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DNA methylation profiling of pediatric brain tumors offers a new way of diagnosing and subgrouping these tumors which improves current clinical diagnostics based on histopathology. We have therefore developed ...
With the emerging interest in phytoplankton research, the need to establish genetic tools for the functional characterization of genes is indispensable. The CRISPR/Cas9 system is now well recognized as an effi...
Comparative analysis of whole genome sequence data from closely related prokaryotic species or strains is becoming an increasingly important and accessible approach for addressing both fundamental and applied ...
Recent interest in reference-free deconvolution of DNA methylation data has led to several supervised methods, but these methods do not easily permit the interpretation of underlying cell types.
Many models of protein sequence evolution, in particular those based on Point Accepted Mutation (PAM) matrices, assume that its dynamics is Markovian. Nevertheless, it has been observed that evolution seems to...
In order to better understand complex diseases, it is important to understand how genetic variation in the regulatory regions affects gene expression. Genetic variants found in these regulatory regions have be...
The increase in human populations around the world has put pressure on resources, and as a consequence food security has become an important challenge for the 21st century. Wheat (Triticum aestivum) is one of the...
There have been great advancements in the field of digital pathology. The surge in development of analytical methods for such data makes it crucial to develop benchmark synthetic datasets for objectively valid...
Sparse Gaussian graphical models are popular for inferring biological networks, such as gene regulatory networks. In this paper, we investigate the consistency of these models across different data platforms, ...
Branch-length parameters are a central component of phylogenetic models and of intrinsic biological interest. Default branch-length priors in some Bayesian phylogenetic software can be unintentionally informat...
The inference of gene regulatory networks (GRNs) from transcriptional expression profiles is challenging, predominantly due to its underdetermined nature. One important consequence of underdetermination is the...
Fish tracking is an important step for video based analysis of fish behavior. Due to severe body deformation and mutual occlusion of multiple swimming fish, accurate and robust fish tracking from video image s...
Identification of associations between marketed drugs and adverse events from the biomedical literature assists drug safety monitoring efforts. Assessing the significance of such literature-derived association...
Phenomics is a field in functional genomics that records variation in organismal phenotypes in the genetic, epigenetic or environmental context at a massive scale. For microbes, the key phenotype is the growth...
The growing complexity of biological experiment design based on high-throughput RNA sequencing (RNA-seq) is calling for more accommodative statistical tools. We focus on differential expression (DE) analysis u...
Integrative analysis of multi-omics data is becoming increasingly important to unravel functional mechanisms of complex diseases. However, the currently available multi-omics datasets inevitably suffer from mi...
Peptide identification based upon mass spectrometry (MS) is generally achieved by comparison of the experimental mass spectra with the theoretically digested peptides derived from a reference protein database....
An exponential growth of high-throughput biological information and data has occurred in the past decade, supported by technologies, such as microarrays and RNA-Seq. Most data generated using such methods are ...
Protein variability can now be studied by measuring high-resolution tolerance-to-substitution maps and fitness landscapes in saturated mutational libraries. But these rich and expensive datasets are typically ...
The Erratum to this article has been published in BMC Bioinformatics 2016 17:439
Next Generation Sequencing (NGS) has dramatically enhanced our ability to sequence genomes, but not to assemble them. In practice, many published genome sequences remain in the state of a large set of contigs....
The original article was published in BMC Bioinformatics 2016 17:161
Model checking has been recently introduced as an integrated framework for extracting information of the phylogenetic trees using temporal logics as a querying language, an extension of modal logics that impos...
Cryo-electron tomography (cryo-ET) enables 3D imaging of macromolecular structures. Reconstructed cryo-ET images have a “missing wedge” of data loss due to limitations in rotation of the mounting stage. Most c...
Targeted sequencing of discrete gene sets is a cost effective strategy to screen subjects for monogenic forms of disease. One method to achieve this pairs microfluidic PCR with next generation sequencing. The ...
Single-cell technologies make it possible to quantify the comprehensive states of individual cells, and have the power to shed light on cellular differentiation in particular. Although several methods have bee...
RNA-binding proteins participate in many important biological processes concerning RNA-mediated gene regulation, and several computational methods have been recently developed to predict the protein-RNA intera...
For clinical genomic studies with high-dimensional datasets, tree-based ensemble methods offer a powerful solution for variable selection and prediction taking into account the complex interrelationships betwe...
Peak calling is a fundamental step in the analysis of data generated by ChIP-seq or similar techniques to acquire epigenetics information. Current peak callers are often hard to parameterise and may therefore ...
