Siqi Pan's Curriculumn Vitae
Email: siqipan2008@outlook.com
Educational Experience go to the top...
Shanghai World Foreign Language Academy (Sept. 2023 – May 2026)
Self-study Languages (Ongoing) View my blogs...
Self-study for Advanced Placement (AP) (May 2024 – May 2025) View Report...
edX online courses (Aug. 2023 – Dec. 2024)
Probability and Statistics in Data Science Using Python - 100/100 View Certificate...
Calculus I: From Functions to Differential Equations - 100/100 View Certificate...
Calculus II: Multivariable Functions - 88/100 View Certificate...
Linear Algebra I: Linear Equations - 100/100 View Certificate...
Linear Algebra II: Matrix Algebra - 100/100 View Certificate...
Linear Algebra III: Determinants and Eigenvalues - 100/100 View Certificate...
Linear Algebra IV: Orthogonality & Symmetric Matrices and the SVD - 100/100 View Certificate...
University of Chicago Summer Session (Jul. 2024)
Course name: Explorations in Neuroscience: Neurons, Behavior, and Beyond
Mentor: Prof. Megan McNulty; University of Chicago;
Final grade: 100/100. View Certificate...
Psychology and Neuroscience Summer School Program (Jul. 2023) View Certificate...
Mentor: Prof. Alexandra Krugliak; Fitzwilliam College of Cambridge University;
Named Top 2 students. View Certificate...
Research Experience go to the top...
A Bioinformatics Study on Designing Soluble Versions of Alpha-synuclein (Aug. 2025 – Jan. 2026) View my blog...
Independent research. Unsuccessful.
I used the QTY code to design soluble versions of alpha-synuclein with the goal of breaking alpha-synuclein aggregates. The structures of native and QTY-designed versions were predicted to investigate their aggregation potential. Results indicated that, although QTY-designed alpha-synuclein has higher solubility, it still shows tendency to aggregate with itself or co-aggregate with native alpha-synuclein.A Structural and Functional Bioinformatics Study of QTY-designed Retinylidene Proteins ( Jan. 2025 – Jul. 2025) View my blog...
Independent research. Published in QRB Discovery by Cambridge University Press.
DOI: https://doi.org/10.1017/qrd.2025.10009
Abstract
Retinylidene proteins are retinal-binding light-sensitive proteins found in organisms ranging from microbes to human. Microbial opsins have been utilized in optogenetics, while animal opsins are essential for vision and light-dependent metabolic functions. However, retinylidene proteins have hydrophobic transmembrane (TM) domains, which makes them challenging to study. In this structural and functional bioinformatics study, I use the QTY (Glutamine, Threonine, Tyrosine) code to design water-soluble QTY analogs of retinylidene proteins, including 9 human and 3 microbial opsins. I provide superpositions of the AlphaFold3-predicted hydrophobic native proteins and their water-soluble QTY analogs, and experimentally-determined structures when available. I also provide a comparison of surface hydrophobicity of the variants. Despite significant changes to the protein sequence (35.53% to 50.24% in the TM domain), protein characteristics and structures are well-preserved. Furthermore, I run molecular dynamics (MD) simulations of native and QTY-designed OPN2 (rhodopsin) and analyze their response to the isomerization of 11-cis-retinal to all-trans-retinal. The results show that the QTY analog has similar functional behavior to the native protein. The findings of this study indicate that the QTY code can be used as a robust tool to design water-solubility retinylidene proteins. These have potential applications in protein studies, therapeutic treatments, and bioengineering.Multimodal Abnormity-Aware Model for Ocular Disease Diagnosis ( Apr. 2024 – Aug. 2024) View my blog...
Independent research. Wrote paper (https://tinyurl.com/3k8kya8p)
Abstract
We devise a novel model, the Multimodal Abnormity-Aware Model (MAAM), for assisting ocular disease diagnosis. MAAM enables input of 2 kinds of ophthalmological images, namely optical coherence tomography (OCT) and color fundus images, and simulates the decision-making process of ophthalmologists by deducing the disease from abnormities. The model is composed of two submodels, the Abnormity Models and the Diagnosis Model, where the Abnormity Models identify OCT and fundus abnormities, and the Diagnosis Model identifies diseases by integrating features from the Abnormity Models. In MAAM, we introduce the fusion mechanism, the concept of codominant abnormities and diseases, and the Abnormity-to-Disease Criteria. The model partly breaks the black box of complex neural network and exposes more interpretable information for the reference of ophthalmologists. We train a proof-of-concept model, capable of identifying 8 OCT abnormities, 11 fundus abnormities, and 12 diseases. It has an overall accuracy of 89%, which verifies the feasibility of MAAM.Internships go to the top...
Communications Intern, The International Brain Bee (IBB) (Jan. 2026 – Present) View Official Site...
- Attend the 2025 IBB NextGen event, held in conjunction with the 2025 Alzheimer's Association International Conference in Toronto, Canada in Jul. 2025; View Certificate...
- Participate in the IBB competition-prep team and design exam questions for the 2025 IBB Championship competition in Nov. 2025.
- Manage social media communications projects.
