Creative Group
Yongyong SHI

Ph.D., Professor, Principal Investigator

Email:shiyongyong@gmail.com

INTRODUCTION
Dr. Shi’s research has been supported by National 863 Project and NSFC. He is honored as 2007 Shanghai Outstanding Young Scientist of Science and Technology and the 2009 Author of Shanghai Excellent Doctoral Dissertation.
RESEARCH INTERESTS
Genetics; Bioinformatics; Nanotechnology; Study the etiology of complex traits.
REPRESENTATIVE PUBLICATIONS

1.Chen P, Pan D, Fan C*, Chen J, Huang K, Wang D, Zhang H, Li Y, Feng G, Liang P, He L, Shi Y*. Gold nanoparticles for high-throughput genotyping of long-range haplotypes. Nature Nanotechnology. 2011 Sep 4;6(10):639-44. doi: 10.1038/nnano.2011.141. (IF: 30.324)

2. Shi Y*, Li L, Hu Z, Li S, Wang S, Liu J, Wu C, He L, Zhou J, Li Z, Hu T, Chen Y, Jia Y, Wang S, Wu L, Cheng X, Yang Z, Yang R, Li X, Huang K, Zhang Q, Zhou H, Tang F, Chen Z, Shen J, Jiang J, Ding H, Xing H, Zhang S, Qu P, Song X, Lin Z, Deng D, Xi L, Lv W, Han X, Tao G, Yan L, Han Z, Li Z, Miao X, Pan S, Shen Y, Wang H, Liu D, Gong E, Li Z, Zhou L, Luan X, Wang C, Song Q, Wu S, Xu H, Shen J, Qiang F, Ma G, Liu L, Chen X, Liu J, Wu J, Shen Y, Wen Y, Chu M, Yu J, Hu X, Fan Y, He H, Jiang Y, Lei Z, Liu C, Chen J, Zhang Y, Yi C, Chen S, Li W, Wang D, Wang Z, Di W, Shen K, Lin D, Shen H, Feng Y, Xie X*, Ma D*. A genome-wide association study identifies two new cervical cancer susceptibility loci at 4q12 and 17q12. Nature Genetics. 2013 Aug;45(8):918-22. doi: 10.1038/ng.2687. Epub 2013 Jun 30. (IF: 36.377)

3.Shi Y*, Hu Z, Wu C, Dai J, Li H, Dong J, Wang M, Miao X, Zhou Y, Lu F, Zhang H, Hu L, Jiang Y, Li Z, Chu M, Ma H, Chen J, Jin G, Tan W, Wu T, Zhang Z, Lin D*, Shen H*. A genome-wide association study identifies new susceptibility loci for non-cardia gastric cancer at 3q13.31 and 5p13.1. Nature Genetics. 2011 Oct 30;43(12):1215-8. doi: 10.1038/ng.978. (IF: 36.377)

4.Shi Y*, Li Z, Xu Q, Wang T, Li T, Shen J, Zhang F, Chen J, Zhou G, Ji W, Li B, Xu Y, Liu D, Wang P, Yang P, Liu B, Sun W, Wan C, Qin S, He G, Steinberg S, Cichon S, Werge T, Sigurdsson E, Tosato S, Palotie A, Nöthen MM, Rietschel M, Ophoff RA, Collier DA, Rujescu D, Clair DS, Stefansson H, Stefansson K, Ji J, Wang Q, Li W, Zheng L, Zhang H, Feng G, He L*. Common variants on 8p12 and 1q24.2 confer risk of schizophrenia. Nature Genetics. 2011 Oct 30;43(12):1224-7. doi: 10.1038/ng.980. (IF: 36.377)

5.Shi Y, Zhao H, Shi Y, Cao Y, Yang D, Li Z, Zhang B, Liang X, Li T, Chen J, Shen J, Zhao J, You L, Gao X, Zhu D, Zhao X, Yan Y, Qin Y, Li W, Yan J, Wang Q, Zhao J, Geng L, Ma J, Zhao Y, He G, Zhang A, Zou S, Yang A, Liu J, Li W, Li B, Wan C, Qin Y, Shi J, Yang J, Jiang H, Xu JE, Qi X, Sun Y, Zhang Y, Hao C, Ju X, Zhao D, Ren CE, Li X, Zhang W, Zhang Y, Zhang J, Wu D, Zhang C, He L*, Chen ZJ*. Genome-wide association study identifies eight new risk loci for polycystic ovary syndrome. Nature Genetics. 2012 Aug 12. doi: 10.1038/ng.2384. [Epub ahead of print] (IF: 36.377)

