Super User

Super User

星期四, 22 10月 2015 11:36

2014

Kang, T., White, J. T., Xie, Z., Benenson, Y., Sontag, E., & Bleris, L. (2013). Reverse Engineering Validation using a Benchmark Synthetic Gene Circuit in Human Cells. ACS Synthetic Biology. doi:10.1021/sb300093y

Kashyap, N., Pham, B., Xie, Z., & Bleris, L. (2013). Transcripts for combined synthetic microRNA and gene delivery. Molecular bioSystems. doi:10.1039/c3mb70043g

Guo W, Chung, W-Y, Qian, M, Pellegrini, M, Zhang, MQ (2013). Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells. NAR. In press.

Guo W, Fiziev P, Yan W, Cokus S, Sun X, Zhang MQ, Chen PY, Pellegrini M (2013) BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC Genomics. 2013 Nov 10;14(1):774.

Jiang R, Zhang X, Zhang MQ (2013) Basics of Bioinformatics: Lecture Notes of Graduate Summer School on Bioinformatics of China. Book, ISBN-10:3642389503, ISBN-13: 978-3642389504. Springer 2013 edition.

Chen Y, Ding Y, Yang L, Yu J, Liu G, Wang X, Zhang S, Yu D, Song L, Zhang H, Zhang C, Huo L, Huo C, Wang Y, Du Y, Zhang H, Zhang P, Na H, Xu S, Zhu Y, Xie Z, He T, Zhang Y, Wang G, Fan Z, Yang F, Liu H, Wang X, Zhang X, Zhang MQ, Li Y, Steinbüchel A, Fujimoto T, Cichello S, Yu J, Liu P. (2013) Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630. NAR, [Epub ahead of print], PMID:24150943.

Tam KW, Zhang W, Soh J, Stastny V, Chen M, Sun H, Thu K, Rios JJ, Yang C, Marconett CN, Selamat SA, Laird-Offringa IA, Taguchi A, Hanash S, Shames D, Ma X, Zhang MQ, Lam WL, Gazdar A (2013) CDKN2A/p16 Inactivation Mechanisms and Their Relationship to Smoke Exposure and Molecular Features in Non-Small-Cell Lung Cancer. J Thorac Oncol. 8:1378-88. PMID:24077454.

Wu D, Gu J, Zhang MQ. (2013) FastDMA: An Infinium HumanMethylation450 Beadchip Analyzer. PLoS One. 2013 Sep 5;8(9):e74275. PMID:24040221.

Kim MV, Ouyang W, Liao W, Zhang MQ, Li MO. (2013) The transcription factor Foxo1 controls central-memory CD8+ T cell responses to infection. Immunity. 39:286-97. PMID:23924514.

Qin J, Li MJ, Wang P, Wong NS, Wong MP, Xia Z, Tsao GS, Zhang MQ, Wang J (2013) ProteoMirExpress: inferring microRNA-centered regulatory networks from high throughput proteomic and mRNA expression data. Mol. Cell. Proteomics, [PubMed – in process] PMID:23924514.

Zhou D, Wu D, Li Z, Qian M, Zhang MQ (2013) Population dynamics of cancer cells with cell-state conversions. Quant. Biol. 2:2095-4689. DOI: 10.1007/s40484-013-0014-2.

Xie W, Schultz M, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tiam S, Hawkins DR, Leung D, Yang H, Wang T, Swanson SA, Zhang J, Zhu Y, Lee AY, Kim A, Nery J, Urich MA, Kuan S, Yen C, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung W, Chi NC, Antosiewicz-Bourget J, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Eckert JR, Ren B (2013) Epigenomic Analysis of Multi-lineage Differentiation of Human Embryonic Stem Cells. Cell, 153:1134-48. PMID:23664764.

Wen-Yu Chung, Robert J. Schmitz, Tanya Biorac, Delia Ye, Miroslav Dudas, Gavin D. Meredith, Christopher C. Adams, Joseph R. Ecker and Michael Q. Zhang (2013) Constructing hepitypes: phasing local genotype and DNA methylation. JNSNE, In press.

May P, Liao W, Wu Y, Shuai B, McCombie WR, Zhang MQ, Liu QA (2013) The Effects of Carbon Dioxide and Temperature on microRNA Expressions in Arabidopsis Development. Nat. Comm. 4:2145. PMID:23900278.
Ma X, Wang YW, Zhang MQ, Gazdar AF (2013) DNA methylation data analysis and its application to cancer research. Epigenomics. 5:301-16. PMID:23750645.

Wu J, Anczuków O, Krainer AR, Zhang MQ*, Zhang C* (2013) OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. Nucl. Acid. Res. 41:5149-5163. PMID:23571760.

Wang C, Zhang MQ, Zhang Z (2013) Computational identification of active enhancers in model organisms. Genomics, Proteomics Bioinformatics, pii:S1672-0229(13)00047-8. PMID:23685394.

Megha Rajaram; Jianping Zhang; Tim Wang; Cem Kuscu; Mamoru Kato; Vladimir Grubor; Robert Weil; Asluag Helland; Anne-Lise Borrenson-Dale; Kathleen Cho; Douglas A Levine; Alan N Houghton; Jedd D Wolchok; Lois Myeroff; Sanford D Markowitz; Michael Zhang; Alex Krasnitz; Robert Lucito; David Mu; Scott Powers (2013) Two Distinct Categories of Focal Deletions in Cancer Genomes. PLoS ONE, 8:e66264. PMID:23805207.

