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2016

Fan Bai's lab

1.  Ma Q, Sowa Y, Baker M*, Bai F* “Conformational spread in the flagellar motor switch in response to CheY-P regulation and motor structural alterations”. Biophysical Journal (*corresponding author) 110 (2016), pp. 1411-1420.

2.  Xue R#, Li R#, Guo H#, Guo L#, Su Z, Ni X, Qi L, Zhang T, Li Q, Zhang Z, Xie XS, Bai F*, Zhang N* “Variable extent of intra-tumor heterogeneity revealed by genomic sequencing of multiple lesions in patients with hepatocellular carcinoma”. Gastroenterology (#equal contribution) (*corresponding author) 150 (2016), pp. 998-1008.

 

Yiqin Gao's lab

1.  Initial hydration behavior of sodium iodide dimer: photoelectron spectroscopy and ab initio calculations, R.Z. Li, G.L. Hou, C.W. Liu, H.G. Xu, X. Zhao*, Y.Q. Gao*, W.J. Zheng*, Phys. Chem. Chem. Phys. 18, 557-565 (2016).

2.  Molecular Dynamic Simulations of the Effects of Trimethylamine-N-oxide/Urea Mixture on the Hydration of Single-Walled Carbon Nanotube Interiors, L.J. Yang, Y.Q. Gao*, Acta Phys-chim Sin 32, 313-320 (2016).

3.  Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling, Y.I Yang, J. Zhang, X. Che, L.J. Yang , Y.Q. Gao*, J. Chem. Phys. 144, 094105 (2016).

4.  Ion Pairing in Alkali Nitrate Electrolyte Solutions, W. J. Xie, Z. Zhang, Y. Q. Gao*, J. Phys. Chem. B 120, 2343-2351 (2016).

5.  Structural Flexibility and Conformation Features of Cyclic Dinucleotides in Aqueous Solutions, X. Che, J. Zhang, Y.Y. Zhu, L.J. Yang, H. Quan, Y.Q. Gao*, J. Phys. Chem. B 120, 2670-2680 (2016).

6.  Direct Oxidation of Aliphatic C–H Bonds in Amino-Containing Molecules under Transition-Metal-Free Conditions, X. Li, X. Che, G.H. Chen, J. Zhang, J.L. Yan, Y.F. Zhang, L.S. Zhang, C.P. Hsu, Y.Q. Gao*, Z.J. Shi*, Org. Lett. 18, 1234-1237 (2016).

7.  Tuning Ice Nucleation with Counterions on Polyelectrolyte Brush Surfaces, Z. He, W.J. Xie, Z. Liu, G. Liu, Z. Wang, Y.Q. Gao*, J. Wang*, Science Advances 2, e1600345 (2016).

8.  Structural Characteristics of Homogeneous Hydrophobic Ionic Liquid-HNO3-H2O Ternary System: Experimental Studies and Molecular Dynamics Simulations, J. Fu, Y.I. Yang, J. Zhang, Q. Chen, X. Shen*, Y.Q. Gao*, J. Phys. Chem. B ASAP, DOI: 10.1021/acs.jpcb.6b01214.

9.  Tautomerization-dependent Recognition and Excision of Oxidation Damage in Base-excision DNA Repair, C.X. Zhu, J. Zhang, L. Lu, C.X. Zhu, L. Lu, J. Zhang, Z. Yue, J. Song, S. Zong, M.H. Liu, O.G. Stoviceke, Y.Q. Gao*, C.Q. Yi*, Proc. Natl. Acad. Sci. U S A (accepted).

 

 

Hao Ge's lab

1.  Ge, H. and Qian, H.: Nonequilibrium thermodynamic formalism of nonlinear chemical reaction systems with Waage–Guldberg’s law of mass action. Chemical Physics 472, 241–248 (2016)

2.  Zhao, Z.Q., Xie, X.S. and Ge, H.: Nonequilibrium Relaxation of Conformational Dynamics Facilitates Catalytic Reaction in an Elastic Network Model of T7 DNA Polymerase. J. Phys. Chem. B 120, 2869?2877 (2016)

 

Yanyi Huang's lab

1.  Yujiao Dang,# Liying Yan,# Boqiang Hu,# Xiaoying Fan, Yixin Ren, Rong Li, Ying Lian, Jie Yan, Qingqing Li, Yan Zhang, Min Li, Xiulian Ren, Jin Huang, Yuqi Wu, Ping Liu, Lu Wen, Chen Zhang, Yanyi Huang,* Fuchou Tang,* Jie Qiao* .Tracing the expression of circular RNAs in human pre-implantation embryos. Genome Biology 17 130 (2016) .doi: 10.1186/s13059-016-0991-3

2.  Chen Cao, Dong Zhou, Tao Chen, Aaron M. Streets,* Yanyi Huang*. Label-free Digital Quantification of Lipid Droplets in Single Cells by Stimulated Raman Microscopy on a Microfluidic Platform. Analytical Chemistry 88 (9), 4931-4939 (2016) .doi: 10.1021/acs.analchem.6b00862

3.  Yu Hou,# Huahu Guo,# Chen Cao, Xianlong Li, Boqiang Hu, Ping Zhu, Xinglong Wu, Lu Wen, Fuchou Tang,* Yanyi Huang,* Jirun Peng*. Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas. Cell Research 26 (3), 304-319 (2016) .doi: 10.1038/cr.2016.23

 

Xiaodong Su's lab

1.  Yu K, Yu Y, Tang X, Chen H, Xiao J, Su XD. “Transcriptome analyses of insect cells to facilitate baculovirus-insect expression.” Protein & Cell. 2016 Mar 26. [Epub ahead of print]

2.  Wang C, Dong X, Han L, Su XD, Zhang Z, Li J, Song J. “Identification of WD40 repeats by secondary structure-aided profile-profile alignment. ” J Theor Biol. 2016 Mar 25. pii: S0022-5193(16)00166-1. doi: 10.1016/j.jtbi.2016.03.025. [Epub ahead of print]

3.  Jianshi Jin, Tengfei Lian, Chan Gu, Kai Yu, Yi Qin Gao, Xiao-Dong Su Mechanistic studies of transcriptional regulation by non-CpG methylated DNA (2016) Scientific Reports accepted

 

Yujie Sun's lab

1.  Xuanze Chen, Zhiping Zeng, Rongqin Li, Boxin Xue, Yujie Sun*, and Peng Xi*, Superior performance with sCMOS over EMCCD in Super-resolution Optical Fluctuation Imaging (SOFI), J Biomed Optics, in press. (*co-corresponding)

2.  Pu Y, Zhao Z, Li Y, Zou J, Ma Q, Zhao Y, Ke Y, Zhu Y, Chen H, Baker MA, Ge H, Sun Y, Xie XS, Bai F, Enhanced Efflux Activity Facilitates Drug Tolerance in Dormant Bacterial Cells, Mol Cell, in press.

3.  Xuanze Chen, Weijian Zong,Rongqin Li, Zhiping Zeng, Jia Zhao, Peng Xi, Liangyi Chen and Yujie Sun, Two-photon light-sheet nanoscopy by ?uorescence ?uctuation correlation analysis, Nanoscale, 2016, 8, 9982–9987.

4.  Wanqing Du, Qian Peter Su, Yang Chen, Yueyao Zhu, Dong Jiang, Yueguang Rong, Senyan Zhang, Yixiao Zhang, He Ren, Chuanmao Zhang, Xinquan Wang, Ning Gao, Yanfeng Wang, Lingfei Sun, Yujie Sun* and Li Yu*, Dev Cell, 2016, 37, 326–336 (*co-corresponding)

5.  Qian Peter Su, Wanqing Du, Qinghua Ji, Boxin Xue, Dong Jiang, Yueyao Zhu, Jizhong Lou, Li Yu*, and Yujie Sun*, Vesicle Size Regulates Nanotube Formation in the Cell, Sci Rep, in press (*co-corresponding)

6.  Xuanze Chen, Mian Wei, M. Mocarlo Zheng, Jiaxi Zhao, Huiwen Hao, Lei Chang, Peng Xi, and Yujie Sun, Study of RNA Polymerase II Clustering inside Live-Cell Nuclei Using Bayesian Nanoscopy, ACS Nano, 2016, 10, 2447–54.

7.  Shipeng Shao, Weiwei Zhang, Huan Hu, Boxin Xue, Jinshan Qin, Chaoying Sun, Yuao Sun, Wensheng Wei, Yujie Sun, Long-term Dual-color Tracking of Genomic Loci by Modified sgRNAs of the CRISPR/Cas9 System, Nucleic Acids Res, 2016, Nucleic Acids Res., 2016, 44, e86.

 

Fuchou Tang's lab

1.  Zhou F, Li X, Wang W, Zhu P, Zhou J, He W, Ding M, Xiong F, Zheng X, Li Z, Ni Y, Mu X, Wen L, Cheng T, Lan Y, Yuan W*, Fuchou Tang*, Liu B*. Tracing haematopoietic stem cell formation at single-cell resolution. Nature, 533: 487-492 (2016) (*: 共同通讯作者).

2.  Wen L*, Tang Fuchou*. Single-cell sequencing in stem cell biology. Genome Biology 2016 17: 71 (2016) (*: 共同通讯作者) (Review).

3.  Hou Y, Guo H, Cao C, Li X, Hu B, Zhu P, Wu X, Wen L, Tang Fuchou*, Huang Y*, Peng J*. Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas. Cell Research 26: 304-319 (2016) (*: 共同通讯作者).

4.  Pan H, Guan D, Liu X, Li J, Wang L, Wu J, Zhou J, Zhang W, Ren R, Zhang W, Li Y, Yang J, Hao Y, Yuan T, Yuan G, Wang H, Ju Z, Mao Z, Li J, Qu J*, Tang Fuchou*, Liu GH*. SIRT6 safeguards human mesenchymal stem cells from oxidative stress by coactivating NRF2. Cell Research 26: 190-205 (2016) (*: 共同通讯作者).

