周 超 Chao Zhou

周超 Chao Zhou

I am a PhD candidate at Shanghai Jiao Tong Univerity joint superivised by Prof. Tao Wang and Prof. Hongyu Zhao.

Study at Yale, 2019.11

Contact

Mailing: Ye jiequan Building, Dongchuan Road 800, Shanghai
Email: rchao.zhou@gmail.com
Github: https://github.com/ZRChao

Education

Ph.D in Biostatistcs, Shanghai Jiao Tong Univerity (2022)
B.S. in Statistics, Sun Yat-Sen Univeristy (2016)

Research

Metagenomics and microbiome research
Genome-wide association study (GWAS) based on the summary statistics
Mendelian Randomization (MR) for casual inference

Publications

2020 & 2021

Bai, J., Bruner, D. W., Fedirko, V., Beitler, J. J., Zhou, C., Gu, J., … & Xiao, C. (2020). Gut microbiome associated with the psychoneurological symptom cluster in patients with head and neck cancers. Cancers, 12(9), 2531.[online]
Xiao, C., Fedirko, V., Beitler, J., Bai, J., Peng, G., Zhou, C., … & Bruner, D. (2021). The role of the gut microbiome in cancer-related fatigue: Pilot study on epigenetic mechanisms. Supportive Care in Cancer, 29(6), 3173-3182.[online]
Zhou, C., Zhao, H., & Wang, T. (2021). Transformation and differential abundance analysis of microbiome data incorporating phylogeny. Bioinformatics, 37(24), 4652-4660.[online][R package]

2022

Zhou, C., Wang, H., Zhao, H., & Wang, T. (2022). fastANCOM: a fast method for analysis of compositions of microbiomes. Bioinformatics, 38(7), 2039-2041.[online][R package]
Liu, T., Zhou, C., Wang, H., Zhao, H., & Wang, T. (2022). phyloMDA: an R package for phylogeny-aware microbiome data analysis. BMC bioinformatics, 23(1), 1-6.[online][R package]
Zhang, C., Zhou, C., et al. (2022). Transmission risk of asymptomatic SARS-CoV-2 infection: a systematic review and meta-analysis. Infectious Medicine (In press). [online]
Ren, Y., Kong, Y., Zhou, X., Genchev, G. Z., Zhou, C., Zhao, H., & Lu, H. (2022). FVC as an adaptive and accurate method for filtering variants from popular NGS analysis pipelines. Communications Biology, 5(1), 1-9.[online]
Deng L, Li P, Zhang X, Jiang Q, Turner D, Zhou C, Gao Y, Qian F, Zhang C, Lu H, Zou H, Vermund SH, Qian HZ. Risk of SARS-CoV-2 reinfection: a systematic review and meta-analysis. Sci Rep. 2022 Dec 1;12(1):20763. doi: 10.1038/s41598-022-24220-7. PMID: 36456577; PMCID: PMC9714387.[online]
Liang W, Zhou C, Wang J, Zhao J, Liu F, Wang G, Xu C, Zhang Y, Wang W, Cai S, Han Y, Chang L, Zhang P. (2022) A prognostic signature based on adenosine metabolism related genes for ovarian cancer. Front Oncol. 2022 Nov 28;12:1003512. doi: 10.3389/fonc.2022.1003512. PMID: 36518306; PMCID: PMC9742553.

Software

I have developed and maintained softwares on my GitHub page.

adaANCOM An R package implemented the parameter estimation of ZIDTM by Expectation-Maximization algorithm, the likelihood ratio test, Bayesian posterior-mean transformation on the phylogenetic tree, and an adaptive analysis of the compostions of microbiome (adaANCOM).
fastANCOM An R package implemented a fast method for analysis of compositions of microbiomes, and also an speedup version of ANCOM based on Mann Whitney U Test.
phyloMDA An R package for phylogeny-aware microbiome data analysis
phyloMAT An R package for analysis of compositions of microbiomes at the community level incorporating phylogenetic tree.

My PhD life

Thanks to all the people I met along the way, I wish all of you will be treated with kindness by the world and accompanied by others with warmth!

The little prince and his roses

Life is a train that keeps moving forward. It is difficult for someone to accompany you from beginning to end. It comes to an end anytime, and wave goodbye gratefully, and finally wish myself closer to happiness!