Jin Gu, Zhenyu Xuan. Inferring the perturbed microRNA regulatory networks in cancer using hierarchical gene co-expression signatures. PLoS ONE 2013, 8(11):e81032.

Dingming Wu, Jin Gu, Michael Zhang. FastDMA: An Infinium HumanMethylation450 Beadchip Analyzer. PLoS ONE 2013, 8(9):e74275.

Ting Wang, Jin Gu, Jun Yuan, Ran Tao, Yanda Li, Shao Li. Inferring pathway crosstalk networks using gene set co-expression signatures. Molecular BioSystems 2013, 9(7):1822-1888.

Rui Li, Tao Ma, Jin Gu, Xujun Liang, Shao Li. Imbalanced network biomarkers for traditional Chinese medicine Syndrome in gastritis patients. Scientific Reports 2013, 3:1543.

Feng Zeng, Rui Jiang, Ting Chen, PyroHMMsnp: a SNP caller for Ion Torrent and 454 sequencing data, Nucleic Acids Research, accepted, 2013.

Li R, Ma T, Gu J, Liang X, Li S. Imbalanced network biomarkers for traditional Chinese medicine Syndrome in gastritis patients. Scientific Reports 2013;3:1543.

Zhang B, Wang X, Li S. An integrative platform of TCM network pharmacology and its application on an herbal formula, Qing-Luo-Yin. Evidence-based.

Zhang B, Liu L, Zhao S, Wang X, Liu L, Li S. Vitexicarpin acts as a novel angiogenesis inhibitor and its target network. Evidence-based Complementary and Alternative Medicine 2013:278405.

Freeberg MA, Han T,Moresco JJ, Kong A, Yang YC2, Lu ZJ2, Yates JR, Kim JK. (2013) Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae. Genome Biology.

Kudron M, Niu W, Lu Z, Wang G, Gerstein M, Snyder M, Reinke V. (2013) Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs. Genome Biology.

Matthew H Larson, Luke A Gilbert, Xiaowo Wang, Wendell A Lim, Jonathan S Weissman & Lei S Qi, CRISPR interference (CRISPRi) for sequence-specific control of gene expression, Nature Protocols, 2013; 8, 2180–2196.

星期四, 22 10月 2015 11:34

2013

Cao C, Jiang W, Wang B, Fang J, Lang J, Tian G*, Jiang J*, and Zhu TF*. (2014) Inhalable microorganisms in Beijing's PM2.5 and PM10 pollutants during a severe smog event. Environ Sci Technol, 48(3):1499-1507, .

Samira Kiani, Jacob Beal, Mohammad R Ebrahimkhani, Jin Huh, Richard N. Hall1, Zhen Xie, Yinqing Li and Ron Weiss*. (2014) CRISPR transcriptional repression devices and layered circuits in mammalian cells. Nature Methods 11, 723-6.

Jonathan Leo Schmid-Burgk, Zhen Xie, Yaakov Benenson*. (2014) Hierarchical ligation-independent assembly of PCR fragments. Methods Molecular Biology 1116:49-58.

Zhen Xie, Liliana Wroblewska and Ron Weiss*. (2014) RNAi synthetic logic circuits for sensing, information processing and actuation. RNA Regulation, Encyclopedia of Molecular Cell Biology and Molecular Medicine. Edition April 2014, ISBN 978-3-527-33156-7-Wiley-VCH, Weinheim (Book chapter).

Jin Gu*#, Yang Chen*, Huiya Huang, Lingyun Yin, Zhen Xie, Michael Zhang#. (2014) Gene module based regulator inference identifying miR-139 as a tumor suppressor in colorectal cancer. Molecular BioSystems, 10(12):3249-3254.

Ting Wang, Jin Gu#, Yanda Li. (2014) Inferring the perturbed microRNA regulatory networks from gene expression data using a network propagation based method. BMC Bioinformatics, 15:255.

Dongfang Wang, Jin Gu#, Ting Wang, Zijian Ding. (2014) OncomiRDB: a database for the experimentally verified oncogenic and tumor-suppressive microRNAs. Bioinformatics, 30(15):2237-2238.

Heidari N, Phanstiel DH, He C, Grubert F, Jahanbanian F, Kasowski M, Zhang MQ, Snyder MP (2014). Genome-wide map of regulatory interactions in the human genome. Genome Res. 24:1905-17.

Sephton CF, Tang AA, Kulkarni A, West J, Brooks M, Stubblefield JJ, Liu Y, Zhang MQ, Green CB, Huber KM, Huang EJ, Herz J, Yu G (2014) Activity-Dependent FUS Dysregulation Disrupts Synaptic Homeostasis. PNAS, 111:E4769-78.

Cheng J, Zhou X, Lu Y, Chen J, Han B, Zhu Y, Liu L, Choy K-W, Han D, Sham PC, Zhang MQ, Zhang X, Yuan H (2014) Exome sequencing identifies a novel frameshift mutation of MYO6 as the cause of autosomal dominant nosyndromic hearing loss in a Chinese family. AHG. In press.

Sheng MM†, Zhong Y†, Chen Y, Du J, Ju X, Zhao C, Zhang G, Zhang L, Liu K, Yang N, Xie P, Li D, Zhang MQ* Jiang C*. (2014) Hsa-miR-1246, hsa-miR-320a and hsa-miR-196b-5p inhibitors can reduce the cytotoxicity of Ebola virus glycoprotein in vitro. Sci China Life Sci 57:959-972.

