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Computational Challenges in Very Large-Scale 'Omics'
Program
Computational Innovation and Data-Driven Biology
Location
Calvin Lab Auditorium
Date
Monday, July 18
–
Thursday, July 21, 2022
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The Workshop
Schedule
Videos
All talks are in PDT Time. Schedule subject to change.
Monday, July 18, 2022
10:30
–
11:15 a.m.
Coffee and Check-In
11:15
–
11:30 a.m.
Opening Remarks
11:30 a.m.
–
12 p.m.
Single Cell Brain Isoforms in Space and Time
Hagen Tilgner (Weill Cornell Medicine)
12
–
12:30 p.m.
Benchmarking, Inference, and in Silico Controls in Single-Cell and Spatial Omics Data Science
Jingyi Jessica Li (University of California, Los Angeles)
12:30
–
1:30 p.m.
Lunch
1:30
–
2 p.m.
Learning Gene Association Networks Using Single-Cell RNA-Seq Data: A Graphical Model Approach
Davide Risso (University of Padova)
2
–
2:30 p.m.
Mapping Gene Regulatory Dependencies with Single-Cell Resolution
Oliver Stegle (German Cancer Research Center, EMBL Heidelberg)
2:30
–
3 p.m.
Break
3
–
3:30 p.m.
Harnessing Multimodal Single-Cell Sequencing Data for Integrative Analysis
Elizabeth Purdom (UC Berkeley)
3:30
–
4 p.m.
Learning From Large-Scale (Single-Cell) ‘Omics’
Lior Pachter (Caltech)
4
–
4:30 p.m.
Break
4:30
–
6 p.m.
Panel Discussion
Tuesday, July 19, 2022
9:30
–
10 a.m.
Coffee and Check-In
10
–
10:30 a.m.
Exploratory and Model-Based Analysis of ScHi-C Data
Sunduz Keles (University of Wisconsin, Madison)
10:30
–
11 a.m.
Break
11
–
11:30 a.m.
The Earth Biogenome Project: Progress and the Challenges Ahead
Harris Lewin (University of California, Davis)
11:30 a.m.
–
12 p.m.
Multiple Sequence Alignment for Predicting Antigen-Antibody Interactions
Kazutaka Katoh (Osaka University)
12
–
1:30 p.m.
Lunch
1:30
–
2 p.m.
Evolution of Germline Mutation Spectrum in Humans
Priya Moorjani (University of California, Berkeley)
2
–
2:30 p.m.
Sequence Bioinformatics at Large Scale: Petabase-Scale Sequence Alignment Catalyses Viral Discovery
Rayan Chikhi (Institut Pasteur)
2:30
–
3 p.m.
Break
3
–
3:30 p.m.
Long-Read Transcriptome Complexity and Cell-Type Regulatory Signatures in ENCODE4
Ali Mortazavi (University of Victoria)
3:30
–
4 p.m.
Leveraging Long Reads Sequencing for Developing a Functional Iso-Transcriptomics Analysis Framework
Ana Conesa (Spanish National Research Council)
4
–
5:30 p.m.
Reception & Poster Session
Wednesday, July 20, 2022
9
–
9:30 a.m.
Coffee and Check-In
9:30
–
10 a.m.
Multi-Omic Integration for Understanding Disease
Ron Shamir (Tel Aviv University)
10
–
10:30 a.m.
The Epigenetic Logic of Gene Activation
Roderic Guigó (Center for Genomic Regulation)
10:30
–
11 a.m.
Break
11
–
11:30 a.m.
Profiling of Antibody Repertoires and Immunoglobulin Loci Enables Large-Scale Analysis of Adaptive Immune Responses
Yana Safonova (Johns Hopkins University)
11:30 a.m.
–
12 p.m.
Leveraging Molecular Data for Drug Discovery
Haiyan Huang (UC Berkeley)
12
–
1 p.m.
Lunch
1
–
1:30 p.m.
The Rewards and Challenges of Constructing Patient Registries in Mexico
Alejandra Medina-Rivera (Universidad Nacional Autónoma de México)
1:30
–
2 p.m.
Whole Genome Methylation Patterns as a Biomarkers for EHR Imputation
Eran Halperin (Optum Labs and UCLA)
2
–
2:30 p.m.
Break
2:30
–
3 p.m.
Biological Discovery and Consumer Genomics Databases Activate Latent Privacy Risk in Functional Genomics Data
Steven Brenner (UC Berkeley)
3
–
3:30 p.m.
How Do We Deliver Precision Health at Scale for All?
Carlos Bustamante (Galatea Bio, Stanford, University of Miami)
3:30
–
5:30 p.m.
Hike
Thursday, July 21, 2022
9
–
9:30 a.m.
Coffee and Check-In
9:30
–
10 a.m.
Longitudinal Phenotypes and Disease Trajectories at Population Scale
Søren Brunak (Novo Nordisk Foundation Center for Protein Research)
10
–
10:30 a.m.
Towards Making Identification of Noncoding Causes of Human Disease Routine
Timothy Reddy (Duke University)
10:30
–
11 a.m.
Break
11
–
11:30 a.m.
New Approaches for Phylogenetic Species Tree Estimation
Tandy Warnow (University of Illinois Urbana-Champaign)
11:30 a.m.
–
12 p.m.
Nanopore Basecalling for Directed Evolution
Ian Holmes (UC Berkeley)
12
–
1:30 p.m.
Lunch
1:30
–
2 p.m.
Breaking the Winner's Curse in Mendelian Randomization: Rerandomized Inverse Variance Weighted Estimator
Jingshen Wang (UC Berkeley)
2
–
2:30 p.m.
Computational Challenges in a Densely Sequenced Tree of Life
Katie Pollard (Gladstone Institute of Data Science & Biotechnology)
2:30
–
2:45 p.m.
Concluding Remarks
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