5.  Yan L, Guo H, Hu B, Li R, Yong J, Zhao Y, Zhi X, Fan X, Guo F, Wang X, Wang W, Wei Y, Wang Y, Wen L, Qiao J*, Tang Fuchou*. Epigenomic landscape of human fetal brain, heart, and liver. Journal Biological Chemistry 291: 4386-4398 (2016) (*: 共同通讯作者).

 

Wensheng Wei's lab

1.  Shao, S., Zhang, W., Hu, H., Xue, B., Qin, J., Sun, C., Sun, Y., Wei, W., and Sun, Y. (2016). Long-term dual-color tracking of genomic loci by modified sgRNAs of the CRISPR/Cas9 system.   Nucleic Acids Res. doi: 10.1093/nar/gkw066.

2.  Zhou Y and Wei W*. (2016) Mapping regulatory elements. Nat Biotechnol 34, 151-152.

3.  Yang J, Guo S, Yuan P and Wei W*. (2016) TALEN – Methods and Protocols: Assembly of Customized TAL Effectors through Advanced ULtiMATE System. Methods Mol Biol. 1338:49-60. (Book chapter)

 

Xiaoliang Xie's lab

1.  Liying Yan,# Lei Huang,# Liya Xu,# Jin Huang,  Fei Ma, Xiaohui Zhu, Yaqiong Tang, Mingshan Liu, Ying Lian, Ping Liu, Rong Li, Sijia Lu, Fuchou Tang,* Jie Qiao,* X. Sunney Xie* "Live Births after Simultaneous Avoidance of Monogenic Diseases and Chromosome Abnormality by NGS with Linkage Analyses” , PNAS 2015-23297 (Accepted)

 

Zemin Zhang's lab

1.   X. Hu and Z. Zhang. (2016) Understanding the Genetic Mechanisms of Cancer Drug Resistance Using Genomic Approaches. Trends In Genetics. 32(2):127-37.

2.    R. Xue, R. Li, H. Guo, L. Guo, Z. Su, X. Ni, L. Qi, T. Zhang, Q. Li, Z. Zhang, X.S. Xie, F. Bai, and N. Zhang. (2016) Variable Extent of Intra-tumor Heterogeneity Revealed by Genomic Sequencing of Multiple Lesions in Patients with Hepatocellular Carcinoma. Gastroenterology. pii: S0016-5085(15)01861-2

 



2015

 Fan Bai's lab

1.  Xue R, Ma Q, Baker M*, Bai F* “A delicate nanoscale motor made by nature - the bacterial flagellar motor”. Advanced Science (*corresponding author) (2015), doi: 10.1002/advs. 201500129.

2.  Xue R#, Li R#, Guo H#, Guo L#, Su Z, Ni X, Qi L, Zhang T, Li Q, Zhang Z, Xie XS, Bai F*, Zhang N* “Genomic Comparison of Multiple Malignant Lesions from Patients with Hepatocellular Carcinoma”. Gastroenterology (#equal contribution) (*corresponding author) (in press)

3.  Chen X, Bai F*. “Single-cell analyses of circulating tumor cells”. Cancer Biology and Medicine (* corresponding author) 12 (2015), pp. 184-192.

4 Guo X*, Jin X, Lv X, Pu Y, Bai F* Real time visualization of perylene nano-clusters (PNCs) in water and their partitioning to graphene surface and macrophage cells. Environmental Science & Technology (*corresponding author) 49 (2015), pp. 7926-7933.

 

Yiqin Gao's lab

1.  Computer simulation studies of AB37-42 aggregation thermodynamics and kinetics in water and salt solution, I.Y. Yang, Y.Q. Gao*, J. Phys. Chem. B 119, 662-670 (2015).

2.  From Thermodynamics to Kinetics: Enhanced Sampling of Rare Events, L. Yang, C.W. Liu, Q. Shao, J. Zhang, Y.Q. Gao*, Acc. Chem. Res 48, 947–955 (2015).

3.  Understanding the Microsolvation of Salts in Molecular Clusters, C.W. Liu, Y.Q. Gao*, Intl. J. Quant. Chem. 115, 541-544 (2015).

4.  Conformational Preadjustment in Aqueous Claisen Rearrangement Revealed by SITS-QM/MM MD Simulations, J. Zhang, I.Y. Yang, L. Yang, Y.Q. Gao*, J. Phys. Chem. B 119, 5518-5530 (2015).

5.  The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells, F. Guo et al., Cell 161, 1437-1452 (2015).

6.  Accurate placement of substrate RNA by Gar1 in H/ACA RNA-guided pseudouridylation, P. Wang, L. Yang, Y.Q. Gao*, X.S. Zhao*, Nucl. Acids Res. 43, 7207-7216 (2015).

7.  Dual Reorientation Relaxation Routes of Water Molecules in Oxyanion’s Hydration Shell: A Molecular Geometry Perspective, W.J. Xie, Y.I. Yang, Y.Q. Gao*, J. Chem. Phys. 143, 224504 (2015).

8.  DNA Structural Correlation in Short and Long Ranges, C. Gu, J. Zhang, Y.I. Yang, X. Chen, H. Ge, Y.J. Sun, X.D. Su, L. Yang, S. Xie*, Y.Q. Gao*, J. Phys. Chem. B 119, 13980-13990 (2015).

9.  Dynamics and Kinetics Study of "In-Water" Chemical Reactions by Enhanced Sampling of Reactive Trajectories, J. Zhang, Y.I. Yang, L. Yang, Y.Q. Gao*, J. Phys. Chem. B 119, 14505-14514 (2015).

 

Hao Ge's lab

1.  Chen, H.Y., Shiroguchi, K., Ge, H. and Xie, X.S.:  Genome-wide study of mRNA degradation and transcript elongation in E.coli.  Mol Syst Biol.  11: 781 (2015)  (co-corresponding author)

2.  Ge, H.:  Macroscopic fluxes and local reciprocal relation in second-order stochastic processes far from equilibrium. J. Stat.  Mech. P01005 (2015)

3.  Ge, H., Qian, H. and Xie, X.S.:  Stochastic phenotype transition of a single cell in an intermediate region of gene state switching. Phys. Rev. Lett. 114, 078101 (2015)

4.  Wen, L., Li, J., Guo, H., Liu, X., Zheng, S., Zhang, D., Zhu, W., Qu, J., Guo, L., Du, D., Jin, X., Zhang, Y., Gao, Y., Shen, J., Ge, H., Tang, F., Huang, Y., Peng, J.:  Genome-scale detection of hypermethylated CpG islands in circulating cell free DNA of hepatocellular carcinoma patients.   Cell Res.  25 (11):1250-64 (2015)

5.  Gu, C., Zhang, J., Yang, Y.I., Chen, X., Ge, H., Sun, Y., Su, X., Yang, L.,  Xie, X.S. and Gao, Y.Q.:  DNA Structural Correlation in Short and Long Ranges. J. Phys. Chem. B. 119(44):13980-90 (2015)

6.  Ge, H.:  Mathematical laws of randomness. In Voices: Expanding the Biology Toolkit.  Cell 163, 1306 (2015)

 

Yanyi Huang's lab

1.  Gang Li,# Wenlu Zheng,# Zitian Chen,# Yu Zhou, Yu Liu, Junrui Yang, Yanyi Huang, Xiaoyu Li* . Design, Preparation, and Selection of DNA-encoded Dynamic Libraries. Chemical Science 6 (12), 7097-7104 (2015) . doi: 10.1039/C5SC02467F

2.  虞之龙,黄岩谊*. 集成微流控芯片在单细胞测序样品制备中的应用(综述). 中国科学 化学 45 (11), 1090-1101 (2015) . doi: 10.1360/N032015-00100 ( 封面论文 )

3.  Lu Wen,# Jingyi Li,# Huahu Guo,# Xiaomeng Liu,# Shengmin Zheng, Dafang Zhang, Weihua Zhu, Jianhui Qu, Limin Guo, Dexiao Du, Xiao Jin, Yuhao Zhang, Yun Gao, Jie Shen, Hao Ge, Fuchou Tang,* Yanyi Huang,* Jirun Peng* . Genome-scale detection of hypermethylated CpG islands in circulating cell-free DNA of hepatocellular carcinoma patients. Cell Research 25 (11), 1250-1264 (2015) . doi: 10.1038/cr.2015.126

4.  满奕, 李昂, 曹德昌, 林金星, 黄岩谊, 荆艳平*. 受激拉曼散射显微技术在生物科学中的应用. 电子显微学报 34 (3), 154-162 (2015) . doi: 10.3969/j.1000-6281.2015.02.014

5.  Tao Chen and Yanyi Huang*. Transient Absorption: A New Modality for Microscopic Imaging of Nanomaterials in Living Cells. Small 11 (38), 4998-5003 (2015) . doi: 10.1002/smll.201500814

6.  Yusi Fu, Chunmei Li, Sijia Lu, Wenxiong Zhou, Fuchou Tang, X. Sunney Xie,* Yanyi Huang*. Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification. Proceedings of the National Academy of Sciences of the United States of America 112 (38), 11923-11928 (2015) . doi: 10.1073/pnas.1513988112

7.  Xiaoying Fan,# Xiannian Zhang,# Xinglong Wu, Hongshan Guo, Yuqiong Hu, Fuchou Tang,* Yanyi Huang*. Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos. Genome Biology 16 148 (2015) . doi: 10.1186/s13059-015-0706-1

8.  Meiling Zhang, Tao Sun, Chongshu Jian, Lei Lei, Peidong Han, Quanlong Lv, Ran Yang, Xiaohai Zhou, Jiejia Xu, Yingchun Hu, Yongfan Men, Yanyi Huang, Chuanmao Zhang, Xiaojun Zhu, Xianhua Wang, Heping Cheng,* Jing- Wei Xiong*. Remodeling of Mitochondrial Flashes in Muscular Development and Dystrophy in Zebrafish. PLOS ONE 10 (7), e0132567 (2015) . doi: 10.1371/journal.pone.0132567

