研究成果

白凡组

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.     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) (2015), doi: 10.1021/acs.est.5b01880

3.     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)

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

  

高毅勤组 

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

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

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

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

 

葛颢组 

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)

 

 

黄岩谊组 

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

 

苏晓东组 

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. 

 

孙育杰组 

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 

 

汤富酬组 

1.      Wen L*, Tang Fuchou*, Charting a Map through the Cellular Reprogramming Landscape. Cell Stem Cell 16: 215-216 (2015) (*: Co-corresponding authors) (Preview).

2.      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, Duan S, Ding Z, Li M, Yi F, Bai R, Wang Y, Chen C, Yang F, Li X, Wang Z, Aizawa E, Goebl A, Soligalla RD, Reddy P, Esteban CR, Tang Fuchou*, Liu GH*, Belmonte JC*. A Werner syndrome stem cell model unveils heterochromatin alterations as a driver of human aging. Science 348: 1160-1163 (2015) (*: Co-corresponding authors).

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 YQ, Tang Fuchou*, Qiao J*. The transcriptome and DNA methylome landscapes of human primordial germ cells. Cell 161: 1437-1452 (2015) (*: Co-corresponding authors).

4.      Wen L*, Tang Fuchou*, How to catch rare cell types. Nature 52: 197-198 (*: Co-corresponding authors) (2015) (Preview).

5.      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) (*: Co-corresponding author).

6.      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) (*: Co-corresponding author).

7.      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) (*: Co-corresponding author).

8.      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).

9.      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) (*: Co-corresponding authors).

10.   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, Belmonte JC, Chen Z, Wang X, Jiang T, Qu J*, Fuchou Tang*, Liu G*. Nature Communications 6: 10068 (2015) (*: Co-corresponding authors).

11.   Huize Pan, Di Guan, Xiaomeng Liu, Jingyi Li, Lixia Wang, Jun Wu, Junzhi Zhou, Weizhou Zhang, Ruotong Ren, Weiqi Zhang, Ying Li, Jiping Yang, Ying Hao, Tingting Yuan, Guohong Yuan, Zhenyu Ju, Zhiyong Mao, Jian Li, Jing Qu*, Fuchou Tang*, Guang-Hui Liu*. SIRT6 safeguards human mesenchymal stem cells from oxidative stress by transactivating NRF2 Cell Research (in press) 

 

魏文胜组 

1.        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)

2.        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.

3.        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.

4.        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.

5.        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.

6.        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.

 

谢晓亮组 

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 

 

张泽民组 

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

4.        (this last paper was largely done at Genentech, but I did quite a bit work at Biopic, so the BIOPIC affiliation was included. )

 

赵新生研究组 

1.   Peng Wang, Lijiang Yang, Yi Qin Gao, Xin Sheng Zhao, Nucleic Acids Res. 2015, on line. “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”.

 



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