2019 Midwest Computational Biology Workshop @ TTIC

September 12-13, 2019

Toyota Technological Institute at Chicago

6045 S. Kenwood Ave, Chicago, IL 60637

The 2019 Midwest Computational Biology Workshop (September 12-13 @ Toyota Technological Institute at Chicago) will explore emerging topics in the field of computational biology, covering a spectrum of algorithmic and machine learning challenges to address biological questions. The workshop will bring together a wide range of participants from different backgrounds and positions and also aims to initiate new interdisciplinary interactions and collaborations. This workshop is part of the 2019 TTI-Chicago Summer Workshop Program. Additional funding has been graciously provided by the National Center for Brain Mapping (NCBM).


Registration is free but limited by seating capacity. Please register using this form.


There is free parking in two commuter parking lots, about 7-10 min walk away, at 60th St and Stony Island Ave and 63rd St and S Kenwood Ave.

There is also free, but limited, street parking on many streets near TTIC (just beware of "permit parking" and "street cleaning" signs!). For example, parking can be found on 61st Street (between Woodlawn Ave and Blackstone Ave) and on Dorchester Street (between 60th and 61st Streets).

Workshop Schedule

Thursday, September 12

8:30-8:55: Continental breakfast at TTIC

8:55-12:15: Metagenomics and Microbiome Session

8:55-9:00: Introductory Remarks, Michael Yu, TTIC

9:00-9:45: Catherine Putonti, Loyola University Chicago. The Urinary Tract Virome and Women’s Health

9:45-10:30: Yuzhen Ye, Indiana University. Computational methods for microbiome-based discovery and application of CRISPR-Cas systems.

10:30-10:45: Snacks and Coffee Break

10:45-11:30: Zhong Wang, Joint Genome Institute. Metagenome Exploration: discover novel microbial species.

11:30-12:15: Fiona Brinkman, Simon Fraser University. The power, the promise - and the pitfalls - of microbiome analyses.

12:15-1:15: Lunch at TTIC

1:15-5:30: Cancer Genomics & Computational Immunology Session

1:15-1:30: Introductory Remarks, Aly A. Khan, University of Chicago

1:30-2:15: Cenk Sahinalp, National Cancer Institute. Tumor evolution modeling through integrative use of bulk and single cell sequencing data

2:15-3:00: Hatice Osmanbeyoglu, University of Pittsburgh. Predictive gene regulatory models for precision medicine

3:00-3:45: Alex Rubinsteyn, Icahn School of Medicine at Mount Sinai. Personalized cancer vaccines

3:45-4:00: Snacks and Coffee Break

4:00-4:45: Kenneth Hoehn, Yale University. Phylogenetic analysis of B cell repertoires

4:45-5:30: Jonathan Carlson, Microsoft Research. The Adaptive-Microsoft Antigen Map Project

5:30-6:15: Reception at TTIC

Friday, September 13

8:30-8:55: Continental breakfast at TTIC

8:55-12:15: Protein Structure Session

8:55-9:00: Introductory Remarks, Jinbo Xu, TTIC

9:00-9:45: Ivan Anishchenko, University of Washington. Improved protein structure prediction using predicted inter-residue orientations.

9:45-10:30: Michael Feig, Michigan State University. High-Resolution structure refinement via MD Simulations.

10:30-10:45: Snacks and Coffee Break

10:45-11:30: Tristan Bepler, MIT. Learning protein sequence embeddings using information from structure.

11:30-12:15: Alex Rives, New York University. Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences.

12:15-1:15: Lunch at TTIC

1:15-4:35: Brain Connectomics Session

1:15-1:20: Introductory Remarks, Michael Yu, TTIC

1:20-2:05: Narayanan "Bobby" Kasthuri, University of Chicago, Argonne National Laboratory.

2:05-2:50: Viren Jain, Google. High-throughput synapse-resolution connectomics in fly, bird, and human brains.

2:50-3:05: Snacks and Coffee Break

3:05-3:50: Olaf Sporns, Indiana University. Network models of brain structure and function.

3:50-4:35: Sarah Muldoon, University at Buffalo. Exploring individual differences through personalized brain network models.

4:35-5:20: Reception at TTIC


  • Michael Yu, TTIC
  • Aly A. Khan, University of Chicago
  • Jinbo Xu, TTIC