BMC Bioinformatics
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Practical application of a Bayesian network approach to poultry epigenetics and stress
BMC Bioinformatics - Tập 23 - Trang 1-16 - 2022
Relationships among genetic or epigenetic features can be explored by learning probabilistic networks and unravelling the dependencies among a set of given genetic/epigenetic features. Bayesian networks (BNs) consist of nodes that represent the variables and arcs that represent the probabilistic relationships between the variables. However, practical guidance on how to make choices among the wide ......
A new protein-ligand binding sites prediction method based on the integration of protein sequence conservation information
BMC Bioinformatics - Tập 12 - Trang 1-7 - 2011
Prediction of protein-ligand binding sites is an important issue for protein function annotation and structure-based drug design. Nowadays, although many computational methods for ligand-binding prediction have been developed, there is still a demanding to improve the prediction accuracy and efficiency. In addition, most of these methods are purely geometry-based, if the prediction methods improve......
Identifying microRNA targets in different gene regions
BMC Bioinformatics - Tập 15 - Trang 1-11 - 2014
Currently available microRNA (miRNA) target prediction algorithms require the presence of a conserved seed match to the 5' end of the miRNA and limit the target sites to the 3' untranslated regions of mRNAs. However, it has been noted that these requirements may be too stringent, leading to a substantial number of missing targets. We have developed TargetS, a novel computational approach for predi......
Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis
BMC Bioinformatics - Tập 11 - Trang 1-11 - 2010
Analysis of data from high-throughput experiments depends on the availability of well-structured data that describe the assayed biomolecules. Procedures for obtaining and organizing such meta-data on genes, transcripts and proteins have been streamlined in many data analysis packages, but are still lacking for metabolites. Chemical identifiers are notoriously incoherent, encompassing a wide range ......
A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes
BMC Bioinformatics - Tập 12 - Trang 1-19 - 2011
Great strides have been made in the effective treatment of HIV-1 with the development of second-generation protease inhibitors (PIs) that are effective against historically multi-PI-resistant HIV-1 variants. Nevertheless, mutation patterns that confer decreasing susceptibility to available PIs continue to arise within the population. Understanding the phenotypic and genotypic patterns responsible ......
Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes
BMC Bioinformatics - Tập 3 - Trang 1-10 - 2002
Gene regulation in eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory elements in the upstream region of eukaryotic genes. The genes are grouped in sets sharing an overrepresented short motif in their upstream sequence. For each set, th......
Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences
BMC Bioinformatics - Tập 10 - Trang 1-24 - 2009
Knowledge of structural class is used by numerous methods for identification of structural/functional characteristics of proteins and could be used for the detection of remote homologues, particularly for chains that share twilight-zone similarity. In contrast to existing sequence-based structural class predictors, which target four major classes and which are designed for high identity sequences,......
BioWord: A sequence manipulation suite for Microsoft Word
BMC Bioinformatics - Tập 13 - Trang 1-7 - 2012
The ability to manipulate, edit and process DNA and protein sequences has rapidly become a necessary skill for practicing biologists across a wide swath of disciplines. In spite of this, most everyday sequence manipulation tools are distributed across several programs and web servers, sometimes requiring installation and typically involving frequent switching between applications. To address this ......
Computing expectation values for RNA motifs using discrete convolutionsAbstract
Background
Computational biologists use Expectation values (E-values) to estimate the number of solutions that can be expected by chance during a database scan. Here we focus on computing Expectation values for RNA motifs defined by single-strand and helix lod-score profiles with variable h... ...
BMC Bioinformatics -
scAnnotatR: framework to accurately classify cell types in single-cell RNA-sequencing data
BMC Bioinformatics - Tập 23 - Trang 1-13 - 2022
Automatic cell type identification is essential to alleviate a key bottleneck in scRNA-seq data analysis. While most existing classification tools show good sensitivity and specificity, they often fail to adequately not-classify cells that are missing in the used reference. Additionally, many tools do not scale to the continuously increasing size of current scRNA-seq datasets. Therefore, additiona......
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