6.Li J, Zhou G, Ji W, Feng G, Zhao Q, Liu J, Li T, Li Y, Chen P, Zeng Z, Wang T, Hu Z, Zheng L, Wang Y, Shen Y, He L, Shi Y*. Common Variants in the BCL9 Gene Conferring Risk of Schizophrenia. Archives of General Psychiatry. 2011 Mar;68(3):232-40. (IF: 15.618)

7. Zeng Z, Wang T, Li T, Li Y, Chen P, Zhao Q, Liu J, Li J, Feng G, He L, Shi Y*. Common SNPs and haplotypes in DGKH are associated with bipolar disorder and schizophrenia in the Chinese Han population. Molecular Psychiatry. 2011 May;16(5):473-5. (IF: 15.470)

8.Chen ZJ*, Zhao H, He L, Shi Y, Qin Y, Shi Y*, Li Z, You L, Zhao J, Liu J, Liang X, Zhao X, Zhao J, Sun Y, Zhang B, Jiang H, Zhao D, Bian Y, Gao X, Geng L, Li Y, Zhu D, Sun X, Xu JE, Hao C, Ren CE, Zhang Y, Chen S, Zhang W, Yang A, Yan J, Li Y, Ma J, Zhao Y. Genome-wide association study identifies susceptibility loci for polycystic ovary syndrome on chromosome 2p16.3, 2p21 and 9q33.3. Nature Genetics. 2011 Jan;43(1):55-9. (IF: 36.377)

9.Hu Z*, Liu Y, Zhai X, Dai J, Jin G, Wang L, Zhu L, Yang Y, Liu J, Chu M, Wen J, Xie K, Du G, Wang Q, Zhou Y, Cao M, Liu L, He Y, Wang Y, Zhou G, Jia W, Lu J, Li S, Liu J, Yang H, Shi Y*, Zhou W*, Shen H*. New loci associated with chronic hepatitis B virus infection in Han Chinese. Nature Genetics. 2013 Oct 27. doi: 10.1038/ng.2809. [Epub ahead of print] (IF: 36.377)

10. Shi YY*, He G*, Zhang Z, Tang W, Zhang J, Zhao Q, Zhang J, Li XW, Xi ZR, Fang C, Zhao XZ, Feng GY, He L*. A study of rare structural variants in schizophrenia patients and normal controls from Chinese Han population. Molecular Psychiatry. 2008 Oct;13(10):911-3. (IF: 15.470)

# Contributed equally to the paper * Corresponding author

Zhuo Wang

Ph.D., Professor, Doctor Mentor

Ph.D in Bioinformatics from Shanghai Jiao Tong University, Postdoc from Institute for Systems Biology in Seattle

Email:zhuowang@sjtu.edu.cn

INTRODUCTION
Dr. Wang's research has been sponsored by NSCF, National Key R&D Program, and Shanghai Municipal Science and Technology. Dr. Wang undertakes the bilingual education of “Systems Biology” for undergraduate students.
RESEARCH INTERESTS
Omics data analysis and integration; Genotype-phenotype association; Identify driver genes and potential targets of complex diseases using machine learning and statistic model. Application of metabolic network model in synthetic biology design.
REPRESENTATIVE PUBLICATIONS

(1) Shen FZ, Sun RL, Li J, Yao J, Price ND, Liu Q, Liu CG, Wang Z*. OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling, PLOS Computational Biology. 2019, 15(3): e1006835.


(2) Zhang H, Wang K, Zhou J, Chen JH, Xu YZ, Wang D, Li XQ, Sun RL, Zhang MC, Wang Z*, Shi YY*. VariFAST: a Variant Filter by Automated Scoring based on Tagged-signatures. BMC Bioinformatics, 2019, 20(Suppl 22): 713.


