Yubao Cheng*, Miao Liu*, Mengwei Hu & Siyuan Wang, TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations, bioRXiv, doi:, (2021). *Co-first authors. (Link).

Miao Liu, Bing Yang, Mengwei Hu, Jonathan S.D. Radda, Yanbo Chen, Shengyan Jin, Yubao Cheng & Siyuan Wang, Chromatin tracing and multiplexed imaging of nucleome architectures (MINA) and RNAs in single mammalian cells and tissue, Nature Protocols, Volume 16, Pages 2667-2697 (2021). (Link).

Yanfang Lu*, Miao Liu*, Jennifer Yang, Sherman M. Weissman, Xinghua Pan#, Samuel G. Katz#, & Siyuan Wang#, Spatial transcriptome profiling by MERFISH reveals fetal liver hematopoietic stem cell niche architecture, Cell Discovery – Nature, in press. *Co-first authors. #Co-corresponding authors.


Mengwei Hu*, Bing Yang*, Yubao Cheng, Jonathan S.D. Radda, Yanbo Chen, Miao Liu & Siyuan Wang, ProbeDealer is a convenient tool for designing probes for highly multiplexed fluorescence in situ hybridization, Scientific Reports, Volume 10, Number 22031, (2020). *Co-first authors. (Link).

Mengwei Hu & Siyuan Wang, Chromatin tracing: Imaging 3D genome and nucleome, Trends in Cell Biology, Volume 31, Issue 1, Pages 5-8, (2020). (Link)

Miao Liu*, Yanfang Lu*, Bing Yang, Yanbo Chen, Jonathan S.D. Radda, Mengwei Hu, Samuel G. Katz & Siyuan Wang, Multiplexed imaging of nucleome architectures in single cells of mammalian tissue, Nature Communications, Volume 11, Number 2907, (2020). *Co-first authors. (Link)

Ahilya N. Sawh, Maxwell E.R. Shafer, Jun-Han Su, Xiaowei Zhuang,  Siyuan Wang & Susan E. Mango, Lamina-Dependent Stretching and Unconventional Chromosome Compartments in Early C. elegans Embryos, Molecular Cell, Volume 78, Issue 1, Pages 96-111, (2020). (Link)


Miao Liu*, Yanfang Lu*, Bing Yang, Yanbo Chen, Jonathan S.D. Radda, Mengwei Hu, Samuel G. Katz & Siyuan Wang, Multiplexed imaging of nucleome architectures in single cells of mammalian tissue,
bioRXiv, doi:, (2019). *Co-first authors. (Link)

Andrew E.S. Barentine, Yu Lin, Miao Liu, Phylicia Kidd, Leonhard Balduf, Michael R. Grace, Siyuan Wang, Joerg Bewersdorf & David Baddeley, 3D Multicolor Nanoscopy at 10,000 Cells a Day, bioRXiv, doi:, (2019). (Link)

2017 (before joining Yale)

Jinrong Wu, Wei Qu, Guangsu Huang, Siyuan Wang, Cheng Huang & Han Liu, Super-Resolution Fluorescence Imaging of Spatial Organization of Proteins and Lipids in Natural Rubber, Biomacromolecules, Volume. 18, Issue 6, Pages 1705-1712, (2017). (Link)


Siyuan Wang, Jun-Han Su, Brian J. Beliveau, Bogdan Bintu, Jeffrey R. Moffitt, Chao-ting Wu & Xiaowei Zhuang, Spatial organization of chromatin domains and compartments in single chromosomes, Science, Volume 353, Issue 6299, Pages 598-602, DOI: 10.1126/science.aaf8084, (2016). (Link) Highlighted in F1000Prime.

Siyuan Wang#, Jun-Han Su, Feng Zhang & Xiaowei Zhuang, An RNA-aptamer-based two-color CRISPR labeling system, Scientific Reports, Volume 6, Article 26857, (2016). #Corresponding author. (Link)

Jeffrey R. Moffitt, Shristi Pandey, Alistair N. Boettiger, Siyuan Wang & Xiaowei Zhuang, Spatial organization shapes the turnover of a bacterial transcriptome, Elife, Volume 5,  Article e13065, (2016). (Link)

Alistair N. Boettiger, Bogdan Bintu, Jeffrey R. Moffitt, Siyuan Wang, Brian J. Beliveau, Geoffrey Fundenberg, Maxim Imakaev, Leonid A. Mirny, Chao-ting Wu & Xiaowei Zhuang, Super-resolution imaging reveals distinct chromatin folding for different epigenetic states, Nature, Volume 529, Pages 418-422, (2016). (Link)


Kok Hao Chen, Alistair N. Boettiger, Jeffrey R. Moffitt, Siyuan Wang & Xiaowei Zhuang, Spatially resolved, highly multiplexed RNA profiling in single cells, Science, Volume 348, Issue 6233, aaa6090, (2015). (Link) Highlighted in F1000Prime.


