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导师介绍
 
张焱 博士 研究员
生物信息学与微量元素代谢调控网络研究组组长

E-mail: yanzhang01@@sibs.ac.cn (发邮件时请删除一个@)

个人简介:
张焱博士1997年毕业于浙江大学医学院临床医学系,获学士学位;2002年于中国医学科学院&北京协和医学院基础医学研究所生物医学工程系获博士学位。2002年-2009年在美国内布拉斯加大学林肯分校担任博士后和高级研究助理。2009年-2011年在美国哈佛医学院&布莱根妇女医院医学系担任讲师。2011年3月任中科院上海生科院系统生物学重点实验室研究员。2012年入选中国科学院“百人计划”。2013年1月起受聘于中科院上海生科院营养科学研究所,担任研究员、研究组组长。

研究领域:
本研究组的研究方向是利用生物信息学的理论和方法,深入研究微量元素(如硒和必需金属)代谢调控网络,并发现相关的新代谢通路、新基因与新调控机制。此外,利用高通量组学数据资源(基因组、转录组、蛋白质组、离子组等),结合系统生物学研究方法和体系的开发,揭示复杂疾病(如糖尿病、肿瘤和AD病等)发生发展的分子机制,寻找生物标记物,并深入探讨微量元素代谢紊乱与复杂疾病的潜在关系。

研究队伍:

近期论文:

