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Knowledge-based Analysis of Microarray Gene Expression Data By Using Support Vector Machines

by Michael P. S. Brown, William Noble Grundy, David Lin, Nello Cristianini, Charles Walsh Sugnet, Terrence S. Furey, Manuel Ares, Jr., David Haussler , 2000
"... We introduce a method of functionally classifying genes by using gene expression data from DNA microarray hybridization experiments. The method is based on the theory of support vector machines (SVMs). SVMs are considered a supervised computer learning method because they exploit prior knowledge of ..."
Abstract - Cited by 514 (8 self) - Add to MetaCart
of gene function to identify unknown genes of similar function from expression data. SVMs avoid several problems associated with unsupervised clustering methods, such as hierarchical clustering and self-organizing maps. SVMs have many mathematical features that make them attractive for gene expression

Clustering Gene Expression Patterns

by Amir Ben-Dor, Ron Shamir, Zohar Yakhini , 1999
"... Recent advances in biotechnology allow researchers to measure expression levels for thousands of genes simultaneously, across different conditions and over time. Analysis of data produced by such experiments offers potential insight into gene function and regulatory mechanisms. A key step in the ana ..."
Abstract - Cited by 446 (11 self) - Add to MetaCart
Recent advances in biotechnology allow researchers to measure expression levels for thousands of genes simultaneously, across different conditions and over time. Analysis of data produced by such experiments offers potential insight into gene function and regulatory mechanisms. A key step

Functional discovery via a compendium of expression profiles. Cell 102:109

by Timothy R. Hughes, Matthew J. Marton , 2000
"... have been devised to survey gene functions en masse either computationally (Marcotte et al., 1999) or experimentally; among these, highly parallel assays of ..."
Abstract - Cited by 537 (8 self) - Add to MetaCart
have been devised to survey gene functions en masse either computationally (Marcotte et al., 1999) or experimentally; among these, highly parallel assays of

Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes

by Audrey P. Gasch, Paul T. Spellman, Camilla M. Kao, Orna Carmel-Harel, Michael B. Eisen, Gisela Storz, David Botstein, Patrick O. Brown, Pamela A. Silver - Mol. Biol. Cell , 2000
"... this article contains data set material, and is available at www.molbiolcell.org. ..."
Abstract - Cited by 743 (21 self) - Add to MetaCart
this article contains data set material, and is available at www.molbiolcell.org.

Multiple sequence alignment with the Clustal series of programs

by Ramu Chenna, Hideaki Sugawara, Tadashi Koike, Rodrigo Lopez, Toby J. Gibson, Desmond G. Higgins, Julie D. Thompson - Nucleic Acids Res , 2003
"... The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also the ..."
Abstract - Cited by 725 (5 self) - Add to MetaCart
The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also

Support Vector Machine Classification and Validation of Cancer Tissue Samples Using Microarray Expression Data

by Terrence S. Furey, Nello Cristianini, Nigel Duffy, David W. Bednarski, Michèl Schummer, David Haussler , 2000
"... Motivation: DNA microarray experiments generating thousands of gene expression measurements, are being used to gather information from tissue and cell samples regarding gene expression differences that will be useful in diagnosing disease. We have developed a new method to analyse this kind of data ..."
Abstract - Cited by 566 (1 self) - Add to MetaCart
Motivation: DNA microarray experiments generating thousands of gene expression measurements, are being used to gather information from tissue and cell samples regarding gene expression differences that will be useful in diagnosing disease. We have developed a new method to analyse this kind of data

Modeling and simulation of genetic regulatory systems: A literature review

by Hidde De Jong - JOURNAL OF COMPUTATIONAL BIOLOGY , 2002
"... In order to understand the functioning of organisms on the molecular level, we need to know which genes are expressed, when and where in the organism, and to which extent. The regulation of gene expression is achieved through genetic regulatory systems structured by networks of interactions between ..."
Abstract - Cited by 729 (15 self) - Add to MetaCart
In order to understand the functioning of organisms on the molecular level, we need to know which genes are expressed, when and where in the organism, and to which extent. The regulation of gene expression is achieved through genetic regulatory systems structured by networks of interactions between

Studies of transformation of Escherichia coli with plasmids

by Douglas Hanahan - J. Mol. Biol , 1983
"... Factors that affect he probability of genetic transformation f Escherichia coli by plasmids have been evaluated. A set of conditions is described under which about one in every 400 plasmid molecules produces a transformed cell. These conditions include cell growth in medium containing elevated level ..."
Abstract - Cited by 1609 (1 self) - Add to MetaCart
, and that the establishment of a transformation event is neither helped nor hindered significantly by the presence of multiple plasmids. 1. Introduct ion Both gram-posit ive and gram-negative bacteria can take up and stably establish

The transcriptional program of sporulation in budding yeast. Science 282:699–705

by S. Chu, I. Herskowitz, Department Of Biochemistry , 1998
"... Diploid cells of budding yeast produce haploid cells through the developmental program of sporulation, which consists of meiosis and spore morphogenesis. DNA microarrays containing nearly every yeast gene were used to assay changes in gene expression during sporulation. At least seven distinct tempo ..."
Abstract - Cited by 490 (9 self) - Add to MetaCart
of coordinately expressed genes. The temporal expression pattern provided clues to potential functions of hundreds of previously uncharacterized genes, some of which have vertebrate homologs that may function during gametogenesis. All sexually reproducing organisms have a specialized developmental pathway

Empirical Bayes Analysis of a Microarray Experiment

by Bradley Efron, Robert Tibshirani, John D. Storey, Virginia Tusher - Journal of the American Statistical Association , 2001
"... Microarrays are a novel technology that facilitates the simultaneous measurement of thousands of gene expression levels. A typical microarray experiment can produce millions of data points, raising serious problems of data reduction, and simultaneous inference. We consider one such experiment in whi ..."
Abstract - Cited by 488 (19 self) - Add to MetaCart
Microarrays are a novel technology that facilitates the simultaneous measurement of thousands of gene expression levels. A typical microarray experiment can produce millions of data points, raising serious problems of data reduction, and simultaneous inference. We consider one such experiment
Results 1 - 10 of 288,735