9.  Zitian Chen, Haifeng Duan,* Shuo Qiao, Wenxiong Zhou, Haiwei Qiu, Li Kang, X. Sunney Xie, Yanyi Huang*. Fluorogenic Sequencing Using Halogen-fluorescein Labeled Nucleotides. ChemBioChem 16 (8), 1153-1157 (2015) . doi: 10.1002/cbic.201500117 ( Featured as Front Cover )

10.  Fenghua Liu, Ruisheng Song, Yuanqing Feng, Jiaojiao Guo, Yanmin Chen, Yong Zhang, Tao Chen, Yanru Wang, Yanyi Huang, Chuan-Yun Li, Chunmei Cao, Yan Zhang, Xinli Hu,* Rui-ping Xiao*. Upregulation of MG53 Induces Diabetic Cardiomyopathy Through Transcriptional Activation of Peroxisome Proliferation-Activated Receptor α. Circulation 131 (9), 795-804 (2015) . doi: 10.1161/CIRCULATIONAHA.114.012285

11.  Jie Shen, Changzu Cai, Zhilong Yu, Yuhong Pang, Ying Zhou, Lili Qian, Wensheng Wei,* Yanyi Huang*. A microfluidic live cell assay to study anthrax toxin induced cell lethality assisted by conditioned medium. Scientific Reports 5 8651 (2015) . doi: 10.1038/srep08651

12.  Xiannian Zhang, Zitian Chen, Yanyi Huang*. A valve-less microfluidic peristaltic pumping method. Biomicrofluidics 9 (1), 014118 (2015) . doi: 10.1063/1.4907982

13.  Jie Shen,# Dongqing Jiang,# Yusi Fu,# Xinglong Wu,# Hongshan Guo, Binxiao Feng, Yuhong Pang, Aaron M. Streets, Fuchou Tang,* Yanyi Huang*. H3K4me3 epigenomic landscape derived from ChIP-Seq of 1,000 mouse early embryonic cells. Cell Research 25 (1), 143-147 (2015) . doi: 10.1038/cr.2014.119

14.  Yinqiu Cui, Li Song, Dong Wei, Yuhong Pang, Ning Wang, Chao Ning, Chunmei Li, Binxiao Feng, Wentao Tang, Hongjie Li, Yashan Ren, Chunchang Zhang, Yanyi Huang,* Yaowu Hu,* Hui Zhou*. Identification of kinship and occupant status in Mongolian noble burials of the Yuan Dynasty through a multidisciplinary approach. Philosophical Transactions of the Royal Society B 370 (1660), 20130378 (2015) . doi: 10.1098/rstb.2013.0378

 

Xiaodong Su's lab

1.  Xiao-Jun Wang, Qin Cao, Yan Zhang and Xiao-Dong Su* “Activation and Regulation of Caspase-6 and Its Role in Neurodegenerative Diseases” Annu. Rev. Pharmacol. Toxicol. 2015;55:553-72. doi: 10.1146/annurev-pharmtox-010814-124414. Epub 2014 Oct 17

2.  Xiao-Dong Su*, Heng Zhang, Thomas C. Terwilliger, Anders Liljas, Junyu Xiao and Yuhui Dong “Protein Crystallography from the Perspective of Technology Developments” (2015) Crystallogr Rev. 2015;21(1-2):122-153.

3.  Chen HM, Yu K, Tang XY, Bao ZS, Jiang T, Fan XL, Chen XW, Su XD. “Enhanced expression and phosphorylation of the MET oncoprotein by glioma-specific PTPRZ1-MET fusions.” FEBS Lett. 2015 Jun 4;589(13):1437-43. doi: 10.1016/j.febslet.2015.04.032. Epub 2015 Apr 29

4.  Gao J, Tao J, Liang W, Zhao M, Du X, Cui S, Duan H, Kan B, Su X*, Jiang Z.* Identification and characterization of phosphodiesterases that specifically degrade 3'3'-cyclic GMP-AMP. Cell Res. 2015 May;25(5):539-50. doi: 10.1038/cr.2015.40. Epub 2015 Apr 3.

5.  Heng Zhang1, Ming-Jie Han1, Jian-Li Tao1, Zhao-Yang Ye, Xiao-Xia Du, Ming-Jing Deng, Xiao-Yan Zhang, Lan-Fen Li, Zheng-Fan Jiang* and Xiao-Dong Su* Rat and human STINGs profile similarly towards anticancer/antiviral compounds Scientific Reports 2015in proof

6.  Gu C, Zhang J, Yang YI, Chen X, Ge H, Sun Y, Su X, Yang L, Xie S, Gao YQ. “DNA Structural Correlation in Short and Long Ranges.” J Phys Chem B. 2015 Nov 5;119(44):13980-90. doi: 10.1021/acs.jpcb.5b06217. Epub 2015 Oct 16.

 

Yujie Sun's lab

1.  Chong Wang, Wanqing Du, Qian Peter Su, Mingli Zhu, Peiyuan Feng, Ying Li,  Yichen Zhou, Na Mi, Yueyao Zhu, Dong Jiang, Senyan Zhang, Zerui Zhang,  Yujie Sun*, Li Yu*Dynamic tubulation of mitochondria drives mitochondrial network formationCell Research 2015 (*co-corresponding)

2.  Na Mi, Yang Chen, Shuai Wang, Mengran Chen, Mingkun Zhao, Guang Yang,  Meisheng Ma, Qian Su, Sai Luo, Jingwen Shi, Jia Xu, Qiang Guo, Ning Gao, Yujie Sun, Zhucheng Chen, Li YuCapZ regulates autophagosomal membrane shaping by promoting actin assembly inside the isolation membraneNature Cell Biology 08/2015

3.  Yongliang Li, Zhen Liu, Yifei Zhang, Qian P. Su, Boxin Xue, Shipeng Shao, Yun Zhu, Xiao Xu, Shicheng Wei, Yujie Sun, Live-cell and super-resolution imaging reveal that the distribution of wall-associated protein A is correlated with the cell chain integrity of Streptococcus mutansMolecular Oral Microbiology 2015

4.  X. Zhang, X. Chen, Z. Zeng, M. Zhang, Y. Sun, P. Xi*, J. Peng*, and P. Xu*,Development of a reversibly switchable protein for super-resolution optical fluctuation imaging, ACS Nano, 2015, doi: 10.1021/ nn5064387.

5.  Wang G, Li Y, Wang P, Liang H, Cui M, Zhu M, Guo L, Su Q, Sun Y, McNutt MA, Yin Y, PTEN regulates RPA1 and protects DNA replication forks, Cell Res. 2015

6.  Gu C, Zhang J, Yang YI, Chen X, Ge H, Sun Y, Su X, Yang L, Xie S1, Gao YQ, DNA Structural Correlation in Short and Long Ranges. J Phys Chem B, 2015, 119(44):13980-90

 

Fuchou Tang's lab

1.  Yan L, Huang L, Xu L, Huang J, Ma F, Zhu X, Tang Y, Liu M, Lian Y, Liu P, Li R, Lu S, Tang Fuchou*, Qiao J*, Xie XS*. Live births after simultaneous avoidance of monogenic diseases and chromosome abnormality by next-generation sequencing with linkage analyses. Proc Natl Acad Sci U S A 112: 15964-15969 (2015) (*: 共同通讯作者).

2.  Wen L*, Tang Fuchou*, How to catch rare cell types. Nature 52: 197-198 (2015) (*: 共同通讯作者) (Preview).

3.  Guo F, Yan L, Guo H, Li L, Hu B, Zhao Y, Yong J, Hu Y, Wang X, Wei Y, Wang W, Li R, Yan J, Zhi X, Zhang Y, Jin H, Zhang W, Hou Y, Zhu P, Li J, Zhang L, Liu S, Ren Y, Zhu X, Wen L, Gao Y, Tang Fuchou*, Qiao J*. The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells. Cell 161: 1437-1452 (2015) (*: 共同通讯作者).

4.  Zhang W, Li J, Suzuki K, Qu J, Wang P, Zhou J, Liu X, Ren R, Xu X, Ocampo A, Yuan T, Yang J, Li Y, Shi L, Guan D, Pan H, Suan S, Ding Z, Li M, Yi F, Bai R, Wang Y, Chen C, Yang F, Li X, Wang Z, Aizawa E, Goebl A, Soligalla RE, Reddy P, Esteban CR, Tang Fuchou*, Liu G* and Izpisua Belmonte JC*. A Human Stem Cell Model of Werner Syndrome Uncovers Heterochromatin Degeneration as an Aging Driver. Science 348: 1160-1163 (2015) (*: 共同通讯作者).

5.  Wen L*, Tang Fuchou*. Charting a Map through the Cellular Reprogramming Landscape. Cell Stem Cell 16: 215-216 (2015) (*: 共同通讯作者) (Preview).

6.  Wen L, Li J, Guo H, Liu X, Zheng S, Zhang D, Zhu W, Qu J, Guo L, Du D, Jin X, Zhang Y, Gao Y, Shen J, Ge H, Tang Fuchou*, Huang Y*, Peng J*. Genome-scale detection of hypermethylated CpG islands in circulating cell-free DNA of hepatocellular carcinoma patients. Cell Research 25: 1250-1264 (2015) (*: 共同通讯作者).

7.  Duan S, Yuan G, Liu X, Ren R, Li J, Zhang W, Wu J, Xu X, Fu L, Li Y, Yang J, Zhang W, Bai R, Yi F, Suzuki K, Gao H, Esteban CR, Zhang C, Izpisua Belmonte JC, Chen Z, Wang X, Jiang T, Qu J*, Tang Fuchou*, Liu GH*. PTEN deficiency reprogrammes human neural stem cells towards a glioblastoma stem cell-like phenotype. Nature Communications 6: 10068 (2015) (*: 共同通讯作者).

8.  Fan X, Zhang X, Wu X, Guo H, Hu Y, Tang Fuchou*, Huang Y*. Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos. Genome Biology 16: 148 (2015) (*: 共同通讯作者).

