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郑何平

发布于:2019-03-18 星期一 11:41:45 点击数:5742

郑何平-1.png    郑何平

 教授,博士生导师。

 E-mail: hz5p@hnu.edu.cn


基本信息

郑何平,男,1979年生,广东汕头。2001年本科毕业于中国科技大学,获得生物科学理学学士学位和计算机技术科学工学学士学位。同年考入弗吉尼亚大学分子生理学与生物物理学系, 2009年获得哲学博士学位。同年于弗吉尼亚大学Wladek Minor教授实验室从事博士后研究,2013年在弗吉尼亚大学任研究科学家,2019年加入湖南大学生物学院,聘为教授。目前在国际学术刊物上发表SCI论文30多篇,包括Nature Protocols,Nucleic Acids Research等知名学术期刊,被引用次数超过1000次。目前担任 Science, Bioinformatics, Scientific Reports, BMC Bioinformatics, Protein Science, PLoS Computational Biology, Journal of Applied Crystallography等多家国际期刊审稿人。


教育背景

2001年8月-2009年8月,美国弗吉尼亚大学,哲学博士,导师:Wladek Minor教授;

1998年9月-2000年7月,中国科学技术大学计算机技术科学学院,工学学士;

1996年9月-2001年7月,中国科学技术大学生命科学学院,理学学士。



工作履历

2019年2月至今,湖南大学生物学院,教授,岳麓学者,博士生导师;

2013年10月-2019年2月,美国弗吉尼亚大学,研究科学家,导师:Wladek Minor教授;

2009年8月-2013年10月,美国弗吉尼亚大学,博士后研究员,导师:Wladek Minor教授。



研究领域

主攻生物信息学中,信息学方法模型和算法开发。专业研究手段包括数据挖掘,建模算法,线性回归,机器学习。使用的技术主要包括:

1.数据分析软件R及其基本操作软件包,包括但不限于:用于数据操作的dplyr,作图的ggplot2等;

2.人工智能机器学习算法软件包,例如:caret,pandas/scikit-learn,H2O.ai等;

3.集群环境 Proxmox,云共享软件开发,软件容器 Singularity,Linux container 或者 Docker;

4.关系数据库 PostgreSQL,分布式数据库MongoDB;

5.MVC框架如Django,Ruby on Rails等;

6.网站服务器Nginx和服务器管理环境node.js;

7.基于bootstrap,web components,React JS或者Angular JS的网页开发;基于Objective-C或者Java的手机App应用开发。

实验室的研究方向还包括以X-射线晶体衍射和冷冻电镜技术为主要手段,结合分子生物学、生物化学、细胞生物学、免疫学、生物物理学等多个学科的方法手段,研究金属结合蛋白以及金属药物与蛋白复合物的结构,阐明其发挥功能的分子机制,并将其应用到诊断治疗、培育养殖上面去。例如:(a)锌依赖性金属蛋白酶SAS1B:该蛋白在卵细胞和癌细胞表面有特异表达,可以作为癌细胞的天然标记蛋白,所以SAS1B 抗体可作为抗癌药物的给药载体。(b)人体血清中转运小分子的白蛋白(Albumin):该蛋白具有锌的特异结合位点,还有可能参与其他金属小分子的转运,在金属结合和转运中起到重要作用。(c)钙结合蛋白AVIL:该蛋白的表达与横纹肌肉瘤密切相关。(d)来自鲤鱼的43kD 锌结合蛋白ZBP:该蛋白作为细胞表面受体参与细胞粘连(cell adhesion),与鲤鱼的消化道组织中经常发现极高浓度的锌有关。


招聘信息:

本实验室长期招聘博士后研究人员和博士研究生、硕士研究生。有意向者请将送本人简历发至:hz5p@hnu.edu.cn。应聘要求如下:

1.硕士研究生以及本科实习生:对科研工作感兴趣,愿意学习某种关键生物信息学、数据科学、或者生物统计学技术,并用于解决生物医学、农学问题者;

2.博士研究生需具备以下至少一项专业背景:生物信息学,计算生物学,统计学,数据科学,计算化学,结构生物学,生物化学与分子生物学,细胞生物学,免疫学;

3.博士后需具备以下至少一项专业背景:生物信息学,计算生物学,统计学,数据科学,计算化学,结构生物学,生物化学与分子生物学,细胞生物学,免疫学,并至少发表一篇第一作者SCI论文;或者熟练掌握上述介绍所使用的1-7中的某项关键技术者。博士后有留校任职机会。课题组将按每人12-30万/年的标准提供优厚的待遇、完善的科研条件,期待您的加盟!


学术成果

1. Majorek KA, Zimmerman MD, Grabowski M, Shabalin I, Zheng H, Minor W (2020)

Assessment of Crystallographic Structure Quality and Protein–Ligand Complex Structure Validation

in Structural Biology in Drug Discovery: Methods, Techniques, and Practices: 253-275. [DOI:10.1002/9781118681121.ch11]

 

2.  Han Y, Yu Y, Liang C, Shi Y, Zhu Y, Zheng H*, Wang J*, Zhang J* (2019)

Fluoride-induced unrestored arrest during haploid period of spermatogenesis via the regulation of DDX25 in rats.

