Single cell technology, advanced imaging & quantitative analysis, cancer-driving cells, target discovery
Our Focus
Our research aims to uncover the mechanisms driving tumor metastasis, tumor progression, and therapy resistance by developing and applying imaging-guided single-cell and spatial omics technologies. By integrating advanced microscopy, computational analysis, and omics profiling, we link dynamic cellular behaviors and morphological phenotypes to their underlying molecular programs.
We develop proprietary platforms, such as FUNseq, BC-seq, and CIN-seq, that enable behavior- and phenotype-coupled sequencing, allowing rare but clinically relevant subpopulations (e.g., migratory, chromosomally unstable, immune-evasive, or drug-resistant cells) to be identified, isolated, and profiled. Using these approaches, we have discovered predictive metastasis signatures and novel mechanisms in head and neck squamous cell carcinoma, and identified actionable pathways associated with chromosomal instability and tumor progression.
To capture tumor-microenvironment interactions, we develop spatial and in situ FUNseq technologies to profile immune niches and dynamic cell states within live tissues and 3D organoid models. In parallel, we apply deep learning models to prospectively predict cell fate decisions, enabling causal dissection of disease-driving processes.
Our work on therapy resistance focuses on DNA damage response dynamics and cancer cell plasticity, including the development of FUN-TRACE and PAINT-seq to uncover epigenetic and pre-existing resistance mechanisms. Together, our integrative approach provides a dynamic, single-cell view of cancer biology with direct translational potential.
About Miao-Ping Chien
Miao-Ping Chien
My Research
Miao-Ping Chien is a multidisciplinary scientist. She obtained her PhD in chemistry and biochemistry at University of California, San Diego, where she successfully invented a nanomaterial that can specifically be targeted to and deposited in tumor tissues for a long period of time, through which the tumor can be detected with conjugated probes (fluorescent or MRI contrast agents) and treated with attached drugs (Doxorubicin). After that, she pursued her postdoctoral training in optical engineering and computational biology with Dr. Adam Cohen at Harvard University, where she developed technologies that are applicable to single cell biology and high-throughput measurements.
In 2017 June, Miao-Ping joined Erasmus MC as a group leader. Her research focuses on developing and applying multidisciplinary technologies (advanced microscopy and imaging, computation, single cell technology and bioinformatics) to investigate the underlying mechanisms of tumorigenesis, particularly of rare cancer-driving cells. Her main research goals are: the creation and application of technology for (early) detection and treatment of tumors, and the creation and application of single cell technology to facilitate the discovery and interpretation of genetic, transcriptomic and proteomic profiles of aberrant (single) cancer cells, with the aim of translating the knowledge gained to clinical applications. She is a founder of UFO Biosciences, which aims to profile rare & cancer-driving cells and identify actionable targets driving clinically relevant tumorigenic phenotypes.
Awards
- 2025: KWF Proof-of-Concept Grant
- 2025: NWO Perspectief Grant
- 2024: ERC Consolidator Grant
- 2024: NWO XL Grant
- 2023: EMC2 Synergy Grant
- 2023: Aspasia Award
- 2022: NWO Vidi Award
- 2022: KWF Public-Private-Partnership Grant, TKI
- 2022: Two Flagship Consortium Grants
- 2022: Computable Award
- 2022: Inspiring Fifty Deep Tech
- 2020: Ammodo Science Award
- 2020: Josephine Nefkens Foundation Grant
- 2020: Erasmus MC-TU Delft Convergence Grant
- 2018: Erasmus MC Fellowship
- 2017: CancerGenomiCs.nl Junior Fellowship
- 2017: NWO Veni Award
Key Publications
- 2025 | Functional Single-Cell Proteomics: Technology and Biological Applications | Pin-Rui Su | Methods in Molecular Biology | View publication
- 2025 | Unraveling the molecular mechanisms underlying spontaneous chromosomal instability through CIN-seq | Pin-Rui Su et al. | bioRxiv | View publication
- 2024 | Investigating the Metabolic Heterogeneity of Cancer Cells Using Functional Single-Cell Selection and nLC Combined with Multinozzle Emitter Mass Spectrometry | Kai-Wen Cheng et al. | Analytical Chemistry | View publication
- 2023 | Instant processing of large-scale image data with FACT, a real-time cell segmentation and tracking algorithm | Ting-Chun Chou et al. | Cell Reports Methods | View publication
- 2023 | Protocol for profiling intratumor heterogeneity using spatially annotated single cell sequencing | Myrthe M. Smit et al. | STAR Protocols | View publication
- 2023 | Spatial Transcriptomic Technologies | Tsai-Ying Chen et al. | Cells | View publication
- 2022 | Linking the genotypes and phenotypes of cancer cells in heterogenous populations via real-time optical tagging and image analysis | Li You et al. | Nature Biomedical Engineering | View publication
- 2022 | Microscopy-based single-cell proteomic profiling reveals heterogeneity in DNA damage response dynamics | Pin-Rui Su et al. | Cell Reports Methods | View publication
- 2022 | Functional single-cell sequencing links dynamic phenotypes to their genotypes | Daan Brinks | Nature Biomedical Engineering | View publication
- 2021 | A Comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis | Li Li et al. | Genome Biology | View publication
- 2021 | Photoactivated voltage imaging in tissue with an archaerhodopsin-derived reporter | M. P. Chien et al. | Science Advances | View publication
Members
| Miao-Ping Chien Group Leader | Cecile Beerens Technician | Jelle Storteboom Post Doc |
| Johanna Vliet Scientist | Junfeng Huang Phd student | Lars van Roemburg PhD student |
| Li You Postdoc fellow | Maria Teresa López Cascales Postdoctoral researcher | Oluwatoba Ajani Phd student |
| Pierangela Chiafele Research Analyst | Reza Ghadiri Rad PhD student | Ting-Chun Chou PhD student |
| Tsai- Ying Chen Phd Student | Swati Garg Project Manager |