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Recent clinical advances in cancer immuno-therapeutics underscore the need for improved understanding of the complex relationship between cancer and the multiple, multi-functional, inter-dependent, cellular an...
Citation: BMC Bioinformatics 2021 22:197
ChIP-seq combines chromatin immunoprecipitation assays with sequencing and identifies genome-wide binding sites for DNA binding proteins. While many binding sites have strong ChIP-seq ‘peak’ observations and a...
Citation: BMC Bioinformatics 2021 22:193
The Cox proportional hazards model is commonly used to predict hazard ratio, which is the risk or probability of occurrence of an event of interest. However, the Cox proportional hazard model cannot directly g...
Citation: BMC Bioinformatics 2021 22:192
Gene Set Analysis (GSA) is arguably the method of choice for the functional interpretation of omics results. The following paper explores the popularity and the performance of all the GSA methodologies and softwa...
Citation: BMC Bioinformatics 2021 22:191
Harmonin Homogy Domains (HHD) are recently identified orphan domains of about 70 residues folded in a compact five alpha-helix bundle that proved to be versatile in terms of function, allowing for direct bindi...
Citation: BMC Bioinformatics 2021 22:190
We previously developed TANTIGEN, a comprehensive online database cataloging more than 1000 T cell epitopes and HLA ligands from 292 tumor antigens. In TANTIGEN 2.0, we significantly expanded coverage in both ...
Citation: BMC Bioinformatics 2021 22(Suppl 8):40
Despite the importance of alternative poly-adenylation and 3′ UTR length for a variety of biological phenomena, there are limited means of detecting UTR changes from standard transcriptomic data.
Citation: BMC Bioinformatics 2021 22:189
The genomics data analysis has been widely used to study disease genes and drug targets. However, the existence of missing values in genomics datasets poses a significant problem, which severely hinders the us...
Citation: BMC Bioinformatics 2021 22:188
Technological and research advances have produced large volumes of biomedical data. When represented as a network (graph), these data become useful for modeling entities and interactions in biological and simi...
Citation: BMC Bioinformatics 2021 22:187
Clustering is a crucial step in the analysis of single-cell data. Clusters identified in an unsupervised manner are typically annotated to cell types based on differentially expressed genes. In contrast, super...
Citation: BMC Bioinformatics 2021 22:186
Microsatellite instability (MSI) is a common genomic alteration in colorectal cancer, endometrial carcinoma, and other solid tumors. MSI is characterized by a high degree of polymorphism in microsatellite leng...
Citation: BMC Bioinformatics 2021 22:185
The interactions of proteins are determined by their sequences and affect the regulation of the cell cycle, signal transduction and metabolism, which is of extraordinary significance to modern proteomics resea...
Citation: BMC Bioinformatics 2021 22:184
The nucleus of eukaryotic cells spatially packages chromosomes into a hierarchical and distinct segregation that plays critical roles in maintaining transcription regulation. High-throughput methods of chromos...
Citation: BMC Bioinformatics 2021 22:183
The rapid spread of the COVID-19 demands immediate response from the scientific communities. Appropriate countermeasures mean thoughtful and educated choice of viral targets (epitopes). There are several artic...
Citation: BMC Bioinformatics 2021 22:182
The widespread use of next-generation sequencing has identified an important role for somatic mosaicism in many diseases. However, detecting low-level mosaic variants from next-generation sequencing data remai...
Citation: BMC Bioinformatics 2021 22:181
Permutation testing is often considered the “gold standard” for multi-test significance analysis, as it is an exact test requiring few assumptions about the distribution being computed. However, it can be comp...
Citation: BMC Bioinformatics 2021 22:180
The rapid advances in next-generation sequencing technologies have revolutionized the microbiome research by greatly increasing our ability to understand diversity of microbes in a given sample. Over the past ...
Citation: BMC Bioinformatics 2021 22:179
The hallmarks of cancer provide a highly cited and well-used conceptual framework for describing the processes involved in cancer cell development and tumourigenesis. However, methods for translating these hig...