This article is part of a Supplement: Volume 17 Supplement 5
Pathway expression is multivariate in nature. Thus, from a statistical perspective, to detect differentially expressed pathways between two conditions, methods for inferring differences between mean vectors ne...
This article is part of a Supplement: Volume 17 Supplement 5
Joint and individual variation explained (JIVE), distinct and common simultaneous component analysis (DISCO) and O2-PLS, a two-block (X-Y) latent variable regression method with an integral OSC filter can all ...
This article is part of a Supplement: Volume 17 Supplement 5
We address the problem of integratively analyzing multiple gene expression, microarray datasets in order to reconstruct gene-gene interaction networks. Integrating multiple datasets is generally believed to pr...
This article is part of a Supplement: Volume 17 Supplement 5
The Erratum to this article has been published in BMC Bioinformatics 2016 17:290
Genome layout and gene regulation appear to be interdependent. Understanding this interdependence is key to exploring the dynamic nature of chromosome conformation and to engineering functional genomes. Eviden...
This article is part of a Supplement: Volume 17 Supplement 5
Text mining and data integration methods are gaining ground in the field of health sciences due to the exponential growth of bio-medical literature and information stored in biological databases. While such me...
This article is part of a Supplement: Volume 17 Supplement 5
Under both physiological and pathological conditions gene expression programs are shaped through the interplay of regulatory proteins and their gene targets, interactions between which form intricate gene regu...
This article is part of a Supplement: Volume 17 Supplement 5
In order to find genetic and metabolic pathways related to phenotypic traits of interest, we analyzed gene expression data, metabolite data obtained with GC-MS and LC-MS, proteomics data and a selected set of ...
This article is part of a Supplement: Volume 17 Supplement 5
Mixed graphical models (MGMs) are graphical models learned over a combination of continuous and discrete variables. Mixed variable types are common in biomedical datasets. MGMs consist of a parameterized joint...
This article is part of a Supplement: Volume 17 Supplement 5
In recent years, high throughput technologies have led to an increase of datasets from omics disciplines allowing the understanding of the complex regulatory networks associated with biological processes. Leaf...
This article is part of a Supplement: Volume 17 Supplement 5
Somatic Hypermutation (SHM) refers to the introduction of mutations within rearranged V(D)J genes, a process that increases the diversity of Immunoglobulins (IGs). The analysis of SHM has offered critical insi...
This article is part of a Supplement: Volume 17 Supplement 5
Next generation sequencing (NGS) produces massive datasets consisting of billions of reads and up to thousands of samples. Subsequent bioinformatic analysis is typically done with the help of open source tools...
The current practice of histopathology review is limited in speed and accuracy. The current diagnostic paradigm does not fully describe the complex and complicated patterns of cancer. To address these needs, w...
Current genome sequencing projects reveal substantial numbers of taxonomically restricted, so called orphan genes that lack homology with genes from other evolutionary lineages. However, it is not clear to wha...
Aptamer-protein interacting pairs play a variety of physiological functions and therapeutic potentials in organisms. Rapidly and effectively predicting aptamer-protein interacting pairs is significant to desig...
Discovery of microRNAs (miRNAs) relies on predictive models for characteristic features from miRNA precursors (pre-miRNAs). The short length of miRNA genes and the lack of pronounced sequence features complica...
The Legumes (Fabaceae) are an economically and ecologically important group of plant species with the conspicuous capacity for symbiotic nitrogen fixation in root nodules, specialized plant organs containing s...
Genomic regions with recurrent DNA copy number variations (CNVs) are generally believed to encode oncogenes and tumor suppressor genes (TSGs) that drive cancer growth. However, it remains a challenge to deline...
The problem of learning causal influences from data has recently attracted much attention. Standard statistical methods can have difficulty learning discrete causes, which interacting to affect a target, becau...
A number of large genomic datasets are being generated for studies of human ancestry and diseases. The ADMIXTURE program is commonly used to infer individual ancestry from genomic data.
Chemical cross-linking combined with mass spectrometry (CX-MS) is a high-throughput approach to studying protein-protein interactions. The number of peptide-peptide combinations grows quadratically with respec...
In this paper, we study the problem of RNA motif search in long genomic sequences. This approach uses a combination of sequence and structure constraints to uncover new distant homologs of known functional RNA...
RNA molecules fold into complex three-dimensional shapes, guided by the pattern of hydrogen bonding between nucleotides. This pattern of base pairing, known as RNA secondary structure, is critical to their cel...
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