刘小乐课题组分享 http://blog.sciencenet.cn/u/CancerBioinfo

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刘小乐 --- 教授

已有 9331 次阅读 2013-7-28 21:12 |个人分类:实验室成员|系统分类:人物纪事|关键词:同济大学,斯坦福大学,计算机科学,哈佛大学,技术学院| 哈佛大学, 计算机科学, 斯坦福大学, 同济大学, 技术学院

个人简介

刘小乐博士,目前美国哈佛大学公共卫生学院与Dana-Farber 癌症研究所终身教授,和Dana-Farber 癌症研究所功能性癌症表观遗传学中心主任,2009年至今担任同济大学生命科学与技术学院讲座教授,2012年被聘为长江讲座教授,现被同济大学聘为千人计划重点学科短期项目教授。刘小乐博士于2002年取得斯坦福大学生物医学信息学博士和计算机科学辅修博士学位。她的主要研究方向是通过整合全基因组ChIP-chip/Seq、核小体定位、组蛋白修饰、基因表达谱、基因组序列等数据,构建计算和统计模型来发现转录与表观遗传在癌症系统中的调控机制。

刘小乐博士在计算生物学、表观遗传学和癌症生物学方面做出了重要贡献,包括开发了许多被广泛应用的算法,发表了第一个高通量人类核小体分布图谱,首次验证表观遗传组动态变化模式可以用来推测出核心转录因子,发现了乳腺癌中的雌激素受体、前列腺癌中的雄激素受体,揭示了EZH2在癌症中的功能转换机制等等。至今,她已在同行评议的国际学术期刊上发表超过100篇文章(其中30篇发表CellNatureScience及其系列上),h-index47,引用次数超过10,000次。她主持并参与了多个研究项目,包括美国卫生部和国防部项目、中国国家自然基金项目和中国973项目等。她获得过多个学术奖项,包括国防部前列腺研究新人奖(2007)、Sloan 基金会研究奖金(2008)等。她担任7本期刊的编委,为21本期刊和3个国际会议审稿。还作为特邀报告人参加了50多场国际学术会议。她培养的1名博士和7名博士后获得了高校和研究机构的终身制(tenure-track)职位,其中2名在加州大学旧金山分校和贝勒医学院已经分别获得了终身(tenured)职位。

刘小乐博士多次回国参加学术交流活动。她在同济大学生物信息学系的建立和成长中起了至关重要的作用。目前正依托同济大学培养数名研究生、博士后,并已取得一些成果,作为通讯或共同通讯作者、以同济大学为第一单位在国际期刊上发表了数篇高水平SCI文章(Bioinfo,Cancer Res, NAR, Nat Prot, NSBM)。在今后的合作计划中,将发挥优势,进一步推动国内外学术交流,建立与生物信息与转化医学结合的科研平台,培养一批高素质创新人才,力争取得建设性的成果。

个人博客网址:http://www.longwoodgenomics.org/ 

哈佛实验室网址:http://liulab.dfci.harvard.edu/ 


获奖与荣誉

1997    Summa cum laude, Highest Departmental Honors in Biochemistry, Sigma Xi, Phi Beta Kappa, Smith College

1997-2000    Lucille P. Markey Biomedical Research Predoctoral Fellowship, Stanford University

2002    Featured by The Chronicle of Higher Education as a “Bioinformatics Whiz” and “Rising Star”

2007-2009    New Investigator Award, Department of Defense Prostate Cancer Research Program

2008-2010    Alfred P. Sloan Research Fellowship

2011-2013    David A. Mazzone Project Development Award

2012    Yangtze River Scholar, Ministry of Education, China

2013    1000 Talent Plan Scholar, China

发表论文

(Selected from over 100 papers, including 51 as the (co)-first or (co)-corresponding authors, 32 papersare in Nature, Science or Cell series;H-index = 47 according to Google Scholar; #Co-first authors;*Co-corresponding authors)

1.     Liu XS, Brutlag DL, Liu JS(2002). An algorithm for finding protein-DNA binding sites with applications tochromatin immunoprecipitation microarray experiments. Nat Biotechnol.20(8):835-9. (cited by 614)

2.     Conlon EM#, Liu XS#,Lieb JD, Liu JS (2003). Integrating regulatory motif discovery and genome-wideexpression analysis. Proc Natl Acad Sci U S A.100(6):3339-44. PMCID: PMC152294. (cited by 333)

3.     Liu Y#, Liu XS#, Wei L, Altman RB, Batzoglou S(2004).  Eukaryotic regulatory elementconservation analysis and identification using compararative genomics.Genome Res. 14(3):451-8.  PMCID:PMC353232.(cited by 149).

