[Crib-list] TODAY.... SPEAKER: Joy Yang (MIT) | CRIBB Seminar | Friday, Oct. 5, 2018 | TIME: 1:00 PM | Room 32-155 (Stata)

[Shirley Entzminger]

 		T O D A Y . . .



     	  COMPUTATIONAL RESEARCH in BOSTON and BEYOND Seminar
 			    (CRIBB)



DATE:		Friday, October 5, 2018

TIME:		1:00 PM - 2:00 PM  ("NEW time")

LOCATION:	Building 32, Room 155 (Stata)

 	   		  Pizza and beverages provided outside
 	   		  Room 155 at 12:45 PM


TITLE:		Statistically Identifying Mechanisms of Phage-host
  		  Interactions in the Nahant Collection


SPEAKER:	Joy Yang  (MIT)


ABSTRACT:

The Polz Lab maintains the Nahant Collection - 243 Vibrio strains challenged by 
241 unique phage, all with sequenced genomes.  This is the largest 
phylogenetically resolved host-range cross test available to date. These host 
strains match to 19 populations that coexist but are ecologically 
differentiated, and the phage fall into around 18 phylogenetically distinct 
groups with diverse infection strategies and morphologies.

This rich data set offers the opportunity to glean mechanistic insights from 
sequencing data, but doing so comes with a few challenges: (1) While the 
diverse population structure of phage and hosts is an interesting feature of 
the data, it means that statistical independence does not apply. Ignoring 
phylogenetic relationships can result in spurious correlations drowning out 
relevant signals. (2) A reasonable model should capture the generally 
lock-and-key nature of infection specificities due to protein interactions. For 
example, a specific methylase may evade a specific restriction modification 
system.

Here, in order to simplify computation, we first screen for genes of interest 
using generalized least squares to account for phylogenetic confounding.  Then 
we build a multivariate model with statistical interaction terms that loosely 
represent putative interactions of host and phage genes.  Finally, because our 
ultimate goal is to facilitate the process of generating testable hypotheses 
about biological mechanisms based on large-scale sequencing data, it is key to 
ensure that the model is interpretable and that the data is explorable by the 
general scientific community.  To this end, we've written an interactive web 
visualization that anyone interested in the Nahant Collection will be able to 
access.

==========================================

Massachusetts Institute of Technology
Cambridge, MA  02139



For information about the Computational Research in Boston and Beyond Seminar 
(CRIBB), please visit...

 		http://math.mit.edu/crib/

===============

Shirley A. Entzminger
Administrative Assistant II
Department of Mathematics
Massachusetts Institute of Technology
77 Massachusetts Avenue
Building 2, Room 350A
Cambridge, MA 02139
PHONE:	(617) 253-4347
FAX:	(617) 253-4358
E-mail:	daisymae at math.mit.edu
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