Main
Jianfeng Sun
computational biology, artificial intelligence, data science
I am working broadly in computational biology at the University of Oxford. I use mathematical algorithms to model biological systems in structural biology, molecular biology and cancer biology. I am carving out a niche for myself as a leading researcher in UMI-assisted research and computational drug discovery.
Education
Ph.D., Dr. rer. nat., Artificial Intelligence Structural Biology
Technical University of Munich
Munich, Germany
2020 - 2017
- biological - protein science, evolutionary biology
- computational - deep learning, statistics
- specifics - deep learning for predicting protein interaction sites
M.Eng., Software Engineering and Computational Biology
Beijing Forestry University
Beijing, China
2014 - 2016
- biological - genetics
- computational - algorithm design, web application development
- specifics - mathematical modelling for quantitative trait loci (QTLs) detection
B.S.Mgt.Sci., Accounting (minor dual-degree)
Nanjing Tech University
Nanjing, China
2014 - 2011
- economics
B.Sci., Information and Computer Science (i.e., Computational Mathematics)
Nanjing Tech University
Nanjing, China
2014 - 2010
- mathematics
- statistics
- programming
Research Experience
Postdoctoral Researcher in Single-cell Sequencing Analysis
University of Oxford
Oxford, United Kingdom
2025 - 2021
- biological - transcriptomics, protein science
- computational - deep learning, statistics
- duty - computational analysis of single-cell data in sarcoma diseases and algorithm design for accurate long-read sequencing technology
Post-doctoral Studies in Transmembrane Proteome Analysis
Technical University of Munich
Munich, Germany
2021 - 2020
- biological - protein isoforms, mutations, variants, interaction sites
- computational - machine learning, statistics
- duty - Occurrences of mutation sites and interaction sites in the human transmembrane proteome
Professional service
Full member of Sigma XI, The Scientific Research Honor Society
Oxford
Oxford, United Kingdom
Current - 2024
Young Editorial Member of iMeta
Oxford
Oxford, United Kingdom
Current - 2024
Thesis
Prediction of residue contacts and interaction sites in transmembrane proteins using deep learning
Technical University of Munich
Munich, Germany
2021 - 2020
- Ph.D. Defense
- committee chairman - Prof. Bernhard Küster
- examiner - Prof. Burkhard Rost
- link - https://mediatum.ub.tum.de/doc/1577512
Academic Publication
Journal Articles, Conference Proceedings, Book Chapters, etc.
Please refer a full list of my publications at the sites below
N/A
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I updated my latest research at these websites on a regular basis. I primarily published articles in the topics of methods, computational tools, and their applications in molecular and disease biology.
Patent
Silkworm silk gland recombinant expression vector for expressing human epidermal growth factor and preparation method and application thereof
China National Intellectual Property Administration (CNIPA)
China
Current - 2022
- inventors - Dingpei Long, Jian Cheng, Jianfeng Sun, Zhonghuai Xiang, and Fangyin Dai (by order)
- patent No. - CN112852876A
- link - https://patents.google.com/patent/CN112852876A/en?oq=cn112852876
- my role - algorithm design for deducing protein functions based on their experimental and predicted structures
I applied the golden rule to a protein material study: protein structures determine their functions. This is used to screen synthetic proteins with similar biological activities to commericialised proteins.
