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

[daisymae@mit.edu]

     	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
-------------- next part --------------
A non-text attachment was scrubbed...
Name: CRIBB Seminar - Joy Yang (MIT) -- Friday, Oct	5-2018.pdf
Type: application/pdf
Size: 962431 bytes
Desc: 
Url : http://mailman.mit.edu/pipermail/crib-list/attachments/20181001/ca3e6be7/attachment.pdf