研究成果

白凡组

1. Du Y, Li R, Chen Z, Wang X, Xu T and Bai F. Mutagenic Factors and Complex Clonal Relationship of Multifocal Urothelial Cell Carcinoma. Eur Urol. 2017;71:841-843.
2. Gao Y, Ni X, Guo H, Su Z, Ba Y, Tong Z, Guo Z, Yao X, Chen X, Yin J, Yan Z, Guo L, Liu Y, Bai F, Xie XS and Zhang N. Single-cell sequencing deciphers a convergent evolution of copy number alterations from primary to circulating tumor cells. Genome Res. 2017;27:1312-1322.
3. Fang Y, Su Z, Xie J, Xue R, Ma Q, Li Y, Zhao Y, Song Z, Lu X, Li H, Peng C, Bai F and Shen B. Genomic signatures of pancreatic adenosquamous carcinoma (PASC). J Pathol. 2017;243:155-159.
4. Li J, Liu K, Chen H, Li R, Drechsler M, Bai F, Huang J, Tang BZ and Yan Y. Functional Built-In Template Directed Siliceous Fluorescent Supramolecular Vesicles as Diagnostics. ACS Applied Materials & Interfaces. 2017;9:21706-21714.
5. Chen XX, Zhong Q, Liu Y, Yan SM, Chen ZH, Jin SZ, Xia TL, Li RY, Zhou AJ, Su Z, Huang YH, Huang QT, Huang LY, Zhang X, Zhao YN, Yun JP, Wu QL, Lin DX, Bai F and Zeng MS. Genomic comparison of esophageal squamous cell carcinoma and its precursor lesions by multi-region whole-exome sequencing. Nat Commun. 2017;8:524.
6. Li Y, Wu S and Bai F. Molecular characterization of circulating tumor cells-from bench to bedside. Semin Cell Dev Biol. 2018;75:88-97.
7. Li R, Li X, Xue R, Yang F, Wang S, Li Y, Shen D, Sun K, Chen K, Weng W, Bai F and Wang J. Early metastasis detected in patients with multifocal pulmonary ground-glass opacities (GGOs). Thorax. 2018;73:290-292.
8. Liu M, Liu Y, Di J, Su Z, Yang H, Jiang B, Wang Z, Zhuang M, Bai F and Su X. Multi-region and single-cell sequencing reveal variable genomic heterogeneity in rectal cancer. BMC Cancer. 2017;17:787.
9. Pu Y, Ke Y and Bai F. Active efflux in dormant bacterial cells - New insights into antibiotic persistence. Drug Resist Updat. 2017;30:7-14.
10. Chen M, Zhao Z, Yang J, Peng K, Baker MA, Bai F and Lo CJ. Length-dependent flagellar growth of Vibrio alginolyticus revealed by real time fluorescent imaging. Elife. 2017;6.
11. Jin X, Guo X, Xu D, Zhao Y, Xia X and Bai F. Single-Cell Real-Time Visualization and Quantification of Perylene Bioaccumulation in Microorganisms. Environ Sci Technol. 2017;51:6211-6219.

