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James W. Fickett

Bio: James W. Fickett is an academic researcher from Los Alamos National Laboratory. The author has contributed to research in topics: Gene & Genome. The author has an hindex of 20, co-authored 33 publications receiving 4061 citations.

Papers
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Journal ArticleDOI
TL;DR: The test has been thoroughly proven on 400,000 bases of sequence data: it misclassifies 5% of the regions tested and gives an answer of "No Opinion" one fifth of the time.
Abstract: We give a test for protein coding regions which is based on simple and universal differences between protein-coding and noncoding DNA. The test is simple enough to use without a computer and is completely objective. The test has been thoroughly proven on 400,000 bases of sequence data: it misclassifies 5% of the regions tested and gives an answer of "No Opinion" one fifth of the time. We predict some new coding and noncoding regions in published sequences.

875 citations

Journal ArticleDOI
TL;DR: This work found that 98% of experimentally defined sequence-specific binding sites of skeletal-muscle-specific transcription factors are confined to the 19% of human sequences that are most conserved in the orthologous rodent sequences, and found that in using this restriction, the binding specificities of all three major muscle- specific transcription factors can be computationally identified.
Abstract: Elucidating the human transcriptional regulatory network is a challenge of the post-genomic era. Technical progress so far is impressive, including detailed understanding of regulatory mechanisms for at least a few genes in multicellular organisms, rapid and precise localization of regulatory regions within extensive regions of DNA by means of cross-species comparison, and de novo determination of transcription-factor binding specificities from large-scale yeast expression data. Here we address two problems involved in extending these results to the human genome: first, it has been unclear how many model organism genomes will be needed to delineate most regulatory regions; and second, the discovery of transcription-factor binding sites (response elements) from expression data has not yet been generalized from single-celled organisms to multicellular organisms. We found that 98% (74/75) of experimentally defined sequence-specific binding sites of skeletal-muscle-specific transcription factors are confined to the 19% of human sequences that are most conserved in the orthologous rodent sequences. Also we found that in using this restriction, the binding specificities of all three major muscle-specific transcription factors (MYF, SRF and MEF2) can be computationally identified.

500 citations

Journal ArticleDOI
TL;DR: A model is generated with predictive capability for identifying muscle-specific regulatory modules that bind to regulatory elements to control gene expression and promises to be easily modified to take advantage of the elucidation of additional factors, cooperation rules, and spacing constraints.

407 citations

Journal ArticleDOI
TL;DR: This paper reviews and synthesizes the underlying coding measures from published algorithms and concludes that a very simple and obvious measure--counting oligomers--is more effective than any of the more sophisticated measures.
Abstract: A number of methods for recognizing protein coding genes in DNA sequence have been published over the last 13 years, and new, more comprehensive algorithms, drawing on the repertoire of existing techniques, continue to be developed. To optimize continued development, it is valuable to systematically review and evaluate published techniques. At the core of most gene recognition algorithms is one or more coding measures--functions which produce, given any sample window of sequence, a number or vector intended to measure the degree to which a sample sequence resembles a window of 'typical' exonic DNA. In this paper we review and synthesize the underlying coding measures from published algorithms. A standardized benchmark is described, and each of the measures is evaluated according to this benchmark. Our main conclusion is that a very simple and obvious measure--counting oligomers--is more effective than any of the more sophisticated measures. Different measures contain different information. However there is a great deal of redundancy in the current suite of measures. We show that in future development of gene recognition algorithms, attention can probably be limited to six of the twenty or so measures proposed to date.

407 citations

Journal ArticleDOI
TL;DR: The GenBank Genetic Sequence Data Bank contains over 5700 entries for DNA and RNA sequences that have been reported since 1967, and the forms in which the database is distributed.
Abstract: The GenBank Genetic Sequence Data Bank contains over 5700 entries for DNA and RNA sequences that have been reported since 1967. This paper briefly describes the contents of the database, the forms in which the database is distributed, and the services we offer to scientists who use the GenBank database.

363 citations


Cited by
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Journal ArticleDOI
Eric S. Lander1, Lauren Linton1, Bruce W. Birren1, Chad Nusbaum1  +245 moreInstitutions (29)
15 Feb 2001-Nature
TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
Abstract: The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

22,269 citations

Journal ArticleDOI
TL;DR: A group of programs that will interact with each other has been developed for the Digital Equipment Corporation VAX computer using the VMS operating system.
Abstract: The University of Wisconsin Genetics Computer Group (UWGCG) has been organized to develop computational tools for the analysis and publication of biological sequence data. A group of programs that will interact with each other has been developed for the Digital Equipment Corporation VAX computer using the VMS operating system. The programs available and the conditions for transfer are described.

14,575 citations

Journal ArticleDOI
Robert H. Waterston1, Kerstin Lindblad-Toh2, Ewan Birney, Jane Rogers3  +219 moreInstitutions (26)
05 Dec 2002-Nature
TL;DR: The results of an international collaboration to produce a high-quality draft sequence of the mouse genome are reported and an initial comparative analysis of the Mouse and human genomes is presented, describing some of the insights that can be gleaned from the two sequences.
Abstract: The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

6,643 citations

01 Aug 2000
TL;DR: Assessment of medical technology in the context of commercialization with Bioentrepreneur course, which addresses many issues unique to biomedical products.
Abstract: BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

4,833 citations

Journal ArticleDOI
TL;DR: This work reviews a general methodology for model-based clustering that provides a principled statistical approach to important practical questions that arise in cluster analysis, such as how many clusters are there, which clustering method should be used, and how should outliers be handled.
Abstract: Cluster analysis is the automated search for groups of related observations in a dataset. Most clustering done in practice is based largely on heuristic but intuitively reasonable procedures, and most clustering methods available in commercial software are also of this type. However, there is little systematic guidance associated with these methods for solving important practical questions that arise in cluster analysis, such as how many clusters are there, which clustering method should be used, and how should outliers be handled. We review a general methodology for model-based clustering that provides a principled statistical approach to these issues. We also show that this can be useful for other problems in multivariate analysis, such as discriminant analysis and multivariate density estimation. We give examples from medical diagnosis, minefield detection, cluster recovery from noisy data, and spatial density estimation. Finally, we mention limitations of the methodology and discuss recent development...

4,123 citations