Workshops

Summer 2022

From Algorithms to Discovery in Genome-Scale Biology and Medicine

Jul 5, 2022 to Jul 8, 2022

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All talks are in Pacific Time. Schedule subject to change.

Tuesday, July 5th, 2022
12:45 pm–1:15 pm		Coffee & Check-In
		Session 1: Gene Regulation
1:15 pm–1:30 pm		Opening Remarks
1:30 pm–2:00 pm		BANKSY: A Spatial Omics Algorithm that Unifies Cell Type Clustering and Tissue Domain Segmentation Shyam Prabhakar (Genome Institute of Singapore)
2:00 pm–2:30 pm		Break
2:30 pm–3:00 pm		Spatial Transcriptomics Identifies Neighbourhoods and Molecular Markers of Alveolar Damage in the Lung for COVID-19 Patients Martin Hemberg (Brigham and Women's Hospital)
3:00 pm–3:30 pm		Landscapes of Human cis-regulatory Elements and Transcription Factor Binding Sites Evolutionarily Constrained in the Mammalian Lineage Zhiping Weng (UMass Chan Medical School)
3:30 pm–5:00 pm		Reception & Poster Session

Wednesday, July 6th, 2022
9:00 am–9:30 am		Coffee & Check-In
		Session 2: Systems Medicine
9:30 am–10:00 am		Formatting Biological Big Data to Enable (Personalized) Systems Pharmacology Patrick Aloy (Institute for Research in Biomedicine)
10:00 am–10:30 am		TBD Jimmie Ye (UCSF)
10:30 am–11:00 am		Break
11:00 am–11:30 am		Genomics of Cancer Noam Shomron (TAU)
11:30 am–12:00 pm		Understanding Molecular Complexity for Precision Medicine Natasa Przulj (ICREA; Barcelona Supercomputing Center; University College London)
12:00 pm–2:00 pm		Lunch
		Session 3: Machine Learning
2:00 pm–2:30 pm		Machine Learning for Single-Cell 3D Epigenomics Jian Ma (Carnegie Mellon University)
2:30 pm–3:00 pm		A Statistical, Reference-Free Algorithm Subsumes Myriad Problems in Genome Science Julia Salzman (Stanford)
3:00 pm–3:30 pm		Break
3:30 pm–4:00 pm		Using Large-Scale Clinico-Genomics Data for in silico Clinical Trials and Precision Oncology James Zou (Stanford University)
4:00 pm–5:30 pm		Future Directions in Genomic Discovery Roded Sharan (TAU) and Nadav Ahituv (UCSF)

Thursday, July 7th, 2022
9:00 am–9:30 am		Coffee & Check-In
		Session 4: Network Biology
9:30 am–10:00 am		Interactome Networks in Genetic and Infectious Diseases Pascal Falter-Braun (Institute of Network Biology - Helmholtz Zentrum Munich)
10:00 am–10:30 am		Long-Range Propagation of Genetic Effects in Molecular Networks Andreas Beyer (CECAD, University of Cologne, Germany)
10:30 am–11:00 am		Break
11:00 am–11:30 am		A Binary Quantitative Interaction Mapping Approach: Elucidating Multiprotein Complexes in Health and Disease Erich Wanker (Max Delbrueck Center for Molecular Medicine)
11:30 am–12:00 pm		A Tyrosine Kinase Protein Interaction Map Reveals Targetable EGFR Network Oncogenesis in Lung Cancer Sourav Bandyopadhyay (UCSF)
12:00 pm–2:00 pm		Lunch
2:00 pm–2:30 pm		Computational Approaches to Study Interactions Between Mutagenic Processes and Cellular Processes Teresa Przytycka (National Center for Biotechnology Information)
2:30 pm–3:00 pm		Mapping Biological Pathways Using Systematic Genetics and Cell Biology Brenda Andrews (University of Toronto)
3:00 pm–3:30 pm		Coffee & Ride
3:30 pm–5:30 pm		Hike in Strawberry Canyon

Friday, July 8th, 2022
9:00 am–9:30 am		Coffee & Check-In
		Session 5: From Genotype to Phenotype
9:30 am–10:00 am		Algorithms for Inferring Phenotypes from Ancient DNA Tony Capra (UCSF)
10:00 am–10:30 am		Predicting the Deleteriousness of Genomic Variants – Big and Small Martin Kircher (BIH @ Charité / University of Luebeck)
10:30 am–11:00 am		Break
11:00 am–11:30 am		How Genome 3D Organization Regulates Alternative Splicing? Gil Ast (Tel Aviv University)
11:30 am–12:00 pm		Determining the Molecular Intermediates Between Genotype and Phenotype David Knowles (Columbia University/New York Genome Center)
12:00 pm–12:30 pm		Distinct Gene Programs Underpinning ‘Disease Tolerance’ and ‘Resistance’ Against Infections Irit Gat-Viks (Tel Aviv University)
12:30 pm–12:45 pm		Closing Remarks