(3) Shen FZ, Wu XT, Shi LX, Zhang H, Chen YM, Qi XQ, Wang Z*, Li X*. Transcriptomic and metabolic flux analyses reveal shift of metabolic patterns during rice grain development, BMC Systems Biology, 2018, 12(Suppl 4):47.


(4) Li J, Sun RL, Ning XJ, Wang XR, Wang Z*. Genome-Scale Metabolic Model of Actinosynnema pretiosum ATCC 31280 and Its Application for Ansamitocin P-3 Production Improvement. Genes 2018, 9, 364, doi:10.3390/genes9070364.


(5) Cui P, Zhong T, Wang Z, Wang T, Zhao H, Liu C, Lu H. Identification of human circadian genes based on time course gene expression profiles by using a deep learning method. Biochim Biophys Acta Mol Basis Dis. 2018 Jun;1864(6 Pt B):2274-2283


(6) Wang Z, Danziger S, Heavner B, Ma SY, Smith J, Li S, Baliga N, Aitchison J, Price N*. Combining Inferred regulatory and mechanistic metabolic networks enhances phenotype prediction in yeast. PLOS Computational Biology. 2017.5.17, 13(5): 0~e1005489


(7) Wang Z, Lu LY, Liu L, Li J. Coordination of plant primary metabolism studied with a constraint-based metabolic model of C3 mesophyll cell. Metabolomics (Los Angel) 2017, 7: 192. doi:10.4172/2153-0769.1000192.


(8) Shen FZ,Li J,Zhu Y,Wang Z*. Systematic investigation of metabolic reprogramming in different cancers based on tissue-specific metabolic models. Journal of Bioinformatics and Computational Biology,2016.10.19, 14(5): 1644001-1~1644001-18.


(9)   Liu L, Shen FZ, Xin CP, Wang Z*. Multi-scale analysis of Arabidopsis response to different CO2 conditions: from gene expression to metabolic flux. Journal of Integrative Plant Biology. 2015, 12370.


(10)   Wang CL, Guo LY, Li YX, Wang Z*. Systematic Comparison of C3 and C4 Plants Based on Metabolic Network Analysis BMC Systems Biology, 2012, 6: S9.


(11)   Wang CL, Guo LY, Wang Z*. Comparative Analysis of C3 and C4 Plants using Constraint-based Model. The Fourth International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications, 2012, Shanghai. (EI)


(12)   Wang J, Wang Y, Wang Z*, Liu L*, Zhu XG*, Ma XT*. Synchronization of cytoplasmic and transferred mitochondrial ribosomal protein gene expression in land plants is linked to Telo-box motif enrichment. BMC Evolutionary Biology, 2011, 11:161.


(13)Chang X, Wang Z, Hao P, Li YY, Li YX*. Exploring mitochondrial evolution and metabolism organization principles by comparative analysis of metabolic networks. Genomics, 2010, 95: 339–344.


(14)Chen Q, Wang Z*, Wei DQ. Progress in the applications of flux analysis of metabolic networks. Chinese science bulletin, 2010, 55(22): 2315-2322.


(15)Wang Z, Zhu XG, Chen YZ, Li YX, Liu L*. Though with constraints imposed by endosymbiosis, preferential attachment is still a plausible mechanism responsible for evolution of chloroplast metabolic network. Journal of Evolutionary Biology, 2009, 22(1): 71-79.


(16)Wang Z, Chen Q, Liu L*. Relationship between topology and functions in metabolic network evolution. Chinese science bulletin, 2009, 54 (5): 776-782.


(17)Wang Z, Zhu XG, Chen YZ, Li YY, Hou J, Li YX*, Liu L*. Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria. BMC Genomics, 2006, 7: 100.


(18)Wang Z, Zhu XG, Chen YZ, Li YX, Liu L*. Comparison of modularization methods in application to different biological networks. Lecture Notes in Computer Science, 2006, 4316: 185-195.


(19)Wang Z, Chen YZ, Li XY*. A brief review of computational gene prediction method. Genomics, Proteomics and Bioinformatics. 2004, 2(4): 216-221.