Environ Pollution 253: 538-551. [Pub Med ID: 31330346]

 

3. Lipowska J, Miks CD, Kwon K, Shuvalova L, Zheng H, Lewiński K, Cooper DR, Shabalin IG, Minor W (2019)

Pyrimidine biosynthesis in pathogens - Structures and analysis of dihydroorotases from Yersinia pestis and Vibrio cholerae.

Int. J. Biol. Macromol. 136: 1176-1187. [Pub Med ID: 31207330]

 

4. Grabowski M, Shabalin I, Porebski PJ, Domagalski MJ, Zheng H, Cooper D, Venkataramany BS, Bourne PE, Minor W (2019)

Data Sharing in Structural Biology: Advances and Challenges

in Data Sharing: Recent Progress and Remaining Challenges - Computer Science, Technology and Applications, Nova Science Publishers, New York : 29-68.

 

5. Handing KB, Niedzialkowska E, Shabalin IG, Kuhn ML, Zheng H*, Minor W* (2018) 

Characterizing metal-binding sites in proteins with X-ray crystallography.

Nat Protoc 13: 1062-1090 [Pub Med ID: 29674755]  

F1000 Recommended Publication

 

6. Hou J, Zheng H*, Tzou WS, Cooper DR, Chruszcz M, Chordia MD, Kwon K, Grabowski M, Minor W* (2018) 

Differences in substrate specificity of V. cholerae FabH enzymes suggest new approaches for the development of novel antibiotics and biofuels.

FEBS J. 285: 2900-2921 [Pub Med ID: 29917313]  

 

7. Porebski PJ, Sroka P, Zheng H, Cooper DR, Minor W (2018) 

Molstack-Interactive visualization tool for presentation, interpretation, and validation of macromolecules and electron density maps.

Protein Sci. 27: 86-94 [Pub Med ID: 28815771]  

 

8. Zhang J, Zhu Y, Shi Y, Han Y, Liang C, Feng Z, Zheng H, Eng M, Wang J (2017) 

Fluoride-Induced Autophagy via the Regulation of Phosphorylation of Mammalian Targets of Rapamycin in Mice Leydig Cells.

J Agric. Food Chem. 65: 8966-8976 [Pub Med ID: 28927274]

 

9. Zheng H, Cooper DR, Porebski PJ, Shabalin IG, Handing KB, Minor W (2017) 

CheckMyMetal: a macromolecular metal-binding validation tool.

Acta Crystallogr D Struct Biol 73: 223-233 [Pub Med ID: 28291757] 

 

10. Zheng H, Langner KM, Shields GP, Hou J, Kowiel M, Allen FH, Murshudov G, Minor W (2017) 

Data mining of iron(II) and iron(III) bond-valence parameters, and their relevance for macromolecular crystallography.

Acta Crystallogr D Struct Biol 73: 316-325 [Pub Med ID: 28375143]  

 

11. Zheng H, Porebski PJ, Grabowski M, Cooper DR, Minor W (2017) 

Databases, Repositories, and Other Data Resources in Structural Biology.

Methods Mol. Biol. 1607: 643-665 [Pub Med ID: 28573593]  

 

12. Zhang J, Zhang Y, Liang C, Wang N, Zheng H, Wang J (2016) 

Choline supplementation alleviates fluoride-induced testicular toxicity by restoring the NGF and MEK expression in mice.

Toxicol Appl Pharmacol. 310: 205-214 [Pub Med ID: 27664006]

 

13. Grabowski M, Langner KM, Cymborowski M, Porebski PJ, Sroka P, Zheng H, Cooper DR, Zimmerman MD, Elsliger MA, Burley SK, Minor W (2016) 

A public database of macromolecular diffraction experiments.

Acta Crystallogr D Struct Biol 72: 1181-1193 [Pub Med ID: 27841751]  

 

14. Hou J, Zheng H, Chruszcz M, Zimmerman MD, Shumilin IA, Osinski T, Demas M, Grimshaw S, Minor W (2015) 

Dissecting the Structural Elements for the Activation of β-Ketoacyl-(Acyl Carrier Protein) Reductase from Vibrio cholerae.

J. Bacteriol. 198: 463-76 [Pub Med ID: 26553852] 

 

15. Zheng H, Mandal A, Shumilin IA, Chordia MD, Panneerdoss S, Herr JC, Minor W (2015) 

Sperm Lysozyme-Like Protein 1 (SLLP1), an intra-acrosomal oolemmal-binding sperm protein, reveals filamentous organization in protein crystal form.

Andrology 3: 756-71 [Pub Med ID: 26198801]  

 

16. Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W (2015) 

Magnesium-binding architectures in RNA crystal structures: validation, binding preferences, classification and motif detection.

