Duncan P. Brown

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Function prediction by homology is widely used to provide preliminary functional annotations for genes for which experimental evidence of function is unavailable or limited. This approach has been shown to be prone to systematic error, including percolation of annotation errors through sequence databases. Phylogenomic analysis avoids these errors in(More)
The Berkeley Phylogenomics Group presents PhyloFacts, a structural phylogenomic encyclopedia containing almost 10,000 'books' for protein families and domains, with pre-calculated structural, functional and evolutionary analyses. PhyloFacts enables biologists to avoid the systematic errors associated with function prediction by homology through the(More)
BACKGROUND Function prediction by transfer of annotation from the top database hit in a homology search has been shown to be prone to systematic error. Phylogenomic analysis reduces these errors by inferring protein function within the evolutionary context of the entire family. However, accuracy of function prediction for multi-domain proteins depends on(More)
The limitations of homology-based methods for prediction of protein molecular function are well known; differences in domain structure, gene duplication events and errors in existing database annotations complicate this process. In this paper we present a method to detect and model protein subfamilies, which can be used in high-throughput, genome-scale(More)
MOTIVATION Automatic clustering of protein sequences is an important problem in computational biology. The recent explosion in genome sequences has given biological researchers a vast number of novel protein sequences. However, the majority of these sequences have no experimental evidence for their molecular function in the cell, and the responsibility for(More)
Background: Function prediction by transfer of annotation from the top database hit in a homology search has been shown to be prone to systematic error. Phylogenomic analysis reduces these errors by inferring protein function within the evolutionary context of the entire family. However, accuracy of function prediction for multi-domain proteins depends on(More)
Serial auditory brainstem (ABR) and middle-latency (AMR) response recordings were made for 12 children (8 male, 4 female) ranging in age from 2 weeks to 10 years. A total of 40 ABR and 32 AMR assessments were carried out at bedside in varied hospital environments, including a pediatric intensive care unit (ICU), a neonatal ICU and an operating room.(More)
Four chimpanzees, 4 rhesus monkeys, and 11 children aged 4-9 yr were assessed under comparable conditions for their ability to make use of colors as symbols of quantity. One particular color represented the quantifier "all"; another represented "some"; another represented "one"; a fourth represented "none." These arbitrarily chosen colors retained their(More)
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