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Research Article
Personalizing treatment regimes based on gene expression profiles of individual tumors will facilitate management of cancer. Although many methods have been developed to identify pathways perturbed in tumors, ...
BMC Bioinformatics 2017 18:317
Published on: 26 June 2017
Software
Given the development of high-throughput experimental techniques, an increasing number of whole genome transcription profiling time series data sets, with good temporal resolution, are becoming available to re...
BMC Bioinformatics 2017 18:316
Published on: 26 June 2017
Software
Systems Biology Markup Language (SBML) is the standard model representation and description language in systems biology. Enriching and analysing systems biology models by integrating the multitude of available...
BMC Bioinformatics 2017 18:314
Published on: 24 June 2017
Software
The multiple sequence alignment (MSA) is a classic and powerful technique for sequence analysis in bioinformatics. With the rapid growth of biological datasets, MSA parallelization becomes necessary to keep it...
BMC Bioinformatics 2017 18:315
Published on: 24 June 2017
Methodology Article
Identifying disease correlated features early before large number of molecules are impacted by disease progression with significant abundance change is very advantageous to biologists for developing early dise...
BMC Bioinformatics 2017 18:313
Published on: 23 June 2017
Correspondence
Bioinformatics has multitudinous identities, organisational alignments and disciplinary links. This variety allows bioinformaticians and bioinformatic work to contribute to much (if not most) of life science r...
BMC Bioinformatics 2017 18:311
Published on: 21 June 2017
Methodology Article
Transcriptomic approaches (microarray and RNA-seq) have been a tremendous advance for molecular science in all disciplines, but they have made interpretation of hypothesis testing more difficult because of the...
BMC Bioinformatics 2017 18:312
Published on: 21 June 2017
Software
Identifying orthologous genes is an initial step required for phylogenetics, and it is also a common strategy employed in functional genetics to find candidates for functionally equivalent genes across multipl...
BMC Bioinformatics 2017 18:310
Published on: 21 June 2017
Methodology Article
Distance based unsupervised clustering of gene expression data is commonly used to identify heterogeneity in biologic samples. However, high noise levels in gene expression data and relatively high correlation...
BMC Bioinformatics 2017 18:309
Published on: 20 June 2017
Methodology Article
Targeted Next Generation Sequencing (NGS) assays are cost-efficient and reliable alternatives to Sanger sequencing. For sequencing of very large set of genes, the target enrichment approach is suitable. However, ...
BMC Bioinformatics 2017 18:306
Published on: 19 June 2017
Methodology Article
Recent advances in bioimaging and automated analysis methods have enabled the large-scale systematic analysis of cellular dynamics during the embryonic development of Caenorhabditis elegans. Most of these analyse...
BMC Bioinformatics 2017 18:307
Published on: 19 June 2017
Methodology Article
Linear scores are widely used to predict dichotomous outcomes in biomedical studies because of their learnability and understandability. Such approaches, however, cannot be used to elucidate biodiversity when ...
BMC Bioinformatics 2017 18:308
Published on: 19 June 2017
Research Article
Colorectal carcinoma evolves through a multitude of molecular events including somatic mutations, epigenetic alterations, and aberrant protein expression, influenced by host immune reactions. One way to interr...
BMC Bioinformatics 2017 18:304
Published on: 17 June 2017
Software
The analysis of viral vector genomic integration sites is an important component in assessing the safety and efficiency of patient treatment using gene therapy. Alongside this clinical application, integration...
BMC Bioinformatics 2017 18:305
Published on: 17 June 2017
Research Article
Accurately predicted contacts allow to compute the 3D structure of a protein. Since the solution space of native residue-residue contact pairs is very large, it is necessary to leverage information to identify...
BMC Bioinformatics 2017 18:303
Published on: 17 June 2017
Methodology article
Central to protein biology is the understanding of how structural elements give rise to observed function. The surfeit of protein structural data enables development of computational methods to systematically ...
BMC Bioinformatics 2017 18:302
Published on: 14 June 2017
Methodology Article
The availability of fast alignment-free algorithms has greatly reduced the computational burden of RNA-seq processing, especially for relatively poorly assembled genomes. Using these approaches, previous RNA-s...
BMC Bioinformatics 2017 18:301
Published on: 13 June 2017
Research article
DNA-binding proteins perform important functions in a great number of biological activities. DNA-binding proteins can interact with ssDNA (single-stranded DNA) or dsDNA (double-stranded DNA), and DNA-binding p...
BMC Bioinformatics 2017 18:300
Published on: 12 June 2017
Software
Genome sequencing provides a powerful tool for pathogen detection and can help resolve outbreaks that pose public safety and health risks. Mapping of DNA reads to genomes plays a fundamental role in this appro...
BMC Bioinformatics 2017 18:299
Published on: 12 June 2017
Research
For fighting cancer, earlier detection is crucial. Circulating auto-antibodies produced by the patient’s own immune system after exposure to cancer proteins are promising bio-markers for the early detection of...
BMC Bioinformatics 2017 18(Suppl 8):244
Published on: 7 June 2017
This article is part of a Supplement: Volume 18 Supplement 8
Research
Alignment-free sequence comparison approaches have been garnering increasing interest in various data- and compute-intensive applications such as phylogenetic inference for large-scale sequences. While k-mer base...
BMC Bioinformatics 2017 18(Suppl 8):238
Published on: 7 June 2017
This article is part of a Supplement: Volume 18 Supplement 8
Methodology
The notion of centrality is used to identify “important” nodes in social networks. Importance of nodes is not well-defined, and many different notions exist in the literature. The challenge of defining centrality...
BMC Bioinformatics 2017 18(Suppl 8):239
Published on: 7 June 2017
This article is part of a Supplement: Volume 18 Supplement 8
Research
Polychromatic flow cytometry is a popular technique that has wide usage in the medical sciences, especially for studying phenotypic properties of cells. The high-dimensionality of data generated by flow cytome...
BMC Bioinformatics 2017 18(Suppl 8):245
Published on: 7 June 2017
This article is part of a Supplement: Volume 18 Supplement 8
Research
The low success rate and high cost of drug discovery requires the development of new paradigms to identify molecules of therapeutic value. The Anatomical Therapeutic Chemical (ATC) Code System is a World Healt...
BMC Bioinformatics 2017 18(Suppl 8):266
Published on: 7 June 2017
This article is part of a Supplement: Volume 18 Supplement 8
Research Article
Proteins recognize many different aspects of RNA ranging from single stranded regions to discrete secondary or tertiary structures. High-throughput sequencing (HTS) of in vitro selected populations offers a la...
BMC Bioinformatics 2017 18:298
Published on: 6 June 2017
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