Upcoming Colloquia

All seminars will be held in the MBI Lecture Hall - Jennings Hall, Room 355 - unless otherwise noted.

March 09, 2015 3:00 - 3:50PM
Host: Dave Terman

When the human visual system is subjected to diffuse flickering light in the range of 5-25 Hz, many subjects report beautiful swirling colorful geometric patterns. In the years since Jan Purkinje first described them, there have been many qualitative and quantitative analyses of the conditions in which they occur. Here, we use a simple excitatory-inhibitory neural network to explain the dynamics of these fascinating patterns. We employ a combination of computational and mathematical methods to show why these patterns arise. We demonstrate that the geometric forms of the patterns are intimately tied to the frequency of the flickering stimuli. We also show that the patters that arise are completely expected based on symmetric bifurcation arguments.

April 06, 2015 3:00 - 3:50PM
Host: Greg Rempala

The three-dimensional (3D) configuration of chromosomes within the eukaryote nucleus is consequential for several cellular functions, including gene expression regulation, and is also associated with cancer-causing translocation events.   While visualization of such architecture remains limited to low resolutions, the ability to infer structures at high resolution has been enabled by recently-devised chromosome conformation capture assays.  In particular, when coupled with next generation sequencing, such methods yield a genome-wide inventory of chromatin interactions.   Various algorithms have been advanced to operate on such data to produce reconstructed 3D configurations.  Several studies have shown that such reconstructions provide added value over raw interaction data with respect to downstream biological analysis.  

However, such added value has yet to be fully realized for higher eukaryotes since no high resolution genome-wide reconstructions have been inferred for these organisms because of computational bottlenecks and organismal complexity.  After overviewing existing reconstruction approaches we propose a two-stage algorithm, deploying multi-dimensional scaling and Procrustes transformation, that overcomes these barriers. 3D architectures for mouse and human are presented and methods for evaluating these solutions discussed.  Finally, reverting to yeast, we demonstrate the advantages bestowed by 3D structures with respect to identifying co-regulatory elements.

TBD
April 20, 2015 3:00 - 3:50PM
Host: Andrej Rotter

Abstract not submitted.

TBD
August 31, 2015 3:00 - 3:50PM
Host: TBD

Abstract not submitted.

TBD
September 21, 2015 3:00 - 3:50PM
Host: TBD

Abstract not submitted.

TBD
October 05, 2015 3:00 - 3:50PM
Host: TBD

Abstract not submitted.

TBD
October 19, 2015 3:00 - 3:50PM
Host: TBD

Abstract not submitted.

TBD
November 02, 2015 3:00 - 3:50PM
Host: TBD

Abstract not submitted.

TBD
November 09, 2015 3:00 - 3:50PM
Host: TBD

Abstract not submitted.