2025
56, Jinchao Lv, Yunhui Kong, Gaowei Wang*, and Chunhe Li*, Decoding stochastic dynamics from single-cell snapshot data: towards therapeutic target identification in diabetes. submitted
55, Juntan Liu, Peijie Zhou*, Qing Nie* and Chunhe Li*, Reconstructing cellular trajectories and landscape from single-cell snapshots via stochastic dynamic optimal transport network. under review
54, Jingyu Dou, Wentao Lyu, Feng Chen, Qing Nie*, Chunhe Li*, Inferring stochastic dynamics by biophysical Neural ODE using single-cell transcriptomics, in revision
53, Feng Chen, Chunhe Li*, Reconstructing gene network structure and dynamics from single cell data. Bioinformatics, in press (2025).
52, Tao Zhu, Chunhe Li*, Xiakun Chu*, Transcriptional Condensates Encode a "Golden Mean" to Optimize Enhancer-Promoter Communication across Genomic Distances. Proc. Natl. Acad. Sci. 122: e2513371122 (2025).
51, Shirui Bian#, Ruisong Zhou#, Wei Lin*, Chunhe Li*, Protocol to quantify high-dimensional energy landscape of oscillatory systems using diffusion decomposition. STAR Protocols 6: 103922 (2025).
50, Jinchao Lv#, Song Zhang#, Chunhe Li*, Landscape control for cell fate transitions. Communications Physics 8: 240 (2025).
49, Shirui Bian#, Ruisong Zhou#, Wei Lin*, Chunhe Li*, Quantifying the energy landscape of high-dimensional oscillatory systems by diffusion decomposition. Cell Reports Physical Science 6: 102405 (2025).
2024
48, Tao Zhu, Chunhe Li*, Xiakun Chu*, Fluctuating chromatin facilitates enhancer-promoter communication by regulating transcriptional clustering dynamics. Journal of Physical Chemistry Letters, Cover Article, 15: 11428−11436 (2024).
47, Zihao Chen#, Jia Lu#, Xing-Ming Zhao, Haiyang Yu*, Chunhe Li*, Energy landscape reveals the underlying mechanism of cancer-adipose conversion in gene network models. Advanced Science 11: 2404854 (2024).
46, Ruisong Zhou, Yuguo Yu, Chunhe Li*, Revealing neural dynamical structure of C. elegans with deep learning. iScience 27: 109759 (2024).
45, Juntan Liu, Chunhe Li*, Data-driven energy landscape reveals critical genes in cancer progression. npj Systems Biology and Applications 10: 27 (2024).
44, Jinchao Lv, Jin Wang*, Chunhe Li*, Landscape quantifies the intermediate state and transition dynamics in ecological networks. PLOS Comput Biol, 20(1): e1011766 (2024).
43, Yun-Jun Sun, Barbara J Sahakian, Christelle Langley, Anyi Yang, Yuchao Jiang, Jujiao Kang, Xingming Zhao, Chunhe Li, Wei Cheng, Jianfeng Feng, Early-initiated childhood reading for pleasure: associations with better cognitive performance, mental well-being and brain structure in young adolescence. Psychological Medicine, 54: 359-373 (2024).
2023
42, Leijun Ye, Jianfeng Feng*, Chunhe Li*, Controlling brain dynamics: landscape and transition path for working memory. PLOS Comput Biol 19(9): e1011446 (2023).
41, Wei Xia, Jie Zou, Xingze Qiu, Feng Chen, Bing Zhu, Chunhe Li, Dong-Ling Deng, Xiaopeng Li*, Configured Quantum Reservoir Computing for Multi-Task Machine Learning. Science Bulletin 68: 2321–2329 (2023).
40, Lin Zhu#, Xin Kang#, Chunhe Li*, and Jie Zheng*, TMELand: An end-to-end pipeline for quantification and visualization of Waddington's epigenetic landscape based on gene regulatory network. IEEE/ACM Transactions on Computational Biology and Bioinformatics, doi: 10.1109/TCBB.2023.3285395 (2023).
39, Peng Ji#, Yufan Wang#, Thomas Peron*, Chunhe Li*, Jan Nagler, Jiulin Du*, Structure and function in artificial, zebrafish and human neural networks. Physics of Life Reviews 45: 74–111 (2023).