9.  Guo H, Zhu P, Guo F, Li X, Wu X, Fan X, Wen L*, Tang Fuchou*. Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing. Nature Protocols 10: 645-659 (2015) (*: 共同通讯作者).

10.  Wu Y, Zhou H, Fan X, Zhang Y, Zhang M, Wang Y, Xie Z, Bai M, Yin Q, Liang D, Tang W, Liao J, Zhou C, Liu W, Zhu P, Guo H, Pan H, Wu C, Shi H, Wu L* , Tang Fuchou*, Li J,* Correction of a Genetic Disease by CRISPR-Cas9-Mediated Gene Editing in Mouse Spermatogonial Stem Cells. Cell Research 25: 67-79 (2015) (*: 共同通讯作者).

11.  Shen J, Jiang D, Fu Y, Wu X, Guo H, Feng B, Pang Y, Streets AM, Tang Fuchou*, Huang Y*. H3K4me3 epigenomic landscape derived from ChIP-Seq of 1 000 mouse early embryonic cells. Cell Research 25: 143-147 (2015) (*: 共同通讯作者).

12Li Z, Gu TP, Weber AR, Shen JZ, Li BZ, Xie ZG, Yin R, Guo F, Liu X, Tang Fuchou, Wang H, Sch?r P, Xu GL. Gadd45a promotes DNA demethylation through TDG. Nucleic Acids Research 43: 3986-3997 (2015).

13.       Chapman AR, He Z, Lu S, Yong J, Tan L, Tang Fuchou, Xie XS. Single cell transcriptome amplification with MALBAC. PLoS One 10: e0120889 (2015).

 

Wensheng Wei's lab

1.  Yan L, Huang L, Xu L, Huang J, Ma F, Zhu X, Tang Y, Liu M, Lian Y, Liu P, Li R, Lu S, Tang Fuchou*, Qiao J*, Xie XS*. Live births after simultaneous avoidance of monogenic diseases and chromosome abnormality by next-generation sequencing with linkage analyses. Proc Natl Acad Sci U S A 112: 15964-15969 (2015) (*: 共同通讯作者).

2.  Wen L*, Tang Fuchou*, How to catch rare cell types. Nature 52: 197-198 (2015) (*: 共同通讯作者) (Preview).

3.  Guo F, Yan L, Guo H, Li L, Hu B, Zhao Y, Yong J, Hu Y, Wang X, Wei Y, Wang W, Li R, Yan J, Zhi X, Zhang Y, Jin H, Zhang W, Hou Y, Zhu P, Li J, Zhang L, Liu S, Ren Y, Zhu X, Wen L, Gao Y, Tang Fuchou*, Qiao J*. The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells. Cell 161: 1437-1452 (2015) (*: 共同通讯作者).

4.  Zhang W, Li J, Suzuki K, Qu J, Wang P, Zhou J, Liu X, Ren R, Xu X, Ocampo A, Yuan T, Yang J, Li Y, Shi L, Guan D, Pan H, Suan S, Ding Z, Li M, Yi F, Bai R, Wang Y, Chen C, Yang F, Li X, Wang Z, Aizawa E, Goebl A, Soligalla RE, Reddy P, Esteban CR, Tang Fuchou*, Liu G* and Izpisua Belmonte JC*. A Human Stem Cell Model of Werner Syndrome Uncovers Heterochromatin Degeneration as an Aging Driver. Science 348: 1160-1163 (2015) (*: 共同通讯作者).

5.  Wen L*, Tang Fuchou*. Charting a Map through the Cellular Reprogramming Landscape. Cell Stem Cell 16: 215-216 (2015) (*: 共同通讯作者) (Preview).

6.  Wen L, Li J, Guo H, Liu X, Zheng S, Zhang D, Zhu W, Qu J, Guo L, Du D, Jin X, Zhang Y, Gao Y, Shen J, Ge H, Tang Fuchou*, Huang Y*, Peng J*. Genome-scale detection of hypermethylated CpG islands in circulating cell-free DNA of hepatocellular carcinoma patients. Cell Research 25: 1250-1264 (2015) (*: 共同通讯作者).

7.  Duan S, Yuan G, Liu X, Ren R, Li J, Zhang W, Wu J, Xu X, Fu L, Li Y, Yang J, Zhang W, Bai R, Yi F, Suzuki K, Gao H, Esteban CR, Zhang C, Izpisua Belmonte JC, Chen Z, Wang X, Jiang T, Qu J*, Tang Fuchou*, Liu GH*. PTEN deficiency reprogrammes human neural stem cells towards a glioblastoma stem cell-like phenotype. Nature Communications 6: 10068 (2015) (*: 共同通讯作者).

8.  Fan X, Zhang X, Wu X, Guo H, Hu Y, Tang Fuchou*, Huang Y*. Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos. Genome Biology 16: 148 (2015) (*: 共同通讯作者).

9.  Guo H, Zhu P, Guo F, Li X, Wu X, Fan X, Wen L*, Tang Fuchou*. Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing. Nature Protocols 10: 645-659 (2015) (*: 共同通讯作者).

10.  Wu Y, Zhou H, Fan X, Zhang Y, Zhang M, Wang Y, Xie Z, Bai M, Yin Q, Liang D, Tang W, Liao J, Zhou C, Liu W, Zhu P, Guo H, Pan H, Wu C, Shi H, Wu L* , Tang Fuchou*, Li J,* Correction of a Genetic Disease by CRISPR-Cas9-Mediated Gene Editing in Mouse Spermatogonial Stem Cells. Cell Research 25: 67-79 (2015) (*: 共同通讯作者).

11.  Shen J, Jiang D, Fu Y, Wu X, Guo H, Feng B, Pang Y, Streets AM, Tang Fuchou*, Huang Y*. H3K4me3 epigenomic landscape derived from ChIP-Seq of 1 000 mouse early embryonic cells. Cell Research 25: 143-147 (2015) (*: 共同通讯作者).

12.  Li Z, Gu TP, Weber AR, Shen JZ, Li BZ, Xie ZG, Yin R, Guo F, Liu X, Tang Fuchou, Wang H, Sch?r P, Xu GL. Gadd45a promotes DNA demethylation through TDG. Nucleic Acids Research 43: 3986-3997 (2015).

13.  Chapman AR, He Z, Lu S, Yong J, Tan L, Tang Fuchou, Xie XS. Single cell transcriptome amplification with MALBAC. PLoS One 10: e0120889 (2015).

14.  Yang J, Guo S, Yuan P and Wei W*. (2016) TALEN – Methods and Protocols: Assembly of Customized TAL Effectors through Advanced ULtiMATE System. Methods Mol Biol. 1338:49-60. (book chapter)

15.  Peng J, Zhou Y, Zhu S and Wei W*. (2015) High-throughput Screens in Mammalian Cells Using the CRISPR-Cas9 System. FEBS Journal 282, 2089–2096.

16.  He R, Peng J, Yuan P, Xu F, Wei W*. (2015) Divergent roles of BECN1 in LC3 lipidation and autophagosomal function. Autophagy 11:5, 740-747.

17.  Ren Q, Li C, Yuan P, Cai C, Luo G, Zhang L and Wei W*. (2015) A Dual-Reporter System for Real-Time Monitoring and High-throughput CRISPR/Cas9 Library Screening of the Hepatitis C Virus. Sci. Rep. 5, 8865; DOI:10.1038/srep08865.

18.  Shen J, Cai C, Yu Z, Pang Y, Zhou Y, Qian L, Wei W* and Huang Y*. (2015) A microfluidic live cell assay to study anthrax toxin induced cell lethality assisted by conditioned medium. Sci. Rep. 5, 8651; DOI:10.1038/srep08651.

19.  Yuan P, Zhang H, Cai C, Zhu S, Zhou Y, Yang X, He R, Li C, Guo S, Li S, Huang T, Feng H and Wei W*. (2015) Chondroitin sulfate proteoglycan 4 functions as the cellular receptor for Clostridium difficile toxin B. Cell Res. 25:157-168.

 

Xiaoliang Xie's lab

1.  Huang, Lei; Ma, Fei; Chapman, Alec; Lu, Sijia and Xie, X. Sunney* "Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications," Annu Rev Genomics Hum Genet 16:79-102, DOI:10.1146/annurev-genom-090413-025352 (2015)

2.  Liying Yan,# Lei Huang,# Liya Xu,# Jin Huang,  Fei Ma, Xiaohui Zhu, Yaqiong Tang, Mingshan Liu, Ying Lian, Ping Liu, Rong Li, Sijia Lu, Fuchou Tang,* Jie Qiao,* X. Sunney Xie* "Live Births after Simultaneous Avoidance of Monogenic Diseases and Chromosome Abnormality by NGS with Linkage Analyses” , PNAS 2015-23297 (Accepted)

3.  Chen, Huiyi; Shiroguchi, Katsuyuki; Ge, Hao; Xie, X. Sunney "Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli," Mol Syst Biol 11:781 DOI:10.15252/msb.20145794 (2015)

4.  Ge, Hao; Qian, Hong; and Xie, X. Sunney "Stochastic Phenotype Transition of a Single Cell in an Intermediate Region of Gene State Switching," Phys Rev Lett 114(7), 078101, DOI:10.1103/PhysRevLett.114.078101 (2015)

5.  Xie, X. Sunney "Single Molecules Meet Genomics: Pinpointing Precision Medicine," JAMA 313, 2021-2022, DOI:10.1001/jama.2015.5533 (2015)

6.  Fu, Yusi; Li, Chunmei; Lu, Sijia; Zhou, Wenxiong; Tang, Fuchou; Xie, X Sunney and Huang, Yanyi "Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification," Proc Natl Acad Sci USA 112(38), 11923–11928, DOI:10.1073/pnas.1513988112 (2015)

7.  Chen, Z., Duan, H., Qiao, S., Zhou, W., Qiu, H., Kang, L., Xie, X. S. and Huang, Y. (2015), Fluorogenic Sequencing Using Halogen-Fluorescein-Labeled Nucleotides. ChemBioChem, 16: 1153–1157. doi: 10.1002/cbic.201500117

