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The analysis of next generation sequencing (NGS) has become a standard task for many laboratories in the life sciences. Though there exists several tools to support users in the manipulation of such datasets o...
The nonparametric trend test (NPT) is well suitable for identifying the genetic variants associated with quantitative traits when the trait values do not satisfy the normal distribution assumption. If the gene...
Automated classification using machine learning often relies on features derived from segmenting individual objects, which can be difficult to automate. WND-CHARM is a previously developed classification algor...
The major mechanism driving cellular differentiation and organism development is the regulation of gene expression. Cis-acting enhancers and silencers have key roles in controlling gene transcription. The genomic...
Computational biologists daily face the need to explore massive amounts of genomic data. New visualization techniques can help researchers navigate and understand these big data. Horizon Charts are a relativel...
One of our goals for the echinoderm tree of life project (http://echinotol.org) is to identify orthologs suitable for phylogenetic analysis from next-g...
Consider the problem of designing a panel of complex biomarkers to predict a patient’s health or disease state when one can pair his or her current test sample, called a target sample, with the patient’s previ...
Drug-target networks are receiving a lot of attention in late years, given its relevance for pharmaceutical innovation and drug lead discovery. Different in silico approaches have been proposed for the identif...
Enrichment analysis of gene expression data is essential to find functional groups of genes whose interplay can explain experimental observations. Numerous methods have been published that either ignore (set-b...
Selecting a parsimonious set of informative genes to build highly generalized performance classifier is the most important task for the analysis of tumor microarray expression data. Many existing gene pair eva...
Here we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT...
Interest in understanding the mechanisms that lead to a particular composition of the Gut Microbiota is highly increasing, due to the relationship between this ecosystem and the host health state. Particularly...
This article is part of a Supplement: Volume 17 Supplement 2
Methods for the integrative analysis of multi-omics data are required to draw a more complete and accurate picture of the dynamics of molecular systems. The complexity of biological systems, the technological ...
This article is part of a Supplement: Volume 17 Supplement 2
Mecp2 null mice model Rett syndrome (RTT) a human neurological disorder affecting females after apparent normal pre- and peri-natal developmental periods. Neuroanatomical studies in cerebral cortex of RTT mous...
This article is part of a Supplement: Volume 17 Supplement 2
Proteins adapt to environmental conditions by changing their shape and motions. Characterising protein conformational dynamics is increasingly recognised as necessary to understand how proteins function. Given...
This article is part of a Supplement: Volume 17 Supplement 2
The reconstruction of reliable graphical models from observational data is important in bioinformatics and other computational fields applying network reconstruction methods to large, yet finite datasets. The ...
This article is part of a Supplement: Volume 17 Supplement 2
Rapid computational and technological developments made large amounts of omics data available in different biological levels. It is becoming clear that simultaneous data analysis methods are needed for better ...
This article is part of a Supplement: Volume 17 Supplement 2
Inflammatory bowel disease (IBD) consists of two main disease-subtypes, Crohn’s disease (CD) and ulcerative colitis (UC); these subtypes share overlapping genetic and clinical features. Genome-wide microarray ...
Next-generation sequencing datasets are becoming more frequent, and their use in population studies is becoming widespread. For non-model species, without a reference genome, it is possible from a panel of ind...
One of the main aims of phylogenomics is the reconstruction of objects defined in the leaves along the whole phylogenetic tree to minimize the specified functional, which may also include the phylogenetic tree...
The original article was published in BMC Bioinformatics 2015 16:65
A rapidly increasing flow of genomic data requires the development of efficient methods for obtaining its compact representation. Feature extraction facilitates classification, clustering and model analysis fo...
As sequencing technologies can help researchers detect common and rare variants across the human genome in many individuals, it is known that jointly calling genotypes across multiple individuals based on link...
Information in the brain is often segregated into spatially organized layers that reflect the function of the embedded circuits. This is perhaps best exemplified in the layering, or lamination, of the retinal ...
Gene co-expression evidenced as a response to environmental changes has shown that transcriptional activity is coordinated, which pinpoints the role of transcriptional regulatory networks (TRNs). Nevertheless,...
All proteins associate with other molecules. These associated molecules are highly predictive of the potential functions of proteins. The association of a protein and a molecule can be determined from their co...
The Erratum to this article has been published in BMC Bioinformatics 2016 17:105
Metabolomics datasets are often high-dimensional though only a limited number of variables are expected to be informative given a specific research question. The important task of selecting informative variabl...
Natural language processing (NLP) applications are increasingly important in biomedical data analysis, knowledge engineering, and decision support. Concept recognition is an important component task for NLP pi...
