Publications

⁺ equal contribution · * corresponding author

Preprint

2026

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

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Peer-reviewed

2026

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(7): 1882–1891.e4

paper

2025

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(24): 6804–6824

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2025

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(9): 101374

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2024

Expanding the coverage of spatial proteomics: a machine learning approach

Huangqingbo Sun, Jiayi Li, Robert F Murphy*

Bioinformatics, 40(2): btae062

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2023

Basal body organization and cell geometry during the cell cycle in Tetrahymena thermophila

Huangqingbo Sun, Adam Soh, Lisa Mitchell, Chad Pearson, Robert F. Murphy*

Molecular Biology of the Cell, 34(6): ar53

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2022

Improving and evaluating deep learning models of cellular organization

Huangqingbo Sun⁺, Xuecong Fu⁺, Serena Abraham, Shen Jin, Robert F. Murphy*

Bioinformatics, 38(23): 5299–5306

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2021

Evaluation of categorical matrix completion algorithms: toward improved active learning for drug discovery

Huangqingbo Sun, Robert F. Murphy*

Bioinformatics, 37(20): 3538–3545

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2020

An Improved Matrix Completion Algorithm for Categorical Variables: Application to Active Learning of Drug Responses

Huangqingbo Sun, Robert F. Murphy*

ICML 2020 Workshop on Real World Experiment Design and Active Learning

paper

2018

A MEMS variable optical attenuator with ultra-low wavelength-dependent loss and polarization-dependent loss

Huangqingbo Sun, Wei Zhou, Zijing Zhang, Zhujun Wan*

Micromachines, 9(12): 632

paper

Book chapters & technical reports

Learning Morphological, Spatial, and Dynamic Models for Cellular and Subcellular Components

Huangqingbo Sun, Robert F. Murphy*

Imaging Cell Signaling — Methods in Molecular Biology, 2800. Humana, New York, NY