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BMCBI
2010
104views more  BMCBI 2010»
13 years 11 months ago
A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-or
Background: G protein-coupled receptors (GPCRs) represent a family of well-characterized drug targets with significant therapeutic value. Phylogenetic classifications may help to ...
Eelke van der Horst, Julio E. Peironcely, Adriaan ...
BMCBI
2010
133views more  BMCBI 2010»
13 years 11 months ago
Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction
Background: With the rapid expansion of DNA sequencing databases, it is now feasible to identify relevant information from prior sequencing projects and completed genomes and appl...
Lance E. Palmer, Mathäus Dejori, Randall A. B...
BMCBI
2010
93views more  BMCBI 2010»
13 years 11 months ago
HAT: Hypergeometric Analysis of Tiling-arrays with application to promoter-GeneChip data
Background: Tiling-arrays are applicable to multiple types of biological research questions. Due to its advantages (high sensitivity, resolution, unbiased), the technology is ofte...
Erdogan Taskesen, Renee Beekman, Jeroen de Ridder,...
BMCBI
2010
118views more  BMCBI 2010»
13 years 11 months ago
Artificial neural networks for the prediction of peptide drift time in ion mobility mass spectrometry
Background: There is an increasing usage of ion mobility-mass spectrometry (IMMS) in proteomics. IMMS combines the features of ion mobility spectrometry (IMS) and mass spectrometr...
Bing Wang, Steve Valentine, Manolo Plasencia, Srir...
BMCBI
2010
117views more  BMCBI 2010»
13 years 11 months ago
New decoding algorithms for Hidden Markov Models using distance measures on labellings
Background: Existing hidden Markov model decoding algorithms do not focus on approximately identifying the sequence feature boundaries. Results: We give a set of algorithms to com...
Daniel G. Brown 0001, Jakub Truszkowski
BMCBI
2010
106views more  BMCBI 2010»
13 years 11 months ago
Predicting MHC class I epitopes in large datasets
Background: Experimental screening of large sets of peptides with respect to their MHC binding capabilities is still very demanding due to the large number of possible peptide seq...
Kirsten Roomp, Iris Antes, Thomas Lengauer
BMCBI
2010
122views more  BMCBI 2010»
13 years 11 months ago
An overview of the CellML API and its implementation
Background: CellML is an XML based language for representing mathematical models, in a machine-independent form which is suitable for their exchange between different authors, and...
Andrew K. Miller, Justin Marsh, Adam Reeve, Alan G...
BMCBI
2010
57views more  BMCBI 2010»
13 years 11 months ago
Predicting Bevirimat resistance of HIV-1 from genotype
Background: Maturation inhibitors are a new class of antiretroviral drugs. Bevirimat (BVM) was the first substance in this class of inhibitors entering clinical trials. While the ...
Dominik Heider, Jens Verheyen, Daniel Hoffmann
BMCBI
2010
104views more  BMCBI 2010»
13 years 11 months ago
Using simple artificial intelligence methods for predicting amyloidogenesis in antibodies
Background: All polypeptide backbones have the potential to form amyloid fibrils, which are associated with a number of degenerative disorders. However, the likelihood that amyloi...
Maria Pamela C. David, Gisela P. Concepcion, Eduar...
BMCBI
2010
183views more  BMCBI 2010»
13 years 11 months ago
SOPRA: Scaffolding algorithm for paired reads via statistical optimization
Background: High throughput sequencing (HTS) platforms produce gigabases of short read (<100 bp) data per run. While these short reads are adequate for resequencing application...
Adel Dayarian, Todd P. Michael, Anirvan M. Sengupt...