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Single-cell sequencing experiments use short DNA barcode ‘tags’ to identify reads that originate from the same cell. In order to recover single-cell information from such experiments, reads must be grouped bas...
Many medical imaging techniques utilize fitting approaches for quantitative parameter estimation and analysis. Common examples are pharmacokinetic modeling in dynamic contrast-enhanced (DCE) magnetic resonance...
Single-molecule localization microscopy is a super-resolution microscopy technique that allows for nanoscale determination of the localization and organization of proteins in biological samples. For biological...
The massive amounts of data from next generation sequencing (NGS) methods pose various challenges with respect to data security, storage and metadata management. While there is a broad range of data analysis p...
The blat is a widely used sequence alignment tool. It is especially useful for aligning long sequences and gapped mapping, which cannot be performed properly by other fast sequence mappers designed for short r...
Graphlets are useful for bioinformatics network analysis. Based on the structure of Hočevar and Demšar’s ORCA algorithm, we have created an orbit counting algorithm, named Jesse. This algorithm, like ORCA, use...
Simulation of genetic variants data is frequently required for the evaluation of statistical methods in the fields of human and animal genetics. Although a number of high-quality genetic simulators have been d...
Selecting animals for breeding in the optimum way plays an essential role for the management of genetic resources and in selective breeding of livestock species. It requires to compute the optimum genetic cont...
Around 1% of human proteins are predicted to contain a disordered and low complexity prion-like domain (PrLD). Mutations in PrLDs have been shown promote a transition towards an aggregation-prone state in seve...
Clustering molecular network is a typical method in system biology, which is effective in predicting protein complexes or functional modules. However, few studies have realized that biological molecules are sp...
Selection of interesting regions from genome wide association studies (GWAS) is typically performed by eyeballing of Manhattan Plots. This is no longer possible with thousands of different phenotypes. There is...
Advances in high-resolution mass spectrometry facilitate the identification of hundreds of metabolites, thousands of proteins and their post-translational modifications. This remarkable progress poses a challe...
Gene Ontology (GO) is a useful resource of controlled vocabulary that provides information about annotated genes. Based on such resource, finding the biological function is useful for biologists to come up wit...
In systems biology, there is an acute need for integrative approaches in heterogeneous network mining in order to exploit the continuous flux of genomic data. Simultaneous analysis of the metabolic pathways an...
Random-effects (RE) models are commonly applied to account for heterogeneity in effect sizes in gene expression meta-analysis. The degree of heterogeneity may differ due to inconsistencies in sample quality. H...
Translational and post-translational control mechanisms in the cell result in widely observable differences between measured gene transcription and protein abundances. Herein, protein complexes are among the m...
Long non-coding RNA (lncRNA) studies play an important role in the development, invasion, and metastasis of the tumor. The analysis and screening of the differential expression of lncRNAs in cancer and corresp...
Canonical correlation analysis (CCA) is a classic statistical tool for investigating complex multivariate data. Correspondingly, it has found many diverse applications, ranging from molecular biology and medic...
Hypothetical proteins [HP] are those that are predicted to be expressed in an organism, but no evidence of their existence is known. In the recent past, annotation and curation efforts have helped overcome the...
Previous cancer genomics studies focused on searching for novel oncogenes and tumor suppressor genes whose abundance is positively or negatively correlated with end-point observation, such as survival or tumor...
Reverse engineering approaches to infer gene regulatory networks using computational methods are of great importance to annotate gene functionality and identify hub genes. Although various statistical algorith...
Skewed X chromosome inactivation (XCI), which is a non-random process, is frequently observed in both healthy and affected females. Furthermore, skewed XCI has been reported to be related to many X-linked dise...
Recent studies have proposed deep learning techniques, namely recurrent neural networks, to improve biomedical text mining tasks. However, these techniques rarely take advantage of existing domain-specific res...
Traditional Map based Cloning approaches, used for the identification of desirable alleles, are extremely labour intensive and years can elapse between the mutagenesis and the detection of the polymorphism. Hi...
The development of high-throughput sequencing and analysis has accelerated multi-omics studies of thousands of microbial species, metagenomes, and infectious disease pathogens. Omics studies are enabling genot...
To further our understanding of immunopeptidomics, improved tools are needed to identify peptides presented by major histocompatibility complex class I (MHC-I). Many existing tools are limited by their relianc...
Tumor samples are heterogeneous. They consist of varying cell populations or subclones and each subclone is characterized with a distinct single nucleotide variant (SNV) profile. This explains the source of ge...
Predicting drug-disease interactions (DDIs) is time-consuming and expensive. Improving the accuracy of prediction results is necessary, and it is crucial to develop a novel computing technology to predict new ...
