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Investigation of outbreaks to identify the primary case is crucial for the interruption and prevention of transmission of infectious diseases. These individuals may have a higher risk of participating in near ...
16S rRNA-gene sequencing is a valuable approach to characterize the taxonomic content of the whole bacterial population inhabiting a metabolic and spatial niche, providing an important opportunity to study bac...
This article is part of a Supplement: Volume 22 Supplement 15
As technical developments in omics and biomedical imaging increase the throughput of data generation in life sciences, the need for information systems capable of managing heterogeneous digital assets is incre...
Colony growth on solid media is a simple and effective measure for high-throughput genomic experiments such as yeast two-hybrid, synthetic dosage lethality and Synthetic Physical Interaction screens. The devel...
Processed pseudogenes (PΨgs) are disabled gene copies that are transcribed and may affect expression of paralogous genes. Moreover, their insertion in the genome can disrupt the structure or the regulatory reg...
Influenza A virus is one of the leading causes of annual mortality. The emerging of novel escape variants of the influenza A virus is still a considerable challenge in the annual process of vaccine production....
This article is part of a Supplement: Volume 22 Supplement 14
Predicting the secondary, i.e. base-pairing structure of a folded RNA strand is an important problem in synthetic and computational biology. First-principle algorithmic approaches to this task are challenging ...
Genes and gene products do not function in isolation but as components of complex networks of macromolecules through physical or biochemical interactions. Dependencies of gene mutations on genetic background (...
Besides Boolean retrieval with medical subject headings (MeSH), PubMed provides users with an alternative way called “Related Articles” to access and collect relevant documents based on semantic similarity. To...
Cell-based models are becoming increasingly popular for applications in developmental biology. However, the impact of numerical choices on the accuracy and efficiency of the simulation of these models is rarel...
Recent development of bioinformatics tools for Next Generation Sequencing data has facilitated complex analyses and prompted large scale experimental designs for comparative genomics. When combined with the ad...
Despite enormous achievements in the production of high-throughput datasets, constructing comprehensive maps of interactions remains a major challenge. Lack of sufficient experimental evidence on interactions ...
Parasites use polymorphic gene families to evade the immune system or interact with the host. Assessing the diversity and expression of such gene families in pathogens can inform on the repertoire or host inte...
Elucidating the modes of action (MoAs) of drugs and drug candidate compounds is critical for guiding translation from drug discovery to clinical application. Despite the development of several data-driven appr...
Imputation of untyped markers is a standard tool in genome-wide association studies to close the gap between directly genotyped and other known DNA variants. However, high accuracy with which genotypes are imp...
Quality control checks are the first step in RNA-Sequencing analysis, which enable the identification of common issues that occur in the sequenced reads. Checks for sequence quality, contamination, and complex...
Fluorescence image analysis in biochemical science often involves the complex tasks of identifying samples for analysis and calculating the desired information from the intensity traces. Analyzing giant unilam...
Computational prediction of the interaction between drugs and protein targets is very important for the new drug discovery, as the experimental determination of drug-target interaction (DTI) is expensive and t...
This article is part of a Supplement: Volume 22 Supplement 12
This article is part of a Supplement: Volume 22 Supplement 12
Bioinformatics is a subject produced by the combination of life science and computer science. It mainly uses computer technology to study the laws of biological systems. The design and realization of DNA circu...
This article is part of a Supplement: Volume 22 Supplement 12
Clustering and feature selection act major roles in many communities. As a matrix factorization, Low-Rank Representation (LRR) has attracted lots of attentions in clustering and feature selection, but sometime...
This article is part of a Supplement: Volume 22 Supplement 12
During the pathogenesisof complex diseases, a sudden health deterioration will occur as results of the cumulative effect of various internal or external factors. The prediction of an early warning signal (pre-...
This article is part of a Supplement: Volume 22 Supplement 12
The identification of cancer types is of great significance for early diagnosis and clinical treatment of cancer. Clustering cancer samples is an important means to identify cancer types, which has been paid m...
This article is part of a Supplement: Volume 22 Supplement 12
Alkaline earth metal ions are important protein binding ligands in human body, and it is of great significance to predict their binding residues.
This article is part of a Supplement: Volume 22 Supplement 12
Metagenomics technology can directly extract microbial genetic material from the environmental samples to obtain their sequencing reads, which can be further assembled into contigs through assembly tools. Clus...
This article is part of a Supplement: Volume 22 Supplement 12
Mining gene regulatory network (GRN) is an important avenue for addressing cancer mechanism. Mutations in cancer genome perturb GRN and cause a rewiring in an orchestrated network. Hence, the exploration of ge...
