Projects per year
Personal profile
Biography
Dr Chen Li is a new Lab Head at the Monash BDI, where he joins the Cancer and Immunity Programs and the Department of Biochemistry and Molecular Biology.
Supported by an ARC Future Fellowship and an NHMRC Ideas Grant, Dr Li’s lab develops cutting-edge computational and experimental multi-omic approaches—including transcriptomics, proteomics, and immunopeptidomics—to decode the complexities of human diseases and drive innovative therapeutic solutions.
Originally trained as a computer scientist, Dr. Li earned his PhD in 2016 under the supervision of A/Prof Ashley Buckle and Prof Jiangning Song at Monash University. His doctoral research focused on developing bioinformatics algorithms and databases to analyse the relationship between protein structure, function, and disease.
Following his PhD, Dr Li joined the laboratories of Prof Anthony Purcell and Prof Jian Li at Monash BDI as a research bioinformatician, expanding his expertise into proteomics and immunopeptidomics. In 2018, he was awarded the prestigious NHMRC CJ Martin Early Career Fellowship (2018–2022), which enabled him to train at ETH Zurich under renowned Swiss biologist Prof Ruedi Aebersold, a pioneer in proteomics and systems biology. There, he developed pipelines for profiling and predicting protein complexes, their perturbations, and functions using Size Exclusion Chromatography (SEC)-Mass Spectrometry (MS) data. Dr Li returned to Monash BDI to continue his research in cancer immunotherapy, supported by a Cure Cancer Australia research grant (2023).
His lab at Monash BDI now leverages machine learning and bioinformatics to integrate and analyse multi-omic data in biomedical contexts, advancing and facilitating the development of novel immunotherapies.
Research interests
Systems Proteomics; Immunopeptidomics; Cancer; Personalised Medicine; Bioinformatics
Expertise related to UN Sustainable Development Goals
In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This person’s work contributes towards the following SDG(s):
Education/Academic qualification
Bioinformatics, PhD, MONASH UNIVERSITY
External positions
Visiting NHMRC CJ Martin Fellow, Eidgenössische Technische Hochschule Zürich (ETH Zürich) (Federal Institute of Technology Zurich)
Mar 2018 → Feb 2020
Collaborations and top research areas from the last five years
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The "dark immunopeptidome" as a source of CD8 T cell epitopes in type 1 diabetes
DiLorenzo, T. P. (Primary Chief Investigator (PCI)), Purcell, A. (Chief Investigator (CI)), Illing, P. (Chief Investigator (CI)), Li, C. (Chief Investigator (CI)), Nakayama, M. (Chief Investigator (CI)) & Kent, S. (Chief Investigator (CI))
1/02/23 → 31/01/26
Project: Research
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Investigation and prediction of colorectal cancer neoepitopes and their immunological responses
Li, C. (Primary Chief Investigator (PCI))
1/03/17 → 29/12/17
Project: Research
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Targeting outer membrane vesicles of Gram-negative ‘superbug’ Acinetobacter baumannii: A systems and computational approach
Li, C. (Chief Investigator (CI)), Morris, F. (Chief Investigator (CI)) & Song, J. (Chief Investigator (CI))
2/01/17 → 30/04/18
Project: Research
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scRCA: A Siamese network-based pipeline for annotating cell types using noisy single-cell RNA-seq reference data
Liu, Y., Li, C., Shen, L. C., Yan, H., Wei, G., Gasser, R. B., Hu, X., Song, J. & Yu, D.-J., May 2025, In: Computers in Biology and Medicine. 190, 13 p., 110068.Research output: Contribution to journal › Article › Research › peer-review
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CTISL: a dynamic stacking multi-class classification approach for identifying cell types from single-cell RNA-seq data
Wang, X., Chai, Z., Li, S., Liu, Y., Li, C., Jiang, Y. & Liu, Q., 1 Feb 2024, In: Bioinformatics. 40, 2, 10 p., btae063.Research output: Contribution to journal › Article › Research › peer-review
Open Access3 Citations (Scopus) -
DeepOCR: A multi-species deep-learning framework for accurate identification of open chromatin regions in livestock
Zhao, L., Hao, R., Chai, Z., Fu, W., Yang, W., Li, C., Liu, Q. & Jiang, Y., Jun 2024, In: Computational Biology and Chemistry. 110, 9 p., 108077.Research output: Contribution to journal › Article › Research › peer-review
Open Access -
Mapping the immunopeptidome of seven SARS-CoV-2 antigens across common HLA haplotypes
Braun, A., Rowntree, L. C., Huang, Z., Pandey, K., Thuesen, N., Li, C., Petersen, J., Littler, D. R., Raji, S., Nguyen, T. H. O., Jappe Lange, E., Persson, G., Schantz Klausen, M., Kringelum, J., Chung, S., Croft, N. P., Faridi, P., Ayala, R., Rossjohn, J. & Illing, P. T. & 6 others, , Dec 2024, In: Nature Communications. 15, 1, 12 p., 7547.Research output: Contribution to journal › Article › Research › peer-review
Open Access4 Citations (Scopus) -
MERITS: a web-based integrated Mycobacterial PE/PPE protein database
He, Z., Wang, C., Guo, X., Sun, H., Bi, Y., Pitt, M. E., Li, C., Song, J., Coin, L. J. M. & Li, F., 2024, In: Bioinformatics Advances. 4, 1, 8 p., vbae035.Research output: Contribution to journal › Article › Research › peer-review
Open Access
Prizes
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2017 Hans Neurath Outstanding Promise Travel Award
Li, C. (Recipient), 2017
Prize: Prize (including medals and awards)
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FAOBMB Young Scientist Prorgam Award
Li, C. (Recipient), Oct 2021
Prize: Prize (including medals and awards)
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Harnessing systems biology by integrating proteomics and immunopeptidomics to understand prostate cancer carcinogenesis, diagnosis and treatment
Li, C. (Recipient), 2018
Prize: Competitive Fellowships
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HUPO 2019 Early Career Research (ECR) Travel Award
Li, C. (Recipient), 27 Jul 2019
Prize: Prize (including medals and awards)
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Briefings in Bioinformatics (Journal)
Li, C. (Peer reviewer)
2017 → …Activity: Publication peer-review and editorial work types › Peer review responsibility
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PLoS ONE (Journal)
Li, C. (Peer reviewer)
2016 → …Activity: Publication peer-review and editorial work types › Peer review responsibility
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Molecular Genetics and Genomics (Journal)
Li, C. (Peer reviewer)
2016 → …Activity: Publication peer-review and editorial work types › Peer review responsibility
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BMC Bioinformatics (Journal)
Li, C. (Peer reviewer)
2016 → …Activity: Publication peer-review and editorial work types › Peer review responsibility
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International Journal of Antimicrobial Agents (Journal)
Li, C. (Peer reviewer)
2016 → …Activity: Publication peer-review and editorial work types › Peer review responsibility
Press/Media
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Our immune system splices together “Frankenstein Proteins”
2/11/18
1 item of Media coverage
Press/Media: Research
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Bioinformatics tool to unearth new pointers to disease
10/07/18
1 item of Media coverage
Press/Media: Research
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Congratulations to our successful NHMRC Fellows
23/10/17
1 item of Media coverage
Press/Media: Research