[Colloquium] Talks at TTIC: Stefan Canzar, Johns Hopkins University

[Dawn Ellis]

When:     Wednesday, March 19th at 11am

Where:    TTIC, 6045 S Kenwood Avenue, 5th Floor, Room #526

Speaker:  Stefan Canzar, Johns Hopkins University

TITLE:     Digging deeper: An algorithm for recovering low-expressed
transcripts
              from RNA-seq

ABSTRACT:

The use of next-generation sequencing technologies to sequence complementary
DNA copies of RNA transcripts (RNA-seq) has proven its potential for the
detection and quantification of (novel) isoforms expressed in a cell.
However, current methods that try to reconstruct the transcriptome from
RNA-seq data still suffer from various simplifications made to cope with
the
combinatorial complexity of the problem. As a consequence, it has been
observed earlier that many false-negative isoforms are due to splice
junctions that remain undiscovered by the preceding read alignment step.

We therefore propose a novel method that for the first time integrates
isoform
discovery and quantificiation based on the complete set of isoforms, that
is,
independent of discovered splice junctions.
After an initial prediction which improves upon predictions of existing
methods in terms of recall and precision, our algorithm digs deeper into the
space of all possible isoforms through an iterative scheme. In each
iteration,
a transcript that improves prediction is determined by solving an integer
linear programming formulation, yielding a boost in recall among
low-expressed transcripts.

The second part of my talk will (briefly) cover the automated assignment of
atoms
to charge groups, required in molecular dynamics simulations. We model the
charge
group assignment as a graph partitioning problem which we show to be
NP-hard
and give an exact algorithm that solves practical problem instances to
provable optimality
in a fraction of a second.

Host:  Jinbo Xu, j3xu at ttic.edu


-- 
*Dawn Ellis*
Administrative Coordinator,
Bookkeeper
773-834-1757
dellis at ttic.edu

TTIC
6045 S. Kenwood Ave.
Chicago, IL. 60637
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