蕭詠然 Siu Weng In, Shirley
Biography
Shirley W. I. Siu, Associate Professor, PhD supervisor.
In 2010, she received her PhD in Natural Sciences from Saarland University, Germany, and worked as a postdoctoral fellow at University of Erlangen-Nuremberg. She was an Assistant Professor at the Department of Computer and Information Science, University of Macau, and an Associate Professor and Research Coordinator at the Institute of Science and Environment, University of Saint Joseph, Macau. In 2023, she joined the Center of Artificial Intelligence driven Drug Discovery at Macau Polytechnic University as an Associate Professor.
Her research focuses on computational drug discovery, cheminformatics, machine learning, biomolecular simulation, and molecular mechanics force fields, etc. Her team pioneers the application of swarm intelligence and machine learning to solve problems in protein-ligand docking, drug target identification, biological activities and toxicity prediction with the goal of finding new chemical and biological agents with pharmaceutical potential.
Shirley has great interest in the biophysics of proteins, membranes and polymers. Using molecular dynamics simulations, she studies antibacterial, anticancer, and neurotoxic peptides and explores their mechanism of action based on conformational dynamics, free energy changes, and interactions with membranes and membrane proteins. Her team is involved in modeling cell membrane lipids and self-assembled monolayers and developing force fields to improve the accuracy of modeling and simulation of biotechnological components such as biosensors.
She has authored or co-authored a total of 55 peer-reviewed journal papers and 18 conference papers. She has led the development of 7 open-source software tools and 5 online platforms. Her research projects have been supported by the Macau Science and Technology Development Fund (FDCT), universities, and foreign foundations. She has led 6 research projects as a Principal Investigator (PI) and participated in 4 projects as a Co-Investigator (Co-PI). She has successfully supervised more than 40 students, including 2 postdocs, 2 PhD students, and 12 master students.
She actively promotes research collaborations and builds academic networks. She has served as a guest editor and reviewer for numerous international peer-reviewed journals (NAR, Bioinformatics, JCIM, JCheminf, Sci Rep, etc.). She has also served as Chair/Co-Chair/organizer (CSBio2016, ICCP2017, ESST2023) and committee member of several computer science and bioinformatics conferences (WAIM, ACCMS, APBC, CEC, IJCNN, ICBBT, ICBEB, ICBCB, ICCST, etc.), and has been invited to speak at international conferences and workshops.
Education and Experiences
Education:
2010-2011 Postdoctoral fellow, University of Erlangen-Nuremberg, Germany
2006-2010 PhD in Natural Sciences, Saarland University, Germany
2003-2006 MSc in Computational Molecular Biology, Saarland University, Germany
1998-2001 MSc in Software Engineering, University of Macau
1993-1997 BSc in Software Engineering, University of Macau
Professional experiences:
2023-Present Associate Professor, Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University
2021-2023 Associate Professor & Research Coordinator, Institute of Science and Environment, University of Saint Joseph, Macau
2012-2021 Assistant Professor, Department of Computer and Information Science, University of Macau
2009-2012 Senior Instructor, Department of Computer and Information Science, University of Macau
2001-2003 Instructor, Department of Computer and Information Science, University of Macau
Research Interests
- Computer Aided Drug Discovery
- Molecular Dynamics
- Cheminformatics
- Machine Learning
- Intelligent Optimization Algorithms
Selected Recent Publications (First or corresponding author)
- Yan, J.; Zhang, B.; Zhou, M.; Kwok, H.F.; Siu, Shirley W. I.* Multi-Branch-CNN: classification of ion channel interacting peptides using multi-branch convolutional neural networks. Computers in Biology and Medicine 2022, 147, 105717.
- Chen, Jiarui; Si, Yain-Whar; Un, Chon-Wai; Siu, Shirley W. I.* Chemical Toxicity Prediction Based on Semi-supervised Learning and Graph Convolutional Neural Network. Journal of Cheminformatics 2021, 13: 93.
- Chen, J.; Cheong, H.H. and Siu, Shirley W. I.* xDeep-AcPEP: Deep Learning Method for Anticancer Peptide Activity Prediction Based on Convolutional Neural Network and Multitask Learning. Journal of Chemical Information and Modeling 2021, 61, 8, 3789–3803.
- Wong, K. M.; Tai, H. K. and Siu, Shirley W. I.* GWOVina: A grey wolf optimization approach for rigid and flexible receptor docking. Chemical Biology & Drug Design 2020, 00: 1-14.
- Yan, J.; Bhadra, P.; Li, A.; Sethiya, P.; Qin, L.; Tai, H. K.; Wong, K. H.; and Siu, Shirley W. I.* Deep-AmPEP30: Improve short antimicrobial peptides prediction with deep learning. Molecular Therapy – Nucleic Acid 2020, 20, 882-894.