This article is part of a Supplement: Volume 22 Supplement 12
Recently, with the foundation and development of gene ontology (GO) resources, numerous works have been proposed to compute functional similarity of genes and achieved series of successes in some research fiel...
This article is part of a Supplement: Volume 23 Supplement 1
Algorithmic cellular segmentation is an essential step for the quantitative analysis of highly multiplexed tissue images. Current segmentation pipelines often require manual dataset annotation and additional t...
Differential isoform usage is an important driver of inter-individual phenotypic diversity and is linked to various diseases and traits. However, accurately detecting the differential usage of different gene t...
Automatic cell type identification is essential to alleviate a key bottleneck in scRNA-seq data analysis. While most existing classification tools show good sensitivity and specificity, they often fail to adeq...
Protein function prediction remains a key challenge. Domain composition affects protein function. Here we present DomFun, a Ruby gem that uses associations between protein domains and functions, calculated usi...
There has been a simultaneous increase in demand and accessibility across genomics, transcriptomics, proteomics and metabolomics data, known as omics data. This has encouraged widespread application of omics d...
DNA methylation is commonly measured using bisulfite sequencing (BS-seq). The quality of a BS-seq library is measured by its bisulfite conversion efficiency. Libraries with low conversion rates are typically e...
Extrachromosomal circular DNAs (eccDNAs) are ring-like DNA structures physically separated from the chromosomes with 100 bp to several megabasepairs in size. Apart from carrying tandemly repeated DNA, eccDNAs ...
Total-RNA sequencing (total-RNA-seq) allows the simultaneous study of both the coding and the non-coding transcriptome. Yet, computational pipelines have traditionally focused on particular biotypes, making as...
The Correction to this article has been published in BMC Bioinformatics 2022 23:209
Accurate cancer classification is essential for correct treatment selection and better prognostication. microRNAs (miRNAs) are small RNA molecules that negatively regulate gene expression, and their dyresgulat...
LINCS, "Library of Integrated Network-based Cellular Signatures", and IDG, "Illuminating the Druggable Genome", are both NIH projects and consortia that have generated rich datasets for the study of the molecu...
The number of studies using single-cell RNA sequencing (scRNA-seq) is constantly growing. This powerful technique provides a sampling of the whole transcriptome of a cell. However, sparsity of the data can be ...
With the precision of the mass spectrometry (MS) going higher, the MS file size increases rapidly. Beyond the widely-used open format mzML, near-lossless or lossless compression algorithms and formats emerged ...
Compound–protein interaction prediction is necessary to investigate health regulatory functions and promotes drug discovery. Machine learning is becoming increasingly important in bioinformatics for applicatio...
This article is part of a Supplement: Volume 22 Supplement 5
Researchers have attempted to apply deep learning methods of artificial intelligence for rapidly and accurately detecting acute lymphoblastic leukemia (ALL) in microscopic images.
This article is part of a Supplement: Volume 22 Supplement 5
Drug combination, offering an insight into the increased therapeutic efficacy and reduced toxicity, plays an essential role in the therapy of many complex diseases. Although significant efforts have been devot...
This article is part of a Supplement: Volume 23 Supplement 1
The recent advancements in high-throughput sequencing have resulted in the availability of annotated genomes, as well as of multi-omics data for many living organisms. This has increased the need for graphic t...
The original article was published in BMC Bioinformatics 2021 22:586
Representations of the relationships among data using networks are widely used in several research fields such as computational biology, medical informatics and social network mining. Recently, complex network...
This article is part of a Supplement: Volume 22 Supplement 15
Glucocorticoid-remediable aldosteronism (GRA) is a form of heritable hypertension caused by a chimeric fusion resulting from unequal crossing over between 11β‐hydroxylase (CYP11B1) and aldosterone synthase (CYP11...
This article is part of a Supplement: Volume 22 Supplement 10
Analysis of dynamic metabolomics data holds the promise to improve our understanding of underlying mechanisms in metabolism. For example, it may detect changes in metabolism due to the onset of a disease. Dyna...
Plant variety identification is the one most important of agricultural systems. Development of DNA marker profiles of released varieties to compare with candidate variety or future variety is required. However...
DNA methylation has long been known as an epigenetic gene silencing mechanism. For a motivating example, the methylomes of cancer and non-cancer cells show a number of methylation differences, indicating that ...
This article is part of a Supplement: Volume 23 Supplement 1
The polygenic risk score (PRS) shows promise as a potentially effective approach to summarize genetic risk for complex diseases such as alcohol use disorder that is influenced by a combination of multiple vari...
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