Chung-Shou Liao

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MOTIVATION With the increasing availability of large protein-protein interaction networks, the question of protein network alignment is becoming central to systems biology. Network alignment is further delineated into two sub-problems: local alignment, to find small conserved motifs across networks, and global alignment, which attempts to find a best(More)
We describe IsoBase, a database identifying functionally related proteins, across five major eukaryotic model organisms: Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, Mus musculus and Homo Sapiens. Nearly all existing algorithms for orthology detection are based on sequence comparison. Although these have been successful in(More)
We propose a novel algorithm, PISwap, for computing global pairwise alignments of protein interaction networks, based on a local optimization heuristic that has previously demonstrated its effectiveness for a variety of other NP-hard problems, such as the Traveling Salesman Problem. Our algorithm begins with a sequence-based network alignment and then(More)
In a graph G, a vertex is said to dominate itself and all of its neighbors. For a fixed positive integer k, the k-tuple domination problem is to find a minimum sized vertex subset in a graph such that every vertex in the graph is dominated by at least k vertices in this set. The current paper studies k-tuple domination in graphs from an algorithmic point of(More)
MOTIVATION The global alignment of protein interaction networks is a widely studied problem. It is an important first step in understanding the relationship between the proteins in different species and identifying functional orthologs. Furthermore, it can provide useful insights into the species' evolution. RESULTS We propose a novel algorithm, PISwap,(More)
To monitor an electric power system by placing as few phase measurement units (PMUs) as possible is closely related to the famous vertex cover problem and domination problem in graph theory. A set S is a power dominating set (PDS) of a graph G = (V,E), if every vertex and every edge in the system is observed following the observation rules of power system(More)
Next-generation sequencing (NGS) technologies have revolutionized the field of genetics and are trending toward clinical diagnostics. Exome and targeted sequencing in a disease context represent a major NGS clinical application, considering its utility and cost-effectiveness. With the ongoing discovery of disease-associated genes, various gene panels have(More)
In this paper, we consider a map labeling problem where the points to be labeled are restricted on a line. It is known that the 1d-4P and the 1d-4S unit-square label placement problem and the Slope-4P unit-square label placement problem can both be solved in linear time and the Slope-4S unit-square label placement problem can be solved in quadratic time in(More)