Publications
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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…
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Reducing Human Fatigue in Interactive Evolutionary Computation through Fuzzy Systems and Machine Learning Systems
We describe two approaches to reducing human fatigue in Interactive Evolutionary Computation (IEC). A predictor function is used to estimate the human user’s score, thus reducing the amount of effort…
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Theorizing The Transformed Classroom: A Sociocultural Interpretation Of The Effects Of Audience Response Systems In Higher Education
This paper explores the theoretical framework needed to explain observed effects of classrooms in which instructors use audience response systems. We propose a sociocultural reinterpretation of the networked classroom in…