研究成果

白凡

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.

 

高毅勤

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).

 

 

葛颢

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)

 

黄岩谊

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

 

苏晓东

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

 

孙育杰

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.

 

汤富酬

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).

 

魏文胜

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)

 

谢晓亮

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)

 

张泽民

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

 



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