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BMCBI
2007
133views more  BMCBI 2007»
15 years 7 months ago
MATLIGN: a motif clustering, comparison and matching tool
Background: Sequence motifs representing transcription factor binding sites (TFBS) are commonly encoded as position frequency matrices (PFM) or degenerate consensus sequences (CS)...
Matti Kankainen, Ari Löytynoja
BMCBI
2007
134views more  BMCBI 2007»
15 years 7 months ago
Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign
Background: Joint alignment and secondary structure prediction of two RNA sequences can significantly improve the accuracy of the structural predictions. Methods addressing this p...
Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathe...
BMCBI
2007
94views more  BMCBI 2007»
15 years 7 months ago
A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays
Background: Affymetrix SNP arrays can interrogate thousands of SNPs at the same time. This allows us to look at the genomic content of cancer cells and to investigate the underlyi...
Philippe Lamy, Claus L. Andersen, Lars Dyrskjot, N...
BMCBI
2007
176views more  BMCBI 2007»
15 years 7 months ago
Correlation-maximizing surrogate gene space for visual mining of gene expression patterns in developing barley endosperm tissue
Background: Micro- and macroarray technologies help acquire thousands of gene expression patterns covering important biological processes during plant ontogeny. Particularly, fait...
Marc Strickert, Nese Sreenivasulu, Björn Usad...
BMCBI
2008
98views more  BMCBI 2008»
15 years 7 months ago
Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios
Background: Illumina Infinium whole genome genotyping (WGG) arrays are increasingly being applied in cancer genomics to study gene copy number alterations and allele-specific aber...
Johan Staaf, Johan Vallon-Christersson, David Lind...
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