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Faulty components in a network need to be localized and repaired to sustain the health of the network. In this paper, we propose a novel approach that carefully combines active and passive measurements to localize faults in wireless sensor networks. More specifically, we formulate a problem of optimal sequential testing guided by end-to-end data. This(More)
Motifs are patterns found in biological sequences that are vital for understanding gene function, human disease, drug design, etc. They are helpful in finding transcriptional regulatory elements, transcription factor binding sites, and so on. As a result, the problem of identifying motifs is very crucial in biology. Many facets of the motif search problem(More)
Detection of rare events happening in a set of DNA/protein sequences could lead to new biological discoveries. One kind of such rare events is the presence of patterns called motifs in DNA/protein sequences. Finding motifs is a challenging problem since the general version of motif search has been proven to be intractable. Motifs discovery is an important(More)
MOTIVATION Exact-match overlap graphs have been broadly used in the context of DNA assembly and the shortest super string problem where the number of strings n ranges from thousands to billions. The length ℓ of the strings is from 25 to 1000, depending on the DNA sequencing technologies. However, many DNA assemblers using overlap graphs suffer from the need(More)
Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories - based on the data structures which they employ. The first class uses an overlap/string graph and the second type uses a de Bruijn graph. However with the(More)
Smart grid is envisioned to incorporate local distributed power generation for better efficiency and flexibility. Distributed generation, when not used carefully, however, may compromise the stability of the grid. Recently, researchers have proposed innovative architectures (e.g., microgrid, LoCal grid) that virtualize a local generator as a constant load,(More)
In this paper, we consider Multiple-Sink Data Collection Problem in wireless sensor networks, where a large amount of data from sensor nodes need to be transmitted to one of multiple sinks. We design an approximation algorithm to minimize the latency of data collection schedule and show that it gives a constant-factor performance guarantee. We also present(More)
The discovery of patterns in DNA, RNA, and protein sequences has led to the solution of many vital biological problems. For instance, the identification of patterns in nucleic acid sequences has resulted in the determination of open reading frames, identification of promoter elements of genes, identification of intron/exon splicing sites, identification of(More)
Sequence assembly from short reads is an important problem in biology. It is known that solving the sequence assembly problem exactly on a bi-directed de Bruijn graph or a string graph is intractable. However, finding a shortest double stranded DNA string (SDDNA) containing all the k-long words in the reads seems to be a good heuristic to get close to the(More)
Protein/Peptide microarrays are rapidly gaining momentum in the diagnosis of cancer. High-density and high-throughput peptide arrays are being extensively used to detect tumor biomarkers, examine kinase activity, identify antibodies having low serum titers and locate antibody signatures. Improving the yield of microarray fabrication involves solving a hard(More)