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Histone modification constitutes a basic mechanism for the genetic regulation of gene expression. In early 2000s, a powerful technique has emerged that couples chromatin immunoprecipitation with high-throughpu...
Citation: BMC Bioinformatics 2021 22:323
Assessing the nucleosome-forming potential of specific DNA sequences is important for understanding complex chromatin organization. Methods for predicting nucleosome positioning include bioinformatics and biop...
Citation: BMC Bioinformatics 2021 22:322
Nucleosome organization is involved in many regulatory activities in various organisms. However, studies integrating nucleosome organization in mammalian genomes are very limited mainly due to the lack of comp...
Citation: BMC Bioinformatics 2021 22:321
Assignment of chemical compounds to biological pathways is a crucial step to understand the relationship between the chemical repertory of an organism and its biology. Protein sequence profiles are very succes...
Citation: BMC Bioinformatics 2021 22:320
An amendment to this paper has been published and can be accessed via the original article.
Citation: BMC Bioinformatics 2021 22:319
The original article was published in BMC Bioinformatics 2021 22:198
Drug-drug interaction (DDI) is a serious public health issue. The L1000 database of the LINCS project has collected millions of genome-wide expressions induced by 20,000 small molecular compounds on 72 cell li...
Citation: BMC Bioinformatics 2021 22:318
To assign structural and functional annotations to the ever increasing amount of sequenced proteins, the main approach relies on sequence-based homology search methods, e.g. BLAST or the current state-of-the-a...
Citation: BMC Bioinformatics 2021 22:317
The novel coronavirus (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2, and within a few months, it has become a global pandemic. This forced many affected countries to take stringent me...
Citation: BMC Bioinformatics 2021 22(Suppl 6):316
This article is part of a Supplement: Volume 22 Supplement 6
Except for bacteria, the taxonomic diversity of the human fecal metagenome has not been widely studied, despite the potential importance of viruses and eukaryotes. Widely used bioinformatic tools contain limit...
Citation: BMC Bioinformatics 2021 22:312
Single-cell RNA sequencing (scRNA-Seq) experiments are gaining ground to study the molecular processes that drive normal development as well as the onset of different pathologies. Finding an effective and effi...
Citation: BMC Bioinformatics 2021 22:309
Circular RNAs (circRNAs) are a class of single-stranded RNA molecules with a closed-loop structure. A growing body of research has shown that circRNAs are closely related to the development of diseases. Becaus...
Citation: BMC Bioinformatics 2021 22:307
Even when microbial communities vary wildly in their taxonomic composition, their functional composition is often surprisingly stable. This suggests that a functional perspective could provide much deeper insi...
Citation: BMC Bioinformatics 2021 22:306
Early detection of bladder cancer remains challenging because patients with early-stage bladder cancer usually have no incentive to take cytology or cystoscopy tests if they are asymptomatic. Our goal is to fi...
Citation: BMC Bioinformatics 2021 22:305
The detection of genome variants, including point mutations, indels and structural variants, is a fundamental and challenging computational problem. We address here the problem of variant detection between two...
Citation: BMC Bioinformatics 2021 22:304
Long-read sequencing is revolutionizing genome assembly: as PacBio and Nanopore technologies become more accessible in technicity and in cost, long-read assemblers flourish and are starting to deliver chromoso...
Citation: BMC Bioinformatics 2021 22:303
Quantitative proteomics studies are often used to detect proteins that are differentially expressed across different experimental conditions. Functional enrichment analyses are then typically used to detect an...
Citation: BMC Bioinformatics 2021 22:302
Network models are well-established as very useful computational-statistical tools in cell biology. However, a genomic network model based only on gene expression data can, by definition, only infer gene co-e...
Citation: BMC Bioinformatics 2021 22:301
Accurate prognosis and identification of cancer subtypes at molecular level are important steps towards effective and personalised treatments of breast cancer. To this end, many computational methods have been...
Citation: BMC Bioinformatics 2021 22:300
Osteoarthritis (OA) is a multifactorial joint degenerative disease with low-grade inflammation. The gut microbiome has recently emerged as an pathogenic factor of OA, and prebiotics supplementation could allev...
Citation: BMC Bioinformatics 2021 22:299
RNA-Seq is a well-established technology extensively used for transcriptome profiling, allowing the analysis of coding and non-coding RNA molecules. However, this technology produces a vast amount of data requ...
Citation: BMC Bioinformatics 2021 22:298
Feature extraction of protein sequences is widely used in various research areas related to protein analysis, such as protein similarity analysis and prediction of protein functions or interactions.
Citation: BMC Bioinformatics 2021 22:297
The increasing use of whole metagenome sequencing has spurred the need to improve de novo assemblers to facilitate the discovery of unknown species and the analysis of their genomic functions. MetaVelvet-SL is...
Citation: BMC Bioinformatics 2021 22(Suppl 6):427
This article is part of a Supplement: Volume 22 Supplement 6
Coxiella burnetii is the Gram-negative bacterium responsible for Q fever in humans and coxiellosis in domesticated agricultural animals. Previous vaccination efforts with whole cell inactivated bacteria or surfac...
Citation: BMC Bioinformatics 2021 22:296
Biomedical named entity recognition is one of the most essential tasks in biomedical information extraction. Previous studies suffer from inadequate annotated datasets, especially the limited knowledge contain...
Citation: BMC Bioinformatics 2021 22:295
While some non-coding RNAs (ncRNAs) are assigned critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a f...
Citation: BMC Bioinformatics 2021 22:294
Brain wave signal recognition has gained increased attention in neuro-rehabilitation applications. This has driven the development of brain–computer interface (BCI) systems. Brain wave signals are acquired usi...