  1. Sun L, Lin J, Du H, Hu C, Huang Z, Lv Z, Zheng C, Shi X, Zhang Y*, Yang Z*. Gender-specific DNA methylome analysis of a Han Chinese longevity population. Biomed Res Int. 2014; in press.
  2. Malinouski M, Hasan NM, Zhang Y, Seravalli J, Lin J, Avanesov A, Lutsenko S, Gladyshev VN. Genome-wide RNAi ionomics screen reveals new genes and regulation of human trace element metabolism. Nat Commun. 2014; 5:3301.
  3. Gladyshev VN, Zhang Y*. Comparative genomics analysis of the metallomes. Met Ions Life Sci. 2013; 12:529-580.
  4. Zhao HW, Lin J, Wang XB, Cheng X, Wang JY, Hu BL, Zhang Y*, Zhang X*, Zhu JH*. Assessing plasma levels of selenium, copper, iron and zinc in patients of Parkinson's disease. PLoS One 2013; 8(12):e83060.
  5. Jiang L, Zhu HZ, Xu YZ, Ni JZ, Zhang Y*, Liu Q*. Comparative selenoproteome analysis reveals a reduced utilization of selenium in parasitic platyhelminthes. PeerJ 2013; 1:e202.
  6. Gobler CJ, Lobanov AV, Tang YZ, Turanov AA, Zhang Y, Doblin M, Taylor GT, Sañudo-Wilhelmy SA, Grigoriev IV, Gladyshev VN. The central role of selenium in the biochemistry and ecology of the harmful pelagophyte, Aureococcus anophagefferens. ISME J. 2013; 7(7):1333-1343.
  7. Li G, Zhang Y*. Progress in bioinformatics studies on trace metals. Prog Chem. 2013; 25(4):446-456.
  8. Yu Y, Wu A, Zhang Z, Yan G, Zhang F, Hu R, Zhang Y*, Zhang K*, Wang F*. Characterization of the GufA Subfamily Member SLC39A11/Zip11 as a Zinc Transporter. J Nutr Biochem, 2013 Oct;24(10):1697-708.
  9. Wen Z, Liu ZP, Liu Z, Zhang Y, Chen L. An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. J Am Med Inform Assoc. 2013 Jul-Aug;20(4):659-67.
  10. Yang XL, Li QR, Ning ZB, Zhang Y*, Zeng R*, Wu JR*. (2012) Identification of complex relationship among protein kinases and substrates during the cell cycle of HeLa cells by phosphoproteomic analysis. Proteomics. 2013 Apr;13(8):1233-46.
  11. Liang X, Kaya A, Zhang Y, Le DT, Hua D, Gladyshev VN. Characterization of methionine oxidation and methionine sulfoxide reduction using methionine-rich cysteine-free proteins. BMC Biochem. 2012; 13:21.
  12. Liu K, Chen K, Zhang Y*. Comparative genomics of trace element-dependent proteomes. Chinese Bulletin of Life Sciences. 2012;24(8):948-965.
  13. Zhang Y*, Lin J, Gao Y. In silico identification of a multi-functional regulatory protein involved in Holliday junction resolution in bacteria. BMC Syst Biol. 2012;6 Suppl 1:S20.
  14. Mariotti M#, Ridge PG#, Zhang Y#, Lobanov AV, Pringle TH, Guigo R, Hatfield DL, Gladyshev VN. Composition and evolution of the vertebrate and mammalian selenoproteomes. PLoS One. 2012;7(3):e33066. (#: co-first authors)
  15. Shchedrina VA, Everley RA, Zhang Y, Gygi SP, Hatfield DL, Gladyshev VN. Selenoprotein K binds multiprotein complexes and is involved in the regulation of endoplasmic reticulum homeostasis. J Biol Chem. 2011;286(50):42937-42948.
  16. Yim SH, Kim YJ, Oh SY, Fujii J, Zhang Y, Gladyshev VN, Rhee SG. Identification and characterization of alternatively transcribed form of peroxiredoxin IV gene that Is specifically expressed in spermatids of postpubertal mouse testis. J Biol Chem. 2011;286(45):39002-39012.
  17. Zhang Y, Rump S, Gladyshev VN. () Comparative genomics and evolution of molybdenum utilization. Coord Chem Rev. 2011;255(9-10):1206-1217.
  18. Zhang Y, Gladyshev VN. Comparative genomics of trace element dependence in biology. J Biol Chem. 2011;286(27): 23623-23629.
  19. Gobler CJ, Berry DL, Dyhrman ST, Wilhelm SW, Salamov A, Lobanov AV, Zhang Y, Collier JL, Wurch LL, Kustka AB, et al. Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics. Proc Natl Acad Sci U S A. 2011;108(11):4352-4357.
  20. Zhang Y, Gladyshev VN.dbTEU: a protein database of trace element utilization. Bioinformatics. 2010;26(5):700-702.
  21. Zhang Y, Gladyshev VN. General trends in trace element utilization revealed by comparative genomic analyses of Co, Cu, Mo, Ni, and Se. J Biol Chem. 2010; 285(5):3393-3405.
  22. Bekaert M, Firth AE, Zhang Y, Gladyshev VN, Atkins JF, Baranov PV. Recode-2: new design, new search tools, and many more genes. Nucleic Acids Res. 2010;38 (Database issue):D69-74.
  23. Shchedrina VA, Zhang Y, Labunskyy VM, Hatfield DL, Gladyshev VN. Structure-function relations, physiological roles, and evolution of mammalian ER-resident selenoproteins. Antioxid Redox Signal. 2010;12(7):839-849.
  24. Zhang Y, Gladyshev VN. Comparative genomics of trace elements: emerging dynamic view of trace element utilization and function. Chem Rev. 2009; 109(10):4828-4861.
  25. Zhang Y, Rodionov DA, Gelfand MS, Gladyshev VN. () Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization. BMC Genomics. 2009;10:78.
  26. Le DT, Lee BC, Marino SM, Zhang Y, Fomenko DE, Kaya A, Hacioglu E, Kwak GH, Koc A, Kim HY, Gladyshev VN. Functional analysis of free methionine-R-sulfoxide reductase from Saccharomyces cerevisiae. J Biol Chem. 2009;284(7):4354-4364.
  27. Hirosawa-Takamori M, Ossipov D, Novoselov SV, Turanov AA, Zhang Y, Gladyshev VN, Krol A, Vorbrüggen G, Jäckle H. A novel stem loop control element-dependent UGA read-through system without translational selenocysteine incorporation in Drosophila. FASEB J. 2009;23(1):107-113.
  28. Kim HY, Zhang Y, Lee BC, Kim JR, Gladyshev VN. () The selenoproteome of Clostridium sp. OhILAs: characterization of anaerobic bacterial selenoprotein methionine sulfoxide reductase A. Proteins. 2009;74(4):1008-1017.
  29. Zhang Y, Gladyshev VN. () Trends in selenium utilization in marine microbial world revealed through the analysis of the global ocean sampling (GOS) project. PLoS Genet. 2008;4(6):e1000095.
  30. Papp LV, Wang J, Kennedy D, Boucher D, Zhang Y, Gladyshev VN, Singh RN, Khanna KK. Functional characterization of alternatively spliced human SECISBP2 transcript variants. Nucleic Acids Res. 2008; 36(22):7192-7206.
  31. Zhang Y, Turanov AA, Hatfield DL, Gladyshev VN. In silico identification of genes involved in selenium metabolism: evidence for a third selenium utilization trait. BMC Genomics. 2008;9:251.
  32. Zhang Y, Gladyshev VN. Molybdoproteomes and evolution of molybdenum utilization. J Mol Biol. 2008;379(4):881-899.
  33. Ridge PG, Zhang Y, Gladyshev VN. Comparative genomic analyses of copper transporters and cuproproteomes reveal evolutionary dynamics of copper utilization and its link to oxygen. PLoS One .2008; 3(1):e1378.
  34. Zhang Y, Zhou Y, Schweizer U, Savaskan NE, Hua D, Kipnis J, Hatfield DL, Gladyshev VN. Comparative analysis of selenocysteine machinery and selenoproteome gene expression in mouse brain identifies neurons as key functional sites of selenium in mammals. J Biol Chem. 2008;283(4):2427-2438.
  35. Zhang Y, Gladyshev VN. High content of proteins containing 21st and 22nd amino acids, selenocysteine and pyrrolysine, in a symbiotic deltaproteobacterium of gutless worm Olavius algarvensis. Nucleic Acids Res. 2007 ;35(15):4952-4963.
  36. Xu XM, Carlson BA, Mix H, Zhang Y, Saira K, Glass RS, Berry MJ, Gladyshev VN, Hatfield DL. Biosynthesis of selenocysteine on its tRNA in eukaryotes. PLoS Biol. 2007;5(1):e4.
  37. Lobanov AV, Fomenko DE, Zhang Y, Sengupta A, Hatfield DL, Gladyshev VN. Evolutionary dynamics of eukaryotic selenoproteomes: large selenoproteomes may associate with aquatic life and small with terrestrial life. Genome Biol. 2007;8(9):R198.
  38. Xu XM, Carlson BA, Zhang Y, Mix H, Kryukov GV, Glass RS, Berry MJ, Gladyshev VN, Hatfield DL. New developments in selenium biochemistry: selenocysteine biosynthesis in eukaryotes and archaea. Biol Trace Elem Res. 2007;119(3):234-241.

编写书籍:

  1. Gladyshev VN, Zhang Y*. The Metallome, in Metals in Cells. Encyclopedia of Inorganic and Bioinorganic Chemistry, John Wiley & Sons, Ltd, 2013; pp. 1-22.
  2. Zhang Y*. Several chapters in Encyclopedia of Systems Biology, Springer, 2013.

 
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