EDUCATION & TRAINING
2020.6 - present Doctor candidate. Genome Editing, Tumor Immunolpgy, Cancer Analysis and Bioinformatics, Peking University. China
2017.9 - 2020.6 Master. Biophysics, Tianjin University. China
2013.9 - 2017.6 Bachelor. Biological Engineering, Hebei University of Technology. China.
- Hao Wu, Dan Wang, Feng Gao, Toward a high-quality pan-genome landscape of Bacillus subtilis by removal of confounding strains, Briefings in Bioinformatics, bbaa013, https://doi.org/10.1093/bib/bbaa013.
- Wu H, Yang ZK, Yang T, Wang D, Luo H, Gao F. Pan-genome landscape of Bacillus subtilis and Escherichia coli. Essential Genes and Genomes: Methods and Protocols.
POSTERS & PRESENTATIONS
- Zhi-Kai Yang, Hao Luo, Chong Peng, Dan Wang, Chun-Lan Quan, Mei-Jing Dong, Hao Wu and Feng Gao. New insights into the genome organization of Saccharomyces cerevisiae based on comparative genomic analysis. The 8th National Conference on Bioinformatics and Systems Biology of China and the 1st (Macao) International Bioinformatics Symposium. 2018.
Maintain and update the laboratory database. Build and maintain laboratory database related websites with PHP and HTML language. Server network and data management.
National Computer Rank Examination Grade 3, Net Technology.
Specific gene editing analysis, special research methods with different contents, from raw data obtained from different gene editing experiments to detection and analysis of editing efficiency and other issues.
Use various programming languages to solve biology-related problems. Use the bash scripting and SHELL statements of the LINUX platform to process data efficiently and quickly, use Python to write programs to simplify the analysis process and solve specific problems, use the R language to draw publication-level article figures, and use machine learning and deep learning networks to explore high-efficiency bioinformatics tools.
Familiar with various databases related to bioinformatics (SRA, ENSEMBL, UCSC, DEG, etc.), various bioinformatics tools (cutadapt, bwa, GATK, bioawk, seqtik, etc.), various bioinformatics file formats (fasta/q , Bed, vcf, sam/bam, etc.). Understand MySql and H2 database, etc.
Familiar with NGS data processing and analysis of various omics data, from the most primitive data quality control, upstream process to downstream analysis. For example, RNA-Seq is used to analyze differential gene expression between samples to reveal changes in transcription levels, Chip-Seq reveals changes in apparent regulatory levels of transcription factors and verification of overexpression results, and WES/call variants analyze synonymous or non-synonymous mutations and between samples to detect the type of differential mutation is related to gene mutation and disease. And also familiar with various bioinformatics related algorithms.
2019.12 - present
Chengqi Yi (PI)
Research on editing efficiency and off-target effects of genome editing is performing, learning basic chemical biology and molecular biology knowledge, and understanding the data and analysis methods of epigenome and epitranscriptomics.
Role: Doctor candidate
2019.10 - 2020.6
Cooperator: He Huang (PI)
Explore key genes or proteins related to pancreatic cancer metastasis by integrating multi-omics methods. I was responsible for all bioinformatics analyses and partial wet experiment verification work, through the integration of multiple omics (genome, transcriptome, proteome, metabolome), and correlated networks analyses between different methods, revealing the key factors related to metastasis. The genome level explored the mutation map and synonymous mutations in the exon region that affect metastasis, the transcriptome level studied the composition of the difference between the metastasis and the primary tumor, and the proteome and metabolome level quantified the differential proteins and metabolites between samples. Finally performed integratiation analysis to reduce target genes and proteins, by screening known experiments and literature, key factors, and verifying regulatory functions through mouse models. (Ongoing)
Role: Graduate Research, Bioinformatics Analysis.
2017.12 - 2020.4
Cooperator: Zexiong Xie
Synthetic biology project: Explore the influence of different sequencing depths of synthetic yeast on development through bedtools. After quality control comparison, GATK was used to detect the rearrangement and recombination phenomena between the chromosomes and the chromosomes of synthetic synV and wild-type V chromosomes carrying loxP sites. In polyploid yeast, the analysis of the differential genes obtained from the transcriptome revealed the copy number variation accompanying polyploid development. (Compeleted)
Role: Graduate Research, Bioinformatics Analysis.
2017.9 - 2018.4
Feng Gao (PI)
On the basis of the Z-curve theory proposed by Academician Zhang Chunting of the research group, the geometric structure of the genome is explored, and the replication origin, protein and non-protein encoding genes, genome islands, and CpG islands on the genome are identified in three-dimensional or high- dimensional space. I participated in the integration of some functions of the GC-profile statistical tool for genome GC content distribution and used Python scripts to write localization tools, also participate in the optimization of the GC-profile front-end and improve the largest essential gene database (DEG database)(Compeleted)
Role: Graduate Research