Liao W, Ouyang W, Zhang MQ, Li MO (2014) Genome Wide Mapping of Foxo1 Binding-sites in Murine T Lymphocytes. Genomics Data, 2:280-281.

Rajagopal N, Ernst J, Ray R, Wu J, Zhang MQ, Kellis M, Ren B (2014) Distinct and Predictive Histone Lysine Acetylation Patterns at Promoters, Enhancers and Gene Bodies. G3, 4:2051-55.

Lu Y, Zhou X, Jin Z, Cheng J, Shen W, Ji F, Liu L, Zhang X, Zhang M, Cao Y, Han D, Choy K, Yuan H. (2014) Resolving the Genetic Heterogeneity of Prelingual Hearing Loss within One Family: Performance Comparison and Application of Two Targeted Next Generation Sequencing Approaches. JHG, 59:599-607.

Li Y, Ehrhardt K, Zhang MQ, Bleris L (2014) Assembly and Validation of Versatile Transcription Activator-Like Effector Libraries. Sci. Rep. 4:4857.

Li L, Tang J, Zhang B, Yang W, Liugao M, Wang R, Tan Y, Fan J, Chang Y, Fu J, Jiang F, Chen C, Yang Y, Gu J, Wu D, Guo L, Cao D, Li H, Cao G, Wu M, Zhang MQ, Chen L, Wang H (2014) Epigenetic modification of MiR-429 promotes liver tumour-initiating cell properties by targeting Rb binding protein 4. Gut 64:156-67.

He C, Wang X*, Zhang MQ* (2014) Nucleosome eviction and multiple co-factor binding predict estrogen receoptor alpha associated long-range interactions. NAR, 42:6935-44.

Li W, Wu J, Kim S-Y, Zhao M, Zhang MQ, Meistrich ML, Mills AA (2014) Chd5 orchestrates chromatin remodeling during sperm development. Nat. Comm. 5:3812.

Xie P, Liu Y, Li Y, Zhang MQ*, Wang X* (2014) MIROR: a method for cell-type specific microRNA occupancy rate prediction. Mol. BioSyst. 10:1377-84.

Li GP, Li M, Zhang YW, Wang D, Li R, Guimera R, Gao J*, Zhang MQ* (2014) ModuleRole: a tool for modulization, role determination and visualization in protein-protein interaction networks. PLoS ONE, 9:e94608.

16. Weyn-Vanhentenryck S, Sun S, Yan Q, Mele A, Farny N, Silver Z, Zhang MQ, Krainer AR, Darnell RB, Zhang C (2014) HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. Cell Reports, S2211-1247(14)00084-9. PMID:24613350.

Zhixing Feng, Jing Li, Jing-Ren Zhang, Xuegong Zhang*. (2014) qDNAmod: a statistical model-based tool to reveal intercellular heterogeneity of DNA modification from SMRT sequencing data, Nucleic Acids Research, 42(22): 13488-13499.

Leying Guan, Qian Yang, Mengting Gu, Liang Chen, Xuegong Zhang*. (2014) Exon expression QTL (eeQTL) analysis highlights distant genomic variations associated with splicing regulation, Quantitative Biology, 2(2): 71-79.

Guang-Zhong Wang, Simone Marini, Xinyun Ma, Qiang Yang, Xuegong Zhang*, Yan Zhu*. (2014) Improvement of Dscam hemophilic binding affinity throughout Drosophila evolution, BMC Evolutionary Biology, 4: 186.

YingXue Li, XueNing Liu, XiaoWo Wang, XueGong Zhang*. (2014) Sequence signatures of genes with accompanying antisense transcripts in Saccharomyces cerevisiae, Science China Life Sciences, 57(1): 52-58.

Xavier Roge, Xuegong Zhang*. (2014) RNAseqViewer: visualization tool for RNA-Seq data, Bioinformatics, 30(6): 891-892.

Yong Chen, Yunfeng Ding, Yi Yang, Jinhai Yu, Guiing Liu, Xumin Wang, Shuyan Zhang, Dan Yu, Lai Song, Hangxiao Zhang, Congyan Zhang, Linhe Huo, Chaoxing Huo, Yang Wang, Yalan Du, Huina Zhang, Peng Zhang, Huimin Na, Shimeng Xu, Yaxin Zhu, Zhensheng Xie, Tong He, Yue Zhang, Guoliang Wang, Zhonghua Fan, Honglei Liu, Xiaowo Wang, Xuegong Zhang, Michael Q. Zhang, Yanda Li, Alexander Steinbuchel, Toyoshi Fujimoto, Simon Cichello, Jun Yu, Pingsheng Liu. (2014) Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630, Nucleic Acids Research, 42(2): 1042-1064.

Shufang Zhang, Xueya Zhou, Shengnan Liu, Tingting Bai, Yingai Zhang, Jing Wang, Shunlan Wang, Xuegong Zhang, Binbin, Wang. (2014) MYH9-related disease: description of a large Chinese pedigree and a survey of reported mutations, Acta Haematologica, 132: 193-198.

Jing Cheng, Xueya Zhou, Yu Lu, Jing Chen, Bing Han, Yuhua Zhu, Liyang Liu, Kwong-Wai Choy, Dongyi Han, Pak C. Sham, Michael Q. Zhang, Xuegong Zhang, Huijun Yuan. (2014) Exom sequencing identifies a novel frameshift mutation of MYO6 as the cause of autosomal dominant nonsyndromic hearing loss in a Chinese Family, Annals of Human Genetics, 78: 410-423.