高毅勤组

1. Che X, Du XX, Cai X, Zhang J, Xie WJ, Long Z, Ye ZY, Zhang H, Yang L, Su XD and Gao YQ. Single Mutations Reshape the Structural Correlation Network of the DMXAA-Human STING Complex. J Phys Chem B. 2017;121:2073-2082.
2. Hou GL, Liu CW, Li RZ, Xu HG, Gao YQ and Zheng WJ. Emergence of Solvent-Separated Na(+)-Cl(-) Ion Pair in Salt Water: Photoelectron Spectroscopy and Theoretical Calculations. J Phys Chem Lett. 2017;8:13-20.
3. Kan Z, Zhu Q, Yang L, Huang Z, Jin B and Ma J. Polarization Effects on the Cellulose Dissolution in Ionic Liquids: Molecular Dynamics Simulations with Polarization Model and Integrated Tempering Enhanced Sampling Method. J Phys Chem B. 2017;121:4319-4332.
4. Xie WJ, Meng L, Liu S, Zhang L, Cai X and Gao YQ. Structural Modeling of Chromatin Integrates Genome Features and Reveals Chromosome Folding Principle. Sci Rep. 2017;7:2818.
5. Zhang J, Zhang Z, Yang YI, Liu S, Yang L and Gao YQ. Rich Dynamics Underlying Solution Reactions Revealed by Sampling and Data Mining of Reactive Trajectories. ACS Cent Sci. 2017;3:407-414.
6. Zhang L, Xie WJ, Liu S, Meng L, Gu C and Gao YQ. DNA Methylation Landscape Reflects the Spatial Organization of Chromatin in Different Cells. Biophys J. 2017;113:1395-1404.
7. Zhang Q, Chen H, Wu T, Jin T, Pan Z, Zheng J, Gao Y and Zhuang W. The opposite effects of sodium and potassium cations on water dynamics. Chem Sci. 2017;8:1429-1435.
8. Zhang Z, Xie WJ, Yang YI, Sun G and Gao YQ. Simulation Studies of the Self-Assembly of Halogen-Bonded Sierpiński Triangle Fractals. Acta Physico-Chimica Sinca. 2017;33:539-547.

葛颢组

1. Ge H and Qian H. Mathematical Formalism of Nonequilibrium Thermodynamics for Nonlinear Chemical Reaction Systems with General Rate Law. Journal of Statistical Physics. 2017;166:190-209.
2. Ge H, Jia C and Jiang D-Q. Cycle symmetry, limit theorems, and fluctuation theorems for diffusion processes on the circle. Stochastic Processes and their Applications. 2017;127:1897-1925.
3. Ai G, Liu P and Ge H. Torque-coupled thermodynamic model for F_oF_1-ATPase; 2017.
4. Yang L, Ma Z, Cao C, Zhang Y, Wu X, Lee R, Hu B, Wen L, Ge H, Huang Y, Lao K and Tang F. MR-seq: measuring a single cell’s transcriptome repeatedly by RNA-seq. Science Bulletin. 2017;62:391-398.
5. Xu B, Ge H and Zhang Z. An efficient and assumption-free method to approximate protein level distribution in the two-states gene expression model. Journal of Theoretical Biology. 2017;433:1-7.

黄岩谊组

1. Chen Z, Zhou W, Qiao S, Kang L, Duan H, Xie XS and Huang Y. Highly accurate fluorogenic DNA sequencing with information theory-based error correction. Nat Biotechnol. 2017;35:1170-1178.
2. Chen T and Huang Y. Label-Free Transient Absorption Microscopy for Red Blood Cell Flow Velocity Measurement in Vivo. Anal Chem. 2017;89:10120-10123.
3. Li S, Chen T, Wang Y, Liu L, Lv F, Li Z, Huang Y, Schanze KS and Wang S. Conjugated Polymer with Intrinsic Alkyne Units for Synergistically Enhanced Raman Imaging in Living Cells. Angew Chem Int Ed Engl. 2017;56:13455-13458.
4. Chen X and Huang Y. Editorial overview: Molecular imaging for seeing chemistry in biology. Curr Opin Chem Biol. 2017;39:iv-v.
5. Liao P and Huang Y. Digital PCR: Endless Frontier of ‘Divide and Conquer’. Micromachines. 2017;8:231.
6. Li C, Yu Z, Fu Y, Pang Y and Huang Y. Single-Cell-Based Platform for Copy Number Variation Profiling through Digital Counting of Amplified Genomic DNA Fragments. ACS Applied Materials & Interfaces. 2017;9:13958-13964.
7. Wu AR, Wang J, Streets AM and Huang Y. Single-Cell Transcriptional Analysis. Annu Rev Anal Chem (Palo Alto Calif). 2017;10:439-462.
8. Yang L, Ma Z, Cao C, Zhang Y, Wu X, Lee R, Hu B, Wen L, Ge H, Huang Y, Lao K and Tang F. MR-seq: measuring a single cell’s transcriptome repeatedly by RNA-seq. Science Bulletin. 2017;62:391-398.
9. Zheng C, Zhang X, Li C, Pang Y and Huang Y. Microfluidic Device for Studying Controllable Hydrodynamic Flow Induced Cellular Responses. Anal Chem. 2017;89:3710-3715.
10. Chen Z, Liao P, Zhang F, Jiang M, Zhu Y and Huang Y. Centrifugal micro-channel array droplet generation for highly parallel digital PCR. Lab Chip. 2017;17:235-240.

