2024
Nikki Bialy, Frank Alber, Brenda Andrews, Michael Angelo, Brian Beliveau, Lacramioara Bintu, Alistair Boettiger, Ulrike Boehm, Claire M. Brown, Mahmoud Bukar Maina, James J. Chambers, Beth A. Cimini, Kevin Eliceiri, Rachel Errington, Orestis Faklaris, Nathalie Gaudreault, Ronald N. Germain, Wojtek Goscinski, David Grunwald, Michael Halter, Dorit Hanein, John W. Hickey, Judith Lacoste, Alex Laude, Emma Lundberg, Jian Ma, Leonel Malacrida, Josh Moore, Glyn Nelson, Elizabeth Kathleen Neumann, Roland Nitschke, Shuichi Onami, Jaime A. Pimentel, Anne L. Plant, Andrea J. Radtke, Bikash Sabata, Denis Schapiro, Johannes Schöneberg, Jeffrey M. Spraggins, Damir Sudar, Wouter-Michiel Adrien Maria Vierdag, Niels Volkmann, Carolina Wählby, Siyuan (Steven) Wang, Ziv Yaniv, Caterina Strambio-De-Castillia, Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data, arXiv:2401.13022, (2024). (Link)
2023
Leon Tejwani*#, Neal G. Ravindra*, Changwoo Lee*, Yubao Cheng*, Billy Nguyen, Kimberly Luttik, Luhan Ni, Shupei Zhang, Logan M. Morrison, John Gionco, Yangfei Xiang, Jennifer Yoon, Hannah Ro, Fatema Haidery, Rosalie M. Grijalva, Eunwoo Bae, Kristen Kim, Regina T. Martuscello, Harry T. Orr, Huda Y. Zoghbi, Hayley S. McLoughlin, Laura P.W. Ranum, Vikram G. Shakkottai, Phyllis L. Faust, Siyuan Wang#, David van Dijk# & Janghoo Lim#, Longitudinal single-cell transcriptional dynamics throughout neurodegeneration in SCA1, Neuron, https://doi.org/10.1016/j.neuron.2023.10.039, (2023). *Co-first authors. #Co-corresponding authors. (Link)
Lauren Dickinson, Wenxin Yuan, Chantal LeBlanc, Geoffrey Thomson, Siyuan Wang & Yannick Jacob, Regulation of gene editing using T-DNA concatenation, Nature Plants, https://doi.org/10.1038/s41477-023-01495-w, (2023). (Link)
Benjamin Patterson*, Bing Yang*, Yoshiaki Tanaka, Kun-Yong Kim, Bilal Cakir, Yangfei Xiang, Jonghun Kim, Siyuan Wang# & In-Hyun Park#, Female naïve human pluripotent stem cells carry X chromosomes with Xa-like and Xi-like folding conformations, Science Advances, Vol 9, Issue 31, DOI: 10.1126/sciadv.adf2245, (2023). *Co-first authors. #Co-corresponding authors. (Link)
Miao Liu*, Shengyan Jin*, Sherry S. Agabiti*, Tyler B. Jensen, Tianqi Yang, Jonathan S. D. Radda, Christian F. Ruiz, Gabriel Baldissera, Mandar Deepak Muzumdar# & Siyuan Wang#, A genome-wide single-cell 3D genome atlas of lung cancer progression, bioRXiv, doi: https://doi.org/10.1101/2023.07.23.550157, (2023). *Co-first authors. #Co-corresponding authors. (Link)
Andrew E. S. Barentine, Yu Lin, Edward M. Courvan, Phylicia Kidd, Miao Liu, Leonhard Balduf, Timy Phan, Felix Rivera-Molina, Michael R. Grace, Zach Marin, Mark Lessard, Juliana Rios Chen, Siyuan Wang, Karla M. Neugebauer, Joerg Bewersdorf & David Baddeley, An integrated platform for high-throughput nanoscopy, Nature Biotechnology, https://doi.org/10.1038/s41587-023-01702-1, (2023). (Link)
Dennis May, Sangwon Yun, David Gonzalez, Sangbum Park, Yanbo Chen, Elizabeth Lathrop, Biao Cai, Tianchi Xin, Hongyu Zhao, Siyuan Wang, Lauren E. Gonzalez, Katie Cockburn, Valentina Greco, Live imaging reveals chromatin compaction transitions and dynamic transcriptional bursting during stem cell differentiation in vivo, eLife, https://doi.org/10.7554/eLife.83444, (2023). (Link)
Yubao Cheng*, Mengwei Hu*, Bing Yang*, Tyler B Jensen*, Tianqi Yang, Ruihuan Yu, Zhaoxia Ma, Jonathan S D Radda, Shengyan Jin, Chongzhi Zang & Siyuan Wang, Perturb-tracing enables high-content screening of multiscale 3D genome regulators, bioRXiv, doi: https://doi.org/10.1101/2023.01.31.525983, (2023). *Co-first authors. (Link).
2022
SenNet Consortium, NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health, Nature Aging, Volume 2, Pages 1090-1100 (2022). (Link).
Dennis May, Sangwon Yun, David Gonzalez, Sangbum Park, Yanbo Chen, Elizabeth Lathrop, Biao Cai, Tianchi Xin, Hongyu Zhao, Siyuan Wang, Lauren E. Gonzalez, Katie Cockburn & Valentina Greco, Live imaging reveals chromatin compaction transitions and dynamic transcriptional bursting during stem cell differentiation in vivo, bioRXiv, doi: https://doi.org/10.1101/2022.10.07.511316, (2022). (Link).
Yubao Cheng & Siyuan Wang, New mechanism of chromatin compartmentalization by BRD2, Trends in Genetics, https://doi.org/10.1016/j.tig.2022.06.016, (2022). (Link).
2021
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, Genome Biology, Volume 22, Number 309, (2021). *Co-first authors. (Link).
Liana Boraas*, Mengwei Hu*, Lauren Thornton, Charles E. Vejnar, Gang Zhen, Antonio J. Giraldez, Christine Mayr, Siyuan Wang# & Stefania Nicoli#, Non-coding function for mRNAs in focal adhesion architecture and mechanotransduction, bioRXiv, doi: https://doi.org/10.1101/2021.10.04.463097, (2021). *Co-first authors. #Co-corresponding authors. (Link).
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: https://doi.org/10.1101/2021.05.12.443887, (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, Volume 7, Number 47 (2021). *Co-first authors. #Co-corresponding authors. (Link)
Featured by Genetic Engineering & Biotechnology News (GEN). (Link)
2020
Mengwei Hu & Siyuan Wang, Chromatin tracing: Imaging 3D genome and nucleome, Trends in Cell Biology, Volume 31, Issue 1, Pages 5-8, (2020). (Link)
Selected as Best of 2021: Trends in Cell Biology. (Link)
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).
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)
Featured by BioArt.
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)
2019
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: https://doi.org/10.1101/2019.12.20.885277, (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: https://doi.org/10.1101/606954, (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)
2016
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)
2015
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.
2014
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.
2013
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). (Link)
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)
2012
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)
2011
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.
2010
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)
2006-2008
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)