Summer Intern, UCSC Science Internship Program (SIP) (Jun. 2025 – Aug. 2025) View Certificate...
Gene Annotation with Comparative Annotation Toolkit. Mentor: Prajna Hebbar.
Study bioinformatics tools such as Verkko, Hifiasm, and CAT. Assemble the genomes of 2 marmosets using 2 different methods. Align the genomes to each other and to other ones. Conduct comparative annotations to identify genes and other regions.Additional Skills go to the top...
Languages
- Mandarin, English, Spanish, French, German (fluent)
- Japanese (elementary)
- Latin, Sanskrit (read & write)
Programming
- Programming languages: Python, C++ and C#
- Development tools: Git, Visual Studio, SQL server
- Website development and database technology
- Deep learning
- Linux system and Bash script
Bioinformatics
- Molecular dynamics simulation: GROMACS, CHARMM-GUI
- Protein structure prediction: AlphaFold, Phyre, Protter
- Visualization: PyMOL, ChimeraX
Others
- Mathematical modeling
- Photography, film shooting and editing
- Social media management
Awards and Honors go to the top...
Academic
International Brain Bee Championship - 2024; Top 3 out of 37 national champions View Certificate...
National Brain Bee - 2024; Champion out of 2542 Contestants in China View Certificate...
High School Mathematical Contest in Modeling (HiMCM) - 2023; Outstanding; global Champion out of 967 teams View Certificate...
British Biology Olympiad (BBO) - 2024; Gold View Certificate...
Australian Science Olympiads-Biology (ASOB) - 2023; High Distinction; global 10% View Certificate...
UK Chemistry Olympiad (UKChO) - 2024; Gold View Certificate...
British Physics Olympiad (BPhO) - 2023; Round 1 Top Gold View Certificate... ; Round 2 Silver View Certificate...
High School
Luo Peiming Scholarship - 2025; Highest scholarship. View Certificate...
Principal's Award - 2025; Top award in high school . View Certificate...
Five-Star Club (Neuroscience Club) - 2025; Top award for clubs . View Certificate...
Five-Star Club (BonVista Accessibility Club) - 2025; Top award for clubs . View Certificate...
Tetragonal Badge - Leadership Awards - 2025 Semester 1 View Certificate...
Tetragonal Badge - Scholarship Awards 1st Prize - 2025 Semester 1 View Certificate...
Tetragonal Badge - Scholarship Awards 1st Prize - 2024 Semester 2 View Certificate...
Tetragonal Badge - Scholarship Awards 1st Prize - 2024 Semester 2 View Certificate...
Trigonal Badge - Innovation Awards - 2024 Semester 1 View Certificate...
Luo Peiming Scholarship - 2022; Highest scholarship. View Certificate...
Community Service
Infinite Visionaries - 2025; Most Promising Club Award to BonVista Accessibility Club View Certificate...
(Infinite Visionaries Award is a global accolade initiated by the Fosun Foundation to honor young individuals who advance the United Nations Sustainable Development Goals (SDGs) through innovative social impact projects.)
Extracurricular Activities go to the top...
Neuroscience Club (President from Sept. 2023)
- Host an undergraduate-level course on neuroscience for the club as the primary instructor, making 13 hours' slides and videos;
- Write and/or edit 27 neuroscience-related articles on WeChat;
- Organize 9 interdisciplinary events in collaboration with 9 different clubs;
Produce Original Neuroscience Course (Apr. 2025 – Present) View my blog...
- Design, write, and produce an original neuroscience course, which covers the major aspects of neuroscience at undergraduate level.
- The course contains 13 episodes in 23 videos, totaling 7 hours' length, with 100,000+ views as of Jan. 2026. (https://tinyurl.com/yy78udb7).
Running Club (Vice President from Feb. 2024)
- Organize events such as helping fellow students learn to guide people with visually impairments;
- Run 30~40 km per month.
Community Service go to the top...
BonVista Accessibility Club (Founder and President from May 2024) View my blogs...
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Promote accessibility awareness:
- Produce 11 documentary interview videos, showing the lives of people with visual impairments and the status quo of accessibility; totaling 5 hours' length, with 36,000+ views as of Jun. 2025 (https://tinyurl.com/dyznn3pz);
- Design 4 issues of accessibility posters for 25 local neighborhoods;
- Publish 23 accessibility-related articles on WeChat;
- Host Accessibility Week at school, collaborating with 7 other clubs to present workshops, acccessible sport, accessible art, and other events;
- Organize 11 inclusive activities with residents with visual impairments and students from Shanghai Blind Child School;
- Investigate the local accessibility infrastructure and submit reports to local government;
beYoureyeS (Facilitator, Professional Running Guide, and Translator from Sept. 2023)
- Participate weekly in events held by beYoureyeS (a non-profit organization for people with visual impairments) for 90+ weekends as of Apr. 2026;
- Organize training sessions and promote the idea of accessibility for over 300 potential guide runners;
- Certified Professional Running Guide;
- Translate 11 monthly newsletters into English as of Sept. 2025;
- Co-author Volunteer Guidebook for Exhibition Activities for People with Visual Impairments;