Transcripts, which have been subject to Post-transcriptional exon shuffling (PTES), have an exon order inconsistent with the underlying genomic sequence. These have been identified in a wide variety of tissues...
The Erratum to this article has been published in BMC Bioinformatics 2016 17:92
In recent years, many studies focused on the description and comparison of large sets of related bacteriophage genomes. Due to the peculiar mosaic structure of these genomes, few informative approaches for com...
With its simple library preparation and robust approach to genome reduction, genotyping-by-sequencing (GBS) is a flexible and cost-effective strategy for SNP discovery and genotyping, provided an appropriate r...
Rice (Oryza sativa L.) is one of the most important cereal crops in the world and its yield is closely related to the photosynthesis efficiency. The chloroplast stromal ridge complex consisting of PsaC-PsaD-PsaE ...
In the context of high-throughput molecular data analysis it is common that the observations included in a dataset form distinct groups; for example, measured at different times, under different conditions or ...
Aligning similar molecular structures is an important step in the process of bio-molecular structure and function analysis. Molecular surfaces are simple representations of molecular structure that are easily ...
Flow cytometry is a widespread single-cell measurement technology with a multitude of clinical and research applications. Interpretation of flow cytometry data is hard; the instrumentation is delicate and can ...
The Erratum to this article has been published in BMC Bioinformatics 2016 17:149
Missing values are commonly present in microarray data profiles. Instead of discarding genes or samples with incomplete expression level, missing values need to be properly imputed for accurate data analysis. ...
This article is part of a Supplement: Volume 17 Supplement 1
A living cell has a complex, hierarchically organized signaling system that encodes and assimilates diverse environmental and intracellular signals, and it further transmits signals that control cellular respo...
This article is part of a Supplement: Volume 17 Supplement 1
Protein solvent accessibility prediction is a pivotal intermediate step towards modeling protein tertiary structures directly from one-dimensional sequences. It also plays an important part in identifying prot...
This article is part of a Supplement: Volume 17 Supplement 1
DNA methylation is an epigenetic modification that plays important roles on gene regulation. Study of whole-genome bisulfite sequencing and reduced representation bisulfite sequencing brings the availability o...
This article is part of a Supplement: Volume 17 Supplement 1
Thyroid carcinomas are known to harbor oncogenic driver mutations and advances in sequencing technology now allow the detection of these in fine needle aspiration biopsies (FNA). Recent work by The Cancer Geno...
This article is part of a Supplement: Volume 17 Supplement 1
Determining differentially expressed genes (DEGs) between biological samples is the key to understand how genotype gives rise to phenotype. RNA-seq and microarray are two main technologies for profiling gene e...
This article is part of a Supplement: Volume 17 Supplement 1
Understanding the mechanisms by which transcription factors (TF) are recruited to their physiological target sites is crucial for understanding gene regulation. DNA sequence intrinsic features such as predicte...
This article is part of a Supplement: Volume 17 Supplement 1
Tuberculosis (TB) is a serious infectious disease in that 90 % of those latently infected with Mycobacterium tuberculosis present no symptoms, but possess a 10 % lifetime chance of developing active TB. To pre...
This article is part of a Supplement: Volume 17 Supplement 1
Non-small cell lung cancer (NSCLC) is one of the leading causes of death globally, and research into NSCLC has been accumulating steadily over several years. Drug repositioning is the current trend in the phar...
This article is part of a Supplement: Volume 17 Supplement 1
Numerous publicly available biomedical databases derive data by curating from literatures. The curated data can be useful as training examples for information extraction, but curated data usually lack the exac...
This article is part of a Supplement: Volume 17 Supplement 1
The Erratum to this article has been published in BMC Bioinformatics 2016 17:84
Data from a plethora of high-throughput sequencing studies is readily available to researchers, providing genetic variants detected in a variety of healthy and disease populations. While each individual cohort...
Branch lengths are an important attribute of phylogenetic trees, providing essential information for many studies in evolutionary biology. Yet, part of the current methodology to reconstruct a phylogeny from g...
Taxonomic assignment is a crucial step in a metagenomic project which aims to identify the origin of sequences in an environmental sample. Among the existing methods, since composition-based algorithms are not...
Technical advances in Next Generation Sequencing (NGS) provide a means to acquire deeper insights into cellular functions. The lack of standardized and automated methodologies poses a challenge for the analysi...
Advances in high throughput technologies and growth of biomedical knowledge have contributed to an exponential increase in associative data. These data can be represented in the form of complex networks of bio...
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