Workshops

Summer 2022

Computational Challenges in Very Large-Scale 'Omics'

Jul 18, 2022 to Jul 21, 2022

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

Monday, July 18th, 2022
10:30 am–11:15 am		Coffee and Check-In
11:15 am–11:30 am		Opening Remarks
11:30 am–12:00 pm		Single Cell Brain Isoforms in Space and Time Hagen Tilgner (Weill Cornell Medicine)
12:00 pm–12:30 pm		Benchmarking, Inference, and in Silico Controls in Single-Cell and Spatial Omics Data Science Jingyi Jessica Li (University of California, Los Angeles)
12:30 pm–1:30 pm		Lunch
1:30 pm–2:00 pm		Learning Gene Association Networks Using Single-Cell RNA-Seq Data: A Graphical Model Approach Davide Risso (University of Padova)
2:00 pm–2:30 pm		Mapping Gene Regulatory Dependencies with Single-Cell Resolution Oliver Stegle (German Cancer Research Center, EMBL Heidelberg)
2:30 pm–3:00 pm		Break
3:00 pm–3:30 pm		Harnessing Multimodal Single-Cell Sequencing Data for Integrative Analysis Elizabeth Purdom (UC Berkeley)
3:30 pm–4:00 pm		Learning From Large-Scale (Single-Cell) ‘Omics’ Lior Pachter (Caltech)
4:00 pm–4:30 pm		Break
4:30 pm–6:00 pm		Panel Discussion

Tuesday, July 19th, 2022
9:30 am–10:00 am		Coffee and Check-In
10:00 am–10:30 am		Exploratory and Model-Based Analysis of ScHi-C Data Sunduz Keles (University of Wisconsin, Madison)
10:30 am–11:00 am		Break
11:00 am–11:30 am		The Earth Biogenome Project: Progress and the Challenges Ahead Harris Lewin (University of California, Davis)
11:30 am–12:00 pm		Multiple Sequence Alignment for Predicting Antigen-Antibody Interactions Kazutaka Katoh (Osaka University)
12:00 pm–1:30 pm		Lunch
1:30 pm–2:00 pm		Evolution of Germline Mutation Spectrum in Humans Priya Moorjani (University of California, Berkeley)
2:00 pm–2:30 pm		Sequence Bioinformatics at Large Scale: Petabase-Scale Sequence Alignment Catalyses Viral Discovery Rayan Chikhi (Institut Pasteur)
2:30 pm–3:00 pm		Break
3:00 pm–3:30 pm		Long-Read Transcriptome Complexity and Cell-Type Regulatory Signatures in ENCODE4 Ali Mortazavi (University of Victoria)
3:30 pm–4:00 pm		Leveraging Long Reads Sequencing for Developing a Functional Iso-Transcriptomics Analysis Framework Ana Conesa (Spanish National Research Council)
4:00 pm–5:30 pm		Reception & Poster Session

Wednesday, July 20th, 2022
9:00 am–9:30 am		Coffee and Check-In
9:30 am–10:00 am		Multi-Omic Integration for Understanding Disease Ron Shamir (Tel Aviv University)
10:00 am–10:30 am		The Epigenetic Logic of Gene Activation Roderic Guigó (Center for Genomic Regulation)
10:30 am–11:00 am		Break
11:00 am–11:30 am		Profiling of Antibody Repertoires and Immunoglobulin Loci Enables Large-Scale Analysis of Adaptive Immune Responses Yana Safonova (Johns Hopkins University)
11:30 am–12:00 pm		Leveraging Molecular Data for Drug Discovery Haiyan Huang (UC Berkeley)
12:00 pm–1:00 pm		Lunch
1:00 pm–1:30 pm		The Rewards and Challenges of Constructing Patient Registries in Mexico Alejandra Medina-Rivera (Universidad Nacional Autónoma de México)
1:30 pm–2:00 pm		Whole Genome Methylation Patterns as a Biomarkers for EHR Imputation Eran Halperin (Optum Labs and UCLA)
2:00 pm–2:30 pm		Break
2:30 pm–3:00 pm		Biological Discovery and Consumer Genomics Databases Activate Latent Privacy Risk in Functional Genomics Data Steven Brenner (UC Berkeley)
3:00 pm–3:30 pm		How Do We Deliver Precision Health at Scale for All? Carlos Bustamante (Galatea Bio, Stanford, University of Miami)
3:30 pm–5:30 pm		Hike

Thursday, July 21st, 2022
9:00 am–9:30 am		Coffee and Check-In
9:30 am–10:00 am		Longitudinal Phenotypes and Disease Trajectories at Population Scale Søren Brunak (Novo Nordisk Foundation Center for Protein Research)
10:00 am–10:30 am		Towards Making Identification of Noncoding Causes of Human Disease Routine Timothy Reddy (Duke University)
10:30 am–11:00 am		Break
11:00 am–11:30 am		New Approaches for Phylogenetic Species Tree Estimation Tandy Warnow (University of Illinois Urbana-Champaign)
11:30 am–12:00 pm		Nanopore Basecalling for Directed Evolution Ian Holmes (UC Berkeley)
12:00 pm–1:30 pm		Lunch
1:30 pm–2:00 pm		Breaking the Winner's Curse in Mendelian Randomization: Rerandomized Inverse Variance Weighted Estimator Jingshen Wang (UC Berkeley)
2:00 pm–2:30 pm		Computational Challenges in a Densely Sequenced Tree of Life Katie Pollard (Gladstone Institute of Data Science & Biotechnology)
2:30 pm–2:45 pm		Concluding Remarks