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Drug voyager: a computational platform for exploring unintended drug action
Abstract Background The dominant paradigm in understanding drug action focuses on the intended therapeutic effects and frequent... -
Ambiguity of non-systematic chemical identifiers within and between small-mol...
Background A wide range of chemical compound databases are currently available for pharmaceutical research. To retrieve compound information, including structures, researchers... -
Assessment of k-mer spectrum applicability for metagenomic dissimilarity anal...
Background A rapidly increasing flow of genomic data requires the development of efficient methods for obtaining its compact representation. Feature extraction facilitates... -
"A scalability study of phylogenetic network inference methods using empirica...
Background Branching events in phylogenetic trees reflect bifurcating and/or multifurcating speciation and splitting events. In the presence of gene flow, a phylogeny cannot be... -
A multiple testing procedure for multi-dimensional pairwise comparisons with ...
Background Often researchers are interested in comparing multiple experimental groups (e.g. tumor size) with a reference group (e.g. normal tissue) on the basis of thousands of... -
Joint use of over- and under-sampling techniques and cross-validation for the...
Background Prediction models are used in clinical research to develop rules that can be used to accurately predict the outcome of the patients based on some of their... -
Bioinformatics identification of new targets for improving low temperature st...
Background Phenotypic studies in Triticeae have shown that low temperature-induced protective mechanisms are developmentally regulated and involve dynamic acclimation processes.... -
A decision analysis model for KEGG pathway analysis
Background The knowledge base-driven pathway analysis is becoming the first choice for many investigators, in that it not only can reduce the complexity of functional analysis... -
IPED: a highly efficient denoising tool for Illumina MiSeq Paired-end 16S rRN...
Background The development of high-throughput sequencing technologies has revolutionized the field of microbial ecology via the sequencing of phylogenetic marker genes (e.g. 16S... -
Leveraging 3D chemical similarity, target and phenotypic data in the identifi...
Background Drug-target identification is crucial to discover novel applications for existing drugs and provide more insights about mechanisms of biological actions, such as... -
Badapple: promiscuity patterns from noisy evidence.
Background Bioassay data analysis continues to be an essential, routine, yet challenging task in modern drug discovery and chemical biology research. The challenge is to infer... -
Addressing inaccuracies in BLOSUM computation improves homology search perfor...
Background BLOSUM matrices belong to the most commonly used substitution matrix series for protein homology search and sequence alignments since their publication in 1992. In...
