1. What made you pursuing a PHD?

My passion for research and desire to deepen my understanding of bioinformatics and its
applications are the driving forces behind my decision to pursue a Ph.D. My undergraduate
research projects allowed me to learn new computational skills and familiarize myself with
bioinformatics tools. The experience of working with biological data and discovering patterns
through data analysis fascinated me, and I realized that I want to continue exploring this field
through advanced research.

As I progressed in my academic journey, I further expanded my knowledge and skills in

bioinformatics and molecular biology, and have gained practical experience in both
computational and wet lab techniques. These experiences have prepared me for the
challenges and demands of graduate-level research.

My goal is to become a proficient and successful researcher, and to make significant

contributions to the field of bioinformatics through my research. Pursuing a Ph.D. will
provide me with the opportunity to work on more complex and diverse research projects and
collaborate with experts in the field. I believe that a Ph.D. program will equip me with the
necessary skills, knowledge, and experience to achieve my research goals and contribute to
scientific advancements.

In summary, my passion for research and my desire to develop my knowledge and skills in
bioinformatics have led me to pursue a Ph.D. program. I am committed to contributing to the
scientific community through innovative research and to becoming a successful researcher.

2. Introduce your major.

My major is bioinformatics, which is an interdisciplinary field that combines biology,

computer science, and statistics. It involves the development and application of
computational methods to analyze and interpret biological data, ranging from DNA and
protein sequences to high-throughput omics data. In my research experience so far, I have
had the opportunity to apply bioinformatics tools to study the epidemiology of viruses, the
effect of conserved RNA structures on ribosome translation rates, and the omics data of
rhizobia. My work has involved analyzing genomic data, transcriptome data, and metadata
using programming languages such as Python, along with online databases and
bioinformatics tools. Additionally, I have experience working in molecular biology and
microbiology labs, performing DNA extractions, PCRs, and agarose gel electrophoresis.
Overall, I believe that bioinformatics plays a crucial role in modern biology and has great
potential to contribute to scientific discoveries in many fields.

3. Introduce your research.

The person writing the passage has experience in bioinformatics, programming, and research.
They have worked on various projects including analyzing epidemiology of coxsackie virus
type A6, studying the effect of conserved RNA structure on ribosome translation rate, and
collating rhizobia omics data. They have experience working in molecular biology and
microbiology labs and have performed DNA extractions, PCRs, and agarose gel
electrophoresis. They have also worked as a server administrator and a teaching assistant,
helping students improve their R programming language skills and perform exploratory
analysis through network thinking in bioinformatics. The person has a passion for research
and intends to pursue a Ph.D.

4. The conclusion of the master’s thesis.

5. Why do you like this major?

There are several reasons why I am passionate about bioinformatics.

Firstly, bioinformatics allows me to combine my interests in both biology and computer

science. Through bioinformatics, I am able to analyze and interpret biological data using
computational methods, which is a very exciting and innovative field.

Secondly, bioinformatics has enormous potential to make significant contributions to

healthcare and medical research. By analyzing large-scale genomic data, we can identify
potential disease-causing genes and develop new treatments that are tailored to an individual's
genetic makeup.

Lastly, bioinformatics is a rapidly evolving field with new techniques and tools being
developed all the time. This means that there are always new and interesting challenges to
tackle and opportunities to learn and grow as a researcher.

Overall, my passion for bioinformatics stems from the unique and exciting opportunities it
offers to make a difference in the world of science and medicine.

6. Why do you choose …… (the major you choose) for master’s

degree.

7.Why do you choose ……(university you applied for) to pursue a

PhD

As a graduate student in bioinformatics, I have always been interested in understanding the

molecular and cellular mechanisms underlying complex diseases. The Hepatology group at
CHROMETA has a proven track record in using cutting-edge technologies like single-cell
sequencing to study liver disease at a molecular level, which is something that aligns with my
research interests. Additionally, the group's emphasis on combining basic and clinical
expertise to develop novel therapeutic strategies is a unique and exciting approach that I
would love to be a part of. Specifically, I am impressed by the group's focus on studying the
role of immune cells in liver disease, and their use of spatial validation techniques to gain a
deeper understanding of immunological and metabolic defects. I believe that my background
in bioinformatics and my skills in data analysis and interpretation could be an asset to the
group's research goals, and I am excited about the prospect of working with such a talented
and driven team of researchers.
8. What are you going to do after graduate?

In the long-term, I am interested in pursuing a career in scientific research, particularly in the

field of translational medicine. I am excited about the opportunity to work with Prof. Schalk
van der Merwe and his team at KU Leuven on this important project studying the molecular
and cellular mechanisms underlying liver disease. Through this PhD program, I hope to gain
a deep understanding of the cutting-edge technologies and techniques used in this field, as
well as to contribute to the discovery of new therapeutic targets for liver disease. Ultimately,
I hope to use the skills and knowledge I gain during this program to continue to make
meaningful contributions to the field of translational medicine.

