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郑何平

发布于:2019-03-18 星期一 11:41:45  点击数:18155

郑老师证件照.jpg    

 

 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40多篇,包括Nature Protocols,Nucleic Acids Research,IUCrJ,Structure 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


virusMED.png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。实验室的研究方向还包括:

1.蛋白设计:蛋白设计中图论 (graph theory) ,表面几何 (geometry) 和机器学习算法的应用。基于病毒蛋白质结构的重组亚单位蛋白疫苗设计(recombinant vaccine design)和纳米抗体设计 (nanobody design)。自主开发了病毒蛋白质 GPS 打卡图谱 (https://virusMED.biocloud.top)。

2.使用数据统计和实践 (benchwork) 结合的方法,对结构生物学方法学的研究,在 Nature Protocols 上发表过两篇论文。

3.生物大分子中金属离子的分析。包括生物大分子中金属离子结合位点的设计和构建 (metal binding site design and engineering)。

4.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,研究蛋白复合物的结构,阐明其发挥功能的分子机制,开发诊断治疗、培育养殖中的应用。


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。
 

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

2020-2022  

    45.    Ye S, Lu C, Qiu Y, Zheng H, Ge X, Wu A, Xia Z, Jiang T, Zhu H, Peng Y.  An atlas of human viruses provides new insights into  diversity and tissue tropism of human viruses. bioRxiv 2021.11.01.466721; doi: https://doi.org/10.1101/2021.11.01.466721.

    44.    Kong Y, Chen J, Chen H, Shen Y, Wang L, Yan Y, Zhou H, Zheng H, Yu F, Ming Z. The Structural and Biochemical Basis for FER  Receptor Kinase Early Signaling Initiation in Arabidopsis. bioRxiv 2022.03.30.486374; doi: https://doi.org/10.1101/2022.03.30.486374.

43.      Zhang H, Chen P, Ma H, Woińska M, Liu D, Cooper DR, Peng G, Peng Y, Deng L*, Minor W*, Zheng H* (2021) VirusMED: an atlas of hotspots of viral proteins. IUCr J.8(6):931-942.

42.    Cai Z, Lu C, He J, Liu L, Zou Y, Zhang Z, Zhu Z, Ge X, Wu A, Jiang T, Zheng H, Peng Y. Identification and characterization of circRNAs encoded by MERS-CoV, SARS-CoV-1 and SARS-CoV-2. Brief Bioinform. 2021 Mar 22;22(2):1297-1308. doi: 10.1093/bib/bbaa334.

41.    Lu C, Zhang Z, Cai Z, Zhu Z, Qiu Y, Wu A, Jiang T, Zheng H, Peng Y. Prokaryotic virus host predictor: a Gaussian model for host  prediction of prokaryotic viruses in metagenomics. BMC Biol. 2021 Jan 14;19(1):5. doi: 10.1186/s12915-020-00938-6.

40.      Zheng HCooper DR, Woińska M, Grabowski M, Shabalin IG, Macnar JM, Gucwa M, Liang X, Edwards  A, Minor W (2021) Structural Biology in the digital age. IUCr J. (in press).

39.      Zhu S, Fu Q, Xu F, Zheng H, Yu F (2021) New paradigms in cell adaptation: decades of discoveries on the CrRLK1L receptor kinase signalling network. New Phytologist Aug 23. doi: 10.1111/nph.17683. Online ahead of print.

38.    Li D, Pan S, Zhang H, Fu Y, Peng Z, Zhang L, Peng S, Xu F, Huang H, Shi R, Zheng H, Peng Y, Tan Z. A comprehensive microsatellite landscape of human Y-DNA at kilobase resolution. BMC Genomics. 2021 Jan 22;22(1):76. doi: 10.1186/s12864-021-07389-5. 

37.      Cooper DR, Grabowski M, Zimmerman MD, Porebski PJ, Shabalin IG, Woinska M, Domagalski MJ, Zheng H, Sroka P, Cymborowski M, Czub MP, Niedzialkowska E, Venkataramany BS, Osinski T, Fratczak Z, Bajor J, Gonera J, MacLean E, Wojciechowska K, Konina K, Wajerowicz W, Chruszcz M, Minor W (2020) State-of-the-Art Data Management: Improving the Reproducibility, Consistency, and Traceability of Structural Biology and in Vitro Biochemical Experiments. Methods Mol Biol 2199: 209-236. Times cited: 2

36.   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.

2015-2019

35.    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. Times cited: 7

34.    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. Times cited: 3

33.   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.

