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- 1From: BMC Bioinformatics. (Vol. 13) Peer-ReviewedBackground With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results...
- 2From: BMC Bioinformatics. (Vol. 13, Issue Suppl 1) Peer-ReviewedBackground The RDF triple provides a simple linguistic means of describing limitless types of information. Triples can be flexibly combined into a unified data source we call a semantic model. Semantic models open new...
- 3From: BMC Bioinformatics. (Vol. 13) Peer-ReviewedBackground Cancers, a group of multifactorial complex diseases, are generally caused by mutation of multiple genes or dysregulation of pathways. Identifying biomarkers that can characterize cancers would help to...
- 4From: BMC Bioinformatics. (Vol. 13, Issue 1) Peer-ReviewedBackground Analyzing regions of the genome where genetic variation is free from the confounding effects of natural selection is essential for many population genetic studies. Several recent studies in humans have...
- 5From: BMC Bioinformatics. (Vol. 13, Issue 1) Peer-ReviewedBackground One of the crucial steps in regulation of gene expression is the binding of transcription factor(s) to specific DNA sequences. Knowledge of the binding affinity and specificity at a structural level...
- 6From: BMC Bioinformatics. (Vol. 13, Issue 1) Peer-ReviewedBackground Self-incompatibility (SI) is a biological mechanism to avoid inbreeding in allogamous plants. In grasses, this mechanism is controlled by a two-locus system (S-Z). Calculation of male and female gamete...
- 7From: BMC Bioinformatics. (Vol. 13, Issue 1) Peer-ReviewedBackground To understand the roles they play in complex diseases, genes need to be investigated in the networks they are involved in. Integration of gene expression and network data is a promising approach to...
- 8From: BMC Bioinformatics. (Vol. 13, Issue 1) Peer-ReviewedBackground The generation of multiple sequence alignments (MSAs) is a crucial step for many bioinformatic analyses. Thus improving MSA accuracy and identifying potential errors in MSAs is important for a wide range...
- 9From: BMC Bioinformatics. (Vol. 13, Issue 1) Peer-ReviewedBackground Currently, there is no open-source, cross-platform and scalable framework for coalescent analysis in population genetics. There is no scalable GUI based user application either. Such a framework and...
- 10From: BMC Bioinformatics. (Vol. 13, Issue 1) Peer-ReviewedBackground RNA secondary structure prediction, or folding, is a classic problem in bioinformatics: given a sequence of nucleotides, the aim is to predict the base pairs formed in its three dimensional conformation....
- 11From: BMC Bioinformatics. (Vol. 13, Issue 1) Peer-ReviewedBackground While the genetics of diploid inheritance are well studied and software for linkage mapping, haplotyping and QTL analysis are available, for tetraploids the available tools are limited. In order to develop...
- 12From: BMC Bioinformatics. (Vol. 13, Issue 1) Peer-ReviewedBackground Next generation sequencing technologies often require numerous primer designs that require good target coverage that can be financially costly. We aimed to develop a system that would implement primer...
- 13From: BMC Bioinformatics. (Vol. 13, Issue 1) Peer-ReviewedBackground Semantic similarity measures estimate the similarity between concepts, and play an important role in many text processing tasks. Approaches to semantic similarity in the biomedical domain can be roughly...
- 14From: BMC Bioinformatics. (Vol. 13, Issue 1) Peer-ReviewedBackground Evolution of splice sites is a well-known phenomenon that results in transcript diversity during human evolution. Many novel splice sites are derived from repetitive elements and may not contribute to...
- 15From: BMC Bioinformatics. (Vol. 13, Issue 1) Peer-ReviewedBackground There has been a long-standing need in biomedical research for a method that quantifies the normally mixed composition of leukocytes beyond what is possible by simple histological or flow cytometric...
- 16From: BMC Bioinformatics. (Vol. 13, Issue 1) Peer-ReviewedBackground Effective quality assessment is an important part of any high-throughput flow cytometry data analysis pipeline, especially when considering the complex designs of the typical flow experiments applied in...
- 17From: BMC Bioinformatics. (Vol. 13, Issue 1) Peer-ReviewedBackground For gene expression or gene association studies with a large number of hypotheses the number of measurements per marker in a conventional single-stage design is often low due to limited resources....
- 18From: BMC Bioinformatics. (Vol. 13, Issue 1) Peer-ReviewedBackground Stratification of patients according to their clinical prognosis is a desirable goal in cancer treatment in order to achieve a better personalized medicine. Reliable predictions on the basis of gene...
- 19From: BMC Bioinformatics. (Vol. 13, Issue 1) Peer-ReviewedBackground The lack of a uniform way for qualitative and quantitative evaluation of vaccine candidates under development led us to set up a standardized scheme for vaccine efficacy and safety evaluation. We developed...
- 20From: BMC Bioinformatics. (Vol. 13, Issue 1) Peer-ReviewedBackground Because biological networks exhibit a high-degree of robustness, a systemic understanding of their architecture and function requires an appraisal of the network design principles that confer robustness....