华侨大学生物医学学院/医学院导师简介：Philipp Kapranov, Ph.D.（菲利普卡帕诺夫 博士)

热门关键词：华侨大学生物医学学院/医学院导师  华侨大学Philipp Kapranov, Ph.D.（菲利普卡帕诺夫 博士  硕士研究生导师  

 

Philipp Kapranov, Ph.D.（菲利普卡帕诺夫 博士） 教授，博士生导师

基因组学研究所所长

国家千人计划特聘教授

福建省百人计划特聘专家

福建省高校领军人才

福建省高端外专团队领军人才

电 话：0592-6167250

E-mail: philippk08@hotmail.com

Philipp Kapranov教授长期从事系统生物学和基因组学功能方面的研究，是人类基因组普遍转录概念的提出者之一，他的成果(“The Dark Genome”)被2010年科学杂志评为过去十年最伟大的发现之一(http://www.aaas.org/news/science-breakthroughs-2010-and-insights-decade)。Philipp Kapranov教授近年来发表国际高水平论文70余篇，包括Nature、Science 、Cell及其子刊近二十篇，在vlincRNAs、ncRNAs分子机制、表达水平、功能机制等方面取得了众多显著成果。

Philipp Kapranov教授是ENCODE、FANTOM5等国际研究合作联盟的成员，同时兼任Nature、Gene、Genome Biology、Genome Research、 PNAS 、Nature Biotechnology 、Nature Genetics等著名杂志的审稿人。

★欢迎生物、医学、数理统计、计算机专业背景的学生报考硕博士生；也欢迎理工科相关专业学生有此类研究兴趣的跨专业申请。

研究领域(Research Area)

Our group combines systems biology, next generation single molecule sequencing and traditional molecular biology to discover the intricacies of molecular processes happening in our cells. Our research interests focus on two main directions:

1. Characterizing the class of very long intergenic non-coding (vlinc) RNAs recently discovered by us using the combination of approaches mentioned above. Specifically, we are interested in role these RNAs play in cancer and early development.

2.Development of new methods of transcriptomics and genomics analyzes using the single-molecule sequencing platform enabling novel biological discoveries.

本实验室结合系统生物学、新一代单分子测序以及传统的分子生物学手段，探索人类细胞中复杂的分子生理过程。主要研究方向包括：

1. 本实验室先前已经发现了一组和细胞多能性和癌症相关的vlincRNAs，应用系统生物学、新一代分子测序以及分子生物学方法鉴别vlincRNAs的功能特性。尤其是这类RNAs在癌症以及早期发育中的作用机制。

2. 在单分子测序平台基础上研发新的技术方法，并将其应用于转录组学以及基因组学分析中，解答更多的生物难题。

代表性论文(Selected Publications)：

1. Kapranov P, et al (1999) A protein phosphatase 2C gene, LjNPP2C1, from Lotus japonicus induced during root nodule development. Proc. Natl. Acad. Sci. USA 96: 1738-1743.

2. Kapranov P, et al  (2001) Nodule-specific regulation of phosphatidylinositol transfer protein expression in Lotus japonicus. Plant Cell 13: 1369-1382.

3. Kapranov P, et al (2002) Large-Scale Transcriptional Activity in Chromosomes 21 and 22. Science, 296: 916-919.

4. Cawley S, Bekiranov S, Ng HH, Kapranov P,et al  (2004) Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116: 499-509.

5. ENCODE Project Consortium (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306: 636-40.

6. Jeon Y, Bekiranov S, Karnani N, Kapranov P, et al . (2005) Temporal profile of replication of human chromosomes. Proc. Natl. Acad. Sci. U S A 102:6419-24.

7. Cheng J*, Kapranov P*,et al  (2005) Transcriptional Maps of 10 Human Chromosomes at 5 Nucleotide Resolution. Science 308: 1149-1154. *equal contribution.

8. Kapranov P,et al  (2005) Examples of Complex Architecture of the Human Transcriptome Revealed by RACE and High Density Tiling Arrays. Genome Research 15: 987-997.

9. Schumacher A, Kapranov P,et al  (2006) Microarray-based DNA methylation profiling: technology and applications. Nucl. Acids Res. 34: 528–542.

10. Manak JR, Dike S, Sementchenko V, Kapranov P,et al  (2006) Biological function of unannotated transcription during the early development of Drosophila melanogaster. Nat. Genet. 38:1151-1158. Epub 2006 Sep.

11. Yang A, Zhu Z, Kapranov P,et al  (2006) Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Mol. Cell. 24: 593-602.

12. Kapranov P,et al  (2007). Genome-wide transcription and the implications for genomic organization. Nat Rev Genet. 8:413-23.

13. Kapranov P, et al . (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316:1484-8.

14. Denoeud F*, Kapranov P*,et al  (2007) Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Research. 17:746-59. *equal contribution.

15. ENCODE Project Consortium. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447:799-816.

16. Djebali S*, Kapranov P*, Foissac S*, Lagarde J*,et al (2008) Efficient targeted transcript discovery via array-based normalization of RACE libraries. Nature Methods 5: 629-635. *equal contribution.

17. Zhang X, …, Kapranov P, Weissman SM, Newburger PE (2009) A myelopoiesis-associated regulatory intergenic non-coding RNA transcript within the human HOXA cluster. Blood 113: 2526-34.

