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BMCBI
2010
95views more  BMCBI 2010»
13 years 5 months ago
Quantifying the relationship between sequence and three-dimensional structure conservation in RNA
Background: In recent years, the number of available RNA structures has rapidly grown reflecting the increased interest on RNA biology. Similarly to the studies carried out two de...
Emidio Capriotti, Marc A. Martí-Renom
BMCBI
2010
161views more  BMCBI 2010»
13 years 5 months ago
GATExplorer: Genomic and Transcriptomic Explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs
Background: Genome-wide expression studies have developed exponentially in recent years as a result of extensive use of microarray technology. However, expression signals are typi...
Alberto Risueño, Celia Fontanillo, Marcel E...
BMCBI
2010
154views more  BMCBI 2010»
13 years 5 months ago
An eScience-Bayes strategy for analyzing omics data
Background: The omics fields promise to revolutionize our understanding of biology and biomedicine. However, their potential is compromised by the challenge to analyze the huge da...
Martin Eklund, Ola Spjuth, Jarl E. S. Wikberg
BMCBI
2010
165views more  BMCBI 2010»
13 years 5 months ago
Bayesian integrated modeling of expression data: a case study on RhoG
Background: DNA microarrays provide an efficient method for measuring activity of genes in parallel and even covering all the known transcripts of an organism on a single array. T...
Rashi Gupta, Dario Greco, Petri Auvinen, Elja Arja...
BMCBI
2010
123views more  BMCBI 2010»
13 years 5 months ago
A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction
Background: Predicting which molecules can bind to a given binding site of a protein with known 3D structure is important to decipher the protein function, and useful in drug desi...
Brice Hoffmann, Mikhail Zaslavskiy, Jean-Philippe ...
BMCBI
2010
112views more  BMCBI 2010»
13 years 5 months ago
In silico fragmentation for computer assisted identification of metabolite mass spectra
Background: Mass spectrometry has become the analytical method of choice in metabolomics research. The identification of unknown compounds is the main bottleneck. In addition to t...
Sebastian Wolf, Stephan Schmidt, Matthias Mül...
BMCBI
2010
132views more  BMCBI 2010»
13 years 5 months ago
Error margin analysis for feature gene extraction
Background: Feature gene extraction is a fundamental issue in microarray-based biomarker discovery. It is normally treated as an optimization problem of finding the best predictiv...
Chi Kin Chow, Hai Long Zhu, Jessica Lacy, Winston ...
BMCBI
2010
107views more  BMCBI 2010»
13 years 5 months ago
Semantic annotation of morphological descriptions: an overall strategy
Background: Large volumes of morphological descriptions of whole organisms have been created as print or electronic text in a human-readable format. Converting the descriptions in...
Hong Cui
BMCBI
2010
139views more  BMCBI 2010»
13 years 5 months ago
RNAstructure: software for RNA secondary structure prediction and analysis
Background: To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of...
Jessica S. Reuter, David H. Mathews
BMCBI
2010
214views more  BMCBI 2010»
13 years 5 months ago
AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number
Background: Clustering the information content of large high-dimensional gene expression datasets has widespread application in "omics" biology. Unfortunately, the under...
Aaron M. Newman, James B. Cooper