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BACKGROUND DNA copy number variation (CNV) has been recognized as an important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used for CNV detection, but the microarray platform has a number of inherent limitations. RESULTS Here, we describe a method to detect copy number variation using shotgun sequencing,(More)
The alignment of sequencing reads against a protein reference database is a major computational bottleneck in metagenomics and data-intensive evolutionary projects. Although recent tools offer improved performance over the gold standard BLASTX, they exhibit only a modest speedup or low sensitivity. We introduce DIAMOND, an open-source algorithm based on(More)
SUMMARY In the context of metagenomics, we introduce a new approach to protein database search called PAUDA, which runs ~10,000 times faster than BLASTX, while achieving about one-third of the assignment rate of reads to KEGG orthology groups, and producing gene and taxon abundance profiles that are highly correlated to those obtained with BLASTX. PAUDA(More)
– Expected to graduate with a Master of Science (MS) degree in Decem-ber 2014. OSDI 14. Brief description: In this project, we are modyfing the distributed version of MySQL database (aka. MySQL cluster) in both design and implementation to support both ACID and BASE semantics in a single database. In the result system, we gain the good performance of BASE(More)
Modeling peer-to-peer (P2P) networks is a challenge for P2P researchers. In this paper, we provide a detailed analysis of large-scale hybrid P2P overlay network topology, using Gnutella as a case study. First, we reexamine the power-law distributions of the Gnutella network discovered by previous researchers. Our results show that the current Gnutella(More)
This paper describes the design, implementation, and evaluation of Callas, a distributed database system that offers to unmodified, transactional ACID applications the opportunity to achieve a level of performance that can currently only be reached by rewriting all or part of the application in a BASE/NoSQL Style. The key to combining performance and ease(More)
— During the past few years, unstructured peer-to-peer (P2P) file-sharing systems have witnessed a significant increase in popularity. However, there lacks a systematic study on graph properties of the overlay topology. In this paper, we use accurate snapshots of the Gnutella overlay that span over roughly three years to explore changes in graph properties(More)
Microorganisms act both as drivers and indicators of perturbations in the marine environment. In an effort to establish baselines to predict the response of marine habitats to environmental change, here we report a broad survey of microbial diversity across the Indian Ocean, including the first microbial samples collected in the pristine lagoon of Salomon(More)