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RNA sequencing is currently the method of choice for genome-wide profiling of gene expression. A popular approach to quantify expression levels of genes from RNA-seq data is to map reads to a reference genome ...
Barcode-based multiplexing methods can be used to increase throughput and reduce batch effects in large single-cell genomics studies. Despite advantages in flexibility of sample collection and scale, there are...
A birth–death process of which the births follow a hypoexponential distribution with L phases and are controlled by an on/off mechanism, is a population process which we call the on/off-seq-L process. It is a sui...
Necrotizing enterocolitis (NEC) is a common, potentially catastrophic intestinal disease among very low birthweight premature infants. Affecting up to 15% of neonates born weighing less than 1500 g, NEC causes...
Named Entity Recognition (NER) and Normalisation (NEN) are core components of any text-mining system for biomedical texts. In a traditional concept-recognition pipeline, these tasks are combined in a serial wa...
This article is part of a Supplement: Volume 22 Supplement 1
DCLEAR is an R package used for single cell lineage reconstruction. The advances of CRISPR-based gene editing technologies have enabled the prediction of cell lineage trees based on observed edited barcodes fr...
Just Another Gibbs Sampling (JAGS) is a convenient tool to draw posterior samples using Markov Chain Monte Carlo for Bayesian modeling. However, the built-in function dinterval() for censored data misspecifies th...
The Correction to this article has been published in BMC Bioinformatics 2022 23:238
lncRNAs play a critical role in numerous biological processes and life activities, especially diseases. Considering that traditional wet experiments for identifying uncovered lncRNA-disease associations is lim...
This article is part of a Supplement: Volume 22 Supplement 5
Given the economic and environmental importance of allopolyploids and other species with highly duplicated genomes, there is a need for methods to distinguish paralogs, i.e. duplicate sequences within a genome...
The prediction of protein secondary structures is a crucial and significant step for ab initio tertiary structure prediction which delivers the information about proteins activity and functions. As the experim...
Ontologies of precisely defined, controlled vocabularies are essential to curate the results of biological experiments such that the data are machine searchable, can be computationally analyzed, and are intero...
Although both copy number variations (CNVs) and single nucleotide variations (SNVs) detected by single-cell RNA sequencing (scRNA-seq) are used to study intratumor heterogeneity and detect clonal groups, a sof...
This article is part of a Supplement: Volume 23 Supplement 3
Genetic risk scores (GRS) summarize genetic features such as single nucleotide polymorphisms (SNPs) in a single statistic with respect to a given trait. So far, GRS are typically built using generalized linear...
Protein–protein interactions have pivotal roles in life processes, and aberrant interactions are associated with various disorders. Interaction site identification is key for understanding disease mechanisms a...
Third-generation sequencing offers some advantages over next-generation sequencing predecessors, but with the caveat of harboring a much higher error rate. Clustering-related sequences is an essential task in ...
Cell and circadian cycles control a large fraction of cell and organismal physiology by regulating large periodic transcriptional programs that encompass anywhere from 15 to 80% of the genome despite performin...
The accuracy of protein 3D structure prediction has been dramatically improved with the help of advances in deep learning. In the recent CASP14, Deepmind demonstrated that their new version of AlphaFold (AF) p...
The original article was published in BMC Bioinformatics 2020 21:534
Upland cotton provides the most natural fiber in the world. During fiber development, the quality and yield of fiber were influenced by gene transcription. Revealing sequence features related to transcription ...
Current protein family modeling methods like profile Hidden Markov Model (pHMM), k-mer based methods, and deep learning-based methods do not provide very accurate protein function prediction for proteins in the t...
Measuring similarity between complex diseases has significant implications for revealing the pathogenesis of diseases and development in the domain of biomedicine. It has been consentaneous that functional ass...
This article is part of a Supplement: Volume 23 Supplement 1
Drug–drug interactions (DDIs) are the reactions between drugs. They are compartmentalized into three types: synergistic, antagonistic and no reaction. As a rapidly developing technology, predicting DDIs-associ...
This article is part of a Supplement: Volume 23 Supplement 1
Locomotive behaviors are a rapid evaluation indicator reflecting whether the nervous system of worms is damaged, and has been proved to be sensitive to chemical toxicity. In many toxicological studies, C. elegans
To date, cancer still is one of the leading causes of death worldwide, in which the cumulative of genes carrying mutations was said to be held accountable for the establishment and development of this disease ...