38, Feng Chen, Yubo Bai, Chunhe Li*, Estimation of non-equilibrium transition rate from gene expression data. Briefings in Bioinformatics, 24: bbad113 (2023).
37, Shirui Bian, Yunxin Zhang*, Chunhe Li*, An improved approach for calculating energy landscape of gene networks from moment equations. Chaos 33: 023116 (2023).
2022
36, Maalavika Pillai#, Zihao Chen#, Mohit Kumar Jolly*, Chunhe Li*, Quantitative landscapes reveal trajectories of cell-state transitions associated with drug resistance in melanoma. iScience 25: 105499 (2022).
35, Feng Chen, Chunhe Li*, Inferring structural and dynamical properties of gene networks from data with deep learning. NAR Genomics and Bioinformatics 4: lqac068 (2022).
34, Jintong Lang and Chunhe Li*, Unraveling the stochastic transition mechanism between oscillation states by landscape and minimum action path theory. Cover Article, Physical Chemistry Chemical Physics 24: 20050 (2022).
33, Nika Shakiba, Chunhe Li, Jordi Garcia-Ojalvo, Kwang-Hyun Cho, Kiran Patil, Aleksandra Walczak, Yang-Yu Liu, Seppe Kuehn, Qing Nie, Allon Klein, Gustavo Deco, Morten Kringelbach, Srividya Iyer-Biswas, How can Waddington-like landscapes facilitate insights beyond developmental biology? Cell Systems 13: 4-9 (2022).
32, Leijun Ye and Chunhe Li*, TGF-Beta Signaling Methods and Protocols: Energy Landscape Analysis of the Epithelial-Mesenchymal Transition Network. Book Chapter, Methods in Molecular Biology (2022).
2021
31, Xiaoguang Li#, Tongkai Li#, Chunhe Li* and Tiejun Li*, Uncovering the cell fate decision in lysis-lysogeny transition and stem cell development via Markov state modeling. J Chem Phys 155: 245101 (2021).
30, Leijun Ye and Chunhe Li*, Quantifying the landscape of decision making from spiking neural networks. Frontiers In Computational Neuroscience 15: 740601 (2021).
29, Jintong Lang, Qing Nie, and Chunhe Li*, Landscape and kinetic path quantify critical transitions in epithelial-mesenchymal transition. Biophysical J. 120: 4484–4500 (2021).
28, Chenyong Zhang and Chunhe Li*, Revealing the mechanism of lymphoid and myeloid cell differentiation and transdifferentiation through landscape quantification. Physical Review Research 3: 013186 (2021).
27, Xin Kang and Chunhe Li*, A dimension reduction approach for energy landscape: Identifying intermediate states in EMT-metastasis network. Advanced Science, 8: 2003133 (2021).
26, Leijun Ye, Zhuoqing Song, and Chunhe Li*, Landscape and flux quantify the stochastic transition dynamics for p53 cell fate decision. J Chem Phys 154: 025101 (2021).
2020
25, Zihao Chen and Chunhe Li*, Quantifying the Landscape and Transition Paths for Proliferation–Quiescence Fate Decisions. J Clin Med 9: 2582 (2020).
24, Xin Kang and Chunhe Li*, Landscape inferred from gene expression data governs pluripotency in embryonic stem cells. Computational and Structural Biotechnology Journal 18: 366–374 (2020).
2019
23, Chunhe Li* and Leijun Ye, Landscape and flux govern cellular mode-hopping between oscillations. J Chem Phys 151: 175101 (2019).
22, Yunbin Zhang, Ning Liu, Wei Lin and Chunhe Li*, Quantifying the interplay between genetic and epigenetic regulations in stem cell development. New Journal of Physics 21: 103042 (2019).
21, Xin Kang, Jin Wang* and Chunhe Li*, Uncovering the underlying relationships among metabolism, epithelial-mesenchymal transitions and cancer metastasis. iScience 21: 754-772 (2019).
20, Yujie Ye, Xin Kang, Jordan Bailey, Chunhe Li*, Tian Hong*, An enriched network motif family regulates multistep cell fate transitions with restricted reversibility. PLoS Comput Biol 15: e1006855 (2019). (* Co-corresponding author)
2018
19, Chunhe Li* and Gabor Balazsi, A landscape view on the interplay between EMT and cancer metastasis. npj Systems Biology and Applications, 4: 34 (2018).
