简介

主要研究领域：

代表论著：

简介

职 称: 研究员

职 务: 博士生导师

研究方向: 系统生物学

1990-1994 四川大学获得生物工程学学士学位,

1994-1997中科院上海细胞所获得硕士学位,

2001-2003衣阿华大学获得计算机硕士学位,

1998-2003衣阿华大学获得遗传学博士学位

2003-2004衣阿华大学从事生物信息学博士后研究

2004-2005明尼苏达大学从事生物信息学博士后研究

2005-2011 西北大学儿科系研究助理教授

2011－至今 中国科学院北京基因组研究所“百人计划”研究员

专利:

1. Xie, H. Selective Enrichment of CpG islands. (U.S Patent Application Serial No. 12/767,382, Pending)

主要研究领域：

DNA甲基化是直接发生在DNA分子上的一种共价修饰，它直接影响了基因组的构象，是基因表达的一种重要调控方式。高度甲基化的DNA往往被组蛋白紧密包裹而处于封闭状态。去甲基化过程导致DNA双链处于放松状态，并可与转录因子结合从而促进基因的表达。正常细胞分化、组织发育以及疾病包括癌症发生发展过程中常伴随着DNA甲基化水平的改变。本项目组前期工作可以分以下四个方向：1）Alu重复序列甲基化分析技术的发展及应用；2）DNA甲基化模式分析法及应用；3）基因组及表观基因组多态性研究； 4）系统生物学及大规模数据库的整合和应用。

本项目组远期目标是在增强对肿瘤发生发展的理解基础上能够提供有效的预防，诊断及治疗手段。在近期内，本项目组的主要研究方向集中于：1）高通量测序相关技术革新及应用； 2）计算生物学及生物信息学在组学（omics）领域的应用。

代表论著：

A. Andrade, M. Wang, M. d. F. Bonaldo, H. Xie* and M. B. Soares*. Submitted. Human genetic and epigenetic variations resulting from Alu retroposition. (*Corresponding authors)

Yadav, A. K., R. Ferrarese, A.P. Masillamani, H. Xie, M.S. Carro, F, Dai, C. Bredel, A. Alvarez, M. B. Soares, G. R. Harsh and M. Bredel. Submitted. Aberrant splicing of the tumor suppressor ANXA7 contributes to self-sufficiency of glioblastomas in oncogenic EGFR signaling.

Xie, H.*, M. Wang, A. Andrade, M. d. F. Bonaldo, V. Galat, K. Arndt, V. Rajaram, S. Goldman, T. Tomita, and M. B. Soares 2011. Genome-wide quantitative assessment of variation in DNA methylation patterns. Nucleic Acids Res. Jan 28. (*Corresponding author)

M. Wang, H. Xie, W. Stellpflug, V. Rajaram, M. d. F. Bonaldo, S. Goldman, T. Tomita, and M. B. Soares 2011. BTECH: A Platform to Integrate Genomic, Transcriptomic and Epigenomic Alterations in Brain Tumors. NeuroInformatics. Jan 6.

Xie, H.*, M. Wang, M. d. F. Bonaldo, V. Rajaram, W. Stellpflug, C. Smith, K. Arndt, S. Goldman, T. Tomita, and M. B. Soares*. 2010. Epigenomic analysis of Alu repeats in human ependymomas. Proc Natl Acad Sci U S A, 107(15): p. 6952-7. (*Corresponding author)

Hamm, C. A., J. W. Stevens, H. Xie, E. F. Vanin, J. A. Morcuende, H. Abdulkawy, S. T. Sredni, J. Bischof, D. Wang, S. Malchenko, M. d. F. Bonaldo, T. L. Casavant, and M. B. Soares. 2010. Microenvironment alters epigenetic and gene expression profiles in Swarm rat chondrosarcoma tumors. BMC Cancer, 10(1):471

Xie, H.*, M. Wang, F. Bonaldo Mde, C. Smith, V. Rajaram, S. Goldman, T. Tomita, and M. B. Soares*. 2009. High-throughput sequence-based epigenomic analysis of Alu repeats in human cerebellum. Nucleic Acids Res 37 (13):4331-4340. (*Corresponding author)

Hamm, C. A., H. Xie, F. Costa, E. F. Vanin, E. A. Seftor, S. T. Sredni, M. F. Bonaldo, M. J. C. Hendrix, and M. B. Soares. 2009. Global demethylation of rat chondrosarcoma cells after treatment with 5-Aza-2-deoxycytidine results in increased tumorigenicity. PLoS One, 4(12): p. e8340.

Xie, H., M. Wang, J. Bischof, F. Bonaldo Mde, and M. B. Soares. 2009. SNP-based prediction of the human germ cell methylation landscape. Genomics 93 (5):434-440.

Yadav, A. K., J. J. Renfrow, D. M. Scholtens, H. Xie, G. E. Duran, C. Bredel, H. Vogel, J. P. Chandler, A. Chakravarti, P. A. Robe, S. Das, A. C. Scheck, J. A. Kessler, M. B. Soares, B. I. Sikic, G. R. Harsh, and M. Bredel. 2009. Monosomy of chromosome 10 associated with dysregulation of epidermal growth factor signaling in glioblastomas. JAMA 302 (3):276-289.

Xie, H.*, M. Wang, Y. Tange, F. Bonaldo Mde, and M. B. Soares. 2009. A primer design algorithm for global analysis of CpG methylation. International Joint Conference on System Biology, Bioinformatics and Intelligent Computing (IJCBS). Proceedings of IEEE:126-130. (*Corresponding author)

Wang, M., H. Xie, S. Mi, and J. Chen. 2007. Recent patents on the identification and clinical application of microRNAs and target genes. Recent Pat DNA Gene Seq 1 (2):116-124.

Dvorak, C. M., M. Hardstedt, H. Xie, M. Wang, K. K. Papas, B. J. Hering, M. P. Murtaugh, and S. C. Fahrenkrug. 2007. Transcriptional profiling of stress response in cultured porcine islets. Biochem Biophys Res Commun 357 (1):118-125.

Ma, S., M. R. Kosorok, J. Huang, H. Xie, L. Manzella, and M. B. Soares. 2006. Robust semiparametric microarray normalization and significance analysis. Biometrics 62 (2):555-561.

Wang, D., J. Huang, H. Xie, L. Manzella, and M. B. Soares. 2005. A robust two-way semi-linear model for normalization of cDNA microarray data. BMC Bioinformatics 6:14.

Xie, H., S. Chen, J. Wang, and X. Ge. 1998. Cloning and sequencing of the variable gene fragments of LC-1 McAb. Journal of cellular and molecular immunology 14 (2):89-92.

Xie, H., and X. Ge. 1997. Recent advance in antibody engineering with functional genomic fragment transplant. Annual report of shanghai immunology society:1-3.

Lu, Y., H. Xie, and X. Ge. 1996. Inhibition of tumor formation in vivo via increasing IL-2 level in microenvironment. Shanghai Journal of Immunology 5 (24-26).