Dr. Sun is a Postdoctoral Scholar in the Department of Bioengineering at Stanford University,
working under the mentorship of Dr. Emma Lundberg. He earned his Ph.D. in Computational Biology at Carnegie Mellon University,
advised by Dr. Robert F. Murphy.
His research interests span computational biology, biostatistics, and statistical learning. Dr. Sun's current work focuses on developing image-derived generative models of biological systems across multiple scales, from cellular to tissue levels. These models are designed to characterize organizational variations across different regions and individuals. Additionally, Dr. Sun maintains an active interest in the theoretical foundations of modern machine learning systems.
His research interests span computational biology, biostatistics, and statistical learning. Dr. Sun's current work focuses on developing image-derived generative models of biological systems across multiple scales, from cellular to tissue levels. These models are designed to characterize organizational variations across different regions and individuals. Additionally, Dr. Sun maintains an active interest in the theoretical foundations of modern machine learning systems.
Huangqingbo (Paul) Sun
sunh at stanford edu
Department of Bioengineering
Stanford University
443 Via Ortega
Stanford, CA 94305
Publications
⁺ equal contribution, * correspondence author
Preprints
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Generative machine learning unlocks the first proteome-wide image of human cells
Huangqingbo Sun, Konstantin Kahnert, Jan N. Hansen, William Leineweber, Mingyang Li, Wanyue Feng, Frederic Ballllosera Navarro, Ulrika Axelsson, Wei Ouyang, Emma Lundberg*
bioRxiv, (2026).
Peer-reviewed papers
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Big1 is a cell-cycle regulator linking cell size to basal body number in Tetrahymena thermophila
Alexander J. Stemm-Wolf, Adam W.J. Soh, Lisa E. Mitchell, Huangqingbo Sun, Erik Collet, Gayatri L. Dholakia, Vikram Raju, Jay R. Hesselberth, J. Matthew Taliaferro, Robert F. Murphy, Lydia R. Heasley, Chad G. Pearson*
Current Biology, 36, no. 7 (2026): p1882-1891.e4.
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Intrinsic Diversity in Primary Cilia Revealed Through Spatial Proteomics
Jan N. Hansen, Huangqingbo Sun⁺, Konstantin Kahnert⁺, Eini Westenius, Alexandra Johannesson, Carmela Villegas, Trang Le, Kalliopi Tzavlaki, Casper Winsnes, Emmie Pohjanen, Anna Mäkiniemi, Jenny Fall, Frederic Ballllosera Navarro, Anna Bäckström, Cecilia Lindskog, Fredric Johansson, Kalle von Feilitzen, Angelica M Delgado-Vega, Anna Martinez Casals, Diana Mahdessian, Mathias Uhlén, Shu-Hsien Sheu, Anna Lindstrand, Ulrika Axelsson, Emma Lundberg*
Cell, 188, no. 24 (2025): 6804-6824.
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Flexible and robust cell type annotation for highly multiplexed tissue images
Huangqingbo Sun, Shiqiu Yu, Anna Martinez Casals, Anna Bäckström, Yuxin Lu, Cecilia Lindskog, Matthew Ruffalo, Emma Lundberg*, Robert F Murphy*
Cell Systems, 16, no. 9 (2025): 101374.
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Expanding the coverage of spatial proteomics: a machine learning approach
Huangqingbo Sun, Jiayi Li, Robert F Murphy*
Bioinformatics, 40, no. 2 (2024): btae062.
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Basal body organization and cell geometry during the cell cycle in Tetrahymena thermophila
Huangqingbo Sun, Adam Soh, Lisa Mitchell, Chad Pearson, and Robert F. Murphy*
Molecular Biology of the Cell, 34, no. 6 (2023): ar53.
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Improving and evaluating deep learning models of cellular organization
Huangqingbo Sun⁺, Xuecong Fu⁺, Serena Abraham, Shen Jin, and Robert F. Murphy*
Bioinformatics, 38, no. 23 (2022): 5299-5306.
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Evaluation of categorical matrix completion algorithms: toward improved active learning for drug discovery
Huangqingbo Sun, and Robert F. Murphy*
Bioinformatics, 37, no. 20 (2021): 3538-3545.
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An Improved Matrix Completion Algorithm For Categorical Variables: Application to Active Learning of Drug Responses
Huangqingbo Sun, and Robert F. Murphy*
ICML 2020 Workshop on Real World Experiment Design and Active Learning, (2020).
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A MEMS variable optical attenuator with ultra-low wavelength-dependent loss and polarization-dependent loss
Huangqingbo Sun, Wei Zhou, Zijing Zhang, and Zhujun Wan*
Micromachines, 9, no. 12 (2018): 632.
Book chapters & technical reports
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Learning Morphological, Spatial, and Dynamic Models for Cellular and Subcellular Components
Huangqingbo Sun, and Robert F. Murphy*
Imaging Cell Signaling, Methods in Molecular Biology, 2800. Humana, New York, NY.