聂金福
文章来源:     发布时间:2018-04-25
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聂金福,中国科学院合肥肿瘤医院医学病理部、中国科学院合肥物质科学研究院医学物理与技术中心分子病理学研究室高级工程师,中国科学院“百人计划”候选人。2000年在美国马凯特大学获计算机及数理统计专业硕士学位,2000年至2012年在威斯康辛医学院及威斯康辛大学莫格里奇研究院从事软件开发和生物信息学研究,2013年至2016年在美国梅奥诊所组建生物信息分析团队。2016年底加入中科院合肥研究院医学物理中心及中科院合肥肿瘤医院。

职称:正高级工程师 中科院“百人计划”

职务:医学病理部生物信息室主任

学科方向:生物信息学

研究领域

精准医疗,生物医学信息学域的高通量基因数据的分析,整合,解和管理

发表论文 

1.Nie J, Stewart R, Zhang H, Thomson JA, Ruan F, Cui X, Wei H. TF-Cluster: A pipeline for identifying functionally coordinated transcription factors via network decomposition of the shared coexpression connectivity matrix (SCCM). BMC Syst Biol. 2011 Apr 15;5:53.

2.Wang L1,Nie J (并列第一作者),Sicotte H, Li L, Eckel-Passow J, SurendraDasari, Vedell J Measure transcript integrity using RNA-seq data. BMC Bioinformatics.2016 Feb 3;17(1):58

3.Du J, Aleff RA, Soragni E, Kalari K, Nie J, Tang X, Davila J, Kocher JP, Patel SV, Gottesfeld JM, Baratz KH, Wieben ED.RNA toxicity and missplicing in the common eye disease fuchs endothelial corneal dystrophy.J Biol Chem. 2015 Mar 6;290(10):5979-90

4.Wang L, Nie J, Kocher JP.PVAAS: identify variants associated with aberrant splicing from RNA-seq.Bioinformatics. 2015 May 15;31(10):1668-70

5.Kalari KR, Nair AA, Bhavsar JD, O'Brien DR, Davila JI, Bockol MA, Nie J, Tang X, Baheti S, Doughty JB, Middha S, Sicotte H, Thompson AE, Asmann YW, Kocher JP.MAP-RSeq: Mayo Analysis Pipeline for RNA sequencingBMC Bioinformatics. 2014 Jun 27;15:224

6.Sun Z, Wu Y, Ordog T, Baheti S, Nie J, Duan X, Hojo K, Kocher JP, Dyck PJ, Klein CJ.Aberrant signature methylome by DNMT1 hot spot mutation in hereditary sensory and autonomic neuropathy 1E. Epigenetics.2014 Aug;9(8):1184-93

7.Hou Z, Meyer S, Propson NE, Nie J, Jiang P, Stewart R, Thomson JA. Characterization and target identification of a DNA aptamer that labels pluripotent stem cellsCell Res.2015 Mar;25(3):390-3

8.Cho M, Oh SS, Nie J, Stewart R, Radeke MJ, Eisenstein M, Coffey PJ, Thomson JA, Soh HTArray-based discovery of aptamer pairs.Anal Chem.2015 Jan 6;87(1):821-8

9.Cho M, Soo Oh S, Nie J, Stewart R, Eisenstein M, Chambers J, Marth JD, Walker F, Thomson JA, Soh HT Quantitative selection and parallel characterization of aptamersProcNatlAcadSciU S A. 2013 Nov 12;110(46):18460-5

10.Meyer S, Maufort JP, Nie J, Stewart R, McIntosh BE, Conti LR, Ahmad KM, Soh HT, Thomson JAhttp://www.ncbi.nlm.nih.gov/pubmed/23967247PLoS One. 2013 Aug 13;8(8):e71798

11.Stewart R, Rascón CA, Tian S, Nie J, Barry C, Chu LF, Ardalani H, Wagner RJ, Probasco MD, Bolin JM, Leng N, Sengupta S, Volkmer M, Habermann B, Tanaka EM, Thomson JA, Dewey CNComparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastemaPLoSComput Biol. 2013;9(3)

12.Kumari S, Nie J, Chen HS, Ma H, Stewart R, Li X, Lu MZ, Taylor WM, Wei H Evaluation of gene association methods for coexpression network construction and biological knowledge discoveryPLoS One. 2012;7(11)

13.Olson CA, Nie J, Diep J, Al-Shyoukh I, Takahashi TT, Al-Mawsawi LQ, Bolin JM, Elwell AL, Swanson S, Stewart R, Thomson JA, Soh HT, Roberts RW, Sun R Single-round, multiplexed antibody mimetic design through mRNA displayAngewChemInt Ed Engl.2012 Dec 7;51(50):12449-53

