Jun Zhang

Mobile: +86 18797521846
Email: 202200300321@mail.sdu.edu.cn
Personal homepage: https://zhangjun640.github.io/
Address: No. 1500, Shunhua Road, Gaoxin District, Jinan, Shandong Province

EDUCATION

Shandong University, Jinan, China
Bachelor of Engineering in Software Engineering
Sept. 2022 – Jul. 2026 (Expected)
GPA: 88.03 / 100

Major Courses:
Advanced Mathematics (96); Linear Algebra (100); Advanced Programming (Bilingual) (90);
Data Structure (Bilingual) (92); Fundamentals of Machine Learning (96); Database System (Bilingual) (91).

Research Interests:
Methylation analysis; Machine learning and deep learning; Single-cell transcriptomics;
Medical image analysis; Multimodal data analysis.

PUBLICATIONS

• Jun Zhang, Jianbo Qiao, Zhiqun Zhao, Chenglin Yin, Junru Jin, Ding Wang, Wenjia Gao, Leyi Wei* :
  Accurate detection and quantification of single-base m6A RNA modification using nanopore signals with multi-view deep learning,
  bioRxiv 2025.08.04.668591; doi:https://doi.org/10.1101/2025.08.04.668591 (NUCLEIC ACIDS RESEARCH, Under review)

• Zhiqun Zhao#, Jun Zhang#, Guangyu Ji, Zhenzhen Zhou, Yaozong Yang, Fengqi Sun and Haiquan Lu* :
  Single-cell transcriptomics reveals spaceflight-induced accelerated aging and impaired recovery in the murine bone marrow.
  npj Microgravity (Under review)

• Jia Liu#, Zhiqun Zhao#, Guangyu Ji#, Jie Lan#, Yuhong Zhang, Qi Liu, Jun Zhang, Yajing Zhang, Guangyao Wei, Fengqi Sun, Yiran Yu, Xiaofeng Jiang, Kai Ji, Qi Mei, Kai Zhang, Zheng Wang* , and Haiquan Lu* :
  Metabolic redundancy of fatty acid desaturation and elongation promotes hypoxia-induced breast cancer stem cell enrichment.
  Submitted

RESEARCH EXPERIENCES

Prediction of RNA Modifications using Nanopore Direct RNA Sequencing Reads

Research Assistant, Research Center of Software and Data Engineering
Jun. 2023 – Aug. 2025

• Processed all raw Nanopore Fast5 files, including base calling, re-squiggle operations, and signal-level analysis, with methylation site information fully extracted. Conducted site-level analysis of RNA methylation data, achieving accurate prediction of methylation sites.
• Applied Multi-view Model to improve the accuracy of RNA methylation prediction, achieving over 5% improvement compared to m6Anet in HEK293T dataset, providing a valuable tool for better predictions.
• Applied Multi-view Model to improve accuracy by over 5% vs m6Anet on HEK293T dataset.
• The core output of this project has been submitted as a manuscript to NUCLEIC ACIDS RESEARCH (Under review).

Single-cell analysis of the impact of age on immune dysregulation and recovery induced by spaceflight

Research Assistant, Cheeloo College of Medicine
Jul. 2024 – Aug. 2025

• Processed the single-cell sequencing data of OSD-402 and OSD-403 from NASA GeneLab, completing all single-cell analyses including quality control, clustering, cell type annotation, subgroup annotation, cell communication, and pseudotime analysis.
• Utilized Seurat, monocle3, and other R packages to perform all of the above analyses.
• The core output of this project has been submitted as a manuscript to npj microgravity (Under review).

Metabolic redundancy of fatty acid desaturation and elongation promotes hypoxia-induced breast cancer stem cell enrichment

Research Assistant, Cheeloo College of Medicine
Jul. 2024 – Mar. 2025

• Performed functional analysis such as GO, KEGG, GSEA and GSVA to identify critical pathways influenced by hypoxia.
• Used the Random Forest algorithm to analyze transcriptomics of hypoxia and normoxia groups, recognizing the hypoxia-associated breast cancer hypoxia signature.
• The core output of this project has been submitted as a manuscript to Science Bulletin (Submitted).

Accurate Prediction of Different RNA Modification Types and Their Interactions Using Nanopore Direct RNA Sequencing Reads

Research Assistant, Research Center of Software and Data Engineering
Jun. 2025 – Present

• Discovered that modification occurrences are not mutually independent, identifying significant long-range dependencies (most over 100bp, even over 1000bp) between modification sites.
• Revealed bidirectional cross-talk between m6A and m5C modifications in HEK293T cell lines; observed that knocking out m6A-specific writer enzymes alters m5C modification levels, and vice-versa.
• Currently collaborating with a biological (wet) lab to design experiments for the biological validation of these computationally predicted modification interactions.

PROJECT EXPERIENCES

Hospital Medical Management System

Project Leader | Jun. 2024 – Aug. 2024
Tech Stack: JavaScript, CSS, HTML, Java, Apache Shiro, MySQL, Vue

• Led the overall project architecture design and technology selection, implementing a decoupled front-end (Vue.js) and back-end (Spring Boot) solution.
• Designed and implemented the security framework using Apache Shiro, delivering user authentication, session management, and Role-Based Access Control (RBAC).
• Developed and managed the core business modules, including backend APIs for drug information, supplier management, inventory (inbound/outbound), and sales statistics.
• Project is open-source: GitHub Link

A Fine-tuned Large Model based on DeepSeek for AI-Assisted

Interviews
Project Leader | Mar. 2025 – Jun. 2025
Tech Stack: Python, PyTorch, QLoRA, Ollama, HTML, Vue 3

• Led the creation and open-sourcing of the world's largest Chinese interview dataset (150k+ entries) by scraping tech communities and generating high-quality Q&A pairs using multiple LLMs (GPT-4o, DeepSeek), successfully publishing it on Hugging Face.
• Directed the technology selection and fine-tuning of the AI interviewer LLM. Employed QLoRA (Unsloth) on a DeepSeek base model, training it on the custom dataset to specialize in generating interview questions, follow-ups, and automated scoring.
• Designed and deployed the project's full-stack architecture: built the frontend application (Vue 3) integrating resume editing, AI polishing, and mock interviews; and deployed the fine-tuned model as an HTTP API service using Ollama.
• Project is open-source: GitHub Link
• Chinese interview datasets are open-source: Hugging Face Link

COMPETITIONS

• Chinese Mathematics Competitions — Second Prize, Shandong Province District (Aug. 2022)
• “Blue Bridge Cup” National Software Engineering Competition — Third Prize, Shandong Province (Apr. 2024)

HONORS & AWARDS

• School Aesthetic Education Scholarship
• First Prize in University Landscape Project Award
• Outstanding Individual in University Social Practice
• Outstanding University Practice Report
• Outstanding University Practice Team
• Shandong University Academic Scholarship (Third Prize)

RESEARCH SKILLS

Programming Languages: Python, R, SQL, C++, Java
Python Packages: Pandas, Matplotlib, Scipy, Numpy, Scanpy, pysam, ont-fast5-api, PyTorch, cellpath, Scikit-learn, etc.
Software & Tools: Guppy, Excel, HTML, IGV, VSCode, RStudio, PyCharm, etc.
Biology Analysis Expertise:

• scRNA analysis (Seurat, Scanpy)
• Spatial transcriptomics analysis
• Machine learning for biology
• Functional enrichment (GO, KEGG, GSVA)
• Clustering and dimensionality reduction for biological data