Structure-aware deep learning enhances m6A prediction and reveals cell type-associated RNA structural signatures.
Mingze Sun#; Di Zhang#*; Zhiyuan Li*; Yihan Lin*
PLOS Computational Biology, 2026, 22(8): e1014649.Research Output
Publications
Work from the lab spanning quantitative single-cell analysis, cellular programming, and synthetic and systems biology.
# equal contribution; * corresponding author
Widespread transcriptional memory shapes heritable states and functional heterogeneity in cancer and stem cells.
Yongjie Lin*; Xiangru Chen; Long Wu; Yutong Zhou; Yihan Lin*
Cell Systems, 2026, 101621.
Navigating high-order protein fitness landscapes via deep learning on directed evolution trajectories.
Chengzhi Song#; Liang Ma#; Lingfeng Xue; Yingfan Xu; Qihan Zhang; Yuxi Liu; Chen Song; Yihan Lin*
Proceedings of the National Academy of Sciences, 2026, 123(22).
Patient-derived organoid-immune co-cultures integrated with multi-omics reveal immunotherapy resistance mechanisms in urothelial carcinoma.
Shan Jiang#; Yuxuan Song#; Yun Peng#; Ran Yan#; Yunze Niu#; Baoqiang Chen; Jiaxing Lin; Jilin Wu; Shixiang Wang; Yiqing Du; Caipeng Qin; Yihan Lin*; Tao Xu*
iMeta, 2026
Orthogonal RNA replication enables directed evolution and Darwinian adaptation in mammalian cells.
Liang Ma; Yihan Lin*
Nature Chemical Biology, 2025, 21(3): 451-463.
Engineering virus-like particles for safe and versatile modeling of SARS-CoV-2 host interaction and immune escape.
Liang Ma#; Yuan Lin#; Siyu Ma; Kai Chen; Yihan Lin*
Communications Biology, 2025, 8(1): 1322.
Decoding cell fate: integrated experimental and computational analysis at the single-cell level.
Yutong Zhou; Shuyang Hou; Xinhao Miao; Guangxin Zhang; Zining Li; Di Zhang*; Yongjie Lin*; Yihan Lin*
Bioinformatics, 2025, 41(11): btaf603.
AI-enabled directed evolution for protein engineering and optimization.
Chengzhi Song; Yihan Lin*
Synthetic Biology Journal, 2025, 6(3): 617-635.
Harnessing the central dogma: Enzyme-driven gene diversification strategies for in cellulo continuous directed evolution.
Liang Ma*; Kai Chen; Yuan Lin; Yihan Deng; Siyu Ma; Yihan Lin*
Fundamental Research, 2025, In press, corrected proof.
Tertiary lymphoid structures are linked to enhanced antitumor immunity and better prognosis in muscle-invasive bladder cancer.
Jiaxing Lin; Shan Jiang; Baoqiang Chen; Yiqing Du; Caipeng Qin; Yuxuan Song; Yun Peng; Mengting Ding; Jilin Wu; Yihan Lin*; Tao Xu*
Advanced Science, 2025, 12(7): 2410998.
Promoter DNA methylation and transcription factor condensation are linked to transcriptional memory in mammalian cells.
Shenqi Fan#; Liang Ma#*; Chengzhi Song; Xu Han; Bijunyao Zhong; Yihan Lin*
Cell Systems, 2024, 15(9): 808-823.e6.
Dissecting and improving gene regulatory network inference using single-cell transcriptome data.
Lingfeng Xue; Yan Wu; Yihan Lin
Genome Research, 2023, 33(9): 1609-1621.
Deciphering a global source of non-genetic heterogeneity in cancer cells.
Jianhan Zhang#; Xu Han#; Liang Ma; Shuhui Xu; Yihan Lin*
Nucleic Acids Research, 2023, 51(17): 9019-9038.
NFAT and NF-kB dynamically co-regulate TCR and CAR signaling responses in human T cells.
Wen Huang; Wei Lin; Baoqiang Chen; Jianhan Zhang; Peifen Gao; Yingying Fan; Yihan Lin*; Ping Wei*
Cell Reports, 2023, 42(7): 112663.
Modulating gene regulation function by chemically controlled transcription factor clustering.
Jiegen Wu#; Baoqiang Chen#; Yadi Liu; Liang Ma; Wen Huang; Yihan Lin*
Nature Communications, 2022, 13(1): 2663.
Profiling transcription factor activity dynamics using intronic reads in time-series transcriptome data.
Yan Wu#; Lingfeng Xue#; Wen Huang#; Minghua Deng; Yihan Lin*
PLOS Computational Biology, 2022, 18(1): e1009762.
Proteomic mapping and targeting of mitotic pericentriolar material in tumors bearing centrosome amplification.
Bingteng Xie; Yang Pu; Fan Yang; Wei Chen; Wei Yue; Jihong Ma; Na Zhang; Yuening Jiang; Jiegen Wu; Yihan Lin; Xin Liang; Chu Wang; Peng Zou*; Mo Li*
Cancer Research, 2022, 82(14): 2576-2592.
Co-condensation between transcription factor and coactivator p300 modulates transcriptional bursting kinetics.
Liang Ma; Zeyue Gao; Jiegen Wu; Bijunyao Zhong; Yuchen Xie; Wen Huang; Yihan Lin*
Molecular Cell, 2021, 81(8): 1682-1697.e7.
Yeast cell fate control by temporal redundancy modulation of transcription factor paralogs.
Yan Wu; Jiaqi Wu; Minghua Deng; Yihan Lin*
Nature Communications, 2021, 12(1): 3145.
Evidence for rate-dependent filtering of global extrinsic noise by biochemical reactions in mammalian cells.
Jiegen Wu; Xu Han; Haotian Zhai; Tingyu Yang; Yihan Lin*
Molecular Systems Biology, 2020, 16(5): e9335.
Dissecting the regulation and function of ATP at the single-cell level.
Jianhan Zhang#; Xu Han#; Yihan Lin*
PLOS Biology, 2018, 16(12): e3000095.