Yu Lu, Xueya Zhou, Zhanguo Jin, Jing Cheng, Weidong Shen, Fei Ji, Liyang Liu, Xuegong Zhang, Michael Zhang, Ye Cao, Dongyi Han, KwongWai Choy, Huijun Yuan. (2014) Resolving the genetic heterogeneity of prelingual hearing loss within one family: performance comparison and application of two targeted next generation sequencing approaches, Journal of Human Genetics, 59: 599-607.

Chao Ye, Xuegong Zhang. (2014) A simulation study on gene expression regulation via stochastic model, Proceedings of the 33rd Chinese Control Conference, pp. 6885-6888, July 28-30, Nanjing, China.

Qifeng Xu, Xuegong Zhang. (2014) Multiclass feature selection algorithms based on R-SVM, IEEE ChinaSIP, 525-529.

Liang X, Li H, Li S*. (2014) A novel network pharmacology approach to analyse traditional herbal formulae: the Liu-wei-di-huang Pill as a case study. Molecular BioSystems 10(5):1014-1022.

Wang L, Wang Y, Hu Q, Li S*. (2014) Systematic analysis of new drug indications by drug-gene-disease coherent subnetworks. CPT: Pharmacometrics and Systems Pharmacology 3:e146.

Liang X, Li H, Tian G, Li S*. (2014) Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer. Scientific Reports 4,4985.

Li S*, Zhang X. (20145) Tongue-coating microbiome characterized by the next-generation sequencing and traditional tongue diagnosis. Encyclopedia of Metagenomics Springer.

Li S*, Fan T, Jia W, Lu A, Zhang W. (2014) Network pharmacology in traditional Chinese medicine. Evidence-based Complementary and Alternative Medicine 138460.

Li H, Zhao L, Zhang B, Jiang Y, Wang X, Guo Y, Liu H, Li S*, Tong X*. (2014) A network pharmacology approach to determine active compounds and action mechanisms of Ge-Gen-Qin-Lian decoction for treatment of Type 2 diabetes. Evidence-based Complementary and Alternative Medicine 2014:495840.

ong Hu, Chao Di, Mingxuan Kai, Yu-Cheng T. Yang, Yang Li, Yunjiang Qiu, Xihao Hu, Kevin Y. Yip, Michael Q. Zhang and Zhi John Lu (2015) A common set of distinct features that characterize noncoding RNAs across multiple species. Nucleic Acids Research 43(1): 104-114.

u-Cheng T. Yang*, Chao Di*, Boqin Hu*, Meifeng Zhou, Yifang Liu, Nanxi Song, Yang Li, Jumpei Umetsu and Zhi John Lu (2015) CLIPdb: a CLIP-seq database for protein-RNA interactions. BMC Genomics In press. (*contributed equally)

hao Di*, Jiapei Yuan*, Yue Wu, Jingrui Li, Huixin Lin, Long Hu, Ting Zhang, Yijun Qi, Mark B. Gerstein, Yan Guo and Zhi John Lu (2014) Characterization of Stress-responsive lncRNAs in Arabidopsis thaliana by Integrating Expression, Epigenetic and Structural Features. The Plant Journal 80:848–861

u ZJ*, Yip KY*, Wang G, Shou C, Hillier LW, et al. (2011) Predicting and characterizing non-coding RNA in C. elegans by integrating conservation, secondary structure and high-throughput sequencing and array data. Genome Research 21: 276-2857 (*contributed equally) [modENCODE special issue – Cover Story]

erstein MB *#, Lu ZJ*, Van Nostrand EL*, Cheng C*, Arshinoff BI*, et al. (2010) Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 330(6012): 1775-1787 (*co-first authors, #corresponding authors) [Cover Story]

Gerstein MB, Joel Rozowsky, Koon-Kiu Yan, Lu Z, Thomas Gingeras and Robert Waterston (2014) Comparative Analysis of the Transcriptome across Distant Species. Nature 512(7515):445-448.

Yang YC, Umetsu J, Lu ZJ (2014) Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae. Science China Life Sciences (Tsinghua Special Issue) 57:1, 22-35

Hu X, Wong TKF, Lu ZJ, Chan TF, Lau TCK, Yiu SM and Yip KY. (2014) Computational Identification of Protein Binding Sites on RNAs using High-Throughput RNA Structure-Probing Data. Bioinformatics vol. 30, no. 8, pp. 1049-1055.

星期四, 22 10月 2015 11:32

2012

Kang, T., White, J. T., Xie, Z., Benenson, Y., Sontag, E., & Bleris, L. (2013). Reverse Engineering Validation using a Benchmark Synthetic Gene Circuit in Human Cells. ACS Synthetic Biology. doi:10.1021/sb300093y

Kashyap, N., Pham, B., Xie, Z., & Bleris, L. (2013). Transcripts for combined synthetic microRNA and gene delivery. Molecular bioSystems. doi:10.1039/c3mb70043g

Guo W, Chung, W-Y, Qian, M, Pellegrini, M, Zhang, MQ (2013). Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells. NAR. In press.

Guo W, Fiziev P, Yan W, Cokus S, Sun X, Zhang MQ, Chen PY, Pellegrini M (2013) BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC Genomics. 2013 Nov 10;14(1):774.

Jiang R, Zhang X, Zhang MQ (2013) Basics of Bioinformatics: Lecture Notes of Graduate Summer School on Bioinformatics of China. Book, ISBN-10:3642389503, ISBN-13: 978-3642389504. Springer 2013 edition.

