Methodology Article
DNA methylation is an important tissue-specific epigenetic event that influences transcriptional regulation of gene expression. Differentially methylated CpG sites may act as mediators between genetic variatio...
BMC Bioinformatics 2017 18:455
Published on: 18 October 2017
Research
Predicting protein complexes from protein-protein interaction (PPI) networks has been studied for decade. Various methods have been proposed to address some challenging issues of this problem, including overla...
BMC Bioinformatics 2017 18(Suppl 12):419
Published on: 16 October 2017
Software
The recent release of the gene-targeted metagenomics assembler Xander has demonstrated that using the trained Hidden Markov Model (HMM) to guide the traversal of de Bruijn graph gives obvious advantage over other...
BMC Bioinformatics 2017 18(Suppl 12):408
Published on: 16 October 2017
Research
Drug Combination is one of the effective approaches for treating complex diseases. However, determining combinative drug pairs in clinical trials is still costly. Thus, computational approaches are used to ide...
BMC Bioinformatics 2017 18(Suppl 12):409
Published on: 16 October 2017
Research
The constant progress in sequencing technology leads to ever increasing amounts of genomic data. In the light of current evidence transposable elements (TEs for short) are becoming useful tools for learning ab...
BMC Bioinformatics 2017 18(Suppl 12):422
Published on: 16 October 2017
Research
Homology search is still a significant step in functional analysis for genomic data. Profile Hidden Markov Model-based homology search has been widely used in protein domain analysis in many different species....
BMC Bioinformatics 2017 18(Suppl 12):414
Published on: 16 October 2017
Research
Genome rearrangements are essential processes for evolution and are responsible for existing varieties of genome architectures. Many studies have been conducted to obtain an algorithm that identifies the minim...
BMC Bioinformatics 2017 18(Suppl 12):427
Published on: 16 October 2017
Research
The binding of small ligands to RNA elements can cause substantial changes in the RNA structure. This constitutes an important, fast-acting mechanism of ligand-controlled transcriptional and translational gene...
BMC Bioinformatics 2017 18(Suppl 12):424
Published on: 16 October 2017
Research
Studies have shown that enhancers are significant regulatory elements to play crucial roles in gene expression regulation. Since enhancers are unrelated to the orientation and distance to their target genes, i...
BMC Bioinformatics 2017 18(Suppl 12):418
Published on: 16 October 2017
Research
A network motif is defined as a statistically significant and recurring subgraph pattern within a network. Most existing instance collection methods are not feasible due to high memory usage issues and provisi...
BMC Bioinformatics 2017 18(Suppl 12):423
Published on: 16 October 2017
Research
Methylation is a common modification of DNA. It has been a very important and hot topic to study the correlation between methylation and diseases in medical science. Because of the special process with bisulfi...
BMC Bioinformatics 2017 18(Suppl 12):410
Published on: 16 October 2017
Research
Genomic structural variants (SV) play a significant role in the onset and progression of cancer. Genomic deletions can create oncogenic fusion genes or cause the loss of tumor suppressing gene function which c...
BMC Bioinformatics 2017 18(Suppl 12):413
Published on: 16 October 2017
Research
Chromosomal deletions represent an important class of human genetic variation. Various methods have been developed to mine “next-generation” sequencing (NGS) data to detect deletions and quantify their clonal ...
BMC Bioinformatics 2017 18(Suppl 12):407
Published on: 16 October 2017
Research
Long non-coding RNA (lncRNA) plays important roles in many biological and pathological processes, including transcriptional regulation and gene regulation. As lncRNA interacts with multiple proteins, predicting l...
BMC Bioinformatics 2017 18(Suppl 12):420
Published on: 16 October 2017
Software
Threshold regression models are a diverse set of non-regular regression models that all depend on change points or thresholds. They provide a simple but elegant and interpretable way to model certain kinds of ...
BMC Bioinformatics 2017 18:454
Published on: 16 October 2017
Research Article
In biomedical articles, a named entity recognition (NER) technique that identifies entity names from texts is an important element for extracting biological knowledge from articles. After NER is applied to art...
BMC Bioinformatics 2017 18:451
Published on: 13 October 2017
Methodology Article
Researchers have previously developed a multitude of methods designed to identify biological pathways associated with specific clinical or experimental conditions of interest, with the aim of facilitating biol...
BMC Bioinformatics 2017 18:453
Published on: 13 October 2017
Meeting abstracts
BMC Bioinformatics 2017 18(Suppl 9):377
Published on: 13 October 2017
This article is part of a Supplement: Volume 18 Supplement 9
Database
Recent advances in omics technology have produced a large amount of liver-related data. A comprehensive and up-to-date source of liver-related data is needed to allow biologists to access the latest data. Howe...
BMC Bioinformatics 2017 18:452
Published on: 13 October 2017
Research Article
DNA microarrays offer motivation and hope for the simultaneous study of variations in multiple genes. Gene expression is a temporal process that allows variations in expression levels with a characterized gene...
BMC Bioinformatics 2017 18:450
Published on: 12 October 2017
Research Article
The prediction of human gene–abnormal phenotype associations is a fundamental step toward the discovery of novel genes associated with human disorders, especially when no genes are known to be associated with ...
BMC Bioinformatics 2017 18:449
Published on: 12 October 2017
Research Article
Predicting disease-associated genes is helpful for understanding the molecular mechanisms during the disease progression. Since the pathological mechanisms of neurodegenerative diseases are very complex, tradi...
BMC Bioinformatics 2017 18:447
Published on: 11 October 2017
Software
Pre-processing of high-throughput sequencing data for immune repertoire profiling is essential to insure high quality input for downstream analysis. VDJPipe is a flexible, high-performance tool that can perfor...
BMC Bioinformatics 2017 18:448
Published on: 11 October 2017
Software
Since experimental elucidation of gene function is often laborious, various in silico methods have been developed to predict gene function of uncharacterized genes. Since functionally related genes are often e...
BMC Bioinformatics 2017 18:444
Published on: 10 October 2017
Research Article
Protein remote homology detection plays a vital role in studies of protein structures and functions. Almost all of the traditional machine leaning methods require fixed length features to represent the protein...
BMC Bioinformatics 2017 18:443
Published on: 10 October 2017
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