9.proposal

10.what difficulties do you expect to encounter during this

project

As a bioinformatics graduate student, I anticipate encountering some challenges during this

project, including:

Complexity of data: The analysis of single-cell transcriptomic data can be complex and may
require specialized skills and experience to perform the analysis accurately.

Limited availability of high-quality data: Generating high-quality single-cell data from

human and mouse models can be challenging, and the availability of such data may be
limited.

Biological interpretation: Translating large amounts of data into meaningful biological

insights can be challenging and may require extensive collaboration with biologists and
clinicians.

Experimental validation: Functionally validating new therapeutic targets using in vitro and in
vivo assays can be time-consuming and require extensive resources.

Communication: Keeping up-to-date with the latest research and effectively communicating
findings with team members and high-level seminars can be a challenge.

However, I am confident that with my previous research experience, strong technical skills,
and ability to learn quickly, I can overcome these challenges and make significant
contributions to the research goals of the laboratory of Prof. Schalk van der Merwe.

11.怎样和其他同时合作，举个例子

12.数据分析，用过哪些包

13.有没有 teaching 经验
As a teaching assistant, Chenglong worked with me for at least four weeks and guided
students to improve their R programming language skills, practice with OMICs data
generated from high-throughput sequencing experiments, and perform exploratory analysis
through network thinking.

I was impressed by her patience, professionalism and responsibility during the teaching
process, even when she met students with less programming experience and weak
bioinformatics backgrounds.

14.tell us about yourself

My name is [Your Name], and I am a research-oriented graduate student specializing in

Bioinformatics. My passion for exploring the intricate mechanisms of biological systems has
led me to work on several exciting research projects.

As a part of my academic pursuits, I have been involved in conducting an extensive literature

review and writing code to process multiple genomic, transcriptomic, metabolomic, and
proteomic datasets. Additionally, I have utilized bioinformatics tools to correct the wrong
classification of rhizobia, explore horizontal gene transfer, and analyze phylogeny. I also
created a website dedicated to rhizobia (https://rhizobiawiki.com).

My research experience includes predicting the conserved RNA structure (CRS) in vivo
based on the transcriptome level, comparing the data of RNA structure in vivo, and exploring
the influence of mRNA conserved structure in the process of translation in vivo. Moreover, I
confirmed the view that the conserved structure in vivo does affect the regulation of ribosome
translation rate, and the conserved structural regions in vivo tend to use fewer rare codons. I
also studied the impact of mRNA secondary structure on the rate of ribosome movement.

Furthermore, I conducted a detailed analysis of the nucleotide and amino acid homology,
phylogeny, mutation site, and recombination of the 46 CVA6 Shandong isolates obtained by
Shandong Academy of Medical Science from 2014 to 2015. I used Mega 5.05, Bioedit,
RaxML, Simplot, and other bioinformatics tools to carry out this analysis.

In my recent work, I established two different prognosis acute liver injury models by giving
mice different doses of APAP and compared their early liver transcriptomes by RNA
sequencing. The study identified Myc, Bag3, and Btc as crucial factors in the adaptive
protective response of DILI. Furthermore, the study showed that Btc plays a crucial role in
adaptive protection response in APAP treatment and is a potential biomarker of drug-induced
liver injury, with good prognosis.

I am eager to further pursue my research interests and contribute to the scientific

community's knowledge base. I believe that the opportunity to undertake doctoral studies will
provide me with a platform to explore novel ideas and further my research aspirations.

Thank you for considering my application.

15.what are your strengths and weaknesses?

Strengths: "I believe that one of my greatest strengths is my ability to work well under
pressure. I am able to stay focused and motivated even when faced with tight deadlines or
challenging projects. Additionally, I am a strong communicator and enjoy collaborating with
others to find solutions to complex problems. For example, on a recent project, I was able to
work closely with my team to successfully deliver a high-quality product on a tight timeline."

weaknesses:I lack clinical knowledge and experience in liver disease research, but I will work
hard to make up for it in the future.In my previous academic career, I focused too much on
learning new bioinformatics techniques and overlooked the spirit of exploring a specific
problem. I hope that during my doctoral studies, I can apply the techniques I have learned to
solve some biologically meaningful questions.

16.what makes you the right candidate for this PhD

As a bioinformatics graduate student, I have gained a strong foundation in the theory and
application of various bioinformatics techniques, as well as experience in conducting
independent research. I believe that my technical skills and research experience, combined
with my passion for exploring novel biological questions, make me an ideal candidate for this
PhD program. Additionally, I am a dedicated and hardworking individual who is committed
to making significant contributions to the field of bioinformatics. I am confident that I have
the necessary skills and drive to excel in this program and make meaningful contributions to
the field.