Chen Y, Ding Y, Yang L, Yu J, Liu G, Wang X, Zhang S, Yu D, Song L, Zhang H, Zhang C, Huo L, Huo C, Wang Y, Du Y, Zhang H, Zhang P, Na H, Xu S, Zhu Y, Xie Z, He T, Zhang Y, Wang G, Fan Z, Yang F, Liu H, Wang X, Zhang X, Zhang MQ, Li Y, Steinbüchel A, Fujimoto T, Cichello S, Yu J, Liu P. (2013) Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630. NAR, [Epub ahead of print], PMID:24150943.

Tam KW, Zhang W, Soh J, Stastny V, Chen M, Sun H, Thu K, Rios JJ, Yang C, Marconett CN, Selamat SA, Laird-Offringa IA, Taguchi A, Hanash S, Shames D, Ma X, Zhang MQ, Lam WL, Gazdar A (2013) CDKN2A/p16 Inactivation Mechanisms and Their Relationship to Smoke Exposure and Molecular Features in Non-Small-Cell Lung Cancer. J Thorac Oncol. 8:1378-88. PMID:24077454.

Wu D, Gu J, Zhang MQ. (2013) FastDMA: An Infinium HumanMethylation450 Beadchip Analyzer. PLoS One. 2013 Sep 5;8(9):e74275. PMID:24040221.

Kim MV, Ouyang W, Liao W, Zhang MQ, Li MO. (2013) The transcription factor Foxo1 controls central-memory CD8+ T cell responses to infection. Immunity. 39:286-97. PMID:23924514.

Qin J, Li MJ, Wang P, Wong NS, Wong MP, Xia Z, Tsao GS, Zhang MQ, Wang J (2013) ProteoMirExpress: inferring microRNA-centered regulatory networks from high throughput proteomic and mRNA expression data. Mol. Cell. Proteomics, [PubMed – in process] PMID:23924514.

Zhou D, Wu D, Li Z, Qian M, Zhang MQ (2013) Population dynamics of cancer cells with cell-state conversions. Quant. Biol. 2:2095-4689. DOI: 10.1007/s40484-013-0014-2.

Xie W, Schultz M, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tiam S, Hawkins DR, Leung D, Yang H, Wang T, Swanson SA, Zhang J, Zhu Y, Lee AY, Kim A, Nery J, Urich MA, Kuan S, Yen C, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung W, Chi NC, Antosiewicz-Bourget J, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Eckert JR, Ren B (2013) Epigenomic Analysis of Multi-lineage Differentiation of Human Embryonic Stem Cells. Cell, 153:1134-48. PMID:23664764.

Wen-Yu Chung, Robert J. Schmitz, Tanya Biorac, Delia Ye, Miroslav Dudas, Gavin D. Meredith, Christopher C. Adams, Joseph R. Ecker and Michael Q. Zhang (2013) Constructing hepitypes: phasing local genotype and DNA methylation. JNSNE, In press.

May P, Liao W, Wu Y, Shuai B, McCombie WR, Zhang MQ, Liu QA (2013) The Effects of Carbon Dioxide and Temperature on microRNA Expressions in Arabidopsis Development. Nat. Comm. 4:2145. PMID:23900278.
Ma X, Wang YW, Zhang MQ, Gazdar AF (2013) DNA methylation data analysis and its application to cancer research. Epigenomics. 5:301-16. PMID:23750645.

Wu J, Anczuków O, Krainer AR, Zhang MQ*, Zhang C* (2013) OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. Nucl. Acid. Res. 41:5149-5163. PMID:23571760.

Wang C, Zhang MQ, Zhang Z (2013) Computational identification of active enhancers in model organisms. Genomics, Proteomics Bioinformatics, pii:S1672-0229(13)00047-8. PMID:23685394.

Megha Rajaram; Jianping Zhang; Tim Wang; Cem Kuscu; Mamoru Kato; Vladimir Grubor; Robert Weil; Asluag Helland; Anne-Lise Borrenson-Dale; Kathleen Cho; Douglas A Levine; Alan N Houghton; Jedd D Wolchok; Lois Myeroff; Sanford D Markowitz; Michael Zhang; Alex Krasnitz; Robert Lucito; David Mu; Scott Powers (2013) Two Distinct Categories of Focal Deletions in Cancer Genomes. PLoS ONE, 8:e66264. PMID:23805207.

Jin Gu, Zhenyu Xuan. Inferring the perturbed microRNA regulatory networks in cancer using hierarchical gene co-expression signatures. PLoS ONE 2013, 8(11):e81032.

Dingming Wu, Jin Gu, Michael Zhang. FastDMA: An Infinium HumanMethylation450 Beadchip Analyzer. PLoS ONE 2013, 8(9):e74275.

Ting Wang, Jin Gu, Jun Yuan, Ran Tao, Yanda Li, Shao Li. Inferring pathway crosstalk networks using gene set co-expression signatures. Molecular BioSystems 2013, 9(7):1822-1888.

Rui Li, Tao Ma, Jin Gu, Xujun Liang, Shao Li. Imbalanced network biomarkers for traditional Chinese medicine Syndrome in gastritis patients. Scientific Reports 2013, 3:1543.

Feng Zeng, Rui Jiang, Ting Chen, PyroHMMsnp: a SNP caller for Ion Torrent and 454 sequencing data, Nucleic Acids Research, accepted, 2013.

Li R, Ma T, Gu J, Liang X, Li S. Imbalanced network biomarkers for traditional Chinese medicine Syndrome in gastritis patients. Scientific Reports 2013;3:1543.

