Page 1 of 227
Determining cell identity in volumetric images of tagged neuronal nuclei is an ongoing challenge in contemporary neuroscience. Frequently, cell identity is determined by aligning and matching tags to an “atlas...
Finding correlation patterns is an important goal of analyzing biological data. Currently available methods for correlation analysis mainly use non-direct associations, such as the Pearson correlation coeffici...
X chromosome inactivation (XCI) is an epigenetic phenomenon that one of two X chromosomes in females is transcriptionally silenced during early embryonic development. Skewed XCI has been reported to be associa...
The effectiveness of biclustering, simultaneous clustering of rows and columns in a data matrix, was shown in gene expression data analysis. Several researchers recognize its potentialities in other research a...
The initial step in comparing mathematical models to experimental data is to do a fit. This process can be complicated when either the mathematical models are not analytically solvable (e.g. because of nonline...
Interpretation of high-throughput gene expression data continues to require mathematical tools in data analysis that recognizes the shape of the data in high dimensions. Topological data analysis (TDA) has rec...
This article is part of a Supplement: Volume 22 Supplement 10
Gene expression is the result of the balance between transcription and degradation. Recent experimental findings have shown fine and specific regulation of RNA degradation and the presence of various molecular...
Nowadays, the inception of computer modeling and simulation in life science is a matter of fact. This is one of the reasons why regulatory authorities are open in considering in silico trials evidence for the ...
This article is part of a Supplement: Volume 22 Supplement 14
Many long non-coding RNAs (lncRNAs) have key roles in different human biologic processes and are closely linked to numerous human diseases, according to cumulative evidence. Predicting potential lncRNA-disease...
Identifying associations among biological variables is a major challenge in modern quantitative biological research, particularly given the systemic and statistical noise endemic to biological systems. Drug se...
The rapid global spread and dissemination of SARS-CoV-2 has provided the virus with numerous opportunities to develop several variants. Thus, it is critical to determine the degree of the variations and in whi...
The original article was published in BMC Bioinformatics 2021 22:553
Using DNA as a storage medium is appealing due to the information density and longevity of DNA, especially in the era of data explosion. A significant challenge in the DNA data storage area is to deal with the...
The mechanism of action for most cancer drugs is not clear. Large-scale pharmacogenomic cancer cell line datasets offer a rich resource to obtain this knowledge. Here, we present an analysis strategy for revea...
The primary determinant of crop yield is photosynthetic capacity, which is under the control of photosynthesis-related genes. Therefore, the mining of genes involved in photosynthesis is important for the stud...
Complex enzymatic models are required for analyzing kinetic data derived under conditions that may not satisfy the assumptions associated with Michaelis–Menten kinetics. To analyze these data, several software...
Stomach adenocarcinoma (STAD) is a common malignant tumor in the world and its prognosis is poor, miRNA plays a role mainly by influencing the expression of mRNAs, and participates in the occurrence and develo...
The Transmembrane Serine Protease 2 (TMPRSS2) of human cell plays a significant role in proteolytic cleavage of SARS-Cov-2 coronavirus spike protein and subsequent priming to the receptor ACE2. Approaching TMP...
When analyzing large datasets from high-throughput technologies, researchers often encounter missing quantitative measurements, which are particularly frequent in metabolomics datasets. Metabolomics, the compr...
When researchers perform gene family analysis, they often analyze the structural characteristics of the gene, such as the distribution of introns and exons. At the same time, characteristic structural analysis...
Due to the high heterogeneity, the early diagnosis and prognostic prediction of hepatic cellular cancer (HCC) is challenging. In this study, we explored the diagnostic and prognostic value of pyroptosis-relate...
Disease detection is an important aspect of biotherapy. With the development of biotechnology and computer technology, there are many methods to detect disease based on single biomarker. However, biomarker doe...
Lung cancer is one of the cancers with the highest mortality rate in China. With the rapid development of high-throughput sequencing technology and the research and application of deep learning methods in rece...
Designing oligonucleotide primers and probes is one of the key steps of various laboratory experiments such as multiplexed PCR or digital multiplexed ligation assays. When designing multiplexed primers and pro...
Boolean networks (BNs) provide an effective modelling formalism for various complex biochemical phenomena. Their long term behaviour is represented by attractors–subsets of the state space towards which the BN...
Clustered regularly interspaced short palindromic repeats (CRISPR) and their spacers are important components of prokaryotic CRISPR-Cas systems. In order to analyze the CRISPR loci of multiple genomes more int...
This article is part of a Supplement: Volume 23 Supplement 3
Archaea are a vast and unexplored domain. Bioinformatic techniques might enlighten the path to a higher quality genome annotation in varied organisms. Promoter sequences of archaea have the action of a plethor...
