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BMCBI
2008
104views more  BMCBI 2008»
13 years 10 months ago
ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS)
Background: Genome survey sequences (GSS) offer a preliminary global view of a genome since, unlike ESTs, they cover coding as well as non-coding DNA and include repetitive region...
Thomas D. Otto, Leonardo H. F. Gomes, Marcelo Alve...
BMCBI
2008
101views more  BMCBI 2008»
13 years 10 months ago
Compressing DNA sequence databases with coil
Background: Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious...
W. Timothy J. White, Michael D. Hendy
BMCBI
2008
102views more  BMCBI 2008»
13 years 10 months ago
Response projected clustering for direct association with physiological and clinical response data
Background: Microarray gene expression data are often analyzed together with corresponding physiological response and clinical metadata of biological subjects, e.g. patients'...
Sung-Gon Yi, Taesung Park, Jae K. Lee
BMCBI
2008
95views more  BMCBI 2008»
13 years 10 months ago
Mining protein networks for synthetic genetic interactions
Background: The local connectivity and global position of a protein in a protein interaction network are known to correlate with some of its functional properties, including its e...
Sri R. Paladugu, Shan Zhao, Animesh Ray, Alpan Rav...
BMCBI
2008
74views more  BMCBI 2008»
13 years 10 months ago
Conditional variable importance for random forests
Carolin Strobl, Anne-Laure Boulesteix, Thomas Knei...
BMCBI
2008
163views more  BMCBI 2008»
13 years 10 months ago
The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology
Background: High-throughput genome biological experiments yield large and multifaceted datasets that require flexible and user-friendly analysis tools to facilitate their interpre...
Frédéric Chalmel, Michael Primig
BMCBI
2008
179views more  BMCBI 2008»
13 years 10 months ago
Bayesian modeling of recombination events in bacterial populations
Background: We consider the discovery of recombinant segments jointly with their origins within multilocus DNA sequences from bacteria representing heterogeneous populations of fa...
Pekka Marttinen, Adam Baldwin, William P. Hanage, ...
BMCBI
2008
170views more  BMCBI 2008»
13 years 10 months ago
Implementing EM and Viterbi algorithms for Hidden Markov Model in linear memory
Background: The Baum-Welch learning procedure for Hidden Markov Models (HMMs) provides a powerful tool for tailoring HMM topologies to data for use in knowledge discovery and clus...
Alexander G. Churbanov, Stephen Winters-Hilt
BMCBI
2008
178views more  BMCBI 2008»
13 years 10 months ago
A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic ana
Background: Protein remote homology detection and fold recognition are central problems in bioinformatics. Currently, discriminative methods based on support vector machine (SVM) ...
Bin Liu, Xiaolong Wang, Lei Lin, Qiwen Dong, Xuan ...