18, Chunhe Li*, Lei Zhang*, Qing Nie*, Landscape reveals critical network structures for sharpening gene expression boundaries. BMC Syst. Biol. 12: 67 (2018).
17, Chunhe Li*, Landscape of gene networks for random parameter perturbation. Cover Article, Integr. Biol. 10, 92-99 (2018).
2017
16, Chunhe Li*, Identifying the optimal anticancer targets from the landscape of a cancer-immunity interaction network. Phys. Chem. Chem. Phys. 19, 7642-7651. (2017).
2016
15, Chunhe Li, Tian Hong, Chiu-Ho Webb, Heather Karner, Sha Sun*, Qing Nie*, A self-enhanced transport mechanism through long noncoding RNAs for X chromosome inactivation. Scientific Reports. 6: 31517 (2016).
14, Chunhe Li*, Tian Hong, and Qing Nie*, Quantifying the landscape and kinetic paths for epithelial-mesenchymal transition from a core circuit. Phys. Chem. Chem. Phys. 18, 17949-17956 (2016). (* Corresponding author)
2015
13, Chunhe Li and Jin Wang*,Quantifying the Landscape for Development and Cancer from a Core Cancer Stem Cell Circuit. Cancer Research, 75(13): 2607-18 (2015). doi: 10.1158/0008-5472.CAN-15-0079.
2014
12, Chunhe Li and Jin Wang*, Landscape and flux reveal a new global view and physical quantification of mammalian cell cycle. Proc. Natl. Acad. Sci. 111, 14130-14135 (2014). [Stony Brook News]: http://sb.cc.stonybrook.edu/news/research/924CancerStudy.php
11, Chunhe Li and Jin Wang*, Quantifying the underlying landscape and paths of cancer. J. R. Soc. Interface. 11:20140774 (2014).
[Stony Brook News]: http://sb.cc.stonybrook.edu/news/research/924CancerStudy.php
2013
10, Chunhe Li and Jin Wang*, Quantifying Waddington landscapes and paths of non-adiabatic cell fate decisions for differentiation, reprogramming and transdifferentiation. J. R. Soc. Interface. 10: 20130787. (2013). http://dx.doi.org/10.1098/rsif.2013.0787
9，Chunhe Li and Jin Wang*, Quantifying Cell Fate Decisions for Differentiation and Reprogramming of a Human Stem Cell Network: Landscape and Biological Paths. PLoS Comut. Biol. 9(8): e1003165 (2013)
2012
8, Chunhe Li, Erkang Wang*, and Jin Wang*, Landscape topography determines global stability and robustness of a metabolic network. ACS Synth. Biol., 2012, 1 (6), pp 229–239.
7, Chunhe Li, Erkang Wang*, and Jin Wang*, Potential flux landscapes determine the global stability of a Lorenz chaotic attractor under intrinsic fluctuations. J. Chem. Phys. 136, 194108 (2012).
2011
6, Chunhe Li, Erkang Wang*, and Jin Wang*, Landscape, Flux, Correlation, Resonance, Coherence, Stability and Key Network Wirings of Stochastic Circadian Oscillation. Biophys. J. 101, 1335-1344 (2011).
5, Chunhe Li, Erkang Wang*, and Jin Wang*, Potential Landscape and Probabilistic Flux of a Predator Prey Network. PLoS One 6, e17888:1-9 (2011).
4, Chunhe Li, Erkang Wang*, and Jin Wang*, Landscape and flux decomposition for exploring global natures of nonequilibrium dynamical systems under intrinsic statistical fluctuations. Chem. Phys. Lett. 505, 75-80 (2011).
3, Jin Wang*, Chunhe Li, Erkang Wang*, and Xidi Wang, A FPT Approach for Predicting Protein Localization from Yeast Genomic Data. PLoS One 6, e14449:1-11 (2011).
2010
2, Jin Wang*, Chunhe Li, and Erkang Wang*, Potential and flux landscapes quantify the stability and robustness of budding yeast cell cycle network. Proc. Natl. Acad. Sci. 107, 8195-8200 (2010).
2009
1, Jin Wang*, Chunhe Li, Erkang Wang*, and Xidi Wang*, Uncovering the rules for protein-protein interactions from yeast genomic data. Proc. Natl. Acad. Sci. 106, 3752-3757 (2009).