Workshop III: Cryo-Electron Microscopy and Beyond - IPAM

Workshop III: Cryo-Electron Microscopy and Beyond

Part of the Long Program Computational Microscopy
November 14 - 18, 2022

Schedule

All times in this Schedule are Pacific Time (PT)

Monday, November 14, 2022

Morning Session

08:00-08:55
Check-In/Breakfast (Hosted by IPAM)
08:55-09:00
Welcome & Opening Remarks: Dean Miguel García-Garibay (Dean of Physical Sciences, UCLA) and Dima Shlyakhtenko (Director, IPAM)
09:00-09:00
Session Chair: Sriram Subramaniam (UBC)
09:00-09:50
Steven Ludtke (Baylor College of Medicine)
Contextual Conformational Variability in CryoEM and CryoET using Deep Learning
10:00-10:15
Break
10:15-11:05
Carlos Oscar Sorzano (Centro Nacional de Biotecnología (CSIS))
Virtual Talk: Overview of the machine and deep learning needs and trends for Single Particle Analysis by Cryo-Electron Microscopy
11:15-11:30
Break
11:30-12:20
Geoffrey Woollard (University of British Columbia)
Using Stochastic variational inference and Computational Optimal Transport for problems in 3D heterogeneity

Afternoon Session

12:30-14:30
Lunch (on your own)
14:30-15:20
Ellen Zhong (Princeton University)
Machine learning for determining protein structure and dynamics from cryo-EM images
15:30-15:50
Break
15:50-16:40
Roy Lederman (Yale University)
Approaches for Exploring the Geometry of Molecular Conformations in Cryo-EM
16:50-17:20
Lightning Poster Presentations
17:20-18:45
Poster Session & Reception (Hosted by IPAM)

Tuesday, November 15, 2022

Morning Session

08:00-09:00
Check-In/Breakfast (Hosted by IPAM)
Session Chair (AM): Joe Kileel (UT Austin)
09:00-09:50
Chris Russo (University of Cambridge)
The potential of electron cryomicroscopy in situ: new technology to identify molecules in cells
10:00-10:15
Break
10:15-11:05
Petar Petrov (University of California, Berkeley (UC Berkeley))
Laser phase-contrast transmission electron microscopy and associated computational opportunities
11:15-11:30
Break
11:30-12:20
Katerina Naydenova (University of Cambridge)
Molecular structure extrapolation to zero dose with cryoEM

Afternoon Session

12:30-14:30
Lunch (on your own)
Session Chair (PM): Roy Lederman (Yale)
14:30-15:20
Serena Yeung (Stanford University)
Virtual Talk: Developing Computer Vision Methods for Segmenting and Analyzing Subcellular Components in Cryo-Electron Tomography
15:30-15:50
Break
15:50-16:40
Nikolaus Grigorieff (University of Massachusetts Medical School)
Detecting Distinct 60S Ribosome Maturation Intermediates in Cells by 2D Template Matching

Wednesday, November 16, 2022

Morning Session

08:00-09:00
Check-In/Breakfast (Hosted by IPAM)
09:00-09:00
Session Chair: Amit Singer (Princeton)
09:00-09:50
Mikhail Kudryashev (Stiftung Max-Delbrück-Centrum für Molekulare Medizin (MDC))
Virtual Talk: High throughput, high performance algorithms for high resolution subtomogram averaging
10:00-10:15
Break
10:15-11:05
Tamir Bendory (Tel Aviv University)
Recovering small molecular structures using cryo-EM
11:15-11:30
Break
11:30-12:20
Joe Kileel (University of Texas at Austin)
Method of moments in cryo-EM

Afternoon Session

12:30-12:40
Group Photo
12:40-14:30
Lunch (on your own)
14:30-15:20
Frederick Poitevin (SLAC National Accelerator Laboratory)
Amortized Inference of Poses for Ab Initio Reconstruction of 3D Molecular Volumes from Experimental Cryo-EM Images
15:30-15:50
Break
15:50-16:40
Tristan Bepler (New York Structural Biology Center (NYSBC))
Detection and segmentation of objects in cryo-electron micrographs using geometric deep learning

Thursday, November 17, 2022

Morning Session

08:00-09:00
Check-In/Breakfast (Hosted by IPAM)
09:00-09:00
Session Chair: Wah Chiu (Stanford)
09:00-09:50
Ayelet Heimowitz (Ariel University)
Virtual Talk: Center of Mass Alignment for Noisy Tomographic Projections
10:00-10:15
Break
10:15-11:05
Pilar Cossio (Flatiron Institute)
Structural-ensemble probability refinement using Cryo-EM particles
11:15-11:30
Break
11:30-12:20
Abhishek Singharoy (Arizona State University West)
Cryo-EM and beyond: Ensemble refinement, free-energy landscapes and molecular dynamics

Afternoon Session

12:30-14:30
Lunch (on your own)
14:30-15:20
Yuehaw Khoo (University of Chicago)
New approaches in simulation of transition paths
15:30-15:50
Break
15:50-16:40
Sonya Hanson (Flatiron Institute)
Better treatments of pose estimation, temperature, noise, and heterogeneity toward understanding biological temperature sensors via cryo-EM

Friday, November 18, 2022

Morning Session

08:00-09:00
Check-In/Breakfast (Hosted by IPAM)
09:00-09:00
Session Chair: Hong Zhou (UCLA)
09:00-09:50
Maya Topf (University of Hamburg)
Virtual Talk: Refinement and validation of atomic models in cryo-EM maps using TEMPy2
10:00-10:15
Break
10:15-11:05
Carlos Esteve-Yague (University of Cambridge)
Spectral decomposition of atomic structures in heterogeneous cryo-EM
11:15-11:30
Break
11:30-12:20
Alberto Bartesaghi (Duke University)
High-throughput cryo-ET: from data acquisition to high-resolution structures

Afternoon Session

12:30-12:30
Conclusion
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