 

Zemin Zhang's lab

1.  X. Hu and Z. Zhang (2015) Understanding the genetic mechanisms of cancer drug resistance using genomic approaches. Trends in Genetics, (in press)

2.  Z. Wang, Z. Shen, Z. Li, J. Duan, S. Fu, Z. Liu, H. Bai, Z. Zhang, J. Zhao, X. Wang, J. Wang (2015) Activation of the BMP-BMPR pathway conferred resistance to EGFR-TKIs in lung squamous cell carcinoma patients with EGFR mutations. Proc Natl Acad Sci U S A. 112:9990-5

3.  F. Gnad*, S. Doll, G. Manning, D. Arnott, Z. Zhang* (2015) Bioinformatics analysis of thousands of TCGA tumors to determine the involvement of epigenetic regulators in human cancer. BMC Genomics. 16:S5

 

Xinsheng Zhao's lab

1.  Peng Wang, Lijiang Yang, Yi Qin Gao*, Xin Sheng Zhao*, Nucleic Acids Res. 2015, 43 (15) September 3, 7207-7216. “Accurate Placement of Substrate RNA by Gar1 in H/ACA RNA-guided Pseudouridylation”. doi: 10.1093/nar/gkv757

2.  Zhi Xin Lyu, Xin Sheng Zhao*, Biochem. Soc. Trans. 2015, 43 (2) April 7, 133-138. “Periplasmic Quality Control in Biogenesis of Outer Membrane Proteins”. doi:10.1042/BST20140217



2014

2014

Yiqin Gao's Lab

  1. Trehalose facilitates DNA melting: a single-molecule optical tweezers study, M., Alireza; B., Sergey; W., Roeland; G, Chan; Y. L. Yang; Y.Q. Gao; S. Tans*, Soft Matter, In press.
  2. Computer simulation studies of AB37-42 aggregation thermodynamics and kinetics in water and salt solution, I. Y. Yang, Y.Q. Gao*, J. Phys. Chem. B DOI: 10.1021/jp502169b
  3. Adsorption of water molecules on sodium-chloride trimer, C.W. Liu, G. L. Hou, W. Zheng*, and Y.Q. Gao*, Theo. Chem. Acc. DOI: 10.1007/s00214-01401550-1
  4. Pairing Preferences of the Model Mono-Valence Mono-Atomic Ions Investigated by Molecular Simulation Q. Zhang, R. Zhang, Y. Zhao, H. Li, Y. Q. Gao*, and W. Zhuang*, J. Chem. Phys. 140,184504 (2014).
  5. Combine Umbrella Sampling with Integrated Tempering Method for Efficient and Accurate Calculation of Free Energy Changes of Complex Energy Surface, M. Yang, L. Yang, Y.Q. Gao*, and H. Hu*, J. Chem. Phys. in Press.
  6. Dynamics of spontaneous flipping of a mismatched base in DNA duplex, Y. Yin, L. Yang, G. Zheng, C. Gu, C. Yi, C. He, Y.Q. Gao* and X. S. Zhao*,  PNAS, 111,8043-8048  (2014).
  7. How Quickly Can a β-hairpin Fold from Its Transition State? B. N. Markiewicz, L. Yang, R.M. Culik, Y.Q. Gao*, F. Gai*, J. Phys. Chem. B 118, 3317-3325 (2014).
  8. Stable salt/water cluster structures reflect the delicacy in the competition between ion-water and water-water interactions, C. Liu, L. Yang, X.-Z. Li, W.-J. Zheng*, and Y. Q. Gao*, J. Phys. Chem. B, 118,743-751 (2014).
  9. On the molecular mechanism of ion specific Hofmeister series, W. J. Xie, C. W. Liu, L. J. Yang, and Y. Q. Gao*, Science China-Chemistry, 57, 36-47 (2014).

 

Hao Ge's Lab

  1. Ge, H.: Time reversibility and nonequilibrium thermodynamics of second-order stochastic processes. Phys. Rev. E 89, 022127 (2014)
  2. Ge, H.: Stochastic Theory of Nonequilibrium Statistical Physics (review). Advances in Mathematics(China) 43, 161-174 (2014)
  3. Chong, S.S., Chen, C.Y., Ge, H. and Xie, X.S.: Mechanism of transcriptional bursting in bacteria. Cell 158, 314–326 (2014)
  4. Ouyang, X.H., Huang, X., Jin, X., Chen, Z., Yang, P.Y., Ge, H., Li, S.G. and Deng, X.W.: Coordinated photomorphogenic UV-B signaling network captured by mathematical modeling. Proc. Nat. Acad. Sci. (2014) (in press)
  5. 赵新生, 高毅勤, 黄岩谊, 孙育杰, 葛颢, 王任小, 徐平勇, 尉志武: 生物物理化学研究进展。化学通报 77, 699 (2014)

 

Yanyi Huang's Lab

  1. Yinqiu Cui, Li Song, Dong Wei, Yuhong Pang, Ning Wang, Chao Ning, Chunmei Li, Binxiao Feng, Wentao Tang, Hongjie Li, Yashan Ren, Chunchang Zhang, Yanyi Huang,* Yaowu Hu,* Hui Zhou*. Identification of kinship and occupant status in Mongolian noble burials of the Yuan Dynasty through a multidisciplinary approach. Philosophical Transactions of the Royal Society B Accepted for publication. (2014).
  2. Jie Shen,# Dongqing Jiang,# Yusi Fu,# Xinglong Wu,# Hongshan Guo, Binxiao Feng, Yuhong Pang, Aaron M. Streets, Fuchou Tang,* Yanyi Huang*.H3K4me3 epigenomic landscape derived from ChIP-Seq of 1,000 mouse early embryonic cells.Cell Research in press. (2014). doi: 10.1038/cr.2014.119
  3. Cheng Cao, Peng Zhao, Ze Li, Zitian Chen, Yanyi Huang, Yu Bai,* Xiaoyu Li*.DNA-Templated Synthesis of Encoded Small Molecules by DNA Self-Assembly.Chemical Communications 50 (75), 10997-10999 (2014). doi: 10.1039/C4CC03380A
  4. Aaron M. Streets, Ang Li, Tao Chen, Yanyi Huang*.Imaging without fluorescence: Non-linear optical microscopy for quantitative cellular imaging (Feature Article).Analytical Chemistry 86 (17), 8506-8513 (2014). doi: 10.1021/ac5013706(Cover article)
  5. Tao Chen,# Shouhui Chen,# Jihan Zhou, Dehai Liang, Xiaoyuan Chen,* Yanyi Huang* . Transient absorption microscopy of gold nanorods as spectrally orthogonal labels in live cells. Nanoscale 6 (18), 10536-10539 (2014). doi: 10.1039/c4nr03413a
  6. Peng Zhao, Zitian Chen, Yizhou Li, Dawei Sun, Yuan Gao, Yanyi Huang,* Xiaoyu Li*. Selection of DNA-Encoded Small Molecule Libraries Against Unmodified and Non-Immobilized Protein Targets. Angewandte Chemie Int. Ed. in press. (2014). doi: 10.1002/anie.201404830
  7. Dino Di Carlo,* Yanyi Huang, Helene Andersson-Svahn. Emerging investigators: new challenges spawn new innovations (Editorial). Lab on a Chip 14 (15), 2599-2600 (2014). doi: 10.1039/c4lc90058h
  8. 赵新生,高毅勤,黄岩谊,孙育杰,葛颢,王任小,徐平勇,尉志武. 生物物理化学研究进展.化学通报 77 (7), 699-702 (2014).
  9. Cuicui Su, Yuqiong Xia, Jianbo Sun, Nan Wang, Lin Zhu, Tao Chen, Yanyi Huang, Dehai Liang*. Liposomes Physically Coated with Peptides: Preparation and Characterization. Langmuir 30 (21), 6219-6227 (2014). doi: 10.1021/la501296r
  10. Aaron M. Streets,# Xiannian Zhang,# Chen Cao, Yuhong Pang, Xinglong Wu, Liang Xiong, Lu Yang, Yusi Fu, Liang Zhao,* Fuchou Tang,* Yanyi Huang*.Microfluidic single-cell whole transcriptome sequencing.Proceedings of the National Academy of Sciences of the United States of America 111 (19), 7048-7053 (2014). doi: 10.1073/pnas.1402030111
  11. Senlian Hong,# Tao Chen,# Yuntao Zhu, Ang Li, Yanyi Huang,* Xing Chen*.Live-cell stimulated Raman scattering imaging of alkyne-tagged biomolecules. Angewandte Chemie Int. Ed. 53 (23), 5827-5831 (2014). doi: 10.1002/anie.201400328
  12. Yuexin Zhou,# Shiyou Zhu,# Changzu Cai,# Pengfei Yuan, Chunmei Li, Yanyi Huang, Wensheng Wei*. High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells. Nature 509 (7501), 487-491 (2014). doi: 10.1038/nature13166
  13. Chunhong Zheng, Hongwei Zhou, Xinxing Liu, Yuhong Pang, Bo Zhang, Yanyi Huang*. Fish in chips: an automated microfluidic device to study drug dynamics in vivo using zebrafish embryos. Chemical Communications 50 (8), 981-984 (2014). doi: 10.1039/C3CC47285J
  14. Aaron M. Streets and Yanyi Huang*. Microfluidics for biological measurements with single-molecule resolution (Review Article). Current Opinion in Biotechnology 25 (1), 69-77 (2014). doi: 10.1016/j.copbio.2013.08.013

 

Fuchou Tang's Lab

  1. Wen L, Tang Fuchou*. Reconstructing Complex Tissues from Single-Cell Analyses. Cell 2014; 157: 771-773 (*: Corresponding author) (Preview).
  2. Streets AM, Zhang X, Cao C, Pang Y, Wu X, Xiong L, Yang L, Fu Y, Zhao L*, Tang Fuchou*, Huang Y*. Microfluidic single-cell whole-transcriptome sequencing. Proc Natl Acad Sci U S A. 2014; 111: 7048-7053 (*: Co-corresponding author).
  3. Wen L, Li X, Yan L, Tan Y, Li R, Zhao Y, Wang Y, Xie J, Zhang Y, Song C, Yu M, Liu X, Zhu P, Li X, Hou Y, Guo H, Wu X, He C*, Li R*, Tang Fuchou*, Qiao J*. Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain. Genome Biology 2014; 15: R49 (*: Co-corresponding author).
  4. Hu X, Zhang L, Mao SQ, Li Z, Chen J, Zhang RR, Wu HP, Gao J, Guo F, Liu W, Xu GF, Dai HQ, Shi YG, Li X, Hu B, Tang Fuchou, Pei D, Xu GL. Tet and TDG Mediate DNA Demethylation Essential for Mesenchymal-to-Epithelial Transition in Somatic Cell Reprogramming. Cell Stem Cell 2014; 14: 512-522.