苏晓东组

1. Che X, Du XX, Cai X, Zhang J, Xie WJ, Long Z, Ye ZY, Zhang H, Yang L, Su XD and Gao YQ. Single Mutations Reshape the Structural Correlation Network of the DMXAA-Human STING Complex. J Phys Chem B. 2017;121:2073-2082.
2. Wang Y, Ning X, Gao P, Wu S, Sha M, Lv M, Zhou X, Gao J, Fang R, Meng G, Su X and Jiang Z. Inflammasome Activation Triggers Caspase-1-Mediated Cleavage of cGAS to Regulate Responses to DNA Virus Infection. Immunity. 2017;46:393-404.
3. Tao J, Zhang XW, Jin J, Du XX, Lian T, Yang J, Zhou X, Jiang Z and Su XD. Nonspecific DNA Binding of cGAS N Terminus Promotes cGAS Activation. J Immunol. 2017;198:3627-3636.
4. Lian TF, Xu YP, Li LF and Su XD. Crystal Structure of Tetrameric Arabidopsis MYC2 Reveals the Mechanism of Enhanced Interaction with DNA. Cell Rep. 2017;19:1334-1342.
5. Da L-T, E C, Shuai Y, Wu S, Su X-D and Yu J. T7 RNA polymerase translocation is facilitated by a helix opening on the fingers domain that may also prevent backtracking. Nucleic Acids Research. 2017;45:7909-7921.
6. Li X, Nai S, Ding Y, Geng Q, Zhu B, Yu K, Zhu W-G, Dong M-Q, Su X-D, Xu X and Li J. Polo-like kinase 1 (PLK1)-dependent phosphorylation of methylenetetrahydrofolate reductase (MTHFR) regulates replication via histone methylation. Cell Cycle. 2017;16:1933-1942.

孙育杰组

1. Li X, Nai S, Ding Y, Geng Q, Zhu B, Yu K, Zhu W-G, Dong M-Q, Su X-D, Xu X and Li J. Polo-like kinase 1 (PLK1)-dependent phosphorylation of methylenetetrahydrofolate reductase (MTHFR) regulates replication via histone methylation. Cell Cycle. 2017;16:1933-1942.
2. Chen X, Li R, Liu Z, Sun K, Sun Z, Chen D, Xu G, Xi P, Wu C and Sun Y. Small Photoblinking Semiconductor Polymer Dots for Fluorescence Nanoscopy. Adv Mater. 2017;29.
3. Chen X, Liu Z, Li R, Shan C, Zeng Z, Xue B, Yuan W, Mo C, Xi P, Wu C and Sun Y. Multicolor Super-resolution Fluorescence Microscopy with Blue and Carmine Small Photoblinking Polymer Dots. ACS Nano. 2017;11:8084-8091.
4. Shao S, Chang L, Sun Y, Hou Y, Fan X and Sun Y. Multiplexed sgRNA Expression Allows Versatile Single Non-repetitive DNA Labeling and Endogenous Gene Regulation. bioRxiv. 2017.
5. Wang S, Ding M, Xue B, Hou Y and Sun Y. Live Cell Visualization of Multiple Protein–Protein Interactions with BiFC Rainbow. ACS Chemical Biology. 2017.
6. Wang S, Ding M, Chen X, Chang L and Sun Y. Development of bimolecular fluorescence complementation using rsEGFP2 for detection and super-resolution imaging of protein-protein interactions in live cells. Biomed Opt Express. 2017;8:3119-3131.
7. Shao S, Chang L, Hou Y and Sun Y. Illuminating the structure and dynamics of chromatin by fluorescence labeling. Frontiers in Biology. 2017;12:241-257.
8. Guan R, Zhang L, Su QP, Mickolajczyk KJ, Chen GY, Hancock WO, Sun Y, Zhao Y and Chen Z. Crystal structure of Zen4 in the apo state reveals a missing conformation of kinesin. Nat Commun. 2017;8:14951.
9. Han X, Li P, Yang Z, Huang X, Wei G, Sun Y, Kang X, Hu X, Deng Q, Chen L, He A, Huo Y, Li D, Betzig E and Luo J. Zyxin regulates endothelial von Willebrand factor secretion by reorganizing actin filaments around exocytic granules. Nat Commun. 2017;8:14639.
10. Fang X, Chen X, Li R, Liu Z, Chen H, Sun Z, Ju B, Liu Y, Zhang S, Ding D, Sun Y and Wu C. Multicolor Photo‐Crosslinkable AIEgens toward Compact Nanodots for Subcellular Imaging and STED Nanoscopy. Small. 2017.

