Artificial intelligence publications
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Optimal Metabolic Route Search Based on Atom Mappings
We present the algorithm used in the new RouteSearch tool within the Pathway Tools software.
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Metabolic Pathways for the Whole Community
Here we adopt the MetaPathways annotation and analysis pipeline and Pathway Tools to construct environmental pathway/genome databases that describe microbial community metabolism using MetaCyc.
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An Operational Semantics for the Goal Life-Cycle in BDI Agents
A fundamental feature of intelligent agents is their ability to deliberate over their goals. Operating in an environment that may change in unpredictable ways, an agent needs to regularly evaluate…
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The EcoCyc Database
This review outlines the data content of EcoCyc and of the procedures by which this content is generated.
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Curation Accuracy of Model Organism Databases
We assessed the accuracy of EcoCyc and CGD by manually selecting curated assertions within randomly chosen EcoCyc and CGD gene pages and by then validating that the data found in…
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A Framework for Application of Metabolic Modeling in Yeast to Predict the Effects of Nssnv in Human Orthologs
Here we present the next step in the workflow toward using yeast metabolic modeling to predict human metabolic behavior resulting from nsSNV.
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A Genome-Scale Metabolic Flux Model of Escherichia coli K-12 Derived from the EcoCyc Database
We present EcoCyc–18.0–GEM, a genome-scale model of the E. coli K–12 MG1655 metabolic network.
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An Autoencoder with Bilingual Sparse Features for Improved Statistical Machine Translation
We propose a natural autoencoder that maps all the discrete and overlapping sparse features for each SCFG rule into a continuous vector, so that the information encoded in sparse feature…
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Addition of Escherichia coli K-12 Growth Observation and Gene Essentiality Data to the Ecocyc Database
We have integrated data on the growth or nongrowth of E. coli K-12 obtained from published observations using a variety of individual media and from high-throughput phenotype microarrays into the…
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Evaluating Multimedia Features and Fusion for Example-Based Event Detection
To study the value of multimedia features and fusion for representing and learning events from a set of example video clips, we created SESAME, a system for video SEarch with…
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Addition of Escherichia coli K–12 Growth-Observation and Gene Essentiality Data to the EcoCyc database
We have integrated data on the growth or nongrowth of E. coli K-12 obtained from published observations using a variety of individual media and from high-throughput phenotype microarrays into the EcoCyc database.
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PortEco: A Resource for Exploring Bacterial Biology through High-Throughput Data and Analysis Tools
PortEco ( http://porteco.org) aims to collect, curate and provide data and analysis tools to support basic biological research in Escherichia coli.