cv
Below you can find the details of my profile. PDf version is also available (see right).
General Information
| Full Name | Yongsoo Kim |
| Date of Birth | 7th Sep 1984 |
| ORCiD | 0000-0002-2995-2131 |
Education
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2007.3-2013.8 PhD (combined with MSc)
POSTECH, Pohang, South Korea - School of Interdisciplinary Bioscience and Bioengineering (I-BIO).
- Joint Participation.
- Machine Learning Lab (Prof. Seungjin Choi).
- Systems Biology Lab (Prof. Daehee Hwang).
- Thesis - “Probabilistic Inference in Context-specific Dynamic Networks"
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2003.3-2007.2 BSc
POSTECH, Pohang, South Korea - Computer Science and Engineering (CSE)
Experience
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2013.9-2014.12 Postdoctoral fellow
Deagu Gyeongbuk Institute of Science & Technology (DGIST), Daegu, South Korea - Systems Biology Lab (Prof. Daehee Hwang)
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2015.1-2018.9 Postdoctoral fellow
- The Netherlands Cancer Institute (the NKI), Plesmanlaan 121, 1066 DX Amsterdam, The Netherlands.
- Joint Participation.
- Wilbert Zwart Group
- Computational Cancer Biology Group (Prof. dr. Lodewyk Wessels)
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2018.10 - current Assistant Professor of multiomics data science
Department of Pathology, Amsterdam UMC - Cancer Center Amsterdam
Open Source Projects
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2021 - 2025 Bayesian Log-normal DEconvolution (BLADE)
- Python package for log-normal deconovlution method. It is mostly succeeded by Statescope.
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2025 - Statescope
- Integrative deconvolution method tailored for cell state analysis. Successor of BLADE. Features pyTorch implementation. R package is also under development.
Honors and Awards
Projects / Fundings
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2024-2029 SPACETIME
- Horizon Europe (co-PI)
- Announcement
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2025-2029 Cell2Sample
- Stitching ADORE
- Announcement
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2024-2029 GEN-BioDORA
- stitching ADORE (co-PI)
- Announcement
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2023-2027 Establishing a Reproducible and Accessible Bioinformatics Framework to determine Tumor microenvironment and heterogeneity
- NWO startergrant
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2023-2026 An affordable RNA profiling-based tumor microenvironment characterization for the optimal care of cervical cancer patients
- HealthHolland
- Accompanying Video
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2022-2026 A comprehensive multi-layer characterization of intra-tumoral heterogeneity in pancreatic ductal adenocarcinoma
- Dutch Cancer Society (KWF - 13774)
- Announcement
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2020-2021 A computational framework to address within-tumour heterogeneity of pancreatic ductal adenocarcinoma
- Stitching Cancer Center Amsterdam
PhD students supervision
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Barbara Andrade Barbosa
- co-promoter
- Thesis title - "Solutions to navigate the oncogenomic maze through advanced computational methods"
- Thesis submitted to reading committee
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Jurriaan Janssen
- co-promoter
- Lung cancer / Deconvolution (Statescope) / Bioinformatics
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Mischa Steketee
- co-promoter (funded by KWF)
- Pancreatic cancer / Deconvolution (Statescope) / Bioinformatics
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Stef Elings
- co-promoter (funded by SPACETIME)
- Lung cancer / Tumor microenvironment / Spatial transcriptome analysis
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Dominika Martinovicová
- co-promoter (funded by SPACETIME)
- Lung cancer / Spatial tarnscriptome anlaysis / Tumor microenvironment
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Nicole Miolato
- co-promoter (funded by Cell2Sample)
- Multi-omics deconvolution