Zhang B, Wang X, Li S. An integrative platform of TCM network pharmacology and its application on an herbal formula, Qing-Luo-Yin. Evidence-based.

Zhang B, Liu L, Zhao S, Wang X, Liu L, Li S. Vitexicarpin acts as a novel angiogenesis inhibitor and its target network. Evidence-based Complementary and Alternative Medicine 2013:278405.

Freeberg MA, Han T,Moresco JJ, Kong A, Yang YC2, Lu ZJ2, Yates JR, Kim JK. (2013) Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae. Genome Biology.

Kudron M, Niu W, Lu Z, Wang G, Gerstein M, Snyder M, Reinke V. (2013) Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs. Genome Biology.

Matthew H Larson, Luke A Gilbert, Xiaowo Wang, Wendell A Lim, Jonathan S Weissman & Lei S Qi, CRISPR interference (CRISPRi) for sequence-specific control of gene expression, Nature Protocols, 2013; 8, 2180–2196.

星期四, 22 10月 2015 11:30

2011

Kang, T., White, J. T., Xie, Z., Benenson, Y., Sontag, E., & Bleris, L. (2013). Reverse Engineering Validation using a Benchmark Synthetic Gene Circuit in Human Cells. ACS Synthetic Biology. doi:10.1021/sb300093y

Kashyap, N., Pham, B., Xie, Z., & Bleris, L. (2013). Transcripts for combined synthetic microRNA and gene delivery. Molecular bioSystems. doi:10.1039/c3mb70043g

Guo W, Chung, W-Y, Qian, M, Pellegrini, M, Zhang, MQ (2013). Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells. NAR. In press.

Guo W, Fiziev P, Yan W, Cokus S, Sun X, Zhang MQ, Chen PY, Pellegrini M (2013) BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC Genomics. 2013 Nov 10;14(1):774.

Jiang R, Zhang X, Zhang MQ (2013) Basics of Bioinformatics: Lecture Notes of Graduate Summer School on Bioinformatics of China. Book, ISBN-10:3642389503, ISBN-13: 978-3642389504. Springer 2013 edition.

Chen Y, Ding Y, Yang L, Yu J, Liu G, Wang X, Zhang S, Yu D, Song L, Zhang H, Zhang C, Huo L, Huo C, Wang Y, Du Y, Zhang H, Zhang P, Na H, Xu S, Zhu Y, Xie Z, He T, Zhang Y, Wang G, Fan Z, Yang F, Liu H, Wang X, Zhang X, Zhang MQ, Li Y, Steinbüchel A, Fujimoto T, Cichello S, Yu J, Liu P. (2013) Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630. NAR, [Epub ahead of print], PMID:24150943.

Tam KW, Zhang W, Soh J, Stastny V, Chen M, Sun H, Thu K, Rios JJ, Yang C, Marconett CN, Selamat SA, Laird-Offringa IA, Taguchi A, Hanash S, Shames D, Ma X, Zhang MQ, Lam WL, Gazdar A (2013) CDKN2A/p16 Inactivation Mechanisms and Their Relationship to Smoke Exposure and Molecular Features in Non-Small-Cell Lung Cancer. J Thorac Oncol. 8:1378-88. PMID:24077454.

Wu D, Gu J, Zhang MQ. (2013) FastDMA: An Infinium HumanMethylation450 Beadchip Analyzer. PLoS One. 2013 Sep 5;8(9):e74275. PMID:24040221.

Kim MV, Ouyang W, Liao W, Zhang MQ, Li MO. (2013) The transcription factor Foxo1 controls central-memory CD8+ T cell responses to infection. Immunity. 39:286-97. PMID:23924514.

Qin J, Li MJ, Wang P, Wong NS, Wong MP, Xia Z, Tsao GS, Zhang MQ, Wang J (2013) ProteoMirExpress: inferring microRNA-centered regulatory networks from high throughput proteomic and mRNA expression data. Mol. Cell. Proteomics, [PubMed – in process] PMID:23924514.

Zhou D, Wu D, Li Z, Qian M, Zhang MQ (2013) Population dynamics of cancer cells with cell-state conversions. Quant. Biol. 2:2095-4689. DOI: 10.1007/s40484-013-0014-2.

Xie W, Schultz M, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tiam S, Hawkins DR, Leung D, Yang H, Wang T, Swanson SA, Zhang J, Zhu Y, Lee AY, Kim A, Nery J, Urich MA, Kuan S, Yen C, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung W, Chi NC, Antosiewicz-Bourget J, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Eckert JR, Ren B (2013) Epigenomic Analysis of Multi-lineage Differentiation of Human Embryonic Stem Cells. Cell, 153:1134-48. PMID:23664764.

Wen-Yu Chung, Robert J. Schmitz, Tanya Biorac, Delia Ye, Miroslav Dudas, Gavin D. Meredith, Christopher C. Adams, Joseph R. Ecker and Michael Q. Zhang (2013) Constructing hepitypes: phasing local genotype and DNA methylation. JNSNE, In press.

May P, Liao W, Wu Y, Shuai B, McCombie WR, Zhang MQ, Liu QA (2013) The Effects of Carbon Dioxide and Temperature on microRNA Expressions in Arabidopsis Development. Nat. Comm. 4:2145. PMID:23900278.
Ma X, Wang YW, Zhang MQ, Gazdar AF (2013) DNA methylation data analysis and its application to cancer research. Epigenomics. 5:301-16. PMID:23750645.

