In honor of Michael Waterman’s 80th birthday, 40 years of Computational Biology,

and the new Quantitative and Computational Biology department!


May 19th – 21st, 2022

Thursday, May 19th, 2022


8:00-9:00 - Conference Registration and Breakfast

9:00-9:05 - Welcome

Remo Rohs, QCB Department Chair


9:05-9:10 - Greeting

Jan Amend, Divisional Dean for Life Sciences, Dornsife College


9:19-9:15 - Greeting

Yannis Yortsos, Dean, Viterbi School of Engineering


9:15-9:25 - Opening Remarks

Andrew Viterbi, USC Life Trustee

9:25-9:30 - Recorded Greeting

Amber Miller, Dean, Dornsife College


9:30-12:30 - Session 1: Structure in Computational Biology


9:30-10:10 - Keynote: Structure-based proteome wide prediction of protein-protein and protein-compound interactions

Barry Honig, Columbia University (on Zoom)


10:10-10:35 - Digitally detangling the 3D genome

Geoffrey Fudenberg, USC              


10:35-10:55 - Coffee Break


10:55-11:20 - Annotating human and mouse candidate cis-regulatory elements in the ENCODE Project

Zhiping Weng, UMass Medical School


11:20-11:45 - Towards reconstructing peta-scale microscopy datasets

Stephan Preibisch, HHMI Janelia Research Campus


11:45-12:10 - Unraveling the mechanistic basis of the CRISPR-Cas revolution through computational methods

Giulia Palermo, UC Riverside            


12:10-12:30 - Group photo


12:30-14:00 - Lunch break


14:00–17:05 - Session 2: Statistics in Computational Biology


14:00-14:40 - Keynote: Veridical data science for biomedical research: discovering predictable and stable non-linear interactions through iRF and epiTree

Bin Yu, UC Berkeley

14:40-15:05 - Deconvolution of DNA damage and repair contributions to the mutational landscape of cancer

Teresa Przytycka, NIH


15:05-15:30 - Exploiting the geometry of Correspondence Analysis: Association Plots and biclustering

Martin Vingron, Max Planck Institute of Molecular Genetics


15:30-15:55 - Quantifying the evolutionary dynamics of tumor progression and metastasis

Christina Curtis, Stanford University


15:55-16:20 - Genomics and AI for immuno-oncology drug discovery

X. Shirley Liu, GV20 Therapeutics


16:20-16:40 - Coffee Break


16:40-18:30 - Poster session


Friday, May 20th, 2022


8:00-9:00 - Breakfast

9:00–12:20 - Session 3:  Algorithms in Computational Biology


9:00-09:40 - Keynote: Utilizing multi-omics, biological networks and medical records to understand cancer 

Ron Shamir, Tel Aviv University

9:40-10:05 - Detecting COVID-19 with genomic sequencing: from bench to vending machine

Eleazar Eskin, UCLA

10:05-10:30 - New methods to characterize VNTR variation in human genomes

Mark Chaisson, USC

10:30-10:50 - Break


10:50-11:15 - Design for inference: the power of random experiments in biology

Aviv Regev, Genentech and Broad Institute (on Zoom)

11:15-11:40 - Toward complete genome assemblies using multiplex de Bruijn graphs

Pavel Pevzner, UCSD

11:40-12:05 - Learning protein-DNA recognition codes using structural mappings

Mona Singh, Princeton University

12:05-12:30 - Reconstructing somatic evolution from multiomic data

Russell Schwartz, Carnegie Mellon University

12:30-14:00 - Lunch break


14:00–17:05 - Session 4: Systems Biology


14:00-14:40 - Keynote: How genomes encode time

Michael Levine, Princeton University

15:05-15:30 - Modeling the dynamics of cell fate decision-making in single cells

Adam MacLean, USC

14:40-15:05 - Upscaling stochastic dynamics in non-linear systems 

Naomi Levine, USC

15:30-15:50 - Coffee Break

15:50-16:30 - Keynote: TBA

Bonnie Berger, MIT

16:30-16:55 - On some open combinatorial problems in computational molecular biology

Lior Pachter, Caltech

16:55-17:20 - The limits of inference from phylogenetic trees  

Matt Pennell, USC and UBC

18:00 - Reception, Town & Gown 


19:00 - Banquet Dinner, Town & Gown 


Remo Rohs, QCB Department Chair

Dinner Remarks

Charles Zukoski, USC Provost

Ming Hsieh, Fulgent Genetics and USC Trustee

Simon Tavaré, Columbia University and USC

Michael Waterman, USC

Saturday, May 21st, 2022
8:00-9:00 - Breakfast


9:00–12:20 - Session 5: Population Genetics and Evolutionary Genomics


9:00-09:40 - Keynote: Modeling and simulation of cancer evolution in single cells

Simon Tavaré, Columbia University and USC


9:40-10:05 - On the number of genealogical ancestors tracing to the source groups of an admixed population  

Jazlyn Mooney, USC

10:05-10:30 - Recursive coalescent computations for multi-species gene genealogies

Noah Rosenberg, Stanford University

10:30-10:50 - Coffee Break


10:50-11:15 - Alignment: it's not only about sequences

Susan Holmes, Stanford University (on Zoom)

11:15-11:40 - Opening black boxes: enhancing statistical rigor in genomics data science                                         

Jingyi Jessica Li, UCLA

11:40-12:05 - Revisiting power in case-control association studies as a function of the case fraction              

Michael ‘Doc’ Edge, USC

12:05-12:30 - Scalable, fast, and statistically consistent species tree estimation addressing both ILS and GDL

Tandy Warnow, UIUC

12:30-14:00 - Lunch break


14:00-14:25 - Back to discrete - in biology, math and AI

Serafim Batzoglou, Seer Inc.

14:24-14:50 - Count statistics for inferring gene-gene interactions and disease-drug associations

Haiyan Huang, UC Berkeley

14:50-5:15 - Characterizing the brain regulatory grammar at a single-cell resolution to highlight disease-driving genetic

and epigenetic dysregulations

Jing Zhang, UC Irvine

15:15-15:40 - Topological data analysis (TDA) and logic on omics data 

Laxmi Parida, IBM

15:40-15:45 - Organization Committee, Closing Remarks, Adjourn
Fengzhu Sun, Conference Chair