Citation: BMC Bioinformatics 2021 22:178
The recent blooming of metabarcoding applications to biodiversity studies comes with some relevant methodological debates. One such issue concerns the treatment of reads by denoising or by clustering methods, ...
Citation: BMC Bioinformatics 2021 22:177
For multivariate data analysis involving only two input matrices (e.g., X and Y), the previously published methods for variable influence on projection (e.g., VIPOPLS or VIPO2PLS) are widely used for variable sel...
Citation: BMC Bioinformatics 2021 22:176
Identifying lncRNA-disease associations not only helps to better comprehend the underlying mechanisms of various human diseases at the lncRNA level but also speeds up the identification of potential biomarkers...
Citation: BMC Bioinformatics 2021 22:175
Supervised learning from high-throughput sequencing data presents many challenges. For one, the curse of dimensionality often leads to overfitting as well as issues with scalability. This can bring about inacc...
Citation: BMC Bioinformatics 2021 22:174
To address the need for easy and reliable species classification in plant genetic resources collections, we assessed the potential of five classifiers (Random Forest, Neighbour-Joining, 1-Nearest Neighbour, a ...
Citation: BMC Bioinformatics 2021 22:173
Protein post-translational modification (PTM) is a key issue to investigate the mechanism of protein’s function. With the rapid development of proteomics technology, a large amount of protein sequence data has...
Citation: BMC Bioinformatics 2021 22:171
The most common measure of association between two continuous variables is the Pearson correlation (Maronna et al. in Safari an OMC. Robust statistics, 2019. https://login.proxy.bib.uottawa.ca/login?url=https:...
Citation: BMC Bioinformatics 2021 22:170
Studies have shown that RNA secondary structure, a planar structure formed by paired bases, plays diverse vital roles in fundamental life activities and complex diseases. RNA secondary structure profile can re...
Citation: BMC Bioinformatics 2021 22:169
Women are at more than 1.5-fold higher risk for clinically relevant adverse drug events. While this higher prevalence is partially due to gender-related effects, biological sex differences likely also impact d...
Citation: BMC Bioinformatics 2021 22:168
Hepatocellular carcinoma (HCC), derived from hepatocytes, is the main histological subtype of primary liver cancer and poses a serious threat to human health due to the high incidence and poor prognosis. This stu...
Citation: BMC Bioinformatics 2021 22:167
Most transcription factors (TFs) compete with nucleosomes to gain access to their cognate binding sites. Recent studies have identified several TF-nucleosome interaction modes including end binding (EB), orien...
Citation: BMC Bioinformatics 2021 22:166
Exploring the relationship between disease and gene is of great significance for understanding the pathogenesis of disease and developing corresponding therapeutic measures. The prediction of disease-gene asso...
Citation: BMC Bioinformatics 2021 22:165
Heritability is a central measure in genetics quantifying how much of the variability observed in a trait is attributable to genetic differences. Existing methods for estimating heritability are most often bas...
Citation: BMC Bioinformatics 2021 22:164
Coronavirus Disease 2019 (COVID-19) is a viral pandemic disease that may induce severe pneumonia in humans. In this paper, we investigated the putative implication of 12 vaccines, including BCG, OPV and MMR in...
Citation: BMC Bioinformatics 2021 22:163
Hidden Markov models (HMM) are a powerful tool for analyzing biological sequences in a wide variety of applications, from profiling functional protein families to identifying functional domains. The standard m...
Citation: BMC Bioinformatics 2021 22:162
Cumulative evidence from biological experiments has confirmed that miRNAs have significant roles to diagnose and treat complex diseases. However, traditional medical experiments have limitations in time-consum...
Citation: BMC Bioinformatics 2021 22:161
As the use of nanopore sequencing for metagenomic analysis increases, tools capable of performing long-read taxonomic classification (ie. determining the composition of a sample) in a fast and accurate manner ...
