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Jinchao Lv, Jin Wang*, Chunhe Li*, Landscape quantifies the intermediate state and transition dynamics in ecological networks. PLOS Comput Biol, 20(1): e1011766. https://doi.org/10.1371/journal.pcbi.1011766 (2024)
Leijun Ye, Jianfeng Feng*, Chunhe Li*, Controlling brain dynamics: landscape and transition path for working memory. PLOS Comput Biol, 19(9): e1011446. (2023)
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, 1-15 (2023)
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)
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)
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)
Feng Chen, Yubo Bai, Chunhe Li*, Estimation of non-equilibrium transition rate from gene expression data. Briefings in Bioinformatics, 24: bbad113 (2023).
Shirui Bian, Yunxin Zhang*, Chunhe Li*, An improved approach for calculating energy landscape of gene networks from moment equations. Chaos 33: 023116 (2023)
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)
Feng Chen, Chunhe Li*, Inferring structural and dynamical properties of gene networks from data with deep learning. NAR Genomics and Bioinformatics 4: lqac068 (2022)
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)
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).
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).
Leijun Ye and Chunhe Li*, Energy Landscape Analysis of the Epithelial-Mesenchymal Transition Network. Book Chapter, Methods in Molecular Biology (2021).
Leijun Ye and Chunhe Li*, Quantifying the landscape of decision making from spiking neural networks. Frontiers In Computational Neuroscience, 15: 740601 (2021).
Jintong Lang, Qing Nie, and Chunhe Li*, Landscape and kinetic path quantify critical transitions in epithelial-mesenchymal transition. Biophysical J. 120: 4484–4500 (2021).
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).
Xin Kang and Chunhe Li*, A dimension reduction approach for energy landscape: Identifying intermediate states in EMT-metastasis network. Advanced Science, 8: 2003133 (2021).
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).
Zihao Chen and Chunhe Li*, Quantifying the Landscape and Transition Paths for Proliferation–Quiescence Fate Decisions. J Clin Med, 9: 2582 (2020).
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).
Chunhe Li* and Leijun Ye, Landscape and flux govern cellular mode-hopping between oscillations. J Chem Phys 151: 175101 (2019).
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).
Xin Kang, Jin Wang* and Chunhe Li*, Exposing the Underlying Relationship of Cancer Metastasis to Metabolism and Epithelial-Mesenchymal Transitions. iScience 21: 754-772 (2019).
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(3): e1006855 (2019). (* corresponding authors)
Chunhe Li* and Gabor Balazsi, A landscape view on the interplay between EMT and cancer metastasis. npj Systems Biology and Applications 4: 34 (2018).
Chunhe Li*, Lei Zhang*, Qing Nie*, Landscape reveals critical network structures for sharpening gene expression boundaries. BMC Systems Biology 12: 67 (2018).
Chunhe Li*, Landscape of gene networks for random parameter perturbation. Journal Cover Article, Integr. Biol. 10, 92-99, (2018). http://dx.doi.org/10.1039/C7IB00198C
Chunhe Li*, Identifying the optimal anticancer targets from the landscape of a cancer-immunity interaction network. Phys. Chem. Chem. Phys. 19, 7642-7651 (2017).
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).
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 authors)
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).
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 BrookNews]: http://sb.cc.stonybrook.edu/news/research/924CancerStudy.php
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
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).
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)
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.
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).
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).
Chunhe Li, Erkang Wang*, and Jin Wang*, Potential Landscape and Probabilistic Flux of a Predator Prey Network. PLoS One 6, e17888:1-9 (2011).
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).
Jin Wang*, Chunhe Li, Erkang Wang*, and Xidi Wang, A FPT Approach for Predicting Protein Localization from Yeast Genomic Data. PLoS One 6, e14449 (2011).
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).
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).
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