4.     Carroll JS, Meyer CA, Song J, Li W, Brodsky AS, HallG, Geistlinger TR, Eeckhoute J, Wang QB, Bekiranov S, Sementchenko V, Fox EA,Silver PA, Gingeras TR, Liu XS*,Brown M* (2006). Genome wide analysis of estrogen receptor binding sites. NatGenet. 38(11):1289-97. (cited by 726)

5.     Ozsolak F#, Song JS#, Liu XS*, Fisher DE* (2007). High-throughputmapping of the chromatin structure of human promoters. Nat Biotechnol.25(2):244-8. (cited by 236)

6.     Lupien M, Eeckhoute J, Meyer CA, Wang Q, Zhang Y, LiW, Carroll JS, Liu XS, Brown M(2008). FoxA1 translates epigenetic signatures into enhancer drivenlineage-specific transcription. Cell. 132(6):958-70.PMCID:PMC2323438. (cited by 375)

7.     Zhang Y#, Liu T#, Meyer CA,Eeckhoute J, Johnson DS, Bernstein B, Nusbaum C, Myers RM, Brown M, Li W*, Liu XS* (2008). Model-based analysis ofChIP-Seq (MACS). Genome Biol.9(9):R137. PMCID:PMC2592715. (cited by 898)

8.     Johnson DS#, Li W#, et al.,Struhl K*, Myers RM*, Lieb JD*, Liu XS*(2008). Systematic evaluation of variability in ChIP-chip experiments usingpredefined DNA targets. Genome Res. 18(3):393-403.PMCID:PMC2259013. (cited by 121)

9.     Wang Q#, Li W#, Zhang Y, Yuan X,Beroukhim R, Wang H, Lupien M, Wu T, Regan MM, Meyer CA, Carroll JS, Manrai AK,Jänne OA, Balk SP, Mehra R, Chinnaiyan AM, Rubin MA, True L, Giorentino M,Fiore C, Loda M, Kantoff PW, Liu XS*,Brown M*. (2009) Androgen receptor regulates a distinct transcription programin androgen-independent prostate cancer. Cell. 138(2):245-56.PMCID:PMC2726827. (cited by 268)

10.  Vastenhouw N#, Zhang Y#, WoodsI, Imam F, Regev A, Liu XS*, RinnJ*, Schier A* (2010). Chromatin signature of embryonic pluripotency isestablished during zygotic genome activation in zebrafish. Nature. 464(7290):922-6.PMCID:PMC2874748. (cited by 95)

11.  He HH#, Meyer C#, Shin H, BaileyS, Wei G, Wang Q, Zhang Y, Xu K, Ni M, Lupien M, Mieczkowski P, Lieb JD, ZhaoK, Brown M*, Liu XS* (2010).Nucleosome dynamics defines transcriptional enhancers. Nat Genet. 42(4):343-7.PMCID:PMC2932437. (cited by 159)

12.  Wu ZJ#, Meyer CA#, Choudhury S,Shipitsin M, Bessarabova M, Nikolsky Y, Sukumar S, Schwartzman A, Liu JS,Polyak K*, Liu XS* (2010). Geneexpression profiling of human breast tissue samples using SAGE-Seq. GenomeRes. 20(12):1730-9. PMCID:PMC2989999. (cited by 21)

13.  Ji H* & LiuXS*. Analyzing ‘omics data using hierarchical models (2010). NatBiotech.28(4):337-40. PMCID: PMC2904972. (cited by 7)

14.  Feng D#, Liu T#, Sun Z, Bugge A,Mullican SE, Liu XS, Lazar MA(2011). A circadian rhythm orchestrated by histone deacetylase 3 controlshepatic lipid metabolism. Science. 331(6022):1315-9.PMCID:PMC3389392. (cited by 110)

