The approximability of shortest path-based graph orientations of protein–protein interaction networks

D Blokh, D Segev, R Sharan - Journal of Computational Biology, 2013 - liebertpub.com
The graph orientation problem calls for orienting the edges of an undirected graph so as to
maximize the number of prespecified source-target vertex pairs that admit a directed path …

Network orientation via shortest paths

D Silverbush, R Sharan - Bioinformatics, 2014 - academic.oup.com
The graph orientation problem calls for orienting the edges of a graph so as to maximize the
number of pre-specified source–target vertex pairs that admit a directed path from the source …

Approximation algorithms for orienting mixed graphs

M Elberfeld, D Segev, CR Davidson… - Theoretical Computer …, 2013 - Elsevier
Graph orientation is a fundamental problem in graph theory that has recently arisen in the
study of signaling-regulatory pathways in protein networks. Given a graph and a list of …

Approximation algorithms and hardness results for shortest path based graph orientations

D Blokh, D Segev, R Sharan - … , CPM 2012, Helsinki, Finland, July 3-5 …, 2012 - Springer
The graph orientation problem calls for orienting the edges of an undirected graph so as to
maximize the number of pre-specified source-target vertex pairs that admit a directed path …

An algorithm for orienting graphs based on cause-effect pairs and its applications to orienting protein networks

A Medvedovsky, V Bafna, U Zwick, R Sharan - … in Bioinformatics: 8th …, 2008 - Springer
We consider a graph orientation problem arising in the study of biological networks. Given
an undirected graph and a list of ordered source-target pairs, the goal is to orient the graph …

Improved orientations of physical networks

I Gamzu, D Segev, R Sharan - … , WABI 2010, Liverpool, UK, September 6-8 …, 2010 - Springer
The orientation of physical networks is a prime task in deciphering the signaling-regulatory
circuitry of the cell. One manifestation of this computational task is as a maximum graph …

Exploiting bounded signal flow for graph orientation based on cause–effect pairs

B Dorn, F Hüffner, D Krüger, R Niedermeier… - Algorithms for Molecular …, 2011 - Springer
Background We consider the following problem: Given an undirected network and a set of
sender–receiver pairs, direct all edges such that the maximum number of" signal flows" …

On the approximability of reachability-preserving network orientations

M Elberfeld, V Bafna, I Gamzu, A Medvedovsky… - Internet …, 2011 - Taylor & Francis
We introduce a graph-orientation problem arising in the study of biological networks. Given
an undirected graph and a list of ordered source–target vertex pairs, the goal is to orient the …

Optimally orienting physical networks

D Silverbush, M Elberfeld, R Sharan - Journal of Computational …, 2011 - liebertpub.com
In a network orientation problem, one is given a mixed graph, consisting of directed and
undirected edges, and a set of source-target vertex pairs. The goal is to orient the undirected …

Connectivity problems on heterogeneous graphs

J Wu, A Khodaverdian, B Weitz, N Yosef - Algorithms for molecular biology, 2019 - Springer
Background Network connectivity problems are abundant in computational biology
research, where graphs are used to represent a range of phenomena: from physical …