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BMCBI
2004
98views more  BMCBI 2004»
8 years 11 months ago
Incidence of "quasi-ditags" in catalogs generated by Serial Analysis of Gene Expression (SAGE)
Background: Serial Analysis of Gene Expression (SAGE) is a functional genomic technique that quantitatively analyzes the cellular transcriptome. The analysis of SAGE libraries rel...
Sergey V. Anisimov, Alexei A. Sharov
BMCBI
2004
97views more  BMCBI 2004»
8 years 11 months ago
Calibration and assessment of channel-specific biases in microarray data with extended dynamical range
Background: Non-linearities in observed log-ratios of gene expressions, also known as intensity dependent log-ratios, can often be accounted for by global biases in the two channe...
Henrik Bengtsson, Göran Jönsson, Johan V...
BMCBI
2004
102views more  BMCBI 2004»
8 years 11 months ago
Detection of transposable elements by their compositional bias
Background: Transposable elements (TE) are mobile genetic entities present in nearly all genomes. Previous work has shown that TEs tend to have a different nucleotide composition ...
Olivier Andrieu, Anna-Sophie Fiston, Dominique Anx...
BMCBI
2004
115views more  BMCBI 2004»
8 years 11 months ago
Quantifying the relationship between co-expression, co-regulation and gene function
Background: It is thought that genes with similar patterns of mRNA expression and genes with similar functions are likely to be regulated via the same mechanisms. It has been diff...
Dominic J. Allocco, Isaac S. Kohane, Atul J. Butte
BMCBI
2004
208views more  BMCBI 2004»
8 years 11 months ago
Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures
Background: Hidden Markov Models (HMMs) have proven very useful in computational biology for such applications as sequence pattern matching, gene-finding, and structure prediction...
Vadim Alexandrov, Mark Gerstein
BMCBI
2004
265views more  BMCBI 2004»
8 years 11 months ago
ASAView: Database and tool for solvent accessibility representation in proteins
Background: Accessible surface area (ASA) or solvent accessibility of amino acids in a protein has important implications. Knowledge of surface residues helps in locating potentia...
Shandar Ahmad, M. Michael Gromiha, Hamed Fawareh, ...
BMCBI
2004
159views more  BMCBI 2004»
8 years 11 months ago
Extractor for ESI quadrupole TOF tandem MS data enabled for high throughput batch processing
Background: Mass spectrometry based proteomics result in huge amounts of data that has to be processed in real time in order to efficiently feed identification algorithms and to e...
Andreas M. Boehm, Robert P. Galvin, Albert Sickman...
BMCBI
2004
323views more  BMCBI 2004»
8 years 11 months ago
Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks
Background: Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true ...
David Adalsteinsson, David McMillen, Timothy C. El...
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