32.    Handing KB, Niedziakowska E, Shabalin IG, Kuhn ML, Zheng H*, Minor W* (2018) Characterizing metal binding sites in proteins with X-ray crystallography. Nature Protocols 13:1062-1090. Times cited: 28

F1000 Recommended Publication

31.   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. Times cited: 1

30.   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. 2018; 27: 86-94. Times cited: 19

29.   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. Times cited: 121

28.   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. Times cited: 10

27.   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(40):8966-8976. Times cited: 26

26.   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. Times cited: 2

25.   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. Toxicology and applied pharmacology 310: 205-214. Times cited: 5

24.   Grabowski M, Langner K, Cymborowski M, Porebski PJ, Sroka P, Zheng H, Cooper DR, Zimmerman MD, Elsliger MA, Burley SK and Minor W (2016) A public database of macromolecular diffraction experiments. Acta Crystallographica Section D Structural biology 72: 1181-1193. Times cited: 64

23.   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(7):3789-801. Times Cited: 49

22.   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(4): 756-71. Times Cited: 4

21.   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: 1-15. Times Cited: 33

20.   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. Journal of Bacteriology 198: 463-76. Times cited: 11

 

2010-2014

19.   Zheng H, Chordia MD, Cooper DR, Chruszcz M, Muller P, Sheldrick GM, Minor W (2014) Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server. Nature Protocols 9:156-170. Times Cited: 173

18.   Zheng H, Hou J, Zimmerman MD, Wlodawer A, Minor W. The future of crystallography in drug discovery. Expert Opin Drug Discov 2014; 9:125-137. Times Cited: 41

17.   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. Times Cited: 13

16.    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. Times cited: 3

15.    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. Times Cited: 6

14.    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 68:632-637. Times Cited: 2

13.    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 169:304-311. Times Cited: 12

12.    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 Sci19:1395-1404. Times Cited: 25

 

2000-2009

11.    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 17:623-632. Times Cited: 40

10.    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 149:2108-2120. Times Cited: 36

9.    Zheng H, Chruszcz M, Lasota P, Lebioda L, Minor W (2008) Data mining of metal ion environments present in protein structures. J Inorg Biochem 102:1765-1776. Times Cited: 199

8.    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. Times Cited: 3

7.    Zheng H, Gawlicka-Chruszcz A, Cymborowski M, Minor W (2007) trans-1-Hydroxy-cyclo-pentan-2-aminium chloride. Acta Crystallographica Section E 63:o2697-o2698.

6.    Zheng H, Zuo Y, 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 15:417-428. Times Cited: 31

5.    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 16:1360-1367. Times Cited: 17

4.    Dong A, Xu X, Edwards AM, MCSG, SGC, Chang C, Chruszcz M, Cuff M, Cymborowski M, Di Leo R, Egorova O, Evdokimova E, Filippova E, Gu J, Guthrie J, Ignatchenko A, Joachimiak A, Klostermann N, Kim Y, Korniyenko Y, Minor W, Que Q, Savchenko A, Skarina T, Tan K, Yakunin A, Yee A, Yim V, Zhang R, Zheng H, Akutsu M, Arrowsmith C, Avvakumov GV, Bochkarev A, Dahlgren LG, Dhe-Paganon S, Dimov S, Dombrovski L, Finerty P,Jr, Flodin S, Flores A, Graslund S, Hammerstrom M, Herman MD, Hong BS, Hui R, Johansson I, Liu Y, Nilsson M, Nedyalkova L, Nordlund P, Nyman T, Min J, Ouyang H, Park HW, Qi C, Rabeh W, Shen L, Shen Y, Sukumard D, Tempel W, Tong Y, Tresagues L, Vedadi M, Walker JR, Weigelt J, Welin M, Wu H, Xiao T, Zeng H, Zhu H (2007) In situ proteolysis for protein crystallization and structure determination. Nat Methods 4:1019-1021. Times Cited: 154

3.   Gawlicka-Chruszcz A, Zheng H, Hyacinth M, Cymborowski M, Sabat M, Minor W (2006) Crystal structure of 2,6 -dichlorobenzaldehyde,C7H4Cl2O. Zeitschrift Fur Kristallograhie 221:545-546. Times Cited: 2

2.   Zimmerman MD, Chruszcz M, Cymborowski M, Zheng H, Minor W (2006) Disodium 4-nitro-phenylphosphate hexa-hydrate. Acta Crystallographica Section E 62:m884-m886. Times Cited: 1

1.  Chruszcz M, Zheng H, Cymborowski M, Gawlicka-Chruszcz A, Minor W (2005) 3-(Morpholinium-1-yl)propane-sulfonate. Acta Crystallographica Section E 61:o3190-o3191. Times Cited: 5