Manfei ZHANG

Associate Professor

Ph.D., Tenure-track Associate Professor
B.S. in Biology, School of Life Sciences, Fudan University
Ph.D. in Human Biology, School of Life Sciences, Fudan University
Postdoc, Human Phenome Institute,Fudan University

Email:zhangmanfei@sjtu.edu.cn, fayfaytwo@aliyun.com

INTRODUCTION

Dr. Zhang. has been dedicated to the quantification and genetic studies on human appearance traits of East Asian populations. She made important contributions in the field of genetic basis of craniofacial phenotypes, mainly including: facial differences between EAS and EUR (Nat Genet, 2022), skull features (J Genet Genomics, 2022), eyebrow thickness (PLoS Genet, 2018), etc. She has authored 16 peer-reviewed publications in 10 different journals. She carried out the youth program of the National Natural Science Foundation of China (NSFC) and the general program of the China Postdoctoral Science Foundation, and participated in the "international human phenotype group program (phase I)" of major science and technology projects in Shanghai. She has won the Shanghai outstanding graduates, the national scholarship for doctoral students and other honors.

RESEARCH INTERESTS

1.      Digital quantification and database construction of craniofacial phenotype

2.      Formation mechanism of individual differences in appearance features (e.g. genetic and evolution mechanism)

3.      The relationship between craniofacial phenotype and mental health and its regulatory mechanism

REPRESENTATIVE PUBLICATIONS

1.       Zhang M*, Wu S*, Du S*, Qian W*, Chen J, et. al. Genetic variants underlying differences in facial morphology in East Asian and European populations. Nature Genetics. 2022. Apr; 54(4):403-411. (IF=41.307

2.       Qian W*, Zhang M*, Wan K*, Xie Y*, Du S, et. al. Genetic evidence for facial variation being a composite phenotype of cranial variation and facial soft tissue thickness. Journal of Genetics and Genomics. 2022. Mar 5:S1673-8527(22)00072-8. (IF=5.723

3.       Wu S*, Zhang M*, Yang X*, Peng F, Zhang J, et. al. Genome-wide association studies and CRISPR/Cas9-mediated gene editing identify regulatory variants influencing eyebrow thickness in humans. PLOS Genetics. 2018 Sep 24; 14(9):e1007640. (IF=6.02

4.       Zhang M*, Li B*, Wu S, Tan J, Yang Y, et. al. A Genome-Wide Association Study of Basal Transepidermal Water Loss Finds that Variants at 9q34.3 Are Associated with Skin Barrier Function. Journal of Investigative Dermatology. 2017 Apr; 137(4):979-982. (IF=7.59

5.       Zhang M*, Wu S*, Zhang J*, Yang Y*, Tan J, et. al. Large-scale genome-wide scans do not support petaloid toenail as a Mendelian trait. Journal of Genetics and Genomics. 2016 Dec 20;43(12):702-704. (IF=5.723

6.       Wang CC*, Yeh HY*, Popov AN*, Zhang HQ*, Matsumura H, … , Zhang M, He G, Yang X, Hu R, Robbeets M, Schiffels S, Kennett DJ, Jin L, Li H, Krause J, Pinhasi R, Reich D. Genomic insights into the formation of human populations in East Asia. Nature. 2021 Mar; 591(7850):413-419. (IF=69.504

7.       Huang Y*, Li D*, Qiao L, Liu Y, Peng Q, Wu S, Zhang M, et. al. A genome-wide association study of facial morphology identifies novel genetic loci in Han Chinese. Journal of Genetics and Genomics. 2021 Mar 20; 48(3):198-207. (IF=5.723

8.       Wu S*, Tan J*, Yang Y*, Peng Q, Zhang M, et. al. Genome-wide scans reveal variants at EDAR predominantly affecting hair straightness in Han Chinese and Uyghur populations. Human Genetics. 2016 Nov; 135(11):1279-1286. (IF=5.881

9.       Peng Q*, Li J*, Tan J*, Yang Y*, Zhang M, et. al. EDARV370A associated facial characteristics in Uyghur population revealing further pleiotropic effects. Human Genetics. 2016 Jan; 135(1):99-108. (IF=5.881