Funding
Cancer Research UK (CRUK) Oxford Development Fund
University of Oxford
Oxford, United Kingdom
2024 - 2023
- Project Title - Single-cell spliceosome map establishment of immune cells
- Award Ref - CRUKDF-MAY23–AC/JS
Software copyright
The web system for differentiating dynamic complex traits based on growth curve
Beijing Forestry University
Beijing, China
2016
- Copyright No. 2016SRBJ047
- Register - Beijing Forestry University
- Developer - Jianfeng Sun
Climate Change Adaptation Information System for Beijing Landscape and Forestry Industry
Beijing Forestry University
Beijing, China
2016 - 2015
- Copyright No. 2016SR098798
- Register - Zhibo Chen & Jianfeng Sun
- Developer - Jianfeng Sun
Scientific program
Workshop in computational single-cell sequencing analysis
Koç University
Istanbul, Turkey
Current - 2022
- my role - teaching assistant
Invited pre-doctoral programs by the International Max Planck Research School for Computational Biology and Scientific Computing (IMPRS-CBSC),
Max Planck Institute for Molecular Genetics
Berlin, Germany
Current - 2017
Conference
2019 international conference on machine learning and cybernetics (ICMLC)
Kobe Convention Center
Kobe, Japan
2019
- The LSTM Network for residue-residue contacts prediction
Open Talk
Artificial Intelligence Applications on Biomedical Data
Zoom online - RobotGym GmbH (German Company)
Oxford, United Kingdom
2025
- Introduction of advanced artificial Intelligence methods, including language models and variational inference techniques, to the application in biomedical fields.
Machine Learning in Structural Biology
Tecent VooV meeting online - Koushare Academic Platform
Munich, Germany
2020
- Presentation and Q&A
Award
Third Prize of The 8th China (Shenzhen) Innovation & Entrepreneurship International Competition (Milan Division)
Milan
Milan, Italy
2024
2nd rank among 20 screened teams in 2020 Munich Impact Hackathon Programming Competition
Munich
Munich, Germany
2020
China National Scholarship
Beijing Forestry University
Beijing, China
2016 - 2015
China National Scholarship
Beijing Forestry University
Beijing, China
2015 - 2014
University Third-prize Scholarship of Nanjing Tech University
Nanjing Tech University
Nanjing, China
2014 - 2013
University First-prize Scholarship of Nanjing Tech University
Nanjing Tech University
Nanjing, China
2013
University Third-prize Scholarship of Nanjing Tech University
Nanjing Tech University
Nanjing, China
2012 - 2011
University Third-prize Scholarship of Nanjing Tech University
Nanjing Tech University
Nanjing, China
2011
University Third-prize Scholarship of Nanjing Tech University
Nanjing Tech University
Nanjing, China
2011 - 2010
Top 8 Finalist in the Nanjing Regional Finals of 2011 China’s Got Talent
Wanda Plaza
Nanjing, China
2011 - 2010
- sponsor of this event - Dagexing Co., Ltd
- kind - dancing
Computational tool
I am passionate about fantastic techniques applied in data science for biological systems. I have developed dozens of tools and methods, with nearly 15 publicly available to check and use. I will release more!!
UMIche
University of Oxford
Oxford, United Kingdom
Current - 2025
- Website - https://2003100127.github.io/umiche
mclUMI
University of Oxford
Oxford, United Kingdom
Current - 2025
- Website - https://2003100127.github.io/mclumi
Tresor
University of Oxford
Oxford, United Kingdom
Current - 2025
- Website - https://2003100127.github.io/tresor
PyPropel
University of Oxford
Oxford, United Kingdom
Current - 2025
- Website - https://2003100127.github.io/pypropel
TMKit
University of Oxford
Oxford, United Kingdom
Current - 2023
- Website - https://2003100127.github.io/tmkit
DeepdlncUD
University of Oxford
Oxford, United Kingdom
Current - 2024
- Website - https://2003100127.github.io/deepdlncud
Drutai
University of Oxford
Oxford, United Kingdom
Current - 2024
- Website - https://2003100127.github.io/drutai
DeepsmirUD
University of Oxford
Oxford, United Kingdom
Current - 2024
- Website - https://2003100127.github.io/deepsmirud
DeepTMInter
Technical University of Munich
Munich, Germany
Current - 2021
- Website - https://2003100127.github.io/deeptminter
DeepHelicon
Technical University of Munich
Munich, Germany
Current - 2020
- Website - https://2003100127.github.io/deephelicon
ResimPy
University of Oxford
Oxford, United Kingdom
Current - 2024
PCSER
University of Oxford
Oxford, United Kingdom
Current - 2025
- Website - https://2003100127.github.io/pcser