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Article
Open AccessA geographically-diverse collection of 418 human gut microbiome pathway genome databases
Advances in high-throughput sequencing are resha** how we perceive microbial communities inhabiting the human body, with implications for therapeutic interventions. Several large-scale datasets derived from ...
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Article
Open AccessMetabolic pathways for the whole community
A convergence of high-throughput sequencing and computational power is transforming biology into information science. Despite these technological advances, converting bits and bytes of sequence information int...
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Chapter and Conference Paper
Dependable Decentralized Cooperation with the Help of Reliability Estimation
Internet supercomputing aims to solve large partitionable computational problems by using vast numbers of computers. Here we consider the abstract version of the problem, where n processors perform t independent ...
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Article
Open AccessMetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information
A central challenge to understanding the ecological and biogeochemical roles of microorganisms in natural and human engineered ecosystems is the reconstruction of metabolic interaction networks from environmen...
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Article
Open AccessExpanding the boundaries of local similarity analysis
Pairwise comparison of time series data for both local and time-lagged relationships is a computationally challenging problem relevant to many fields of inquiry. The Local Similarity Analysis (LSA) statistic i...
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Chapter and Conference Paper
An Improved Stemming Approach Using HMM for a Highly Inflectional Language
Stemming is a common method for morphological normalization of natural language texts. Modern information retrieval systems rely on such normalization techniques for automatic document processing tasks. High q...
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Chapter and Conference Paper
Self-stabilizing Resource Discovery Algorithm
Massive distributed cooperative computing in networks involves marshaling large collections of network nodes possessing the necessary computational resources. In order for the willing nodes to act in a concert...
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Article
Microbial ecology of expanding oxygen minimum zones
Oxygen minimum zones (OMZs) are oxygen-starved regions of the ocean that are currently expanding owing to the warming of the water column that is induced by gl...
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Chapter and Conference Paper
Robust Network Supercomputing without Centralized Control
Internet supercomputing provides means for harnessing the power of a vast number of interconnected computers. With this come the challenges of marshaling distributed resources and dealing with failures. Tradit...
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Chapter and Conference Paper
Node Discovery in Networks
This paper abstracts the problem of network nodes discovering one another in a network of unknown size using all-to-all gossip. The problem is studied in terms of evolving directed graphs where vertices repres...
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Chapter and Conference Paper
Robust Network Supercomputing with Malicious Processes
Internet supercomputing is becoming a powerful tool for harnessing massive amounts of computational resources. However in typical master-worker settings the reliability of computation crucially depends on the ...
