Ka Yee Yeung, Ph.D.
About
Degrees
Introduction
My research focuses on the development of data science tools, their application to computational biology and the development of interoperable tools to enhance the reproducibility of research. My research focuses on the development of optimized methods and cloud-enabled software tools to facilitate the reproducible analyses of big biomedical data. I also develop machine learning methods that blend both computer science and statistics for applications in bioinformatics.
Current Research
I am the MPI of the NIH-funded MorPhiC (Molecular Phenotypes of Null Alleles in Cells, https://morphic.bio/) program. The goal of this program is to better understand the function of every human gene. My lab is primarily responsible for processing data generated in the MorPhiC program. My lab aims to deliver the latest technological advances in containers and cloud computing to a typical biomedical researcher with limited resources who works with big data. Specifically, we develop user-friendly and performance optimized software platforms to enable biomedical researchers to efficiently analyze and integrate diverse biomedical datasets. We have a training portal at https://biodepot.github.io/training/.
Honors and Awards
Recipient of the 2019 Distinguished Research Award at University of Washington Tacoma.
Graphical and Interactive Spatial Proteomics Image Analysis Workflow. Pritpal Singh, Jocelyn H Wright, Kimberly S Smythe, Bryce N Fukuda, Ling-Hong Hung, Cecilia CS Yeung, Ka Yee Yeung. GigaByte 2026, DOI 10.46471.
A prospective observational study of lifestyle behaviors and biomarkers to promote cardiometabolic health in healthcare workers during the COVID-19 pandemic. Mary McCarthy, Zachary Colburn, Laurel Gillette, Nancy Hodge, Ling-Hong Hung, Bryce Fukuda, Daniel Rhee, Joshua Sakai, Ka Yee Yeung. Frontiers in Molecular Biosciences 2026, 13:1714752.
MorPhiC consortium: Towards functional characterization of all human genes. Mazhar Adli, Laralynne Przybyla, Tony Burdett, Paul W. Burridge, Pilar Cacheiro, Howard Y. Chang, Jesse M. Engreitz, Luke A. Gilbert, William J. Greenleaf, Li Hsu, Danwei Huangfu, Ling-Hong Hung, Anshul Kundaje, Sheng Li, Helen Parkinson, Xiaojie Qiu, Paul Robson, Stephan C. Schurer, Ali Shojaie, William C. Skarnes, Damian Smedley, Lorenz Studer, Wei Sun, Dusica Vidovic, Thomas Vierbuchen, Brian S. White, Ka Yee Yeung, Feng Yue, Ting Zhou and The MorPhiC Consortium. Nature 2025, 638, 351-359.
Harmonizing and integrating the NCI Genomic Data Commons through accessible, interactive, and cloud-enabled workflows. Ling-Hong Hung, Bryce Fukuda, Robert Schmitz, Varik Hoang, Wes Lloyd, Ka Yee Yeung. PLOS One 2025, 20(3): e0318676.
Biodepot Launcher: An App to Install, Manage and Launch Bioinformatics Workflows. Ling-Hong Hung, Thomas Dahlstrom, Johnalbert Garnica, Emmanuel Munoz, Robert Schmitz, Ka Yee Yeung. GigaByte DOI 10.46471/gigabyte.146.
Container Profiler: Profiling Resource Utilization of Containerized Big Data Pipelines. Varik Hoang, Ling-Hong Hung, David Perez, Huazeng Deng, Raymond Schooley, Niharika Arumilli, Ka Yee Yeung, Wes Lloyd. Gigascience, Volume 12, 2023, giad069.
Rapid detection of myeloid neoplasm fusions using Single Molecule Long-Read Sequencing. Olga Sala-Torra, Shishir Reddy, Ling-Hong Hung, Lan Beppu, David Wu, Jerald Radich, Ka Yee Yeung, Cecilia CS Yeung. PLOS Global Public Health 3(9): e0002267.
Cloud-enabled Biodepot workflow builder integrates image processing using Fiji with reproducible data analysis using Jupyter notebooks. Ling-Hong Hung, Evan Straw, Shishir Reddy, Robert Schmitz, Zachary Colburn, and Ka Yee Yeung. Scientific Reports 12: 14920 (2022).
A graphical, interactive and GPU-enabled workflow to process long-read sequencing data. Shishir Reddy, Ling-Hong Hung, Olga Sala-Torra, Jerald Radich, Cecilia CS Yeung, Ka Yee Yeung. BMC Genomics 22, Article number: 626 (2021).
Building containerized workflows using the BioDepot-workflow-Builder (BwB). Ling-Hong Hung, Jiaming Hu, Trevor Meiss, Alyssa Ingersoll, Wes Lloyd, Daniel Kristiyanto, Yuguang Xiong, Eric Sobie, Ka Yee Yeung. Cell Systems 2019, volume 9, issue 5, pages 508-514.E3.
Holistic optimization of RNA-seq workflow for multi-threaded environments. Ling-Hong Hung, Wes Lloyd, Radhika Agumbe Sridhar, Saranya Devi Athmalingam Ravishankar, Yuguang Xiong, Eric Sobie, Ka Yee Yeung. Bioinformatics 2019, volume 35, issue 20, pages 4173-4175.