15. Ni M#, Chen Y#,Bailey ST, Imai Y, Liu XS*, Brown M*(2011). Targeting androgen receptor in estrogen receptor-negative breastcancer. Cancer Cell. 20(1):119-31. PMCID:PMC3180861. (cited by 67)

16. Liu T#, Ortiz JA#,Taing L, Meyer CA, Lee B, Zhang Y, Shin HG, Wong SS, Ma J, Lei Y, Pape UJ,Poidinger M, Chen Y, Yeung K, Brown M*, Turpaz Y*, Liu XS* (2011). Cistrome: an integrative platform fortranscriptional regulation studies. Genome Biol. 12(8):R83. PMCID:PMC3245621. (cited by 49)

17. Tang Q, Chen Y,Meyer CA, Geistlinger T, Lupien M, Wang Q, Liu T, Zhang Y, Brown M*, Liu XS* (2011). A comprehensive view ofnuclear receptor cancer cistromes. Cancer Res. 71(22):6940-7. (cited by1)

18. He HH#, Meyer CA#,Chen MW, Jordan C, Brown M*, Liu XS*(2012). Differential DNase I hypersensitivity reveals factor-dependentchromatin dynamics. Genome Res. 22(6):1015-25. PMCID:PMC3371710.(cited by 13)

19. Feng J#, Liu T#, Qin B, Zhang Y*, Liu XS*(2012). Identifying ChIP-seq enrichment using MACS. Nat Protoc 7(9):1728-1740.(cited by 7)

20. Bailey ST#, Shin H#, Westerling T, Liu XS*, Brown M* (2012).Estrogen receptor prevents p53-dependent apoptosis in breast cancer. Proc NatlAcad Sci USA 109(44):18060-5. PMCID:PMC3497783.

21.  Xu K#, Wu ZJ#, Anna C. GronerAC, He HH, Cai C, Lis RT, Wu X, Stack EC, Loda M, Liu T, Xu H, Cato L, ThorntonJE, Gregory RI, Morrissey M, Vessella RL, Montironi R, Magi-Galluzzi C, KantoffPW, Balk SP, Liu XS*, Brown M*(2012). EZH2 Oncogenic activity in castration resistant prostate cancer ispolycomb-independent. Science. 338(6113):1465-9. PMCID:PMC3625962.(cited by 17)

22.  Trynka G, Han B, Sandor C,Xu H, Stranger BE, Liu XS, Raychaudhuri S (2012). Chromatin marksidentify critical cell types for fine mapping complex trait variants. Nat Genet.151(6):1200-13.(cited by 5)

23. Chen Y#,Negre N#, Mieczkowska JO, Li Q, Zhang Y, He HH, Kim TK, GreenbergME, Ruan Y, Bickel PJ, Wold BJ, Myers RM, White KP*, Lieb JD*, Liu XS* (2012). Systematic evaluationof the factors that influence the fidelity of ChIP-seq experiment usingultra-deep sequencing data. Nat Method. 9(6):609-14.

24. Choudhury S#, Almendro V#, Merino VF#, Wu Z#, Maruyama R#, et al, Liu XS, SukumarS, Polyak K. Molecular Profiling of Human Mammary Gland Links Breast CancerRisk to a p27+ Cell Population with Progenitor Characteristics.Cell Stem Cell.Epub.

25.  Du Z#, Fei T#, Verhaak RG, Su Z,Zhang Y, Brown M*, Chen Y*, Liu XS* (2013). Integrative genomic analyses reveal clinically relevant long noncodingRNAs in human cancer. Nat Struct Mol Biol. 2013 doi:10.1038/nsmb.2591. Epub.

个人爱好

  • 和两个宝贝儿子玩

  • 旅游 (马上要去 Banff)

  • 运动 (游泳,划船,滑雪,跑步)

  • 种花 (最喜欢 bulbs, 尤其是 Amaryllis)

  • 做饭 (钻研如何在最短时间内做出最可口的饭菜)

  • 古典音乐 (最爱 Mozart)

  • 读书 (Audible 上的传记)





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