Publications
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Identifying Candidate Genes Using The BioWarehouse: A Case Study
The BioWarehouse is an open source data warehousing environment focused on supporting bioinformatics databases (DBs). BioWarehouse integrates public source DBs such as Swiss-Prot and GenBank into a unified normalized schema…
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The complete genome sequence of Francisella tularensis, the causative agent of tularemia
We report the complete genome sequence of a highly virulent isolate of F. tularensis. The sequence uncovers previously uncharacterized genes encoding type IV pili, a surface polysaccharide and iron-acquisition systems.
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A Collaborative Framework for Managing Uncertainty and Cognitive Bias
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Expansion of the BioCyc Collection of Pathway/Genome Databases to 160 Genomes
This paper discusses the computational methodology by which the BioCyc collection has been expanded, and presents an aggregate analysis of the collection that includes the range of number of pathways…
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Online Query Relaxation via Bayesian Causal Structures Discovery
We introduce a novel algorithm, TOQR, for relaxing failed queries over databases, that is, over-constrained DNF queries that return an empty result.
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Querying and Computing with BioCyc Databases
We describe multiple methods for accessing and querying the complex and integrated cellular data in the BioCyc family of databases.
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Morphology induction from term clusters
We address the problem of learning a morphological automaton directly from a monolingual text corpus without recourse to additional resources.
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Modeling Prosodic Feature Sequences for Speaker Recognition
We describe a novel approach to modeling idiosyncratic prosodic behavior for automatic speaker recognition.
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Liquid-phase deposition of single-phase alpha-copper-indiumdiselenide,
Based on the first complete CuInSe phase diagram, which was recently established, we propose a new method for making single-phase copper-indium-diselenide (CuInSe2) films for high-specific-power photovoltaic applications: liquid-phase deposition.
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The ICSI-SRI-UW Metadata Extraction System
We describe a state-of-the-art system for automatic detection of "metadata" in both broadcast news and spontaneous telephone conversations, developed as part of the DARPA EARS Rich Transcription program.
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A Wizard of Oz framework for collecting spoken human-computer dialogs
This paper describes a data collection process aimed at gathering human-computer dialogs in high-stress or “busy” domains where the user is concentrating on tasks other than the conversation, for example,…
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SVM Modeling of “SNERF-Grams” for Speaker Recognition
We describe a new approach to modeling idiosyncratic prosodic behavior for automatic speaker recognition. The approach computes prosodic features by syllable, and models the syllable-feature sequences using support vector machines…