Invited talk on AI for GI disease care

Join the lab

We welcome graduate students and postdoctoral researchers with backgrounds in statistics, bioinformatics, computer science, epidemiology or food science. Experience with R or Python is helpful, and curiosity matters more than a perfect match.

Send a short note about your interests and a CV.

Email Amrita