About Me
I come, I live, I die.
I earned a master’s degree in biology, with a specialization in bioinformatics, from Beijing Normal University in 2018. I have been studying and working on problems related to: 1) genome assembly, genome annotation, and phylogenetic analysis of microbes; 2) improving the computational efficiency of bioinformatics tools; 3) cell-type identification based on RNA-seq data.
My study and research interests include the origins of life, cellular mechanisms, organization mechanisms of multicellular organisms, the generation of intelligence of neural systems, and cancer therapy. I use computational approaches to explore these questions.
I am always curious about the world, and learning new things excites me. Applying what I have learned to solve real-world problems gives me a sense of control over my life and the ability to make a positive impact. I prefer to work independently at first and then communicate my ideas to others in a clear, concise, and accurate manner.
Education
Ph.D. student in Biology
Shandong University
09/2024 - 07/2025
Qindao, CN
I quite the doctorate project on July 1, 2025.
Master of Science in Biology
Beijing Normal University
09/2015 - 07/2018
Beijing, CN
Thesis:
Title: An analysis of codon bias between intrinsically disordered regions and structural domains of orthologous single-copy genes from human, chimpanzee and mouse genomes.
Summary: Codon bias, the unequal usage of synonymous codons, can significantly influence biological processes and organism fitness. The project compared the codon bias of orthologous single-copy genes in IDRs and SDs across the human, chimpanzee, and mouse genomes. Our results show that about 3% of orthologous single-copy genes in human and chimpanzee are significantly different in codon bias between IDRs and SDs, and about 1% in mouse genome. There are 7 gene families in which each gene is an IDRs strong codon bias gene, and 13 gene families in which each gene is an IDRs weak codon bias gene.
Bachelor of Science in Biotechnology
Inner Mongolia University
09/2011 - 07/2015
Huhhot, CN
Paper:
Title: Structure-function relationship analysis of 20 kinds of flavonoids of inhibiting HepG2 cell proliferation.
Summary: Flavonoids is a kind of polyphenolic substances and distribute in vegetables and fruits broadly. Flavonoids have different anticancer activity due to different structure. The project compare the anti-proliferation activity of 20 kinds of flavonoids, and analyze structure-function relationship between flavonoids and anticaner activity. The research find that: 1) flavones is more efficient than flavanones; 2) flavones’ basic structure is important to its anticancer activity; 3) flavanones have weak anticancer function may be cause by losing of 23 doubly bond; 4) 5’ have a group is important to its function; 5) phenyl B connect to 3 point is important to its anticancer activity.
Experience
Research Assistant
Shao Lab, Shandong University
09/2023 - 08/2024
Qingdao, CN
Responsibilities:
I primarily serve as a supporter in bioinformatics for other members of the lab.
Research Assistant
Yang Lab, Westlake University
03/2021 - 03/2023
Hangzhou, CN
Responsibilities:
1) manage and download data; 2) install software and provide technical support for Linux usage; 3) address issues of software which developed by the lab; 4) develope software.
Freelance
Home
10/2019 - 02/2021
Yantai, CN
Things:
I learned knowledge of computer systems, networks, and mathematics.
Research Assistant
Feng Lab, Institute of Microbiology, CAS
07/2018 - 10/2019
Beijing, CN
Responsibilities:
1) develope software; 2) genome assembly, genome annotation, and phylogenetic analysis of microbes.
Projects
Background and Targets:
A meaningful file, whether text or binary, always has a specific structure or layout to represent information. There is a need to accurately describe a file’s structure and the meaning of that structure. I developed this markup language to meet that need.
Background and Targets:
Several file formats are commonly used to store GWAS-related data, including PLINK, BGEN, BAM, and BESD files. However, different software tools are required to perform operations such as printing basic file information, extracting subsets of data, and converting binary data into plain text. The project has two main objectives: 1) develop a C library that contain the core functions which is necessary for working with these file formats; 2) create a utility based on the library that can perform operations on these files easily.
Background and Targets:
The project developed a set of tools for: 1) parsing commonly used bioinformatics files; 2) performing phylogenetic tree analysis; 3) detecting long repeats in genomes.
Skills
Computer:
Python and C Programming, A good user of linux systerm, Computer network, front-end web developing, Vector graph and raster graph mapulation.
Bioinformatics:
Genome assembly of microbes, Phylogenetic tree analysis.
Biology:
Cell culture, Animal dissection, Bacterial culture, PCR analysis, Color spectrum.
Language:
IELTS: 6
Courses
Graduate:
Protein Structure and Functions, Biochemistry and Moleculer Biology, Cell Skeleton, Advanced Cell Biology, Advanced Developmental Biology.
Bioinfomatics, Linux Operation System, Computational Biology(Perl and R Programming).
Undergraduate:
Advanced Mathmatics B, Collage Physics B, Collage Chemistry 1 to 3(Inorganic Chemistry, Organic Chemistry, Physical Chemistry).