Siyuan Wang, Jeffrey R. Moffitt, Graham T. Dempsey, X. Sunney Xie & Xiaowei Zhuang, Characterization and development of photoactivatable fluorescent proteins for single-molecule–based superresolution imaging, PNAS, Volume 111, Issue 23, Pages 8452-8457, (2014). (Link) Highlighted in F1000Prime.


Xinliang Xu, Hao Ge, Chan Gu, Yi Qin Gao, Siyuan S. Wang, Beng Joo Reginald Thio, James T. Hynes, X. Sunney Xie & Jianshu Cao, Modeling spatial correlation of DNA deformation: DNA allostery in protein binding, The Journal of Physical Chemistry B, Volume 117, Issue 42, Pages 13378-13387, (2013). (Link)

Sangjin Kim, Erik Brostromer, Dong Xing, Jianshi Jin, Shasha Chong, Hao Ge, Siyuan Wang, Chan Gu, Lijiang Yang, Yi Qin Gao, Xiao-dong Su, Yujie Sun & X. Sunney Xie, Probing Allostery Through DNA, Science, Volume 339, Issue 6121, Pages 816-819, (2013). (PDF)

Siyuan Wang & Ned S. Wingreen, Cell shape can mediate the spatial organization of the bacterial cytoskeleton, Biophysical Journal, Volume 104, Issue 3, Pages 541-552, (2013). (Link)

Siyuan Wang# & Joshua W. Shaevitz, The mechanics of shape in prokaryotes, Frontiers in Bioscience (Scholar Edition), Volume 5, Pages 564-574, (2013). #Corresponding author. (Link)


Siyuan Wang, Leon Furchtgott, Kerwyn Casey Huang & Joshua W. Shaevitz, Helical insertion of peptidoglycan produces chiral ordering of the bacterial cell wall, PNAS, Volume 109, Issue 10, Pages E595-E604, (2012). (Link)


Siyuan Wang, Mechanics, dynamics and organization of the bacterial cytoskeleton and cell wall, Ph. D. Dissertation, Princeton University, (2011). (Link)

Sven van Teeffelen, Siyuan Wang, Leon Furchtgott, Kerwyn Casey Huang, Ned S. Wingreen, Joshua W. Shaevitz & Zemer Gitai, The bacterial actin MreB rotates, and rotation depends on cell-wall assembly, PNAS, Volume 108, Issue 38, Pages 15822-15827, (2011). (Link) Highlighted by HFSP.


Siyuan Wang, Hugo Arellano-Santoyo, Peter A. Combs & Joshua W. Shaevitz, Actin-like cytoskeleton filaments contribute to cell mechanics in bacteria, PNAS, Volume 107, Issue 20, Pages 9182-9185, (2010). (Link)

Siyuan Wang, Hugo Arellano-Santoyo, Peter A. Combs & Joshua W. Shaevitz, Measuring the Bending Stiffness of Bacterial Cells Using an Optical Trap, JoVE, Volume 38, doi: 10.3791/2012, (2010). (Link)


Ming Ni*, Siyuan Wang* & Qi Ouyang, Modelling the SOS response by semi-stochastic simulation, Chinese Physics Letters, Volume 25, Number 7, Pages 2702-2705, (2008). *Co-first authors. (Link)

Ming Ni, Siyuan Wang, Jikun Li & Qi Ouyang, Simulating the temporal modulation of inducible DNA damage response in Escherichia coli, Biophysical Journal, Volume 93, Issue 1, Pages 62-73, (2007). (Link)

Siyuan Wang, Yuping Zhang & Qi Ouyang, Stochastic model of coliphage lambda regulatory network, Physical Review E, Volume 73, Issue 4, Article 041922, (2006). (Link)