14.Gong Q, Wang J, Ahmad KM, Csordas AT, Zhou J, Nie J, Stewart R, Thomson JA, Rossi JJ, Soh HTSelection strategy to generate aptamer pairs that bind to distinct sites on protein targetsAnal Chem. 2012 Jun 19;84(12):5365-71

15.Howden SE, Gore A, Li Z, Fung HL, Nisler BS, Nie J, Chen G, McIntosh BE, Gulbranson DR, Diol NR, Taapken SM, Vereide DT, Montgomery KD, Zhang K, Gamm DM, Thomson JA. Genetic correction and analysis of induced pluripotent stem cells from a patient with gyrate atrophy. 116.ProcNatlAcadSci U S A. 2011 Apr 19;108(16):6537-42.

16.Cho M, Xiao Y, Nie J, Stewart R, Csordas AT, Oh SS, Thomson JA, Soh HT. Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing. ProcNatlAcadSci U S A. 2010 Aug 31;107(35):15373-8.

17.Sengupta S, Nie J, Wagner RJ, Yang C, Stewart R, Thomson JA. MicroRNA 92b controls the G1/S checkpoint gene p57 in human embryonic stem cells. Stem Cells.  2009 Jul;27(7):1524-8.

18.Wei H, Kuan PF, Tian S, Yang C, Nie J, Sengupta S, Ruotti V, Jonsdottir GA, Keles S, Thomson JA, Stewart R. A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets. Nucleic Acids Res. 2008 May;36(9):2926-38.

19.Pan G, Tian S, Nie J, Yang C, Ruotti V, Wei H, Jonsdottir GA, Stewart R, Thomson JA. Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. Cell Stem Cell. 2007 Sep 13;1(3):299-312.

20.Wei H, Kuan PF, Tian S, Yang C, Nie J, Sengupta S, Ruotti V, Jonsdottir GA, Keles S, Thomson JA, Stewart R.  A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets.Nucleic Acids Res. 2008 May;36(9):2926-38. 

21.Yu J, Vodyanik MA, Smuga-Otto K, Antosiewicz-Bourget J, Frane JL, Tian S, Nie J, Jonsdottir GA, Ruotti V, Stewart R, Slukvin II, Thomson JA. Induced pluripotent stem cell lines derived from human somatic cells. Science. 2007 Dec 21;318(5858):1917-20.

22.Twigger SN, Pasko D, Nie J, Shimoyama M, Bromberg S, Campbell D, Chen J, dela Cruz N, Fan C, Foote C, Harris G, Hickmann B, Ji Y, Jin W, Li D, Mathis J, Nenasheva N, Nigam R, Petri V, Reilly D, Ruotti V, Schauberger E, Seiler K, Slyper R, Smith J, Wang W, Wu W, Zhao L, Zuniga-Meyer A, Tonellato PJ, Kwitek AE, Jacob HJ. Tools and strategies for physiological genomics: the Rat Genome Database. Physiol Genomics. 2005 Oct 17;23(2):246-56.

23.de la Cruz N, Bromberg S, Pasko D, Shimoyama M, Twigger S, Chen J, Chen CF, Fan C, Foote C, Gopinath GR, Harris G, Hughes A, Ji Y, Jin W, Li D, Mathis J, Nenasheva N, Nie J, Nigam R, Petri V, Reilly D, Wang W, Wu W, Zuniga-Meyer A, Zhao L, Kwitek A, Tonellato P, Jacob H. 25.The Rat Genome Database (RGD): developments towards a phenome database.Nucleic Acids Res. 2005 Jan 1;33.

24.Kwitek AE, Gullings-Handley J, Yu J, Carlos DC, Orlebeke K, Nie J, Eckert J, Lemke A, Andrae JW, Bromberg S, Pasko D, Chen D, Scheetz TE, Casavant TL, Soares MB, Sheffield VC, Tonellato PJ, Jacob HJ. High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Genome Res. 2004 Apr;14(4):750-7.

25.Twigger SN, Nie J, Ruotti V, Yu J, Chen D, Li D, Mathis J, Narayanasamy V, Gopinath GR, Pasko D, Shimoyama M, De La Cruz N, Bromberg S, Kwitek AE, Jacob HJ, Tonellato PJ. Integrative genomics: in silico coupling of rat physiology and complex traits with mouse and human data. Genome Res. 2004 Apr;14(4):651-60.

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