A web portal for exploring kinase-substrate interactions
A web portal for exploring kinase-substrate interactions. Sekar, John A P.; Li, Yan Chak; Pandey, Gaurav; Schlessinger, Avner; npj Systems Biology and Applications, 2024.
CV
Education
- M.Phil. in Bioengineering (BIEN), The Hong Kong University of Science and Technology, 2019
- Thesis: ‘Deep Learning Enables Instance Edge Detection of Vertebral Bodies on X-ray Images’
- B.Eng. in Computer Engineering (CPEG), The Hong Kong University of Science and Technology, 2017
- Minor in Mathematics
Work experience
- Nov 2019 to Nov 2025: Bioinformatician
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai
- Develop machine learning methods to analyze biomedical data.
- Design website to share and visualize data resources to the general public.
- Teaching assistant of ‘Machine Learning for Biomedical Data Science’ (Spring I 2020 & 2021).
- Supervisor: Prof. Gaurav Pandey.
- Aug 2019 to Oct 2019: Consultant
- Department of Industrial Engineering & Decison Analytics,The Hong Kong University of Science and Technology
- Develop Smart Fever Screening System with ZED stereo camera & FLIR thermal camera
- Supervisor: Prof. Richard H.Y. So
- Jun 2015 to Aug 2015: Summer Intern
- Hong Kong Telecom (HKT) Limited
- Feb 2015 to May 2015: Part-time Tutor
- Pigeon City Creative Computing Training Centre
- Jun 2013 to Aug 2013: Technical Support
- SkyWare Communication Limited
Publications
A comprehensive exploration of the druggable conformational space of protein kinases using AI-predicted structures
A comprehensive exploration of the druggable conformational space of protein kinases using AI-predicted structures. Herrington, Noah B.; Stein, David; Li, Yan Chak; Pandey, Gaurav; Schlessinger, Avner; PLOS Computational Biology, 2024.
A comprehensive youth diabetes epidemiological dataset and web portal: Resource Development and Case Studies
A comprehensive youth diabetes epidemiological dataset and web portal: Resource Development and Case Studies. McDonough, Catherine; Li, Yan Chak; Vangeepuram, Nita; Liu, Bian; Pandey Gaurav. JMIR Public Health and Surveillance, 2024.
Machine learning-driven identification of air toxic combinations associated with asthma symptoms among elementary school children in Spokane, Washington, USA
Machine learning-driven identification of air toxic combinations associated with asthma symptoms among elementary school children in Spokane, Washington, USA. Amiri Solmaz, Li, Yan Chak, Buchwald Dedra, Pandey Gaurav. Science of The Total Environment, 2024.
eipy: An Open-Source Python Package for Multi-modal Data Integration using Heterogeneous Ensembles
eipy: An Open-Source Python Package for Multi-modal Data Integration using Heterogeneous Ensembles. Bennett, Jamie J.R.; Li, Yan Chak; Pandey, Gaurav; arXiv, 2023.
KinAce: a web portal for exploring kinase-substrate interactions
KinAce: a web portal for exploring kinase-substrate interactions. Sekar, John A P.; Li, Yan Chak; Pandey, Gaurav; Schlessinger, Avner; bioRxiv, 2023.
Exploring the Druggable Conformational Space of Protein Kinases Using AI-Generated Structures
Exploring the Druggable Conformational Space of Protein Kinases Using AI-Generated Structures. Herrington, Noah B.; Stein, David; Li, Yan Chak; Pandey, Gaurav; Schlessinger, Avner; bioRxiv, 2023.
Facilitating youth diabetes studies with the most comprehensive epidemiological dataset available through a public web portal
Facilitating youth diabetes studies with the most comprehensive epidemiological dataset available through a public web portal. McDonough, Catherine; Li, Yan Chak; Vangeepuram, Nita; Liu, Bian; Pandey Gaurav. medRxiv, 2023.