汤富酬组

1. Zhu P, Guo H, Ren Y, Hou Y, Dong J, Li R, Lian Y, Fan X, Hu B, Gao Y, Wang X, Wei Y, Liu P, Yan J, Ren X, Yuan P, Yuan Y, Yan Z, Wen L, Yan L, Qiao J and Tang F. Single-cell DNA methylome sequencing of human preimplantation embryos. Nat Genet. 2018;50:12-19.
2. Liu J, Liu W, Yang L, Wu Q, Zhang H, Fang A, Li L, Xu X, Sun L, Zhang J, Tang F and Wang X. The Primate-Specific Gene TMEM14B Marks Outer Radial Glia Cells and Promotes Cortical Expansion and Folding. Cell Stem Cell. 2017;21:635-649 e8.
3. Wen L and Tang F. Single cell epigenome sequencing technologies. Mol Aspects Med. 2018;59:62-69.
4. Guo F, Li L, Li J, Wu X, Hu B, Zhu P, Wen L and Tang F. Single-cell multi-omics sequencing of mouse early embryos and embryonic stem cells. Cell Res. 2017;27:967-988.
5. Yang J, Li J, Suzuki K, Liu X, Wu J, Zhang W, Ren R, Zhang W, Chan P, Izpisua Belmonte JC, Qu J, Tang F and Liu GH. Genetic enhancement in cultured human adult stem cells conferred by a single nucleotide recoding. Cell Res. 2017;27:1178-1181.
6. Li L, Dong J, Yan L, Yong J, Liu X, Hu Y, Fan X, Wu X, Guo H, Wang X, Zhu X, Li R, Yan J, Wei Y, Zhao Y, Wang W, Ren Y, Yuan P, Yan Z, Hu B, Guo F, Wen L, Tang F and Qiao J. Single-Cell RNA-Seq Analysis Maps Development of Human Germline Cells and Gonadal Niche Interactions. Cell Stem Cell. 2017;20:891-892.
7. Zhu C, Gao Y, Guo H, Xia B, Song J, Wu X, Zeng H, Kee K, Tang F and Yi C. Single-Cell 5-Formylcytosine Landscapes of Mammalian Early Embryos and ESCs at Single-Base Resolution. Cell Stem Cell. 20:720-731.e5.
8. Guo H, Hu B, Yan L, Yong J, Wu Y, Gao Y, Guo F, Hou Y, Fan X, Dong J, Wang X, Zhu X, Yan J, Wei Y, Jin H, Zhang W, Wen L, Tang F and Qiao J. DNA methylation and chromatin accessibility profiling of mouse and human fetal germ cells. Cell Res. 2017;27:165-183.
9. Yang L, Ma Z, Cao C, Zhang Y, Wu X, Lee R, Hu B, Wen L, Ge H, Huang Y, Lao K and Tang F. MR-seq: measuring a single cell’s transcriptome repeatedly by RNA-seq. Science Bulletin. 2017;62:391-398.