Wu J, Anczuków O, Krainer AR, Zhang MQ*, Zhang C* (2013) OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. Nucl. Acid. Res. 41:5149-5163. PMID:23571760.

Wang C, Zhang MQ, Zhang Z (2013) Computational identification of active enhancers in model organisms. Genomics, Proteomics Bioinformatics, pii:S1672-0229(13)00047-8. PMID:23685394.

Megha Rajaram; Jianping Zhang; Tim Wang; Cem Kuscu; Mamoru Kato; Vladimir Grubor; Robert Weil; Asluag Helland; Anne-Lise Borrenson-Dale; Kathleen Cho; Douglas A Levine; Alan N Houghton; Jedd D Wolchok; Lois Myeroff; Sanford D Markowitz; Michael Zhang; Alex Krasnitz; Robert Lucito; David Mu; Scott Powers (2013) Two Distinct Categories of Focal Deletions in Cancer Genomes. PLoS ONE, 8:e66264. PMID:23805207.

Jin Gu, Zhenyu Xuan. Inferring the perturbed microRNA regulatory networks in cancer using hierarchical gene co-expression signatures. PLoS ONE 2013, 8(11):e81032.

Dingming Wu, Jin Gu, Michael Zhang. FastDMA: An Infinium HumanMethylation450 Beadchip Analyzer. PLoS ONE 2013, 8(9):e74275.

Ting Wang, Jin Gu, Jun Yuan, Ran Tao, Yanda Li, Shao Li. Inferring pathway crosstalk networks using gene set co-expression signatures. Molecular BioSystems 2013, 9(7):1822-1888.

Rui Li, Tao Ma, Jin Gu, Xujun Liang, Shao Li. Imbalanced network biomarkers for traditional Chinese medicine Syndrome in gastritis patients. Scientific Reports 2013, 3:1543.

Feng Zeng, Rui Jiang, Ting Chen, PyroHMMsnp: a SNP caller for Ion Torrent and 454 sequencing data, Nucleic Acids Research, accepted, 2013.

Li R, Ma T, Gu J, Liang X, Li S. Imbalanced network biomarkers for traditional Chinese medicine Syndrome in gastritis patients. Scientific Reports 2013;3:1543.

Zhang B, Wang X, Li S. An integrative platform of TCM network pharmacology and its application on an herbal formula, Qing-Luo-Yin. Evidence-based.

Zhang B, Liu L, Zhao S, Wang X, Liu L, Li S. Vitexicarpin acts as a novel angiogenesis inhibitor and its target network. Evidence-based Complementary and Alternative Medicine 2013:278405.

Freeberg MA, Han T,Moresco JJ, Kong A, Yang YC2, Lu ZJ2, Yates JR, Kim JK. (2013) Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae. Genome Biology.

Kudron M, Niu W, Lu Z, Wang G, Gerstein M, Snyder M, Reinke V. (2013) Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs. Genome Biology.

Matthew H Larson, Luke A Gilbert, Xiaowo Wang, Wendell A Lim, Jonathan S Weissman & Lei S Qi, CRISPR interference (CRISPRi) for sequence-specific control of gene expression, Nature Protocols, 2013; 8, 2180–2196.

    2014年8月6日清华大学生命科学学院邓海腾课题组在《Molecular & Cellular Proteomics》上在线发表了题为"Down-regulation of Rab 5C-dependent Endocytosis and Glycolysis in Cisplatin-resistant Ovarian Cancer Cell Lines"的研究论文。该论文通过定量蛋白质组学分析,发现了多个与卵巢癌细胞顺铂耐药性相关的因素,包括Rab 5C调控的内吞作用,糖酵解相关蛋白和波形蛋白的下调,以及抗氧化蛋白的上调,为系统理解卵巢癌细胞的耐药机制提供了实验依据。


  耐药性一直是卵巢癌临床治疗上的屏障,严重影响卵巢癌患者的生存率。本项工作通过对非耐药的卵巢癌细胞进行顺铂递增浓度的处理和筛选,建立起了顺铂耐药的细胞系;然后利用TMT标记的定量蛋白质组学方法,鉴定出卵巢癌细胞A2780及其顺铂耐药细胞A2780-DR中有差异表达的蛋白340个;并利用生物信息学的方法对这些差异蛋白进行功能的分析及分类。其中,作者发现Rab 5C在耐药细胞中的表达是下调的。Rab 5C调控细胞的内吞过程。为了证明Rab 5C的下调影响顺铂在细胞中的积累从而导致耐药。作者对A2780细胞中的Rab5C进行了shRNA介导的基因沉默, 结果发现基因沉默可增加细胞对顺铂的耐药性;相反,过表达Rab 5C可使细胞对顺铂更加敏感。这些结果显示卵巢癌细胞的耐药性由多个因素决定,包括Rab 5C和Rab 11B调控的细胞內吞作用。


  本论文的通讯作者为清华大学生命科学学院的邓海腾教授,该课题组的二年级博士生霍祎是该论文的并列第一作者,生物医学测试中心蛋白质化学平台的技术人员参与了该项工 作的样品分析。该研究受国家自然科学基金(31270871)和清华-北大生命科学联合中心经费的支持。

0827 t2

星期四, 22 10月 2015 09:46

聚焦超声外科的兴起

清华大学生物医学工程系

时间:5月20日19:00
地点:医学科学楼B321
报告人:重庆医科大学生物医学工程学院 王智彪教授


报告摘要
上个世纪40年代,美国科学家J.G Lynn首次提出将体外发射的超声波聚焦到体内对肿瘤进行手术治疗的设想。随后英、美、日、法、德、以等国也纷纷投入大量人力物力到该领域的研究。