 

Xinsheng Zhao's Lab

  1. 1 Guangqiao Liu, Guangtao Song, Danyang Zhang, Dejiu Zhang, Zhikai Li, Zhixin Lyu, Jianshu Dong, John Achenbach, Weimin Gong, Xin Sheng Zhao, Knud H Nierhaus, Yan Qin, Nat. Struct. Mol. Biol. 2014, on line. “EF-G catalyzes tRNA translocation by disrupting interactions between decoding center and codon–anticodon duplex”. doi:10.1038/nsmb.2869
  2. 2 赵新生, 高毅勤, 黄岩谊, 孙育杰, 葛 颢, 王任小, 徐平勇, 尉志武, 化学通报, 2014, 77 (7), 699 – 702. “生物物理化学研究进展”.
  3. 3 Dongchun Ni, Yan Wang, Xu Yang, Haizhen Zhou, Xiaomin Hou, Baohua Cao, Zhixin Lu, Xinsheng Zhao, Kun Yang, and Yihua Huang, FASEB J. 2014, 28 (6), 2677 – 2685. “Structural and functional analysis of the ?-barrel domain of BamA from Escherichia coli”. doi: 10.1096/fj.13-248450
  4. 4 Yandong Yin, Lijiang Yang, Guanqun Zheng, Chan Gu, Chengqi Yi, Chuan He, Yi Qin Gao, and Xin Sheng Zhao, Proc. Natl. Acad. Sci. U.S.A 2014, 111 (22), 8043 – 8048. “Dynamics of spontaneous flipping of a mismatched base in DNA duplex”. doi: 10.1073/pnas.1400667111
  5. 5 Xi Ge, Zhi-Xin Lyu, Yang Liu, Rui Wang, Xin Sheng Zhao, Xinmiao Fu, Zengyi Chang, J. Bacteriol. 2014, 196 (3), 672 – 680. “Identification of FkpA as a Key Quality Control Factor for the Biogenesis of Outer Membrane Proteins under Heat Shock Conditions”. doi: 10.1128/JB.01069-13
  6.  

 


2013

2013

Yujie Sun-Fan Bai-Sunney Xiaoliang Xie's Lab

1. He Y, Tsutsui M, Scheicher RH, Bai F, Taniguchi M, Kawai T “Thermophoretic manipulation of DNA translocation through nanopores”. ACS Nano 7 (2013), pp 538–546.

2. Sangjin Kim&, Erik Broströmer&, Dong Xing&, Jianshi Jin&, Shasha Chong, HaoGe, Siyuan Wang, Chan Gu, Lijiang Yang, Yi Qin Gao, Xiao-dong Su*, Yujie Sun*, X. SunneyXie*, Probing Allostery Through DNA. Science 2013, 339:816-819.

3. Ni X#, Zhuo M#, Su Z#, Duan J#, Gao Y#, Wang Z#, Zong C#, Bai H, Chapman A, Zhao J, Xu L, An T, Ma Q, Wang Y, Wu M, Sun Y, Wang S, Li Z, Yang X, Yong J, Su X, Lu Y, Bai F*, Xie XS*, Wang J* “Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients” Proceedings of the National Academy of Sciences USA (#equal contribution)(*corresponding author) 110 (2013), pp21083-21088.

4.Bai F, Che YS, Kami-ike N, Ma Q, Minamino T, Sowa Y, Namba K. “Populational heterogeneity vs. temporal fluctuation in Escherichia coli flagellar motor switching.” Biophysical Journal 105 (2013), pp 2123-2129.

 

Fuchou Tang's Lab

1.      Hou Y, Fan W, Yan L, Li R, Lian Y, Huang J, Li J, Xu L, Tang Fuchou*, Xie XS*, Qiao J*. Genome Analyses of Single Human Oocytes. Cell 2013; 155:1492-1506 (*: Co-corresponding author).

2.      Guo H, Zhu P, Wu X, Li X, Wen L, Tang Fuchou*. Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing. Genome Research 2013; 23: 2126-2135 (*: corresponding author). 

3.      Yan L, Yang M, Guo H, Yang L, Wu J, Li R, Liu P, Lian Y, Zheng X, Yan J, Huang J, Li M, Wu X, Wen L, Lao K, Li R*, Qiao J*, Tang Fuchou*. Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nature Structural & Molecular Biology 2013; 20: 1131-1139 (*: co-corresponding author). 

4.      Gan H, Wen L, Liao S, Lin X, Ma T, Liu J, Song CX, Wang M, He C, Han C*, Tang Fuchou*. Dynamics of 5-hydroxymethylcytosine during mouse spermatogenesis. Nature Communications 2013; 4: 1995 (*: co-corresponding author).

5.      Magnúsdóttir E, Dietmann S, Murakami K, Günesdogan U, Tang Fuchou, Bao S, Diamanti E, Lao K, Gottgens B, Surani MA. A tripartite transcription factor network regulates primordial germ cell specification in mice. Nature Cell Biology 2013; 15: 905-915.

6.      Zhang RR, Cui QY, Murai K, Lim YC, Smith ZD, Jin S, Ye P, Rosa L, Lee YK, Wu HP, Liu W, Xu ZM, Yang L, Ding YQ, Tang Fuchou, Meissner A, Ding C, Shi Y, Xu GL. Tet1 Regulates Adult Hippocampal Neurogenesis and Cognition. Cell Stem Cell 2013; 13: 237-245.

7.      Grabole N, Tischler J, Hackett JA, Kim S, Tang Fuchou, Leitch HG, Magnúsdóttir E, Surani MA. Prdm14 promotes germline fate and naive pluripotency by repressing FGF signalling and DNA methylation. EMBO Reports 2013; 14: 629-637.

 

Xinsheng Zhao's Lab

1. Peng Wang, Lijiang Yang, Pengcheng Liu, Yi Qin Gao, and Xin Sheng Zhao, Chem.-Eur. J. accepted. “Single Molecule Detection Reveals Knot Sliding in TrmD Denaturation”. doi: 10.1002/chem.201203809

2. Yandong Yin, Rongfeng Yuan, Xin Sheng Zhao, J. Phys. Chem. Lett. 2013, 4 (2), 304-309. “Amplitude of relaxations in fluorescence correlation spectroscopy for fluorophores that diffuse together”. doi: 10.1021/jz301871f

 

Yanyi Huang's Lab

1. Aaron M. Streets and Yanyi Huang. Chip in a Lab: Microfluidics for Next Generation Life Science Research. Biomicrofluidics 7 (1), 011302 (2013) . doi: 10.1063/1.4789751

2.Bo Xian, Jie Shen, Weiyang Chen, Na Sun, Nan Qiao, Dongqing Jiang, Tao Yu, Yongfan Men, Zhijun Han, Yuhong Pang, Matt Kaeberlein, Yanyi Huang,* Jing-Dong J. Han.* WormFarm: A quantitative control and measurement device towards automated C. elegans aging analysis. Aging Cell 2012, published online. doi:10.1111/acel.12063

3. Tao Chen,# Feng Lu,# Aaron M. Streets, Peng Fei, Junmin Quan, Yanyi Huang*. Optical Imaging of the Non-fluorescent Nanodiamonds in Live Cells Using Transient Absorption Microscopy. Nanoscale 5 (11), 4701-4705 (2013) . doi: 10.1039/C3NR00308F

 

Xiaodong Su's Lab

1. Sangjin Kim&, Erik Broströmer&, Dong Xing&, Jianshi Jin&, Shasha Chong, HaoGe, Siyuan Wang, Chan Gu, Lijiang Yang, Yi Qin Gao, Xiao-dong Su*, Yujie Sun*, X. SunneyXie*, Probing Allostery Through DNA. Science 2013, 339:816-819.