Nucleic Acids Res. 43: 3789-801 [Pub Med ID: 25800744] 

 

17. Zheng H, Handing KB, Zimmerman MD, Shabalin IG, Almo SC, Minor W (2015) 

X-ray crystallography over the past decade for novel drug discovery - where are we heading next?

Expert Opin Drug Discov 10: 975-89 [Pub Med ID: 26177814] 

 

18. Zheng H, Hou J, Zimmerman MD, Wlodawer A, Minor W (2014) 

The future of crystallography in drug discovery.

Expert Opin Drug Discov 9: 125-37 [Pub Med ID: 24372145] 

 

19. Zheng H, Chordia MD, Cooper DR, Chruszcz M, Müller P, Sheldrick GM, Minor W (2014) 

Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server.

Nat Protoc 9: 156-70 [Pub Med ID: 24356774]  

 

20. Domagalski MJ, Zheng H, Zimmerman MD, Dauter Z, Wlodawer A, Minor W (2014) 

The quality and validation of structures from structural genomics.

Methods Mol. Biol. 1091: 297-314 [Pub Med ID: 24203341] 

 

21. Luo HB, Knapik AA, Petkowski JJ, Demas M, Shumilin IA, Zheng H, Chruszcz M, Minor W (2013) 

Biophysical analysis of the putative acetyltransferase SACOL2570 from methicillin-resistant Staphylococcus aureus.

J. Struct. Funct. Genomics 14: 97-108 [Pub Med ID: 23963951] 

 

22. Hou J, Wojciechowska K, Zheng H, Chruszcz M, Cooper DR, Cymborowski M, Skarina T, Gordon E, Luo H, Savchenko A, Minor W (2012) 

Structure of a short-chain dehydrogenase/reductase from Bacillus anthracis.

Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 68: 632-7 [Pub Med ID: 22684058]

 

23. Zheng H, Filippova EV, Tkaczuk KL, Dworzynski P, Chruszcz M, Porebski PJ, Wawrzak Z, Onopriyenko O, Kudritska M, Grimshaw S, Savchenko A, Anderson WF, Minor W (2012) 

Crystal structures of putative phosphoglycerate kinases from B. anthracis and C. jejuni.

J. Struct. Funct. Genomics 13: 15-26 [Pub Med ID: 22403005]  

 

24. Sledz P, Zheng H, Murzyn K, Chruszcz M, Zimmerman MD, Chordia MD, Joachimiak A, Minor W (2010) 

New surface contacts formed upon reductive lysine methylation: improving the probability of protein crystallization.

Protein Sci. 19: 1395-404 [Pub Med ID: 20506323] 

 

25. Luo HB, Zheng H, Zimmerman MD, Chruszcz M, Skarina T, Egorova O, Savchenko A, Edwards AM, Minor W (2010) 

Crystal structure and molecular modeling study of N-carbamoylsarcosine amidase Ta0454 from Thermoplasma acidophilum.

J. Struct. Biol. 169: 304-11 [Pub Med ID: 19932181] 

 

26. Chruszcz M, Zimmerman MD, Wang S, Koclega KD, Zheng H, Evdokimova E, Kudritska M, Cymborowski M, Savchenko A, Edwards A, Minor W (2008) 

Function-biased choice of additives for optimization of protein crystallization - the case of the putative thioesterase PA5185 from Pseudomonas aeruginosa PAO1.

Cryst Growth Des 8: 4054-4061 [Pub Med ID: 19898606] 

 

27. Jha KN, Shumilin IA, Digilio LC, Chertihin O, Zheng H, Schmitz G, Visconti PE, Flickinger CJ, Minor W, Herr JC (2008) 

Biochemical and structural characterization of apolipoprotein A-I binding protein, a novel phosphoprotein with a potential role in sperm capacitation.

Endocrinology 149: 2108-20 [Pub Med ID: 18202122] 

 

28. Chruszcz M, Potrzebowski W, Zimmerman MD, Grabowski M, Zheng H, Lasota P, Minor W (2008) 

Analysis of solvent content and oligomeric states in protein crystals--does symmetry matter?

Protein Sci. 17: 623-32 [Pub Med ID: 18359856] 

 

29. Zheng H, Chruszcz M, Lasota P, Lebioda L, Minor W (2008) 

Data mining of metal ion environments present in protein structures.

J. Inorg. Biochem. 102: 1765-76 [Pub Med ID: 18614239]  

 

30. Petkowski JJ, Chruszcz M, Zimmerman MD, Zheng H, Skarina T, Onopriyenko O, Cymborowski MT, Koclega KD, Savchenko A, Edwards A, Minor W (2007)

Crystal structures of TM0549 and NE1324--two orthologs of E. coli AHAS isozyme III small regulatory subunit.

Protein Sci. 16: 1360-7. [Pub Med ID: 17586771]

 

31. Zuo Y, Zheng H, Wang Y, Chruszcz M, Cymborowski M, Skarina T, Savchenko A, Malhotra A, Minor W (2007)

Crystal structure of RNase T, an exoribonuclease involved in tRNA maturation and end turnover.

Structure 15: 417-28. [Pub Med ID: 17437714]