A minimum-labeling approach for reconstructing protein networks across multiple conditions

Arnon Mazza, Irit Gat-Viks, Hesso Farhan, Roded Sharan

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review


The sheer amounts of biological data that are generated in recent years have driven the development of network analysis tools to facilitate the interpretation and representation of these data. A fundamental challenge in this domain is the reconstruction of a protein-protein subnetwork that underlies a process of interest from a genome-wide screen of associated genes. Despite intense work in this area, current algorithmic approaches are largely limited to analyzing a single screen and are, thus, unable to account for information on condition-specific genes, or reveal the dynamics (over time or condition) of the process in question. Here we propose a novel formulation for network reconstruction from multiple-condition data and devise an efficient integer program solution for it. We apply our algorithm to analyze the response to influenza infection in humans over time as well as to analyze a pair of ER export related screens in humans. By comparing to an extant, single-condition tool we demonstrate the power of our new approach in integrating data from multiple conditions in a compact and coherent manner, capturing the dynamics of the underlying processes.

Original languageEnglish
Title of host publicationAlgorithms in Bioinformatics - 13th International Workshop, WABI 2013, Proceedings
PublisherSpringer Verlag
Number of pages12
ISBN (Print)9783642404528
StatePublished - 2013
Event13th Workshop on Algorithms in Bioinformatics, WABI 2013 - Sophia Antipolis, France
Duration: 2 Sep 20134 Sep 2013

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume8126 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference13th Workshop on Algorithms in Bioinformatics, WABI 2013
CitySophia Antipolis


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