Combi Seminars
Co-sponsored by the Department of Genomes Sciences and the Computational Molecular Biology (CMB) Program, the Combi Seminars focus specifically on developments in molecular and computational biology-related research and often feature UW faculty and researchers from regionally affiliated centers and institutes.
All Combi Seminars take place on Wednesdays from 1:30 - 2:30 in Foege Auditorium unless otherwise noted. | remote viewing option
compbio-seminars [ a t ] cs.washington.edu -- Biology seminar announcements from all around campus. Subscribe or unsubscribe at http://mailman.cs.washington.edu/mailman/listinfo/compbio-seminars
Please follow this link for a listing of past seminars. Some talks will be recorded and those links will be made available on the past seminars page for 2 weeks.
Winter 2026
2/25 - Dr. Emek Demir | OHSU
"From Fragments to Systems: How can we assemble biological mechanisms in the age of AI?"
Modern cancer research routinely generates petabytes of data across vast spatial and molecular scales. Our primary focus is to build interpretable and steerable AI models of disease that integrates with existing biological and clinical knowledge. I will present two recent tools developed by our teams towards this goal: (i) UniVI is a scalable framework designed to unify multimodal single-cell data. UniVI learns distinct but aligned embedding spaces for each modality. This approach enables consistent cross-modal integration, denoising, and label transfer without the need for pre-annotated reference atlases or curated feature graphs. (ii) MiroSCOPE is an AI-driven digital pathology platform for the systematic annotation of functional tissue units (FTUs). While cell-level modeling provides high resolution, it often overlooks the structural organization of FTUs—the repeating units (such as glands or stromal compartments) essential to tissue function and pathological grading. MiroSCOPE provides an end-to-end, "human-in-the-loop" workflow that integrates multiclass segmentation models with curation-specific features. Using this system, we have annotated over 100.000 FTUs across 200 prostate cancer samples, creating a high-quality resource for the community and facilitating the use of complex structural information in clinical assessments.
Dr. Emek Demir is an Associate Professor at Oregon Health & Science University (OHSU), where he leads a research program dedicated to transforming high-dimensional molecular and imaging data into mechanistic biological knowledge. His interdisciplinary background began at Bilkent University, where he earned both an M.S. in Molecular Biology and Genetics and a Ph.D. in Computer Science. He subsequently joined the Computational Biology Center at Memorial Sloan-Kettering Cancer Center (MSKCC), first as a Postdoctoral Fellow under Chris Sander and later serving as the Manager of the Pathway Commons resource. Emek currently holds faculty appointments at OHSU within the Department of Molecular and Medical Genetics, the Division of Oncological Sciences, and the Department of Biomedical Engineering and multiple leadership positions within the Knight Cancer Institute.
At MSKCC, Emek spearheaded the development of the BioPAX community standard and Pathway Commons, which remains the largest curated repository of human molecular pathways. His team developed a suite of algorithms that utilize these resources as a sophisticated scientific inference engine. By searching thousands of curated biochemical reactions, these tools identify the specific causal chains that explain observed changes in "omic" profiles, providing a mechanistic lens through which to view complex cancer biology.
Since moving to OHSU, Emek’s research has pivoted toward tumor heterogeneity modeling and the expansion of causal inference through AI-Human collaboration. As part of two major DARPA programs, his lab developed AI tools for "human-in-the-loop" curation and agents that can be orchestrated together to solve intricate inference problems. In a current collaboration with NVIDIA, his team is scaling these ideas to the multicellular level—using AI to segment and annotate Functional Tissue Units in the context of prostate, breast, and pancreatic tumors.
3/4 - Dr. Sheng Wang | University of Washington
3/11 - Dr. Ali Shojaie | University of Washington
Spring 2026
4/1 - Dr. Manu Setty | FHCC
4/8 - Dr. Frank Rosenzweig | Georgia Tech
4/15
4/22 - postdoctoral research talk: Dr. Chelsea Lin
4/29 - Dr. Kelley Harris | University of Washington
5/6 - Dr. Cole Trapnell | University of Washington
5/13 -
Postdoctoral Research Talks: two speakers per session
5/20 - reserved for postdoctoral research talks (two speakers per session)
5/27 - reserved for postdoctoral research talks (two speakers per session)
6/3 - reserved for postdoctoral research talks (two speakers per session)