Honglei Zhou

I'm a research assistant professor and senior software engineer at Jiangsu Province Hospital in Nanjing, where my primary focus is on developing bioinformatics analysis platforms, conducting research data analysis, and collaborating with physicians to address real-world challenges.

Before I join Jiangsu Province Hospital, I worked as senior software engineer in MarkLogic in San Mateo, where I mainly involved in developing an AWS Spot Fleet-based MarkLogic DB SaaS service.

I also have sereral years of experience in Start-up companies. From 2022 to 2024, I worked as part-time software engineer in Paigo to design and develop the Paigo backend customer service API, and implement frontend dashboard feature. From 2018 to 2020, I joined Bliss Motors as a founding member, working on the full development stack of Bliss Motors' services and creating a chatbot named Telle Chat. In 2017, I worked as project manager in a next-generation sequencing company named CD Genomics.

Email  /  CV  /  Google Scholar  /  Github

Education

I earned my Master’s degree in Computer Science from the University of Chicago in 2018. Prior to that, I completed my Ph.D. study in Biochemistry and Molecular Biology at the Computational Medicine Center of Thomas Jefferson University, under the supervision of Prof. Isidore Rigoutsos. I received my Bachelor’s degree in Biology from Wuhan University in 2010.

Work Experience

I have worked on multiple projects in both academia and industry, as listed below.

We developed a bioinformatics analysis platform with an intuitive dashboard, allowing scientists to conduct data analysis without needing to write code.

Paigo features an agent that collects resource metrics from clients, and it also supports clients sending resource metrics via REST APIs. The platform provides a dashboard where clients can define resource units used for billing their customers.

To reduce costs while still meeting client service-level agreements, I explored using AWS Spot Fleets as a more cost-effective alternative for clusters.

Our chatbot has a frontend built using JavaScript with the Vue.js framework, allowing it to be embedded in the website as an iframe. The backend consists of multiple microservices that handle chat functionality and other services.

We implemented a job-level monitoring system within the platform in HPC cluster. This system monitors key metrics—such as CPU usage, memory, I/O, and network activity—at the job level, as each job runs within a container.

Research Experience

I have also contributed to several research projects on diseases, with the findings published in peer-reviewed journals as listed below.

1. Ji W#, Zhou H#, Liang W#, Zhang W, Gong B, Yin T, Chu J, Zhuang J, Zhang J, Luo Y, Liu Y, Gao J, Yin Y. SSK1-Loaded Neurotransmitter-Derived Nanoparticles for Alzheimer's Disease Therapy via Clearance of Senescent Cells. Small. 2024 Mar

2. Lei Li, Yinjiao Fei, Tianfu Dong, Yuxin Song, Xiu Chen, Heda Zhang, Honglei Zhou*, Mingxing Liang*, Jinhai Tang*,IFI30 as a key regulator of PDL1 immunotherapy prognosis in breast cancer, International Immunopharmacology, 2024 May

3. Shao X, Yang D, Shan L, Yan X, Xu D, Li L, Sun Y, Yu Q, Zhou H*, Ding Y*, Tang J*. TH-4000, a hypoxia-activated pan-HER inhibitor, shows excellent preclinical efficacy for the treatment of HER2+ breast cancer. Arch Toxicol. 2024 Jan

4. Gong B, Zhang W, Cong W, Gu Y, Ji W, Yin T, Zhou H, Hu H, Zhuang J, Luo Y, Liu Y, Gao J, Yin Y. Systemic Administration of Neurotransmitter-Derived Lipidoids-PROTACs-DNA Nanocomplex Promotes Tau Clearance and Cognitive Recovery for Alzheimer's Disease Therapy. Adv Healthc Mater. 2024 Jul

5. Wang DD, Jiang LH, Zhang J, Chen X, Zhou HL, Zhong SL, Zhang HD. Androgen receptor expression and clinical characteristics in breast cancer. World J Surg Oncol. 2024 Sep

6. Wenquan Chen, Hao Li, Dandan Wang, Sujin Yang, Junchen Hou, Honglei Zhou, Jinhai Tang, Jian Zhang,HJURP indicates poor prognosis of female breast cancer by promoting cell proliferation and migration,Genes & Diseases,2023 Oct

7. Shurui Xuan, Yuan Ma, Honglei Zhou, Shengwei Gu, Xin Yao, Xiaoning Zeng, The implication of dendritic cells in lung diseases: Immunological role of Toll-like receptor 4, Genes & Diseases,2023 Apr

8. Liang M, Fei Y, Wang Y, Chen W, Liu Z, Xu D, Shen H, Zhou H*, Tang J*. Integrative analysis of the role of BOLA2B in human pan-cancer. Front Genet. 2023 Feb

9. Yang K, Wang YL, Zhu Z, Cao XH, Liang MX, Xu D, Fei YJ, Yang SY, Zhou HL, Tang JH. CBX3 promotes breast cancer progression and high level of CBX3 predicts poor prognosis in patients. Neoplasma. 2023 Feb

10. Fang Z, Shen HY, Xu Q, Zhou HL, Li L, Yang SY, Zhu Z, Tang JH. PUS1 is a novel biomarker for predicting poor outcomes and triple-negative status in breast cancer. Front Oncol. 2022 Nov

11. Mogilyansky E, Clark P, Quann K, Zhou H, Londin E, Jing Y, Rigoutsos I. Post-transcriptional Regulation of BRCA2 through Interactions with miR-19a and miR-19b. Front Genet. 2016 Aug

12. Zhou H, Telonis AG, Jing Y, Xia NL, Biederman L, Jimbo M, Blanco F, Londin E, Brody JR, Rigoutsos I. GPRC5A is a potential oncogene in pancreatic ductal adenocarcinoma cells that is upregulated by gemcitabine with help from HuR. Cell Death Dis. 2016 Jul

13. Zhou H, Rigoutsos I. MiR-103a-3p targets the 5' UTR of GPRC5A in pancreatic cells. RNA. 2014 Sep.

The design and code of this website is adapted from Jon Barron's site.