Publications
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The Outcomes of Pathway Database Computations Depend on Pathway Ontology
Different biological notions of pathways are used in different pathway databases. Those pathway ontologies significantly impact pathway computations.
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Learning Theories And Education: Toward A Decade Of Synergy
Our goal is to provide an overview of important aspects of human learning that are particularly relevant to educators.
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MetaCyc: a multiorganism database of metabolic pathways and enzymes
MetaCyc contains metabolic pathways, enzymatic reactions, enzymes, chemical compounds, genes and review-level comments.
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Escherichia coli K-12: a cooperatively developed annotation snapshot 2005
The goal of this group project has been to coordinate and bring up-to-date information on all genes of Escherichia coli K-12. Annotation of the genome of an organism entails identification…
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The Pathway Tools Cellular Overview Diagram and Omics Viewer
Pathway Tools supports interrogation and exploration of cellular biochemical networks through the overview diagram and a software component called the Omics Viewer.
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Evidence supporting predicted metabolic pathways for Vibrio cholerae: gene expression data and clinical tests
Using the completed V.cholerae genome sequence and PathoLogic software, we created VchoCyc, a pathway-genome database that predicted 171 likely metabolic pathways in the bacterium.
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Advanced Patterns and Matches in Link Analysis
The Link Analysis Workbench (LAW) is a tool for detecting and monitoring situations of interest using inexact matching of graphical patterns.
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Washington State Achievers Scholarship Program Case Study: Final Report
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Creating Fungal Pathway/Genome Databases Using Pathway Tools
The Pathway Tools software allows a group of scientists to create, update, and publish on the Web an evolving knowledge resource describing the genome and biochemical networks of the organism.
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Detecting Action Items in Multi-party Meetings: Annotation and Initial Experiments
This paper presents the results of initial investigation and experiments into automatic action item detection from transcripts of multi-party human-human meetings.
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One-To-One Technology-Enhanced Learning: An Opportunity For Global Research Collaboration
We see that ready-to-hand access creates the potential for a new phase in the evolution of technology-enhanced learning (TEL), characterized by “seamless learning spaces” and marked by continuity of the…
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Predicting State Test Scores Better With Intelligent Tutoring Systems: Developing Metrics To Measure Assistance Required
Our approach is to use data that the system collected through a year to tracking student learning and thus estimate their performance on a high-stake state test (MCAS) at the…