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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Effects of Nicotine Deprivation and Replacement on Bold-Fmri Response to Smoking Cues as a Function of DRD4 Vntr Genotype
INTRODUCTION: Reactivity to smoking cues is an important factor in the motivation to smoke and has been associated with the dopamine receptor 4 variable number tandem repeat (DRD4 exon III…
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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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A Nonlinear Real Arithmetic Fragment
We present a new procedure for testing satisability (over the reals) of a conjunction of polynomial equations.
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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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Yices 2.2
We describe the latest release of Yices, namely, Yices 2.2. We present the tool’s architecture and discuss the algorithms it implements, and we describe recent developments such as support for…
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N-CANDA Data Integration: Anatomy of an Asynchronous Infrastructure for Multi-Site, Multi-Instrument Longitudinal Data Capture
The concepts implemented in N-CANDA’s data collection system helped reduce project start-up time by several months.
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A Tale of Two Solvers: Eager and Lazy Approaches to Bit-Vectors
In this paper we describe the architecture and features of our lazy solver (LBV). We provide a comparative analysis of the eager and lazy approaches, and show how they are…
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Evaluation of Functional Activity and Aggregation Properties of Hemopressin
We tested the hemopressin peptide for CB1 receptor agonist and antagonist activity in cAMP and β-arrestin recruitment assay and found it to be inactive.
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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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Multi-source anomaly detection: using across-domain and across-time peer-group consistency checks
We present robust anomaly detection in multi-dimensional data.
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Methodology Considerations in School Mental Health Research
This paper reviews key steps needed to effectively study SMH research questions. Considerations around research designs, methods for describing effects and outcomes, issues in measurement of process and outcomes, and…