Yichun He

I'm a 5th year Ph.D. candidate at Harvard SEAS and the Broad Institute of MIT and Harvard. I'm fortunate to be advised by Prof. Jia Liu and Prof. Xiao Wang. My research focuses on exploring the complex biological systems spanning molecular features, cell identities, tissue structures, functions and behaviors through the application of artificial intelligence (AI) in spatial multi-omics and brain machine interfaces.

Previously, I interned in Prof. Aviv Regev's lab at Genentech with Hanchen Wang and Paula Coelho during the summer of 2024.

I received my B.E. in Electrical Engineering from University of Science and Technology of China with the highest honor.

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Research

I am passionate about accelerating discovery in biology through advanced AI approaches. My work spans multiple directions, including: (1) Scalable AI for characterizing whole-brain spatial single-cell gene expression, (2) Contextual AI for bridging gene expression with spatial contexts and molecular features, (3) Multi-modal AI for integrating diverse biological data, (4) Real-time AI for dynamic biological processes, and (5) Agentic AI for autonomous biological experimental planning, data analysis, and discovery.

Representative papers are highlighted. # Co-first authors; * Corresponding authors.

Scalable AI for characterizing whole-brain spatial single-cell gene expression
	Spatial Atlas of the Mouse Central Nervous System at Molecular Resolution Hailing Shi#, Yichun He#, Yiming Zhou#, Jiahao Huang, Kamal Maher, Brandon Wang, Zefang Tang, Shuchen Luo, Peng Tan, Morgan Wu, Zuwan Lin, Jingyi Ren, Yaman Thapa, Xin Tang, Ken Y. Chan, Benjamin E. Deverman, Hao Shen, Albert Liu, Jia Liu* & Xiao Wang* Nature, 2023 Github Cover and Perspective highlight in Nature as part of collection for whole mouse brain spatial atlas, "BRAIN Initiative Cell Census Network 2.0 – Whole Mouse Brain". Google Map of the Mouse Brain at Molecular Resolution.
	ClusterMap for multi-scale clustering analysis of spatial gene expression Yichun He#, Xin Tang#, Jiahao Huang, Jingyi Ren, Haowen Zhou, Kevin Chen, Albert Liu, Hailing Shi, Zuwan Lin, Qiang Li, Abhishek Aditham, Johain Ounadjela, Emanuelle I. Grody, Jian Shu, Jia Liu* & Xiao Wang* Nature Communications, 2021 ClusterMap package Research develops new way to map RNAs in the cell.
	Controlling organoid symmetry breaking uncovers an excitable system underlying human axial elongation Giridhar M. Anand, Heitor C. Megale, Sean H. Murphy, Theresa Weis, Zuwan Lin, Yichun He, Xiao Wang, Jia Liu, Sharad Ramanathan* Cell, 2023
Contextual AI for bridging gene expression with spatial contexts and molecular features
	Towards a universal spatial molecular atlas of the mouse brain Yichun He, Hao Sheng, Hailing Shi, Wendy Xueyi Wang, Zefang Tang, Jia Liu, and Xiao Wang bioRxiv, 2024 Data portal of the molecular common coordinate framework (molCCF) FuseMap package
	Spatiotemporally resolved transcriptomics reveals the subcellular RNA kinetic landscape Jingyi Ren#, Haowen Zhou#, Hu Zeng#, Connie Kangni Wang, Jiahao Huang, Xiaojie Qiu, Xin Sui, Qiang Li, Xunwei Wu, Zuwan Lin, Jennifer A. Lo, Kamal Maher, Yichun He, Xin Tang, Judson Lam, Hongyu Chen, Brian Li, David E. Fisher, Jia Liu & Xiao Wang* Nature Methods, 2023
	Scalable spatial single-cell transcriptomics and translatomics in 3D thick tissue blocks Xin Sui#, Jennifer A. Lo#, Shuchen Luo, Yichun He, Zefang Tang, Zuwan Lin,Yiming Zhou, Wendy Xueyi Wang, Jia Liu, Xiao Wang* bioRxiv, 2024
Multi-modal AI for integrating diverse biological data
	Multi-task learning for single-cell multi-modality biology Xin Tang#, Jiawei Zhang#, Yichun He#, Xinhe Zhang, Zuwan Lin, Sebastian Partarrieu, Emma Bou Hanna, Zhaolin Ren, Hao Shen, Yuhong Yang, Xiao Wang, Na Li, Jie Ding* & Jia Liu* Nature Communications, 2023 UnitedNet package Editor highlights in Biotechnology and Methods and Computational Science.
	Multimodal charting of molecular and functional cell states via in situ electro-seq Qiang Li#, Zuwan Lin#, Ren Liu#, Xin Tang#, Jiahao Huang, Yichun He, Xin Sui, Weiwen Tian, Hao Shen, Haowen Zhou, Hao Sheng, Hailing Shi, Ling Xiao, Xiao Wang, Jia Liu Cell, 2023 Cover highlight in Cell Perspective highlight in Nature Methods
Real-time AI for dynamic biological processes
	End-to-end multimodal deep learning for real-time decoding of months-long neural activity from the same cells Yichun He#, Arnau Marin-Llobet#, Hao Sheng, Ren Liu, Jia Liu* bioRxiv, 2024 AutoSort package
	Soft bioelectronics for cardiac interfaces Xin Tang#, Yichun He# Jia Liu, Biophysics Reviews*, 2022
	Brain implantation of tissue-level-soft bioelectronics via embryonic development Hao Sheng#, Ren Liu#, Qiang Li#, Zuwan Lin#, Yichun He, Thomas Blum, Hao Zhao, Xin Tang, Wenbo Wang, Lishuai Jin, Zheliang Wang, Emma Hsiao, Paul Le Floch, Hao Shen, Ariel J. Lee, Rachael Alice Jonas-Closs, James Briggs, Siyi Liu, Daniel Solomon, Xiao Wang, Nanshu Lu, and Jia Liu* bioRxiv, 2024
Agentic AI for autonomous biological discovery
	An autonomous agent for scientific discovery in spatial biology Hanchen Wang#, Yichun He#, Paula Coelho#..., Aviv Regev In preparation, 2024
	Fine-Tuning Discrete Diffusion Models via Reward Optimization with Applications to DNA and Protein Design Chenyu Wang#, Masatoshi Uehara#, Yichun He, Amy Wang, Tommaso Biancalani, Avantika Lal, Tommi Jaakkola, Sergey Levine, Hanchen Wang, Aviv Regev arxiv, 2024