在中国,从上世纪80年代开始,重庆医科大学联合南京大学、上海交通大学、中国科学院声学研究所、西安交通大学等单位潜心于聚焦超声外科技术的生物医学工程理论与临床相结合的研究。科研团队用实验科学的方法,从数千吨离体牛肝实验,再发展到小鼠、兔、香猪到恒河猴等动物实验,完成了上万例动物实验,对超声在组织内聚焦规律及剂量学等关键问题进行了深入研究,首次提出“生物学焦域”(Biological Focal Region,BFR)概念,以及生物学焦域与超声在理想声场中的声学焦域(Acoutic Focal Region,AFR)的对比定量研究。通过对生物学效应、治疗剂量学、组织声环境以及改变组织声环境等的研究,初步建立了聚焦超声外科的基础理论体系。

以此为基础,相继开发出了聚焦超声外科的设备,形成了临床方案,培养了世界上首批聚焦超声外科的专科医生,并在全球率先推向临床应用。全世界第一例聚焦超声保肢治疗骨肿瘤、保乳治疗乳腺癌、保肝治疗肝癌、保子宫治疗子宫肌瘤等均诞生在中国,患者至今生存长达15年以上。迄今为止,超声治疗系列化设备已在全球2000余家医院安装使用,累计治疗肿瘤及非肿瘤患者200余万例。

王智彪,医学博士,妇产科主任医师,重庆医科大学生物医学工程学院教授、博士生导师,超声医疗国家工程研究中心主任,中国生物医学工程学会副理事长。国家杰出青年基金获得者,973项目及自然基金委重大科研仪器设备研制专项首席科学家。主要研究方向:超声治疗学、妇产科学。多年来致力于妇科常见疾病子宫肌瘤、子宫腺肌病、宫颈炎症相关疾病以及外阴白色病变的微无创治疗。始终以“治疗——让病人受伤害更小”为从医理念。自1988年起,带领多学科专家团队研制出具有我国完全自主知识产权的大型治疗设备——“高强度聚焦超声肿瘤治疗系统”及CZF型超声波妇科治疗仪等,实现了“体外对体内疾病治疗”的医学梦想。2000年获得国家技术发明二等奖;2008年获得何梁何利基金“科学与技术进步奖”;2010年获得国家科技进步二等奖。

 

Geometric tools for biomedical image analysis - 清华大学生物医学工程系

时间:5月21日下午3:00
地点:医学科学楼B321
报告人:Tao Ju, PhD (Associate Professor, Department of Computer Science and Engineering at the Washington University in St. Louis)


报告摘要
While medical imaging has afforded a vast and quickly growing amount of spatial data, there is still a significant gap between "image'' and "knowledge''. In my work I explored the use of geometric tools and algorithms to help doctors and medical researchers make better sense of their images. In this talk, I will present two such examples. I will show how geometric skeletons are used to understand 3D biological shapes, from proteins to aneurysms, and how deformable atlases allow comparative analysis of 2D and 3D anatomic images.


Tao Ju is an Associate Professor in the Department of Computer Science and Engineering at the Washington University in St. Louis. He is the Ambassador for MISA to Tsinghua University. He graduated from Tsinghua in 2000 with a Bachelor Degree majoring in English and minoring in Computer Science, and he obtained his M.S. and PhD degrees in Computer Science from Rice University in 2005. He conducts research in computer graphics and bio-medical applications. He has served on the program committees of top-tier conferences including ACM Siggraph and Eurographics, and is currently an associate editor of journals IEEE Transactions on Visualization and Computer Graphics, Computer-Aided Design and Graphical Models. He has received a number of grant awards from NSF and NIH, including an NSF CAREER award in 2009.

 

After the talk, a quick introduction about Dept. of Biomedical Engineering of Washington University and research work, together with an introduction of Washington University in St. Louis and its McDonnell International Scholars Program, will be shared by Drs.  Yan LIU and Jiayu LI, respectively.

 

 

 

姓名

录取单位

姓名

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安子玄

生命学院

朱芮葆

生命学院

崔进

生命学院

白雪

生命中心

董俊凯

生命学院

曹雪雅

生命中心

冯佳颖

生命学院

程稼萱

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韩鸽

生命学院

邓强

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胡易

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方谦

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金杰

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韩再铭

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雷博

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黄亮

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李沁

生命学院

黄雪婷

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医学院

王玉

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闫坤

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于磊

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朱林

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    以上是经三方招生委员会面试后形成的拟录取名单,之后将进行资格复审,以下情况资格复审不能通过:

   1)录取单位调剂后没有进行有效报名的人员;

    2)自身情况介绍、成绩排名、档案材料以及报名时递交的其他材料中有弄虚作假者;

    3)其他特殊情况。

      资格复审未通过者将被取消录取资格。

     生命学院、医学院基础医学系、清华大学-北京大学生命科学联合中心

                                   2015年10月19日

星期四, 15 10月 2015 07:02

科普教育

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec consectetur, nibh ut feugiat placerat, orci lacus accumsan erat, eget porttitor arcu velit a lacus. Sed tempus bibendum risus, nec dignissim sem vestibulum ut. Nam iaculis aliquam elementum. Nunc sed dignissim sapien.

 

星期四, 15 10月 2015 03:24

测试下载2

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