Guest: Yanni Sun, City University of Hong Kong

 

Title: Illuminate dark matters in microbial communities via deep learning (BIO, CS, DSA)

 

Date/Time: April 24 2025, 11:00

 

Location: https://sabanciuniv.zoom.us/j/92169771869, Meeting ID: 921 6977 1869, Passcode: 303889

 

Abstract: Viruses are the most abundant and diverse entities on Earth, playing critical roles in health and ecology. Yet, the vast majority of viruses remain undiscovered, constituting a significant portion of the so-called "viral dark matter." Traditional approaches, such as isolating viruses in the laboratory, are often labor-intensive, time-consuming, and costly. As a result, there is a growing need for efficient computational methods to identify and analyze viruses. In this talk, I will present our recent research on virus characterization and analysis, leveraging high-throughput sequencing data and advanced deep learning models. By utilizing state-of-the-art deep learning frameworks—such as Transformers, graph convolutional networks, and biological sequence foundation models—we address several key challenges in virology, including virus identification in metagenomic data and virus-host prediction. Drawing inspiration from natural language processing (NLP), we employ contextualized embedding models like Transformers to decode the "language" of viruses, enabling deeper insights into their structure and function. To make these tools accessible to users with minimal bioinformatics expertise, we have integrated our computational pipelines into an intuitive, easy-to-use webserver for virus identification and analysis (https://phage.ee.cityu.edu.hk/). This platform streamlines virus characterization and empowers researchers to explore the hidden world of viruses with unprecedented efficiency. Finally, I will present our recent finding of using our developed methods/tools to identify core virome in healthy people. 

 

Bio: Yanni Sun is an Associate Professor in the Department of Electrical Engineering at City University of Hong Kong. Before she joined CityU, she was an Associate Professor with tenure at Michigan State University (USA). She received the B.S., M.S. degrees from Xi'an JiaoTong University (China), and the Ph.D. degree from Washington University in Saint Louis, USA, all in Computer Science. Her research interests include: computational biology, bioinformatics, deep learning-based sequence analysis, BIG genomic data mining, algorithm design and software development. In particular, she is interested in applying computational models, algorithms, machine learning/deep learning/data mining methods to analyze biological data. She was a recipient of NSF CAREER Award (USA) in 2010 while she was working at MSU