 

Hao Ge's Lab

1. Kim, S., Broströmer, E., Xing, D., Jin, J.S., Chong, S.S., Ge, H., Wang, S.Y., Gu, C., Yang, L., Gao, Y.Q., Su, X.D., Sun, Y.J. & Xie, X.S.: Probing allostery through DNA. Science 339 816 (2013)

2. Ge, H. and Qian, H.: Dissipation, generalized free energy, and a self-consistent nonequilibrium thermodynamics of chemically driven open systems. Phys. Rev. E 87 062125 (2013)

3. Xu, X.L., Ge, H., Gu, C., Gao, Y. Q., Wang, S.Y., Thio, B., Hynes, J., Xie, X.S. and Cao, J.S.: Modeling spatial correlation of DNA deformation: DNA allostery in protein binding. J. Phys. Chem. B 117, 13378−13387 (2013) (co-first-author)

 


2012

2012

Hao Ge's Lab
1. Ge, H., Pressé, S., Ghosh, K. and Dill, K.: Markov processes follow from the principle of maximum caliber. J. Chem. Phys. 136, 064108 (2012) (Research highlighted)
2. Ge, H.: Multivariable fluctuation theorems in the steady-state cycle kinetics of single enzyme with competing substrates. J. Phys. A: Math. Theor. 45 215002 (2012) (Research highlighted)
3. Ge, H. and Qian, H.: Landscapes of nongradient dynamics without detailed balance: stable limit cycles and multiple attractors. Chaos: An interdisciplinary journal of nonlinear science 22, 023140 (2012)
4. Ge, H. and Qian, H.: Analytical mechanics in stochastic dynamics: most probable path, large-deviation rate function and Hamilton–Jacobi equation. International Journal of Modern Physics B 26, 1230012 (2012)
5. Qian, H. and Ge, H.: Mesoscopic Biochemical Basis of Isogenetic Inheritance and Canalization: Stochasticity, Nonlinearity, and Emergent Landscape. Molecular & cellular biomechanics, 9, 1-16 (2012)
6. Zhang, Y.X., Ge, H. and Qian, H.: One-Dimensional Birth-Death Process and Delbruck-Gillespie Theory of Mesoscopic Nonlinear Chemical Reactions. Studies in applied mathematics 129, 328–345 (2012)
7. Kim, S., Broströmer, E., Xing, D., Jin, J., Chong, S., Ge, H., Wang, S., Su, X.D., Sun, Y. & Xie, X.S.: Probing allostery through DNA. Science (in press) (2013)

Yanyi Huang's Lab
1. Peng Fei, Zitian Chen, Yongfan Men, Ang Li, Yiran Shen, Yanyi Huang.* A compact optofluidic cytometer with integrated liquid-core /PDMS- cladding waveguides. Lab on a Chip 2012, 12(19), 3700-3706.
2. Chunhong Zheng, Zhilong Yu, Ying Zhou, Louis Tao, Yuhong Pang, Tao Chen, Xiannian Zhang, Haiwei Qiu, Hongwei Zhou, Zitian Chen, Yanyi Huang.* Live cell imaging analysis of the epigenetic regulation of the human endothelial cell migration at single cell resolution. Lab on a Chip 2012, 12(17), 3063-3072. 
3. Yongfan Men, Qiang Yu, Zitian Chen, Jianbin Wang, Yanyi Huang,* Hongwei Guo.* A high-throughput imaging system to quantitatively analyze the growth dynamics of plant seedlings. Integrative Biology 2012, 4(8), 945-952.
4. Zhilong Yu, Tao Chen, Xiannian Zhang, Dan Fu, Xin Liao, Jie Shen, Xinxing Liu, Bo Zhang, X. Sunney Xie, Xiaodong Su, Junyuan Chen,* Yanyi Huang.* Label-free chemical imaging in vivo: three-dimensional non-invasive microscopic observation of amphioxus notochord through stimulated Raman scattering (SRS). Chemical Science 2012, 3(8), 2646-2654.
5. Chunhong Zheng, Jingwen Wang, Yuhong Pang, Jianbin Wang, Wenbin Li, Zigang Ge,* Yanyi Huang.* High-throughput immunoassay through in-channel microfluidic patterning. Lab on a Chip 2012, 12(14), 2487-2490. (featured as inside front cover of the issue)
6. Yongfan Men, Yusi Fu, Zitian Chen, Peter A. Sims, William J. Greenleaf, Yanyi Huang.* Digital polymerase chain reaction in an array of femtoliter PDMS microreactors. Analytical Chemistry 2012, 84(10), 4262-4266.
7. Wentao Li, Tao Chen, Zitian Chen, Peng Fei, Zhilong Yu, Yuhong Pang, Yanyi Huang.* Squeeze-chip: A finger controlled microfluidic flow network device and its application to biochemical assays. Lab on a Chip 2012, 12(9), 1587-1590.
8. Peng Fei, Zhilong Yu, Xu Wang, Peter J. Lu, Yusi Fu, Zi He, Jingwei Xiong, Yanyi Huang.* High dynamic range optical projection tomography (HDR-OPT). Optics Express 2012, 20(8), 8824-8836.
9. Chunhong Zheng, Gui’e Chen, Yuhong Pang, Yanyi Huang.* An Integrated Microfluidic Device for Long-term Culture of Isolated Single Mammalian Cells. Science China Chemistry 2012, 55(4), 502-507. (featured as front cover of the issue) 
10. Ying Zhou, Yuhong Pang, Yanyi Huang.* Openly Accessible Microfluidic Liquid Handlers for Automated High-throughput Nanoliter Cell Culture. Analytical Chemistry 2012, 84(5), 2576-2584.
11. Chunhong Zheng, Liang Zhao, Gui’e Chen, Ying Zhou, Yuhong Pang, Yanyi Huang.* Quantitative Study of the Dynamic Tumor-endothelial Cell Interactions through an Integrated Microfluidic Coculture System. Analytical Chemistry 2012, 84(4), 2088-2093. 
12. Jie Shen, Ying Zhou, Tu Lu, Junya Peng, Zhixiang Lin, Lei Huang, Yuhong Pang, Li Yu, Yanyi Huang.* An Integrated Chip for Immunofluorescence and Its Application to Analyze Lysosomal Storage Disorders. Lab on a Chip 2012, 12, 317-324.
13. Tao Chen, Zhilong Yu, Xiannian Zhang, X. Sunney Xie, Yanyi Huang.* Coherent Raman Scattering Microscopy. (review article in Chinese) Scientia Sinica Chimica, 2012, 42(1), 1-16. (featured as back cover of the issue) 

Ruiqiang Li's Lab
1.Lu S, Zong C, Fan W, Yang M, Li J, Chapman AR, Zhu P, Hu X, Xu L, Yan L, Bai F, Qiao J, Tang F, Li R, Xie XS. (2012)Probing meiotic recombination and aneuploidy of single sperm cells by whole-genome sequencing. Science. 338(6114):1627-30. 
2. Guo, S., Zhang, J., Sun, H., Salse, J., Lucas, W., et. al. (2012)“The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions.” Nature Genetics. doi:10.1038/ng.2470
3. Li, S., Li, R., Li, H., et. al. (2012) “SOAPindel: Efficient identification of indels from short paired reads.” Genome Res. doi: 10.1101/gr.132480.111
4. Luo, R., Liu, C., …, Li, R., and Ting, H. (2012) “Efficient SNP-sensitive alignment and database-assisted SNP calling for low coverage samples.” ACM-BCB 12: 163-169. doi: 10.1145/2382936.2382957
5. Li, M., Wu, H., …, Li, R. #, Li, X. (2012) “Co-methylated genes in different adipose depots of pig are associated with metabolic, inflammatory and immune processes.” Int. J. Biol. Sci. 8(6):831-837. doi: 10.7150/ijbs.4493
6. Li, M., Wang, T., …, Li, R. #, Li, X. (2012) “Genome-wide DNA methylation changes between the superficial and deep backfat tissues of the pig.” Int. J. Mol. Sci. 13: 7098-7108. doi:10.3390/ijms13067098
7. Li, M., Wu, H., Luo, Z., …, Li, X., Li, R. # (2012) “An atlas of DNA methylomes in porcine adipose and muscle tissues.” Nature Comm doi:10.1038/ncomms1854
8. Fan, W., Li, R. #, (2012) “Test driving genome assemblers.” Nature Biotech [news & views] 30:330-331. doi: 10.1038/nbt.2172.
9. Liu, C., Wong, T., … Li, R. #, Lam, T. (2012) “SOAP3: ultra-fast GPU-based parallel alignment tool.” Bioinformatics. 28(6):878-9. doi:10.1093
10. Hvilsom, C., Qian, Y., …, Li, R., et. al. (2012) “Extensive X-linked adaptive evolution in central chimpanzees.” PNAS. doi:10.1073/pnas.1106877109
11. Jin L, Zhang M, Ma J, Zhang J, Zhou C, et al. (2012) “Mitochondrial DNA Evidence Indicates the Local Origin of Domestic Pigs in the Upstream Region of the Yangtze River.” PLoS ONE 7(12): e51649. doi:10.1371/journal.pone.0051649

Xiaodong Su's Lab
1. Cao Q, Wang XJ, Liu CW, Liu DF, Li LF, Gao YQ, Su XD*. “Inhibitory mechanism of caspase-6 phosphorylation revealed by crystal structures, molecular dynamics (MD) simulations and biochemical assays.” (2012) J Biol Chem. 287(19):15371-9. 
2. Kai-Tuo Wang, Benoit Desmolaize, Jie Nan, Xiao-Wei Zhang, Lan-Fen Li, Stephen Douthwaite* & Xiao-Dong Su* “Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA.” Nucleic acid research (2012) in press 
3. Li, D., Fu, T.-M., Nan, J., Liu, C., Li, L.-F., Su, X.-D*. “Structural basis for the autoinhibition of the C-terminal kinase domain of human RSK1” (2012) Acta Crystallogr D Biol Crystallogr. 2012 Jun; 68(Pt 6):680-5. 
4. H. Zhang, Z.-Q. Gao, L.-F. Li, X.-D. Su, Y.-H. Dong, Wen-Jia Wang, Guang-Feng Liu, Eleonora V. Shtykova, Jian-Hua Xu, Lan-Fen Li, Xiao-Dong Su*, Yu-Hui Dong* “The crystal structure of the MPN domain from the COP9 signalosome subunit CSN6” (2012) FEBS letters, 586(8):1147-53.
5. Yi-He Huang, Xiang-Yu Liu, Xiao-Xia Du, Zheng-Fan Jiang & Xiao-Dong Su* “The Structural Basis for the Sensing and Binding of Cyclic di-GMP by STING” (2012) Nature Structural & Molecular Biology, 2012 Jun 24;19(7):728-30. 
6. Chen Wang, Xiao-fang Cao , Xiang Liu, Lan-fen Li and Xiaodong Su* “Preliminary Crystallographic Analysis of the Hypothetical Protein SMU_2142 from Streptococcus mutans” (2012) Acta Crystallogr Sect F Struct Biol Cryst Commun. F68, 565-568 
7. Zhilong Yu, Tao Chen, Xiannian Zhang, Dan Fu, Xin Liao, Jie Shen, Xinxing Liu, Bo Zhang, X. Sunney Xie, Xiao-dong Su, Junyuan Chen,* Yanyi Huang.* “Label-free chemical imaging in vivo: three-dimensional non-invasive microscopic observation of amphioxus notochord through stimulated Raman scattering (SRS)”. Chemical Science 2012, 3(8), 2646-2654.
8. Xue-Xin Fan, Yan-Feng Zhou, Xiang Liu, Lanfen Li, and Xiao-Dong Su “Ellman’s Reagent DTNB in promoting Crystallization and Structural Determination of Anabeana CcbP” (2012) Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Nov 1;68 (Pt 11):1409-14.
9. Yu-He Liang, Rong Gao, and Xiao-Dong Su* “Structural Insights into the Broadened Substrate Profiles of an Extended-Spectrum β-Lactamase OXY-1-1 from Klebsiella oxytoca” (2012) Acta Crystallogr Sect D Struct Biol (2012) Nov;68(Pt 11):1460-7. 
10. Zhang H, Gao ZQ, Su XD, Dong YH. * “Crystal structure of type VI effector Tse1 from Pseudomonas aeruginosa” (2012) FEBS Lett. 2012 Jun 29. [Epub ahead of print] 
11. Wang Z, Wu Y, Li L, Su XD* “Intermolecular recognition revealed by the complex structure of human CLOCK-BMAL1 basic helix-loop-helix domains with E-box DNA.(2012) Cell Research 2012 Dec 11. doi: 10.1038/cr.2012.170. [Epub ahead of print]
12. Sun X, Wang Y, Zhang J, Tu J, Wang XJ, Su XD, Wang L, Zhang Y * “Tunneling-nanotube direction determination in neurons and astrocytes.” Cell Death Dis. 2012 Dec 6; 3:e438. doi: 10.1038/cddis.2012.177

