Kuang Lab Wins Outstanding Student Paper Award at ISMB Conference
Department of Computer Science & Engineering PhD student Charlie Broadbent won the Ian Lawson Van Toch Memorial Award for Outstanding Student Paper at the 32nd Conference on Intelligent Systems for Molecular Biology (ISMB) in Montreal, Canada. His paper titled, “Deciphering High-order Structures in Spatial Transcriptomes with Graph-guided Tucker Decomposition” was co-authored by labmate Tianci Song and their advisor Professor Rui Kuang. The Outstanding Student Paper award is given to the student who presents the most thought-provoking or original paper at the conference, as judged by a panel of experts. This award is the only conference-wide paper award given in the conference this year.
“It’s definitely an important award considering the significance of the ISMB conference,” said Broadbent. “There is a lot of competition from many different countries to even get your paper accepted at the conference, let alone to get the Outstanding Student Paper Award. It definitely makes me feel good about the research that I have been doing over the last five years. It’s nice that other people in the field think that it is significant.”
Broadbent’s paper focuses on the development of a high-order factorization method for spatial transcriptomics that finds a compressed representation of gene activities in the spatial context of a micro-environment among cells. This method allows for the capturing and visualization of biologically important tissue regions and the identification of associated gene modules. This process can collectively help biologists better understand how cells may differ in functionality by their spatial arrangement in a tissue. This work is funded by NSF under project BIO DBI IIBR 2042159: Mining Spatial and Single-cell Transcriptomes to Understand Cell Locality and Heterogeneity in Tissues.
“Our focus is on detecting and visualizing gene activities at spatial locations in tissues so that biologists can look at which genes play important roles in different regions of the tissue,” said Kuang. “This is critical for understanding tumor progression, embryo development, and other important applications. We are among the first few groups that are focusing on detection and visualization (of gene modular activities) in a spatial context, and we use advanced tensor-based methods for this application. This is a unique computational challenge. Charlie has been working on a tensor-based representation and model using high-order graph regularization for component detection and visualizations, which is a very advanced, highly-technical method. Charlie has done a great job deriving everything with his lab mate.”
Broadbent is a fifth-year PhD candidate focusing on spatial transcriptomic data. He hopes to finish his thesis in the next two years and apply to researcher positions in academia and industry.
“This is definitely an exciting, growing field,” said Broadbent. “We work with spatial transcriptomic data, which at a high level allows biologists to record how genes might be expressed in different locations on a tissue. One use case is to help biologists understand how cancerous tumors can evolve depending on a cell’s location within the tissue. Our work could also help target specific genes that are worsening certain cancers. At a high level, we are working to understand how cells function within a certain space in a tissue.”
ISMB is the flagship conference in International Society for Computational Biology (ISCB), and considered the top conference in this area. The Ian Lawson Van Toch Memorial Award for Outstanding Student Paper is given in memory of Ian Lawson Van Toch, a 23 year old medical biophysics graduate student at the University of Toronto who passed away in August 2007. This award is funded by the Princess Margaret Hospital Foundation. For more information about the award and a list of past recipients, please visit the ISMB website.