A typical Copy Number Variations (CNVs) detection process based on the depth of coverage in the Whole Exome Sequencing (WES) data consists of several steps: (I) calculating the depth of coverage in sequencing ...
Drug repurposing aims at finding new targets for already developed drugs. It becomes more relevant as the cost of discovering new drugs steadily increases. To find new potential targets for a drug, an abundanc...
Transcription factor (TF) binding motifs are identified by high throughput sequencing technologies as means to capture Protein-DNA interactions. These motifs are often represented by consensus sequences in for...
In higher eukaryotes, the three-dimensional (3D) organization of the genome is intimately related to numerous key biological functions including gene expression, DNA repair and DNA replication regulations. Alt...
Long non-coding RNAs (lncRNAs) play a crucial role in diverse biological processes and have been confirmed to be concerned with various diseases. Largely uncharacterized of the physiological role and functions...
This article is part of a Supplement: Volume 22 Supplement 12
Genome-wide protein-DNA binding is popularly assessed using specific antibody pulldown in Chromatin Immunoprecipitation Sequencing (ChIP-Seq) or Cleavage Under Targets and Release Using Nuclease (CUT&RUN) sequ...
To construct gene co-expression networks, it is necessary to evaluate the correlation between different gene expression profiles. However, commonly used correlation metrics, including both linear (such as Pear...
Dengue is a common vector-borne disease in tropical countries caused by the Dengue virus. This virus may trigger a disease with several symptoms like fever, headache, nausea, vomiting, and muscle pain. Indeed,...
Differential co-expression network analysis has become an important tool to gain understanding of biological phenotypes and diseases. The CSD algorithm is a method to generate differential co-expression networ...
The investigation of possible interactions between two proteins in intracellular signaling is an expensive and laborious procedure in the wet-lab, therefore, several in silico approaches have been implemented ...
PubMed contains millions of abstracts that co-mention terms that describe drugs with other biomedical terms such as genes or diseases. Unique opportunities exist for leveraging these co-mentions by integrating...
Naturally existing and human-produced heavy metals are released into the environment and cannot be completely decomposed by microorganisms, but they continue to accumulate in water and sediments, causing organ...
This article is part of a Supplement: Volume 22 Supplement 5
Prediction of drug–drug interactions (DDIs) can reveal potential adverse pharmacological reactions between drugs in co-medication. Various methods have been proposed to address this issue. Most of them focus o...
CRISPR/Cas9 technology has become an important tool to generate targeted, highly specific genome mutations. The technology has great potential for crop improvement, as crop genomes are tailored to optimize spe...
Nerve discharge is the carrier of information transmission, which can reveal the basic rules of various nerve activities. Recognition of the nerve discharge rhythm is the key to correctly understand the dynami...
This article is part of a Supplement: Volume 22 Supplement 3
The original article was published in BMC Bioinformatics 2021 22:144
The liquid–liquid phase separation (LLPS) of biomolecules in cell underpins the formation of membraneless organelles, which are the condensates of protein, nucleic acid, or both, and play critical roles in cel...
Degeneracy—the ability of structurally different elements to perform similar functions—is a property of many biological systems. Highly degenerate systems show resilience to perturbations and damage because th...
Knowledge of protein motions is significant to understand its functions. While currently available databases for protein motions are mostly focused on overall domain motions, little attention is paid on local ...
Gene ontology (GO) enrichment analysis is frequently undertaken during exploration of various -omics data sets. Despite the wide array of tools available to biologists to perform this analysis, meaningful visu...
Generating chromosome-scale haplotype resolved assembly is important for functional studies. However, current de novo assemblers are either haploid assemblers that discard allelic information, or diploid assemble...
Quantitative trait locus (QTL) analysis allows to identify regions responsible for a trait and to associate alleles with their effect on phenotypes. When using biallelic markers to find these QTL regions, two ...
For the past decades, benefitting from the rapid growth of protein sequence data in public databases, a lot of machine learning methods have been developed to predict physicochemical properties or functions of...
Microscopic examination of human blood samples is an excellent opportunity to assess general health status and diagnose diseases. Conventional blood tests are performed in medical laboratories by specialized p...
With the development of HiC technology, more and more HiC sequencing data have been produced. Although there are dozens of packages that can turn sequencing data into contact maps, there is no appropriate tool...
Osteoporosis is a common metabolic skeletal disease and usually lacks obvious symptoms. Many individuals are not diagnosed until osteoporotic fractures occur. Bone mineral density (BMD) measured by dual-energy...
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