魏文胜组

1. Zhang Y, Liu L, Guo S, Song J, Zhu C, Yue Z, Wei W and Yi C. Deciphering TAL effectors for 5-methylcytosine and 5-hydroxymethylcytosine recognition. Nat Commun. 2017;8:901.
2. Zhu S, Zhou Y and Wei W. Genome-Wide CRISPR/Cas9 Screening for High-Throughput Functional Genomics in Human Cells. Methods in molecular biology (Clifton, NJ). 2017;1656:175-181.
3. He R, Peng J, Yuan P, Yang J, Wu X, Wang Y and Wei W. Glucosyltransferase Activity of Clostridium difficile Toxin B Triggers Autophagy-mediated Cell Growth Arrest. Sci Rep. 2017;7:10532.
4. Fan H, Qiao L, Kang KD, Fan J, Wei W and Luo G. Attachment and Postattachment Receptors Important for Hepatitis C Virus Infection and Cell-to-Cell Transmission. Journal of virology. 2017;91.
5. Zhou Y, Wang P, Tian F, Gao G, Huang L, Wei W and Xie XS. Painting a specific chromosome with CRISPR/Cas9 for live-cell imaging. Cell Res. 2017;27:298-301.
6. Hu H, Zhang H, Wang S, Ding M, An H, Hou Y, Yang X, Wei W, Sun Y and Tang C. Live visualization of genomic loci with BiFC-TALE. Sci Rep. 2017;7:40192.

谢晓亮组

1. Chen C, Xing D, Tan L, Li H, Zhou G, Huang L and Xie XS. Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI). Science. 2017;356:189-194.
2. Zhou Y, Wang P, Tian F, Gao G, Huang L, Wei W and Xie XS. Painting a specific chromosome with CRISPR/Cas9 for live-cell imaging. Cell Res. 2017;27:298-301.
3. Xu J, Zhang Z, Niu W, Yang Q, Yao G, Shi S, Jin H, Song W, Chen L, Zhang X, Guo Y, Su Y, Hu L, Zhai J, Zhang Y, Dong F, Gao Y, Li W, Bo S, Hu M, Ren J, Huang L, Lu S, Xie XS and Sun Y. Mapping allele with resolved carrier status of Robertsonian and reciprocal translocation in human preimplantation embryos. Proc Natl Acad Sci U S A. 2017;114:E8695-E8702.

张泽民组

1. Zheng C, Zheng L, Yoo JK, Guo H, Zhang Y, Guo X, Kang B, Hu R, Huang JY, Zhang Q, Liu Z, Dong M, Hu X, Ouyang W, Peng J and Zhang Z. Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing. Cell. 2017;169:1342-1356 e16.
2. Tang Z, Li C, Kang B, Gao G, Li C and Zhang Z. GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Res. 2017;45:W98-W102.
3. Fonseca NA, He Y, Greger L, Brazma A and Zhang Z. Comprehensive genome and transcriptome analysis reveals genetic basis for gene fusions in cancer. bioRxiv. 2017.
4. Calabrese C, Lehmann K-V, Urban L, Liu F, Erkek S, Fonseca N, Kahles A, Kilpinen-Barrett LH, Markowski J, Waszak S, Korbel J, Zhang Z, Brazma A, Raetsch G, Schwarz R and Stegle O. Assessing the Gene Regulatory Landscape in 1,188 Human Tumors. bioRxiv. 2017.
5. Ji Y, Yang C, Tang Z, Yang Y, Tian Y, Yao H, Zhu X, Zhang Z, Ji J and Zheng X. Adenylate kinase hCINAP determines self-renewal of colorectal cancer stem cells by facilitating LDHA phosphorylation. Nat Commun. 2017;8:15308.
6. Tang Z, Li C, Zhang K, Yang M and Hu X. GE-mini: a mobile APP for large-scale gene expression visualization. Bioinformatics. 2017;33:941-943.

赵新生组

1. Meng L, He S and Zhao XS. Determination of Equilibrium Constant and Relative Brightness in FRET-FCS by Including the Third-Order Correlations. J Phys Chem B. 2017;121:11262-11272.
2. Zhang J, Pan B, Li Z, Sheng Zhao X and Huang L. Kinetic insights into the temperature dependence of DNA strand cleavage and religation by topoisomerase III from the hyperthermophile Sulfolobus solfataricus. Sci Rep. 2017;7:5494.


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