Developing better digital health measures of Parkinson’s disease using free living data and a crowdsourced data analysis challenge
Developing better digital health measures of Parkinson’s disease using free living data and a crowdsourced data analysis challenge. Sieberts, Solveig K; Borzymowski, Henryk; Guan, Yuanfang; Huang, Yidi; Matzner, Ayala; Page, Alex; … ; Li, Yan-Chak; … ; Stanescu, Ana; … ; Pandey, Gaurav; Shawen, Nicholas; Synder, Phil; Omberg, Larsson. PLOS Digital Health 2 (3), e0000208. 2023.
Integrating multimodal data through interpretable heterogeneous ensembles
Integrating multimodal data through interpretable heterogeneous ensembles, Li, Yan Chak; Wang, Linhua; Law, Jeffrey; Murali, TM; Pandey, Gaurav. Bioinformtics Advances, Volume 2, Issue 1, 2022, vbac065
Machine learning–driven identification of early-life air toxic combinations associated with childhood asthma outcomes
Li, Yan-Chak; Hsu, Hsiao-Hsien Leon; Chun, Yoojin; Chiu, Po-Hsiang; Arditi, Zoe; Claudio, Luz; Pandey, Gaurav; Bunyavanich, Supinda. The Journal of Clinical Investigation. 2021. 131(22).
Clinical features of COVID-19 mortality: development and validation of a clinical prediction model
Clinical features of COVID-19 mortality: development and validation of a clinical prediction model. Yadaw, Arjun S; Li, Yan-chak; Bose, Sonali; Iyengar, Ravi; Bunyavanich, Supinda; Pandey, Gaurav. The Lancet Digital Health. 2020. 2(10).
Automatic instance-edge detection network (AID-Net)-vertebral edge detection by deep learning
Yan Li, Jing Chin, Yixiang Wang, Richard So, "Automatic instance-edge detection network (AID-Net)-vertebral edge detection by deep learning." European Journal of Clinical Investigation, 2019.
Talks/Conference Presentations
Integrating multimodal data through interpretable heterogeneous ensembles
Conference & Poster Presentation at Intelligent Systems for Molecular Biology (ISMB) 2022, Madison, Wisconsin
Predicting biomedical characteristics and outcomes using Ensemble Integration
Work In Progress(WIP) talk at Icahn School of Medicine at Mount Sinai, New York, US
Automatic Instance-edge Detection Network (AID-Net) - vertebral edge detection by deep learning
Conference Presentation at European Society for Clinical Investigation(ESCI) Congress, Coimbra, Portugal
Fast similarity measure of SWATH-MS by Cosine Similarity of Random Pairs(CS-RP)
Conference Presentation at Asia Oceania Mass Spectrometry Conference (AOMSC) 2017, Biopolis, Singapore
Teaching
- Spring I 2020 & 2021: Teaching Assistant
- Icahn School of Medicine at Mount Sinai
- BMI3002 Machine Learning for Biomedical Data Science
- Spring I 2018 & 2019: Teaching Assistant
Skills
- Machine learning model development
- Programming Languages:
- Python: Numpy, OpenCV, Pytorch, Scikit-learn, Pandas etc.
- R, R Markdown
- Javascript, Vue.js
- MATLAB, C, C++, CUDA C
- Others:
- High Performance Computing, Oracle Cloud, Google Cloud
- Firebase, Basic SQL
- Google Analytics
Academic Services
- Conference Reviewer:
- IEEE Big Data 2020, 2022
- ACM-BCB 2021-2023
- ISMB 2022, 2023
- ACM-SIGKDD 2022
Voluntary Services/Part-time Job Experiences
- SUG mentor of Hall II (Vertex), HKUST, 2016-2017
- Student Helper, Computer Science System Office, HKUST, 2016-2017
- Student Helper, Institute of Emerging Market Studies, HKUST, 2015-2017
- President, Nature Club, HKUSTSU, 2014-2015
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