AI Center - AI for Health Series - Prof. Dr. Valentina Boeva, ETHZ
Event details
| Date | 15.01.2025 |
| Hour | 13:00 › 14:00 |
| Speaker | Prof. Dr. Valentina Boeva |
| Location | Online |
| Category | Conferences - Seminars |
| Event Language | English |
Host: Dr. Dorina Thanou
Title
Harnessing attention mechanisms to decode chromatin interactions in rare and unexplored cell types
Abstract
Chromatin interactions provide insights into which DNA regulatory elements connect with specific genes, informing the activation or repression of gene expression. Understanding these interactions is crucial for assessing the role of non-coding mutations or changes in chromatin organization due to cell differentiation or disease. Hi-C and single-cell Hi-C experiments can reveal chromatin interactions, but these methods are costly and labor-intensive. Here, I will introduce our computational approach, UniversalEPI, an attention-based deep ensemble model that predicts regulatory interactions in unseen cell types with a receptive field of 2 million nucleotides, relying solely on DNA sequence data and chromatin accessibility profiles. Demonstrating significantly better performance than state-of-the-art methods, UniversalEPI, with a much lighter architecture, effectively predicts chromatin interactions across malignant and non-malignant cancer cell lines (Speaman’s Rho of > 0.9 on unseen cell types). This model represents a significant advancement in in-silico 3D chromatin modeling, essential for exploring genetic variant impacts on diseases and monitoring chromatin architecture changes in organism development.
Bio
Prof. Dr. Valentina Boeva is a Tenure Track Assistant Professor at the Department of Computer Science, ETH Zurich, where she leads the Computational Cancer Genomics Group. Her research focuses on developing computational methods for multi-omics data integration to understand the epigenetic and transcriptional plasticity of cancer cells. Before joining ETH Zurich in 2019, Prof. Boeva led the Computational Epigenetics of Cancer laboratory at Inserm's Cochin Institute in Paris. She holds a Ph.D. in Bioengineering and Bioinformatics from Lomonosov Moscow State University. Throughout her career, Prof. Boeva has made contributions to the field of computational cancer genomics with developing methods for the analysis of DNA sequencing data, bulk and single-cell transcriptomics and epigenomics data, and, recently, spatial transcriptomics and proteomics.
Title
Harnessing attention mechanisms to decode chromatin interactions in rare and unexplored cell types
Abstract
Chromatin interactions provide insights into which DNA regulatory elements connect with specific genes, informing the activation or repression of gene expression. Understanding these interactions is crucial for assessing the role of non-coding mutations or changes in chromatin organization due to cell differentiation or disease. Hi-C and single-cell Hi-C experiments can reveal chromatin interactions, but these methods are costly and labor-intensive. Here, I will introduce our computational approach, UniversalEPI, an attention-based deep ensemble model that predicts regulatory interactions in unseen cell types with a receptive field of 2 million nucleotides, relying solely on DNA sequence data and chromatin accessibility profiles. Demonstrating significantly better performance than state-of-the-art methods, UniversalEPI, with a much lighter architecture, effectively predicts chromatin interactions across malignant and non-malignant cancer cell lines (Speaman’s Rho of > 0.9 on unseen cell types). This model represents a significant advancement in in-silico 3D chromatin modeling, essential for exploring genetic variant impacts on diseases and monitoring chromatin architecture changes in organism development.
Bio
Prof. Dr. Valentina Boeva is a Tenure Track Assistant Professor at the Department of Computer Science, ETH Zurich, where she leads the Computational Cancer Genomics Group. Her research focuses on developing computational methods for multi-omics data integration to understand the epigenetic and transcriptional plasticity of cancer cells. Before joining ETH Zurich in 2019, Prof. Boeva led the Computational Epigenetics of Cancer laboratory at Inserm's Cochin Institute in Paris. She holds a Ph.D. in Bioengineering and Bioinformatics from Lomonosov Moscow State University. Throughout her career, Prof. Boeva has made contributions to the field of computational cancer genomics with developing methods for the analysis of DNA sequencing data, bulk and single-cell transcriptomics and epigenomics data, and, recently, spatial transcriptomics and proteomics.
Practical information
- Informed public
- Free
- This event is internal