Citation: BMC Bioinformatics 2021 22:160
Deep immune receptor sequencing, RepSeq, provides unprecedented opportunities for identifying and studying condition-associated T-cell clonotypes, represented by T-cell receptor (TCR) CDR3 sequences. However, ...
Citation: BMC Bioinformatics 2021 22:159
Synthetic long reads (SLR) with long-range co-barcoding information are now widely applied in genomics research. Although several tools have been developed for each specific SLR technique, a robust standalone ...
Citation: BMC Bioinformatics 2021 22:158
Large-scale biological data sets are often contaminated by noise, which can impede accurate inferences about underlying processes. Such measurement noise can arise from endogenous biological factors like cell ...
Citation: BMC Bioinformatics 2021 22:157
Translation is a fundamental process in gene expression. Ribosome profiling is a method that enables the study of transcriptome-wide translation. A fundamental, technical challenge in analyzing Ribo-Seq data i...
Citation: BMC Bioinformatics 2021 22:156
Model averaging has attracted increasing attention in recent years for the analysis of high-dimensional data. By weighting several competing statistical models suitably, model averaging attempts to achieve sta...
Citation: BMC Bioinformatics 2021 22:155
A growing body of evidence has shown the association between tuberculosis (TB) infection and lung cancer. However, the possible effect of strain‐specific behavior of Mycobacterium tuberculosis (M.tb) population, ...
Citation: BMC Bioinformatics 2021 22:154
Given expression data, gene regulatory network(GRN) inference approaches try to determine regulatory relations. However, current inference methods ignore the inherent topological characters of GRN to some exte...
Citation: BMC Bioinformatics 2021 22:153
Recent studies have confirmed that N7-methylguanosine (m7G) modification plays an important role in regulating various biological processes and has associations with multiple diseases. Wet-lab experiments are cos...
Citation: BMC Bioinformatics 2021 22:152
A number of predictive models for aquatic toxicity are available, however, the accuracy and extent of easy to use of these in silico tools in risk assessment still need further studied. This study evaluated th...
Citation: BMC Bioinformatics 2021 22:151
Currently, no proven effective drugs for the novel coronavirus disease COVID-19 exist and despite widespread vaccination campaigns, we are far short from herd immunity. The number of people who are still vulne...
Citation: BMC Bioinformatics 2021 22:150
A common approach for sequencing studies is to do joint-calling and store variants of all samples in a single file. If new samples are continually added or controls are re-used for several studies, the cost an...
Citation: BMC Bioinformatics 2021 22:149
Storage of genomic data is a major cost for the Life Sciences, effectively addressed via specialized data compression methods. For the same reasons of abundance in data production, the use of Big Data technolo...
Citation: BMC Bioinformatics 2021 22:144
Epigenome-wide association studies (EWAS) and differential gene expression analyses are generally performed on tissue samples, which consist of multiple cell types. Cell-type-specific effects of a trait, such ...
Citation: BMC Bioinformatics 2021 22:141
Spliced leader (SL) trans-splicing replaces the 5′ end of pre-mRNAs with the spliced leader, an exon derived from a specialised non-coding RNA originating from elsewhere in the genome. This process is essential f...
Citation: BMC Bioinformatics 2021 22:140
The rapidly increasing dimensionality and throughput of flow and mass cytometry data necessitate new bioinformatics tools for analysis and interpretation, and the recently emerging single-cell-based algorithms...
Citation: BMC Bioinformatics 2021 22:138
View featured videos from across the BMC-series journals
Speed
70 days to first decision for reviewed manuscripts only
44 days to first decision for all manuscripts
163 days from submission to acceptance
36 days from acceptance to publication
Citation Impact
3.242 - 2-year Impact Factor
3.213 - 5-year Impact Factor
1.156 - Source Normalized Impact per Paper (SNIP)
1.626 - SCImago Journal Rank (SJR)
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