Benchen Ye

Education

Soochow University 2016.9 - 2019.12

Suzhou, Jiangsu

• M.S. in Medical Systems Biology
• Advised by Bairong Shen

Anhui University 2011.9 - 2015.5

Hefei, Anhui

• B.E. in Bioengineering

Publications

CBD: a biomarker database for colorectal cancer.

Xueli Zhang, Xiao-Feng Sun, Yang Cao, Benchen Ye, Qiliang Peng, Xingyun Liu, Bairong Shen, Hong Zhang.
Database (Oxford) 2018 (IF 2.593).
[PDF] [BibTeX] [www]

CRC-EBD: Epigenetic Biomarker Database for Colorectal Cancer

Xingyun Liu, Xueli Zhang, Jing Chen, Benchen Ye, Shumin Ren, Yuxin Lin, Xiao-Feng Sun, Hong Zhang, and Bairong Shen.
Front Genet. 2020 (IF 3.256).
[PDF] [BibTeX] [www]

Systems Health: A Transition from Disease Management Toward Health Promotion.

Li Shen, Benchen Ye, Huimin Sun, Yuxin Lin, Herman van Wietmarschen, Bairong Shen.
Evaluation and Usability of Programming Languages and Tools (IF 2.453)
[PDF] [BibTeX] [www]

Project

Master thesis: Characterization of Network Feature Cancer Driver Genes.

• Summaried four types of cancer driver genes with literature support.
  
• Analysed the enrichment features of network topology centraility of those cancer driver genes.
  
• Builded a better predictor model for cancer driver genes based on Random forests.
  

Update: A cancer biomarker database for microRNA

• Collected 624 literatures about cancer miRNA biomarkers (2014-2016)

A biomarker database for colorectal cancer.

• Discuss the database framework and establish the data selection criteria.
• Collected 470 literatures about colorectal cancer biomarkers(2010-2014)

Experience

GENEWIZ 2019.12 - 2020.7

Bioinformatics Engineer
16S/18S/ITS/23S sequencing data bioinformatics analysis project;
Optimize species diversity analysis process to improve efficiency;
Debug species identification software(python);

Zhejiang University, School of Public Health 2020.8 - 2021.4

Research Assistant
Manage the cohort’s questionnaire database;
clean and preprocess the questionnaire data;
AES Encrypt sensitive data;
statistical workload—Weekly report and monthly report, and visualization;

Honors & Awards

Second prize, Scholarship of School Soochow University, 2018
Second prize, Scholarship of School Soochow University, 2017
Second prize, Scholarship of School Soochow University, 2016
Third prize, Scholarship of School Anhui University, 2013
Third prize, Scholarship of School Anhui University, 2012

SKILLS AND TECHNIQUES

Fields: network modeling, statistic analysis and visualization, database construction, text mining, machine learning
Skills: R, Linux, Python, SQL, pytorch, docker, office, photoshop, HTML, PHP