Modern plant taxonomy reflects phylogenetic relationships among taxa based on proposed morphological and genetic similarities. However, taxonomical relation is not necessarily reflected by close overall resemb...
Non-co-linear (NCL) transcripts consist of exonic sequences that are topologically inconsistent with the reference genome in an intragenic fashion (circular or intragenic trans-spliced RNAs) or in an intergenic f...
3D segmentation is often a prerequisite for 3D object display and quantitative measurements. Yet existing voxel-based methods do not directly give information on the object surface or topology. As for spatiall...
Genome-wide DNA copy number changes are the hallmark events in the initiation and progression of cancers. Quantitative analysis of somatic copy number alterations (CNAs) has broad applications in cancer resear...
Protein sequence alignment analyses have become a crucial step for many bioinformatics studies during the past decades. Multiple sequence alignment (MSA) and pair-wise sequence alignment (PSA) are two major ap...
This article is part of a Supplement: Volume 19 Supplement 19
The detection and interpretation of CNVs are of clinical importance in genetic testing. Several databases and web services are already being used by clinical geneticists to interpret the medical relevance of i...
This article is part of a Supplement: Volume 19 Supplement 19
Cyclic peptide-based drug discovery is attracting increasing interest owing to its potential to avoid target protein depletion. In drug discovery, it is important to maintain the biostability of a drug within ...
This article is part of a Supplement: Volume 19 Supplement 19
Previous studies have suggested deep learning to be a highly effective approach for screening lead compounds for new drugs. Several deep learning models have been developed by addressing the use of various kin...
This article is part of a Supplement: Volume 19 Supplement 19
Identifying protein-protein interactions (PPIs) is of paramount importance for understanding cellular processes. Machine learning-based approaches have been developed to predict PPIs, but the effectiveness of ...
This article is part of a Supplement: Volume 19 Supplement 19
N6-methyladensine (m6A) is a common and abundant RNA methylation modification found in various species. As a type of post-transcriptional methylation, m6A plays an important role in diverse RNA activities such...
This article is part of a Supplement: Volume 19 Supplement 19
The default mode network (DMN) in resting state has been increasingly used in disease diagnosis since it was found in 2001. Prior work has mainly focused on extracting a single DMN with various techniques. How...
This article is part of a Supplement: Volume 19 Supplement 19
Identifying specific residues for protein-DNA interactions are of considerable importance to better recognize the binding mechanism of protein-DNA complexes. Despite the fact that many computational DNA-bindin...
This article is part of a Supplement: Volume 19 Supplement 19
Distinction between pre-microRNAs (precursor microRNAs) and length-similar pseudo pre-microRNAs can reveal more about the regulatory mechanism of RNA biological processes. Machine learning techniques have been...
This article is part of a Supplement: Volume 19 Supplement 19
Many evidences have demonstrated that circRNAs (circular RNA) play important roles in controlling gene expression of human, mouse and nematode. More importantly, circRNAs are also involved in many diseases thr...
This article is part of a Supplement: Volume 19 Supplement 19
Establishing the relationship between microbiota and specific diseases is important but requires appropriate statistical methodology. A specialized feature of microbiome count data is the presence of a large n...
This article is part of a Supplement: Volume 19 Supplement 19
Estimating heterogeneous treatment effect is a fundamental problem in biological and medical applications. Recently, several recursive partitioning methods have been proposed to identify the subgroups that res...
This article is part of a Supplement: Volume 19 Supplement 19
Early and accurate identification of potential adverse drug reactions (ADRs) for combined medication is vital for public health. Existing methods either rely on expensive wet-lab experiments or detecting exist...
This article is part of a Supplement: Volume 19 Supplement 19
Finding peptides with high binding affinity to Class I major histocompatibility complex (MHC-I) attracts intensive research, and it serves a crucial part of developing a better vaccine for precision medicine. ...
This article is part of a Supplement: Volume 19 Supplement 19
Type 2 diabetes (T2D) is one of the most common chronic diseases. Studies on T2D are mainly built upon bulk-cell data analysis, which measures the average gene expression levels for a population of cells and c...
This article is part of a Supplement: Volume 19 Supplement 19
miRBase is the primary repository for published miRNA sequence and annotation data, and serves as the “go-to” place for miRNA research. However, the definition and annotation of miRNAs have been changed signif...
This article is part of a Supplement: Volume 19 Supplement 19
Direct-coupling analysis (DCA) is a method for protein contact prediction from sequence information alone. Its underlying principle is parameter estimation for a Hamiltonian interaction function stemming from ...
Accurate gene regulatory networks can be used to explain the emergence of different phenotypes, disease mechanisms, and other biological functions. Many methods have been proposed to infer networks from gene e...
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