Citation: BMC Bioinformatics 2021 22(Suppl 6):195
This article is part of a Supplement: Volume 22 Supplement 6
Taxonomic assignment is a key step in the identification of human viral pathogens. Current tools for taxonomic assignment from sequencing reads based on alignment or alignment-free k-mer approaches may not perfor...
Citation: BMC Bioinformatics 2021 22(Suppl 6):194
This article is part of a Supplement: Volume 22 Supplement 6
Genomic reads from sequencing platforms contain random errors. Global correction algorithms have been developed, aiming to rectify all possible errors in the reads using generic genome-wide patterns. However, ...
Citation: BMC Bioinformatics 2021 22(Suppl 6):142
This article is part of a Supplement: Volume 22 Supplement 6
Recent advances in simultaneous measurement of RNA and protein abundances at single-cell level provide a unique opportunity to predict protein abundance from scRNA-seq data using machine learning models. Howev...
Citation: BMC Bioinformatics 2021 22(Suppl 6):139
This article is part of a Supplement: Volume 22 Supplement 6
The rapid development of single-cell RNA sequencing (scRNA-seq) enables the exploration of cell heterogeneity, which is usually done by scRNA-seq data clustering. The essence of scRNA-seq data clustering is to...
Citation: BMC Bioinformatics 2021 22(Suppl 6):130
This article is part of a Supplement: Volume 22 Supplement 6
Nucleosome plays an important role in the process of genome expression, DNA replication, DNA repair and transcription. Therefore, the research of nucleosome positioning has invariably received extensive attent...
Citation: BMC Bioinformatics 2021 22(Suppl 6):129
This article is part of a Supplement: Volume 22 Supplement 6
Understanding the functional effects of non-coding variants is important as they are often associated with gene-expression alteration and disease development. Over the past few years, many computational tools ...
Citation: BMC Bioinformatics 2021 22(Suppl 6):128
This article is part of a Supplement: Volume 22 Supplement 6
Drug repositioning, meanings finding new uses for existing drugs, which can accelerate the processing of new drugs research and development. Various computational methods have been presented to predict novel d...
Citation: BMC Bioinformatics 2021 22(Suppl 3):293
This article is part of a Supplement: Volume 22 Supplement 3
An amendment to this paper has been published and can be accessed via the original article.
Citation: BMC Bioinformatics 2021 22:292
The original article was published in BMC Bioinformatics 2021 22:60
DNA-Binding Proteins (DBP) plays a pivotal role in biological system. A mounting number of researchers are studying the mechanism and detection methods. To detect DBP, the tradition experimental method is time...
Citation: BMC Bioinformatics 2021 22(Suppl 3):291
This article is part of a Supplement: Volume 22 Supplement 3
The quality of gene annotation determines the interpretation of results obtained in transcriptomic studies. The growing number of genome sequence information calls for experimental and computational pipelines ...
Citation: BMC Bioinformatics 2021 22:290
Germline cells are important carriers of genetic and epigenetic information transmitted across generations in mammals. During the mammalian germline cell development cycle (i.e., the germline cycle), cell pote...
Citation: BMC Bioinformatics 2021 22:289
As a common and abundant RNA methylation modification, N6-methyladenosine (m6A) is widely spread in various species' transcriptomes, and it is closely related to the occurrence and development of various life pro...
Citation: BMC Bioinformatics 2021 22:288
Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capt...
Citation: BMC Bioinformatics 2021 22:287
Cancer is one of the major causes of death worldwide. To treat cancer, the use of anticancer peptides (ACPs) has attracted increased attention in recent years. ACPs are a unique group of small molecules that c...
Citation: BMC Bioinformatics 2021 22:286
Many important applications in bioinformatics, including sequence alignment and protein family profiling, employ sequence weighting schemes to mitigate the effects of non-independence of homologous sequences a...
Citation: BMC Bioinformatics 2021 22:285
Direct link between metabolism and cell and organism phenotype in health and disease makes metabolomics, a high throughput study of small molecular metabolites, an essential methodology for understanding and d...
Citation: BMC Bioinformatics 2021 22:284
The combination of the bisulfite treatment and the next-generation sequencing is an important method for methylation analysis, and aligning the bisulfite-treated reads (BS-reads) is the critical step for the d...
Citation: BMC Bioinformatics 2021 22:283
With the rapid development of accurate sequencing and assembly technologies, an increasing number of high-quality chromosome-level and haplotype-resolved assemblies of genomic sequences have been derived, from...
Citation: BMC Bioinformatics 2021 22:282
Single-cell RNA sequencing (scRNA-seq) has emerged has a main strategy to study transcriptional activity at the cellular level. Clustering analysis is routinely performed on scRNA-seq data to explore, recogniz...
Citation: BMC Bioinformatics 2021 22:280
The investigation of molecular alterations associated with the conservation and variation of DNA methylation in eukaryotes is gaining interest in the biomedical research community. Among the different determin...
Citation: BMC Bioinformatics 2021 22:278
A Correction to this paper has been published: https://doi.org/10.1186/s12859-021-03979-y
Citation: BMC Bioinformatics 2021 22:276
The original article was published in BMC Bioinformatics 2021 22:61
Histone post-translational modifications (PTMs) play an important role in our system by regulating the structure of chromatin and therefore contribute to the regulation of gene and protein expression. Irregula...
Citation: BMC Bioinformatics 2021 22:275
Clinically effective and safe genotyping relies on correct reference sequences, often represented by haplotypes. The 1000 Genomes Project recorded individual genotypes across 26 different populations and, usin...
Citation: BMC Bioinformatics 2021 22:273
Biomedical question answering (QA) is a sub-task of natural language processing in a specific domain, which aims to answer a question in the biomedical field based on one or more related passages and can provi...
Citation: BMC Bioinformatics 2021 22:272
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