Yujie Sun-Fan Bai-Sunney Xiaoliang Xie's Lab
1. Caporizzo, MA; Sun, Y; Goldman, YE; Composto, RJ, Nanoscale Topography Mediates the Adhesion of F-Actin, Langmuir 2012, 28, 12216 -12224.
2. Jianglan Liu, Yuting Zhao, Yujie Sun, Bing He, Changsong Yang, Tatyana Svitkina, Yale E. Goldman, and Wei Guo, “Exo70 Stimulates the Arp2/3 Complex for Lamellipodia Formation and Directional Cell Migration.” Curr. Biol. 2012,22, 1–7.
3. Beausang JF, Sun Y, Quinlan ME, Forkey JN, Goldman YE., “Orientation and Rotational Motions of Single Molecules by Polarized Total Internal Reflection Fluorescence Microscopy (polTIRFM).” Cold Spring Harb Protoc. 2012,5,535-545.
4. He Y, Tsutsui M, Scheicher RH, Bai F, Taniguchi M, Kawai T “Thermophoretic manipulation of DNA translocation through nanopores”. ACS Nano (2012), in press. 
5. Hu X, Yuan J, Shi Y, Lu J, Liu B, Li Z, Chen Z, Mu D, Zhang H, Li N, Yue Z, Bai F, Li H, Fan W “pIRS: Profile based illumina pair-end reads simulator”. Bioinformatics 28 (2012), pp. 1533-1535
6. Bai F, Wu Z, Jin J, Hochendoner P, Xing J. “Slow protein conformational change, allostery and network dynamics”, Protein-Protein Interactions-Computational and Experimental Tools, Dr. Weibo Cai (Ed.), ISBN: 978-953-51-0397-4, (2012), In Tech. 
7. Ma Q, Nicolau D, Berry R, Maini P. Bai F* “Conformational spread in the flagellar motor switch: a model study”. PLoS Computational Biology (*corresponding author) (2012), doi:10.1371/ journal.pcbi.1002523 
8. Bai F, Minamino T, Wu Z, Namba K, Xing J. “Coupling between switching regulation and torque generation in bacterial flagellar motor”. Physical Review Letters 108 (2012), 178105.

Xinsheng Zhao's Lab
1. Xinxing Yang, Jingqi Duan, Shuang Li, Peng Wang, Shoucai Ma, Keqiong Ye, Xin Sheng Zhao, Nucleic Acids Res. 2010, 40 (21), 10925-10936. “Kinetic and thermodynamic characterization of the reaction pathway of box H/ACA RNA-guided pseudouridine formation”. 
2. Zhi-Xin Lyu, Qiang Shao, Yi Qin Gao, Xin Sheng Zhao, PLoS ONE 2012, 7 (9), e46068. “Direct Observation of the Uptake of Outer Membrane Proteins by the Periplasmic Chaperone Skp”. 
3. Jing Ge, Zhao Fang Liu, Xin Sheng Zhao, Chin. J. Chem. 2012, 30 (9), 2023-2028. “Cocaine Detection in Blood Serum Using Aptamer Biosensor on Gold Nanoparticles and Progressive Dilution”. 
4. Yandong Yin, Peng Wang, Xin Xing Yang, Xun Li, Chuan He, Xin Sheng Zhao, Chem. Commun. 2012, 48 (59), 7413-7415. “Panorama of DNA hairpin folding observed via diffusion-decelerated fluorescence correlation spectroscopy”.

2011

2011

17. Liu X, Zhang H, Wang XJ, Li LF, Su XD. “Get phases from arsenic anomalous scattering: de novo SAD phasing of two protein structures crystallized in cacodylate buffer”. PLoS One. 2011;6(9):e24227. Epub 2011 Sep 2. 
16. Zeyong Zhi, Pengcheng Liu, Peng Wang, Yanyi Huang, Xin Sheng Zhao. “Domain Specific Folding Kinetics of Staphylococcal Nuclease Observed through Single-Molecule FRET in Microfluidic Mixer”. ChemPhysChem 2011, 12(18), 3515-3518. 
15. Yiandong Yin, Xin Sheng Zhao. "Kinetics and dynamics of DNA hybridization". Acc. Chem. Res. 2011, 44 (11), 1172-1181. 
14. Peng Fei, Zi He, Chunhong Zheng, Tao Chen, Yongfan Men, Yanyi Huang.* “Discretely Tunable Optofluidic Compound Microlenses”. Lab on a Chip 2011, 11(17), 2835-2841. (featured as back cover of the issue) [Highlighted in Nature Photonics] 
13. Liang Zhao, Jie Shen, Hongwei Zhou, Yanyi Huang.* “Integrated Microfluidic Chips”. Chinese Science Bulletin 2011, 56(23), 1855-1870. (review article in Chinese) 
12. Xiao-Dong Su, Frank J. Jin. Davydov-Pang model: An improved Davydov protein soliton theory Comment on “The theory of bio-energy transport in the protein molecules and its properties” by Xiaofeng Pang. Phys Life Rev. 2011 Aug 26. 
11. Ze-Yong Zhi, Peng-Cheng Liu, Yan-Yi Huang, Xin-Sheng Zhao. “A Microfluidic Mixer for Single-Molecule Kinetics Experiments”. Acta Physico-Chimica Sinica 2011, 27(8), 1990-1995. 
10. Yujie Sun and Yale E. Goldman. “Lever-Arm Mechanics of Processive Myosins”. Biophysical Journal 2011,101, 1-11. 
9. Yiandong Yin, Xin Sheng Zhao, “Kinetics and dynamics of DNA hybridization”. Acc. Chem. Res. 2011, on line, DOI: 10.1021/ar200068j. 
8. Xun Li, Yandong Yin, Xinxing Yang, Zeyong Zhi, and Xin Sheng Zhao, “Temperature Dependence of Interaction between Double Stranded DNA and Cy3 or Cy5”. Chem. Phys. Lett. 2011, 513 (4-6), 271-275. 
7. Si Wu, Xi Ge, Zhixin Lv, Zeyong Zhi, Zengyi Chang, and Xin Sheng Zhao, “Interaction between Bacterial Outer Membrane Proteins and Periplasmic Quality Control Factors: A Kinetic Partitioning Mechanism”. Biochem. J. 2011, 438 (3), 505-511. 
6. Fei Liu, Kangmin He, Xinxing Yang, Ning Xu, Zhangyi Liang, Ming Xu, Xinsheng Zhao, Qide Han, Youyi Zhang. “1A-Adrenergic Receptor Induces Activation of Extracellular Signal-Regulated Kinase 1/2 through Endocytic Pathway”. PLoS One 2011, 6 (6), e21520. 
5. Xun Li, Ruixue Zhu, Anchi Yu, and Xin Sheng Zhao, “Ultrafast Photoinduced Electron Transfer between Tetramethylrhodamine and Guanosine in Aqueous Solution”. J. Phys. Chem. B 2011, 115 (19), 6265-6271. 
4. Ruixue Zhu, Xun Li, Xin Sheng Zhao, and Anchi Yu. “Photophysical Properties of Atto655 Dye in the Presence of Guanosine and Tryptophan in Aqueous Solution”. J. Phys. Chem. B 2011, 115 (17), 5001-5007. 
3 Zhao Fang Liu, Jing Ge, and Xin Sheng Zhao. “Quantitative detection of adenosine in urine using silver enhancement of aptamer-gold nanoparticle aggregation and progressive dilution”. Chem. Commun. 2011, 47 (17), 4956–4958. 
2. Fuchou Tang, Lao K, Surani MA. “Development and applications of single-cell transcriptome analysis”. Nature Methods 2011; 8: S6-S11 (Review). 
1. Li, J. K; Sullan, R. M. A.; Zou, S.; Li, I. T. S.; Sun, Yujie.; Walker, G. C. (2011). Polymer Nanomechanics in Comprehensive Polymer Science, Matyjaszewski K. ; Möller, M., eds. (Academic Press, London) 
 

2010

2010

1. Xiaodong Su, JS Jin, X. Sunney Xie. “Enzyme Catalysis and Gene Expression Studies at Single Molecule Level”. Acta Phys. Chim. Sin.(Chinese), 2010, 26(7): 1976-87.