My name is Fang Hailing, and I was born in 1992 in Shandong province of China.
I study biology and earned a Master of Science degree in Biology in 2018. My recent work focuses on computational biology, including biological data analysis and software development. I believe that computers are important tools for solving problems in biology. My interests include the origins of life, cellular mechanisms, the development of multicellular systems, and the nervous system. I have many other interests, however, I have chosen to focus on biology for now because life is short.
I'm always curious about the world, and learning new things excites me. Applying what I've learned to solve real-world problems gives me a sense of control over my life and the ability to make a positive difference in the world. While having many interests may be a good thing about me, it also poses a problem. It means that my time is split, and I need to balance it with my career. it challenging for me to sustain my interest in things after gaining a general understanding of them, which makes it difficult for me to persist and become deeply familiar with my interests. I struggle with serious procrastination, and if I aim for perfection, I may never even get started.
I may be a good person and be just. I prefer to work alone first and then communicate my ideas with others. Although I am introverted and hesitant to meet new people, I am talkative around my friends. Nonetheless, I recognize that I still have a long way to go in getting to know myself better.
Education
Master of Science in Biology
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. It also analyzed the characteristics of genes that showed different codon bias between IDRs and SDs. Our results indicated 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. GO (Gene Ontology) and protein domains enrichment analysis show that there are no significantly GO terms and structure domains was enriched within IDRs strong codon bias genes and genes that from gene families in which each gene is an IDRs strong codon bias gene. The protein domains enrichment results show that the C2H2 zinc figure is significantly increased of IDRs weak codon genes of every species. There is only C2H2 zinc figures were enriched within genes that from gene families in which each gene is an IDRs weak codon bias gene, and more than 30% of those genes of every species contain this structure.
Bachelor of Science in Biotechnology
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 has wide biological activities, such as Antioxidant activity, antibacterial, anti-inflammatory and anticancer. Flavonoids have different anticancer activity due to different structure, The project compare the anti-proliferation activity of 20 kinds of flavonoids using CCK-8 method, and analyze structure-function by flavonoids’ anti-proliferation activity to find out the important efficient structure. The research find that: flavones is more efficient than flavanones flavanonols and flavonols indicating flavones’ basic structure is important to its anticancer function, flavanones have weak anticancer function may be cause by losing of 23 doubly bond, 5’ have a group is important to its function, Phenyl B connect to 3 point is important. By the way, two compound from Coralhead Plant Seed have not efficient function.
Experienc
Research Assistant
Works:
I primarily serve as a supporter in bioinformatics for other members of the lab.
Research Assistant
Works:
My main responsibility in the lab is to manage data. The volume of data is at the petabyte level, so I am responsible for ensuring the integration of the data and backing it up. I also download data for members of the lab. Additionally, I assist group members with software installation and provide technical support for issues such as Linux usage, software bugs, and network problems. I am also one of the maintainers of the lab's software and website. In addition, I participate in some of the lab's projects and assist with software development.
Freelance
Things:
I visited Yantai, a beautiful coastal city, where I took some time to relax and also carried out my learning plan. This plan included studying computer systems, networks, and mathematics. Additionally, I even had the chance to learn the basics of skateboarding while I was there.
Research Assistant
Works:
This is my first job, and my main responsibility here is to offer technical support and software development. I also have the opportunity to participate in some projects. This job allows me to apply what I learned in college and gain new knowledge, such as the phylogenetics of microbiology. Additionally, I also went to the Shenzhen CDC to participate in a project aimed at improving the quality of hospital services.
Projects
Status:
Ongoing, active.
Background and Targets:
In my work in software development, I often need to parse files, which can be either binary or plaintext. To understand the structure and content of these files, I typically refer to documentation in the form of descriptive text or tables that outline the meaning of each field and its associated data type. My goal is to create an easy-to-use and accurate markup language that can be used to describe the layout of both binary and plaintext files. Once I have designed this language, I plan to use it to document commonly used file formats in the biological field and other areas. The docs of this project is located at file-format.
Progress:
A draft version of the language has been written, and three file formats have been documented using this language. However, the language still needs a lot of revision and improvement. Please see My Documentation for details.
Status:
Ongoing, active.
Background and Targets:
Several file formats are commonly used to store GWAS related data, including PLINK files, BGEN files, BAM files, and BESD files. However, different software is required to perform operations such as printing basic file information, extracting partial data from files, and transforming binary data into plain text. In addition, some of these software packages lack help messages in the command line. Furthermore, some of the file formats lack APIs for programming languages. My project has two main objectives. First, I aim to develop C libraries that will contain the core functions necessary for working with these file formats, as well as Python APIs that can be used to interface with the C libraries from Python. Second, I plan to use these libraries to create a software utility that can perform operations on these files more easily. The repository is located at gwastools.
Progress:
The C libraries for the PLINK file and BOD have been completed. However, more coding work and iterations are needed to finalize this project.
Status:
Occasional.
Background and Targets:
I planned and carried out this project during I worked at IMCAS. As my work continued, I wrote numerous scripts and tools to fulfill my daily work requirements, and some of the code I created is reusable. In this project, I developed several Python classes to process commonly used bioinformatics data. Additionally, I collected several useful tools that I developed, including those for phylogenetic tree building, collapsing and clustering, and long repeated sequence calling, and added them to this project. The code of for this project is on biotools.
Progress:
Classes for handling FASTA and GFF data has been completed. And I have distributed them via PyPI as a Python library named 'biobrary'. I have integrated phylogenetic tree clustering and collapsing tools. However, I still need to integrate the code for calling long repeating sequences in genomes.
Skills
Biology:
Cell culture, Animal dissection, Bacterial culture, PCR analysis, Color spectrum.
I acquired the skills during my undergraduate studies through theoretical and experimental classes, and I need to review and refresh my knowledge before using them.
Bioinformatics:
Genome assembly of microbio, Phylogenetic tree analysis.
I acquired that knowledge during my graduate studies and subsequently through my work.
Computer:
Python and C Programming, Good user of linux systerm, Computer network, front-end web developing, Vector graph and raster graph mapulation.
I have chosen Python and C as my programming languages for my productive activities. I use Python for daily system management tasks, writing short scripts, programming tools that don't require high efficiency, and prototyping software. I use C for programming when software requires high speed. Mixing these two languages would be good practice for my future work. Additionally, I am proficient in Linux and have used it as my primary operating system for about five years. I develop software and perform my daily tasks using this system.
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. Long repetitive sequences are frequently found in bacterial genomes, and they often consist of short repeated segments arranged in a particular pattern. For example, long repetitive sequences may be constructed by four short repeated segments, labeled A, B, C, and D. In some cases, the C and D segments may be inverted. These sequences should be classified into the same type of long repetitive sequences. 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 sample 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:
In this project, my main contribution is programming. Specifically, I am responsible for programming tasks. Under Ting's supervision, I built the data portal called BrainMeta. The website is based on the open project Pheweb, and I ran the data parse process of it and modified the webpage to adapt to our demands. And also, I implemented the permutation module of 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 primarily assisted with phylogenetic tree clustering in this project. When a phylogenetic tree contains thousands of nodes, manual analysis such as clustering nodes can become difficult. To address this, I developed a tool that automatically clusters the tree. My tool divides the nodes into groups based on a threshold and collapses the nodes in the same group. This produces a simplified tree that can be easily plotted. 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. As a result, the running time for the module was reduced from about 2 hours to several tens of seconds for the same data, compared to the original R script implementation.
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.
My Timeline
—2025
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.
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.