Completing SBGN-AF networks by logic-based hypothesis finding

Yoshitaka Yamamoto, Adrien Rougny, Hidetomo Nabeshima, Katsumi Inoue, Hisao Moriya, Christine Froidevaux, Koji Iwanuma

研究成果

1 被引用数 (Scopus)

抄録

This study considers formal methods for finding unknown interactions of incomplete molecular networks using microarray profiles. In systems biology, a challenging problem lies in the growing scale and complexity of molecular networks. Along with high-throughput experimental tools, it is not straightforward to reconstruct huge and complicated networks using observed data by hand. Thus, we address the completion problem of our target networks represented by a standard markup language, called SBGN (in particular, Activity Flow). Our proposed method is based on logic-based hypothesis finding techniques; given an input SBGN network and its profile data, missing interactions can be logically generated as hypotheses by the proposed method. In this paper, we also show empirical results that demonstrate how the proposed method works with a real network involved in the glucose repression of S. cerevisiae.

本文言語English
ホスト出版物のタイトルFormal Methods in Macro-Biology - First International Conference, FMMB 2014, Proceedings
編集者Carla Piazza, François Fages
出版社Springer Verlag
ページ165-179
ページ数15
ISBN(電子版)9783319103976
ISBN(印刷版)9783319103976
出版ステータスPublished - 2014

出版物シリーズ

名前Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
8738
ISSN(印刷版)0302-9743
ISSN(電子版)1611-3349

ASJC Scopus subject areas

  • 理論的コンピュータサイエンス
  • コンピュータサイエンス一般

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