Cell Biology, Biochemistry, Genetics, Moleculer Biology, Genetic Engineering, Cell Engineering.
Plant Biology, Animal Biology, Microbiology, Animal Histology, Animal Physiology.
Rewards
Graduate:
Graduate Second-class Scholarship(twich), Graduate New Student Scholarship.
Undergraduate:
Excellent Student Scholarship, Outstanding Graduate of the School, Triple-A Student.
Publications
Zhang, G., Yao, S., Liu, Y., Fang, H., Song, Y., Wang, C., Wei, D., Feng, J., 2023. Systematic discovery of a new catalogue of tyrosine-type integrases in bacterial genomic islands. Applied and Environmental Microbiology 89, e01738-22
Contribution:
Assist in identifying long repeats within bacterial genomes. I developed a program that can identify long repetitive sequences, even when their short segments contain variations. This program can now identify long repetitive sequences that follow a particular simple segment pattern.
Qi, T., Wu, Y., Fang, H., Zhang, F., Liu, S., Zeng, J., Yang, J., 2022. Genetic control of RNA splicing and its distinct role in complex trait variation. Nature Genetics 54, 1355–1363.
Contribution:
I built the data portal called BrainMeta. The website is based on the open project Pheweb, and I ran the data parsing process of Pheweb and modified the webpage to meet our needs. I also implemented the permutation module named THISTLE.
Tang, N., Hu, J., Zhao, Y., Song, Y., Wang, C., Zhang, G., Wei, D., Fang, H., Li, C., Jia, R., Feng, J., 2022. In vivo evolution of carbapenem resistance in hypervirulent Klebsiella pneumoniae in a patient undergoing long-term treatment. Journal of Antimicrobial Chemotherapy 77, 531–533.
Contribution:
I assisted with phylogenetic tree clustering in this project. When a phylogenetic tree contains thousands of nodes, manually analyzing such tree become difficult. To address this, I developed a tool that automatically clusters the tree. The code is stored in repository biotools.
Jiang, L., Zheng, Z., Fang, H., Yang, J., 2021. A generalized linear mixed model association tool for biobank-scale data. Nature Genetics 53, 1616–1621.
Contribution:
I implemented the ACAT module based on R scripts provided by Longda. I improved the efficiency of the module by optimizing the data structure and program design.
Zhang, C., Ju, Y., Tang, N., Li, Y., Zhang, G., Song, Y., Fang, H., Yang, L., Feng, J., 2020. Systematic analysis of supervised machine learning as an effective approach to predicate β-lactam resistance phenotype in Streptococcus pneumoniae. Briefings in Bioinformatics 21, 1347–1355.
Contribution:
I helped with rechecking the correctness of previously used protein data.
Personal Summary
I am passionate about learning and technology, and have a curious mind about many subjects, including biology, computers, and electronics. I hold strong moral values and strive for self-improvement. I am easy to get along with and value peaceful relationships. Before undertaking any task, I prefer to acquire a systematic understanding of the relevant background knowledge.
Timeline
—2028
On 3nd October, 2025, I turned 33 years old. Version 34, Darkbeam.
On 1st July, 2025, I quite the doctorate project.
—2025
On 3nd October, 2024, I turned 32 years old. Version 33, Littlewonder.
On 3nd October, 2023, I turned 31 years old. Version 32, Softwind.
On 3nd October, 2022, I turned 30 years old. Version 31, Circleend.
—2022
Began learning violin.
On May 1st, 2021, I started my second job as a research assistant at Westlake University.
Learned basic of skateboard.
In October 2019, I quit my job and moved to Yantai to live a jobless life for 9 months, during which time I focused on learning math and computer-related topics.
On October 3rd, 2019, I turned 28 years old. Version 29.
—2019
Had my first job as a research assitant in Institute of Microbiology.
I graduated from BNU
I got my master degree.
In October 2016, I decided to change my major and began studying bioinformatics.
On October 3rd, 2016, I was 27 years old. Version 28.
—2016
In July 2015, I graduated from IMU and went to Beijing Normal University in the same year.
Got my bachelor degree.
—2013
Proved L'Hopital's Rule independently.
Near the end of my 1st year in university, I recovered from a severe illness, and I still don't know the cause of it.
In September 2011, I started attending Inner Mongolia University.
In Oct 2010, I was 18 years old.
—2010
In 2nd grade, we organized a student campaign to reject summer and winter holiday homework.
In 2008, I went to high school.
—2007
In 2nd grade, I won an award for painting.
In July 2005, I graduated from primary school and went to middle school in the same year.
In 6th grade, I received my first academic award for achieving a good grade in math.
—2004
In 3rd grade, our school shut down, and we moved to a new school where I met my old friends. They are important to me.
In 3rd grade, I rolled down a hill and injured my right wrist. I was very ill, but I survived.
—2001
In September 1999, I went to primary school.
—1998
—1995
—1992
I was born on October 3rd, 1992.
It is most important day to me.