Yanjun Li

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Yanjun Li

Assistant Professor (AI Initiative)
Department of Medicinal Chemistry, College of Pharmacy
University of Florida
1345 CENTER DR, MSB P6-33, Gainesville, FL 32610

Phone: (352) 273-9957
E-mail: yanjun.li AT ufl.edu OR yanjun.li.uf AT gmail.com

Google Scholar, GitHub, Twitter

Biography

Dr. Yanjun Li is a tenure-track Assistant Professor (AI Initiative) in the Department of Medicinal Chemistry at the College of Pharmacy, University of Florida. His research interests span the fields of deep learning, AI-driven drug discovery, and computational biology, with a particular emphasis on deep generative modeling for de novo molecule design and geometric deep learning for molecular recognition. Dr. Li’s work aims to develop innovative AI algorithms to tackle foundational life science challenges with broad scientific impacts and to optimize and automate real-world drug discovery and design pipelines.

Before joining the University of Florida, Dr. Li successively worked as a Senior Research Scientist at the Institute of Deep Learning, Baidu Research USA, Sunnyvale, California, and at Calico Life Sciences, an Alphabet-founded research lab for human aging research. He received his Ph.D. in computer science from the University of Florida (2021), advised by Dr. Dapeng Oliver Wu and Dr. Xiaolin (Andy) Li. He received his dual M.E. from the University of Electronic Science and Technology of China and Waseda University (2015) and B.E. from University of Electronic Science and Technology of China (2012).

Research Interests

  • Deep Learning and AI-driven Drug Discovery

    • Molecule Design and Optimization

      • Deep Generative Modeling for de novo Small Molecule, RNA, and Protein Design and Optimization, etc.
    • Molecular Recognition

      • Geometric Deep Learning for Molecular Interaction Prediction, e.g., Protein-protein, Protein-ligand, RNA-ligand, etc.
    • Computational Biology

      • Genetic Variant Effect Prediction, Single-Cell RNA-sequencing, Spatial Transcriptomics, Image-based Profiling Analysis, etc.

    Openings

    Dr. Li's lab is always seeking self-motivated Ph.D. students, postdoc associate, as well as graduate and undergraduate research assistants, who are interested in AI-driven Drug Discovery.
    If interested, please send your CV and unofficial transcripts to yanjun.li AT ufl.edu. For more detailed information, please follow the link.

    News

    • 06/2024: Our paper "Morphological profiling for drug discovery in the era of deep learning" has been accepted by Briefings in Bioinformatics.

    • 05/2024: Tzu-Tang Lin (MS student, Genetics, Bioinformatics, and Computational Biology, Virginia Tech) joined the lab as a PhD student. Welcome Tzu-Tang!

    • 04/2024: The UF College of Pharmacy was ranked as the No. 4 best pharmacy college in America by US News. Congratulations to UF College of Pharmacy!

    • 04/2024: Our book chapter "Analysis and Visualization of Single-Cell Sequencing Data with Scanpy and MetaCell: A Tutorial" has been accepted by Methods in Molecular Biology.

    • 04/2024: Our paper "Identifying acute illness phenotypes via deep temporal interpolation and clustering network on physiologic signatures" has been accepted by Nature Scientific Reports.

    • 03/2024: We received a UF Health Cancer Center Pilot Grant ($100K, PI: Yanjun Li) on Harnessing AI for RNA-targeted Drug Discovery. Thanks, UF Health Cancer Center!

    • 03/2024: We received a UF Health Cancer Center Pilot Grant ($100K, PI: Hendrik Luesch and Ben Shen) on Natural Product Drug Discovery via Morphological Profiling. Thanks, UF Health Cancer Center!

    • 02/2024: We received a Florida Cancer Innovation Fund Award ($750K, PI: Jessica Childs-Disney) on AI-driven Small Molecule Medicine Discovery Targeting Oncogenic RNAs. Thanks, Florida Department of Health!

    • 02/2024: We received a Florida Cancer Innovation Fund Award ($213K, PI: Yousong Ding) on Enhancing Cancer Diagnosis and Treatment through Innovative Protein Engineering. Thanks, Florida Department of Health!

    • 02/2024: Dr. Li was invited as the reviewer for KDD 2024 and ISMB 2024.

    • 01/2024: Dr. Li was invited as a chair for AI-driven Drug Discovery Session at 2024 UF Drug Discovery Symposium.

    • 01/2024: Tingyi Li (MS students, Computer Science, UF) and Hanbo Yang (MS student, Electrical and Computer Engineering, UF) joined the lab as research assistants. Welcome Tingyi and Hanbo!

    • 01/2024: Our paper "Extracellular Vesicles for Developing Targeted Hearing Loss Therapy" has been accepted by Journal of Controlled Release. (Cover Art)

    • 12/2023: We received a NIH Targeted Genome Editor Delivery (TARGETED) Challenge Phase I Winner Award (PI: Mei He). Thanks, NIH!

    • 10/2023: Our paper "BatmanNet: Bi-branch Masked Graph Transformer Autoencoder for Molecular Representation" has been accepted by Briefings in Bioinformatics.

    • 10/2023: Dr. Li was invited as a panel speaker at the BioTrends Session “Acceleration of Generative AI/Machine Learning in the Life Sciences” for the BioFlorida Annual Conference.

    • 09/2023: Junge Gu and Riddhish Thakare (MS students, Computer Science, UF) joined the lab as research assistants. Welcome Junge and Riddhish!

    • 09/2023: Dr. Li was invited as the reviewer for the GenBio workshop at NeurIPS 2023 and SDM 2024.

    • 08/2023: Dr. Li has officially joined the UF Health Cancer Center, an NCI-Designated Cancer Center.

    • 06/2023: Shiyu Jiang (MS student, Computer Science, JHU) joined the lab as a research assistant. Welcome Shiyu!

    • 05/2023: Weihang You (MS student, Computer Science, UF) joined the lab as a research assistant. Welcome Weihang!

    • 04/2023: Dr. Li was invited as the program committee for KDD 2023 and AAAI 2024.

    • 04/2023: Dr. Li was invited to give a talk at The Wertheim UF Scripps Institute Chemical Biology & 5th UF Drug Discovery Symposium.

    • 03/2023: Dr. Li officially started his position as an Assistant Professor (AI Initiative) in the Department of Medicinal Chemistry at the University of Florida, College of Pharmacy. Go Gators!!!

    Education

    • Ph. D. in Computer Science, University of Florida, Gainesville, FL, USA, 2021

    • M. E. in Communication and Information System, University of Electronic Science and Technology of China, Chengdu, China, 2015

    • M. E. in Information, Production and Systems Engineering, Waseda University, Kitakyushu, Japan, 2015

    • B. E. in Information Engineering, University of Electronic Science and Technology of China, Chengdu, China, 2012