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

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

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

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

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