17.what can you bring to this research group

18.how did you hear about this position

I learned about this position through my own research of graduate programs in

bioinformatics. I was looking for a PhD program that aligned with my research interests and
provided the opportunity to work with renowned researchers in the field. I came across this
program and was immediately drawn to its strong emphasis on interdisciplinary collaboration
and cutting-edge research. As such, I believe that this program is the perfect fit for me, and I
am excited to apply and contribute to its research community.

19.what's your ideal work environment

As a bioinformatics graduate student, my ideal work environment would be one that fosters
collaboration and allows for open communication among team members. In addition, I thrive
in an environment that encourages independent thinking and creativity, as well as a
dedication to continuous learning and professional development.

Finally, I value a workplace that provides the necessary resources and tools to support my
research and professional growth, such as access to the latest software and technologies, as
well as opportunities for training and mentorship.

Overall, my ideal work environment would be one that is collaborative, innovative, inclusive,
and supportive of my professional development.
20.谈谈你对这个岗位项目的看法，你觉得有趣的想要 explore 的点 Talk
about your views on this post project, what do you find
interesting and want to explore

I find the project described in the job description very exciting and full of potential for novel
discoveries. The use of single cell sequencing technology and functional assays to uncover
the molecular and cellular mechanisms underlying liver disease is a cutting-edge approach
that has the potential to lead to the discovery of new therapeutic targets. Specifically, I am
interested in exploring the role of myeloid-derived cells in the circulation or from other organ
sites in contributing to cirrhosis-associated complications or disease progression in the liver.
Additionally, I would be interested in examining how the insights into immune cell function
and metabolism can aid in the design of novel therapeutic strategies for patients with liver
disease. Overall, I believe that this project offers a unique opportunity to work in a highly
collaborative and stimulating research environment and to contribute to the improvement of
patient care.

21.谈谈你觉得可以用在这个项目的 skill 和 method，哪些是你不会的，

不会的准备怎么学

22.说一说过去学习新技能的经历

As a bioinformatics graduate student, I have had several opportunities to learn new skills and
apply them to my research. One example of this was when I learned how to perform
transcriptomic analysis using R programming. This was a new skill for me, and I found it
challenging at first. However, with the guidance of my supervisor and through online courses
and tutorials, I was able to gradually improve my programming skills and use this new
knowledge to analyze complex RNA-seq datasets in my research project.

23.编程怎么样，有过软件开发的经验吗 How about programming, do

you have experience in software development?

24.给我一个例子，说明你的创新能力，解决问题得能力 .Give me an
example of your ability to innovate and solve problems

During my graduate studies, I was working on a project that involved analyzing the genomic
and transcriptomic data of a particular species of rhizobial bacteria, and developing a
database to store and organize this data. One of the main challenges I encountered was the
lack of standardization in the field, which made it difficult to integrate data from different
studies and organisms. In addition, the quality of the available data was often poor, with
incomplete or inconsistent annotations and a lack of standardized metadata.

To address these challenges, I developed a novel approach that combined existing data
integration and standardization techniques with new methods based on machine learning and
natural language processing. This allowed me to identify and correct errors in the data, and
standardize the annotations and metadata. I also developed a new method for integrating
transcriptomic data with genomic data, which allowed me to identify novel gene expression
patterns and regulatory mechanisms.

As a result of this approach, I was able to build a comprehensive database of rhizobial

genomics and transcriptomics that was more accurate, complete, and standardized than any
existing resource. This database has been used by researchers around the world to discover
new genes, pathways, and regulatory networks, and has led to several high-impact
publications.

Overall, I believe that this example demonstrates my ability to think creatively and develop
innovative solutions to complex problems. It also highlights my skills in data analysis,
machine learning, and natural language processing, which are essential in the field of
bioinformatics.

25.phd 你觉得最大的挑战是什么

26.XXX 问题能不能用 XXX 来实现

27.生物出身还是 CS 出身

28.熟悉的编程语言，以及水平大概如何

29.有没有 NGS 经验，细节

I have extensive experience with Next Generation Sequencing (NGS) technologies

Specifically, in my work with rhizobial genomics, transcriptomics, and metabolomics, I have
experience with data preprocessing, quality control, read alignment, and gene expression
analysis.

Furthermore, I have experience in integrating multi-omics data, such as genomics,

transcriptomics, and metabolomics, to create comprehensive databases. In my work with
rhizobial genomics, transcriptomics, and metabolomics, I have constructed a comprehensive
database that includes both the raw sequencing data and the processed results.

Overall, my experience in NGS and bioinformatics has prepared me to work with large-scale
genomic and transcriptomic datasets, and has provided me with a strong foundation for
analyzing and interpreting NGS data in various research projects."

30.想要做的研究

31.软件的代码全是自己写的吗