Gene co-expression networks (GCNs) can be used to determine gene regulation and attribute gene function to biological processes. Different high throughput technologies, including one and two-channel microarray...
A genome-wide association study (GWAS) correlates variation in the genotype with variation in the phenotype across a cohort, but the causal gene mediating that impact is often unclear. When the phenotype is pr...
Dimension reduction and variable selection play a critical role in the analysis of contemporary high-dimensional data. The semi-parametric multi-index model often serves as a reasonable model for analysis of s...
De novo genome assembly typically produces a set of contigs instead of the complete genome. Thus additional data such as genetic linkage maps, optical maps, or Hi-C data is needed to resolve the complete structur...
Recently, we developed a mathematical model for identifying putative competing endogenous RNA (ceRNA) interactions. This methodology has aroused a broad acknowledgment within the scientific community thanks to...
Current gene regulatory network (GRN) inference methods are notorious for a great number of indirect interactions hidden in the predictions. Filtering out the indirect interactions from direct ones remains an ...
Circular RNAs (circRNAs) are a class of non-coding RNAs formed by pre-mRNA back-splicing, which are widely expressed in animal/plant cells and often play an important role in regulating microRNA (miRNA) activi...
To reduce drug side effects and enhance their therapeutic effect compared with single drugs, drug combination research, combining two or more drugs, is highly important. Conducting in-vivo and in-vitro experim...
Orphan gene play an important role in the environmental stresses of many species and their identification is a critical step to understand biological functions. Moso bamboo has high ecological, economic and cu...
With the development of modern sequencing technology, hundreds of thousands of single-cell RNA-sequencing (scRNA-seq) profiles allow to explore the heterogeneity in the cell level, but it faces the challenges ...
Circular RNAs (circRNAs) play essential roles in cancer development and therapy resistance. Many studies have shown that circRNA is closely related to human health. The expression of circRNAs also affects the ...
Improving the prediction of structures, especially those containing pseudoknots (structures with crossing base pairs) is an ongoing challenge. Homology-based methods utilize structural similarities within a fa...
Drug discovery is time-consuming and costly. Machine learning, especially deep learning, shows great potential in quantitative structure–activity relationship (QSAR) modeling to accelerate drug discovery proce...
This article is part of a Supplement: Volume 23 Supplement 3
Although single-cell RNA sequencing of xenograft samples has been widely used, no comprehensive bioinformatics pipeline is available for human and mouse mixed single-cell analyses. Considering the numerous hom...
Quantification of gene expression from RNA-seq data is a prerequisite for transcriptome analysis such as differential gene expression analysis and gene co-expression network construction. Individual RNA-seq ex...
Recent deep sequencing technologies have proven to be valuable resources to gain insights into the expression profiles of diverse tRNAs. However, despite these technologies, the association of tRNAs with diver...
As many complex omics data have been generated during the last two decades, dimensionality reduction problem has been a challenging issue in better mining such data. The omics data typically consists of many f...
This article is part of a Supplement: Volume 23 Supplement 3
T cell receptors (TCRs) play critical roles in adaptive immune responses, and recent advances in genome technology have made it possible to examine the T cell receptor (TCR) repertoire at the individual sequen...
Histone Mark Modifications (HMs) are crucial actors in gene regulation, as they actively remodel chromatin to modulate transcriptional activity: aberrant combinatorial patterns of HMs have been connected with ...
Polyploidy and heterokaryosis are common and consequential genetic phenomena that increase the number of haplotypes in an organism and complicate whole-genome sequence analysis. Allele balance has been used to...
The widely spreading coronavirus disease (COVID-19) has three major spreading properties: pathogenic mutations, spatial, and temporal propagation patterns. We know the spread of the virus geographically and te...
This article is part of a Supplement: Volume 23 Supplement 3
SNARE proteins play an important role in different biological functions. This study aims to investigate the contribution of a new class of molecular descriptors (called SNARER) related to the chemical-physical...
Over the past decade, experimental procedures such as metabolic labeling for determining RNA turnover rates at the transcriptome-wide scale have been widely adopted and are now turning to single cell measureme...
View featured videos from across the BMC-series journals
Speed
15 days to first decision for all manuscripts
70 days to first decision for reviewed manuscripts only
163 days from submission to acceptance
36 days from acceptance to publication
Citation Impact
3.169 - 2-year Impact Factor
3.629 - 5-year Impact Factor
1.276 - Source Normalized Impact per Paper (SNIP)
1.567 - SCImago Journal Rank (SJR)
Usage
6,337,109 Downloads (2021)
5089 Altmetric Mentions