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In this paper, we consider the Minimum Independent Dominating Set problem and develop exact exponential algorithms that break the trivial O(2 |V |) bound. A simple O * (√ 3 |V |) time algorithm is developed to solve this problem on general graphs. For sparse graphs, e.g. graphs with degree bounded by 3 and 4, we show that a few new branching techniques can(More)
Searching genomes for RNA secondary structure with computational methods has become an important approach to the annotation of non-coding RNAs. However, due to the lack of efficient algorithms for accurate RNA structure-sequence alignment, computer programs capable of fast and effectively searching genomes for RNA secondary structures have not been(More)
It is well known that TCP does not perform well in networks with large propagation delay and high link loss probability , which are typical in hybrid space-terrestrial networks. Implementing Automatic-Repeat-Request (ARQ) retransmission over satellite links in hybrid networks has been proposed to enhance TCP performance by hiding the link losses from TCP.(More)
Computational alignment of a biopolymer sequence (e.g., an RNA or a protein) to a structure is an effective approach to predict and search for the structure of new sequences. To identify the structure of remote homologs, the structure-sequence alignment has to consider not only sequence similarity, but also spatially conserved conformations caused by(More)
UNLABELLED An important but difficult problem in proteomics is the identification of post-translational modifications (PTMs) in a protein. In general, the process of PTM identification by aligning experimental spectra with theoretical spectra from peptides in a peptide database is very time consuming and may lead to high false positive rate. In this paper,(More)
De novo sequencing and spectral alignment are computationally important for the prediction of new protein peptides via tandem mass spectrometry (MS/MS). Both approaches are established upon the problem of finding the longest antisymmetric path on formulated graphs. The problem is of high computational complexity and the prediction accuracy is compromised(More)