18. Affymetrix/Cold Spring Harbor Laboratory ENCODE Transcriptome Project (2009)

Cold Spring Harbor Laboratory: Fejes-Toth K*,et al ;

Affymetrix: Kapranov P*, et al ;

Post-transcriptional processing generates a diversity of 5’-modified long and short RNAs. Nature 457:1028-32.*equal contribution.

19. Kapranov P (2009) From transcription start site to cell biology. Genome Biology 2009, 10: 217.

20. Kapranov P (2009) Studying chromosome-wide transcriptional networks: new insights into disease? Genome Medicine 1: 50

21. Makrythanasis P, Kapranov P, et al ; (2009) Variation in Novel Exons (RACEfrags) of the MECP2 Gene in Rett Syndrome Patients and Controls. Hum Mutat. 30:E866-79

22. Plessy C, …, Kapranov P, Wang H, Davis CA, Gingeras TR, Kawai J, Daub CO, Hayashizaki Y, Gustincich S, Carninci P. (2010) Linking new promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nature Methods 7: 528-34.

23. Ozsolak F, Kapranov P, et al ; (2010) Genome-wide Profiling of Polyadenylation Sites by Direct RNA Sequencing. Cell 143: 1018-1029.

24. Kapranov P*, Ozsolak F*, Kim SW*, Foissac F*, et al ; (2010) Novel class of human RNA species associated with gene termini suggests an uncharacterized RNA copying mechanism. Nature 466:642-6.*equal contribution.

25. modENCODE Consortium (2010) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330:1787-97.

26. Graveley BR, …, Kapranov P, …, Celniker SE. (2010) The developmental transcriptome of Drosophila melanogaster. Nature 471:473-9.

27. Kapranov P, St. Laurent G et al ; (2010) The majority of total nuclear-encoded non-ribosomal RNA in a human cell is “dark matter” unannotated RNA. BMC Bio 8:149.

28. Pastor WA, …, Kapranov P, Tahiliani M, Daley GQ, Liu XS, Ecker JR, Milos PM, Agarwal S, Rao A (2011) Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature 473:394-7. [Epub 2011 May 8.].

29. Kapranov P, St Laurent G (2012) Dark Matter RNA: Existence, Function, and Controversy. Front Genet. 3:60. [Epub 2012 Apr 23].

30. St Laurent G, Savva YA, Kapranov P (2012) Dark matter RNA: an intelligent scaffold for the dynamic regulation of the nuclear information landscape. Front Genet. 3:57. [Epub 2012 Apr 25].

31. Kapranov P, St. Laurent G (2012) Genomic "dark matter": implications for understanding human disease mechanisms, diagnostics, and cures. Front Genet. 3:95.

32. ENCODE Project Consortium (2012) Landscape of transcription in human cells. Nature 489:101-8.

33. ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57-74.

34.Khare T, …, Kapranov P, Kustra R, Labrie V, Klimasauskas S, Petronis A (2012) 5-hmC in the brain: abundance in synaptic genes and differences at the exon-intron boundary. Nature Str & Mol Bio 19:1037-43.

35. St Laurent G 3rd, …, Kapranov P. (2012) Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells. BMC Genomics 13(1):504.

36. St. Laurent G, Shtokalo D, Tackett MR, Yang Z, Vyatkin Y, Milos PM, Seilheimer B, McCaffrey TA, Kapranov P (2013) On the Importance of Small Changes in RNA Expression. Methods 63(1): 18-24.

37. St Laurent G, Shtokalo D, Dong B, Tackett MR, Fan X, Lazorthes S, Nicolas E, Sang N, Triche TJ, McCaffrey TA, Xiao W, Kapranov P (2013) VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer. Genome Biol 14(7):R73.

38. Savva YA, Jepson JE, Chang YJ, Whitaker R, Jones BC, St Laurent G, Tackett MR, Kapranov P, Jiang N, Du G, Helfand SL, Reenan RA (2013) RNA editing regulates transposon-mediated heterochromatic gene silencing. Nature Commun 4:2745

39. St Laurent G, Vyatkin Y, Kapranov P. (2014) Dark matter RNA illuminates the puzzle of genome-wide association studies. BMC Medicine 12:97.

40. Lazorthes S, Vallot C,…, Kapranov P, Mann C, Trouche D, Nicolas E. (2015) A vlincRNA participates in senescence maintenance by relieving H2AZ-mediated repression at the INK4 locus. Nature Communications 6:5971.

41. St Laurent G, Wahlestedt C, Kapranov P. (2015) The Landscape of long noncoding RNA classification. Trends Genet 3:239-51.

42. Pastori C, Kapranov P, …, Wahlestedt C. (2015) The Bromodomain protein BRD4 controls HOTAIR, a long noncoding RNA essential for glioblastoma proliferation. Proc Natl Acad Sci U S A. 2015 112:8326-31

43. St Laurent G, …, Wahlestedt C, Kapranov P. (2016) Functional annotation of the vlinc class of non-coding RNAs using systems biology approach. Nucleic Acids Res. 2016 Mar 21. pii: gkw162.

 

期刊审稿人（REVIEW ACTIVITIES）:

Nature

Gene

Genome Biology

Genome Research

PNAS

Nature Biotechnology

Nature Genetics

Nucleic Acids Research

Molecular Cancer

PLOS

BMC Genomics

Frontiers

Scientific reports

期刊编辑（EDITING OF PROFESSIONAL JOURNALS）:

Frontiers in Non-Coding RNA

www.frontiersin.org

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