Jean-Philippe Vert 博士 (Ecole des Mines de Paris, France http://cbio.ensmp.fr/~jvert）<br>
講演日時：7/14 15:00-17:00<br>
講演場所：伊都キャンパス ウェスト2号館10階 1019号室（セミナー室1）<br>
題目: Global alignment of protein-protein interaction networks by graph matching methods<br>
概要:
Aligning protein?protein interaction (PPI) networks of different
species has drawn a considerable interest recently. This problem is
important to investigate evolutionary conserved pathways or protein
complexes across species, and to help in the identification of
functional orthologs through the detection of conserved interactions.
It is, however, a difficult combinatorial problem, for which only
heuristic methods have been proposed so far. In this work we
reformulate the PPI alignment as a graph matching problem, and
investigate how state-of-the-art graph matching algorithms can be
used for that purpose. We differentiate between two alignment problems,
depending on whether strict constraints on protein matches are given,
based on sequence similarity, or whether the goal is instead to find
an optimal compromise between sequence similarity and interaction
conservation in the alignment. We propose new methods for both cases,
and assess their performance on the alignment of the yeast and fly
PPI networks. The new methods consistently outperform state-of-the-art
algorithms, retrieving in particular 78% more conserved interactions
than IsoRank for a given level of sequence similarity. This is a joint
work with Mikhail Zaslavskiy and Francis Bach.<br>
Link:
http://dx.doi.org/10.1093/bioinformatics/btp196