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Polyploidy is very common in plants and can be seen as one of the key drivers in the domestication of crops and the establishment of important agronomic traits. It can be the main source of genomic repatternin...
Citation: BMC Bioinformatics 2021 22:146
Telomeres, nucleoprotein structures comprising short tandem repeats and delimiting the ends of linear eukaryotic chromosomes, play an important role in the maintenance of genome stability. Therefore, the deter...
Citation: BMC Bioinformatics 2021 22:145
Recently, many computational methods have been proposed to predict cancer genes. One typical kind of method is to find the differentially expressed genes between tumour and normal samples. However, there are a...
Citation: BMC Bioinformatics 2021 22:143
Flow and mass cytometry are important modern immunology tools for measuring expression levels of multiple proteins on single cells. The goal is to better understand the mechanisms of responses on a single cell...
Citation: BMC Bioinformatics 2021 22:137
Numerous studies have demonstrated that long non-coding RNAs are related to plenty of human diseases. Therefore, it is crucial to predict potential lncRNA-disease associations for disease prognosis, diagnosis ...
Citation: BMC Bioinformatics 2021 22:136
Combined whole-genome sequencing (WGS) and RNA sequencing of cancers offer the opportunity to identify genes with altered expression due to genomic rearrangements. Somatic structural variants (SVs), as identif...
Citation: BMC Bioinformatics 2021 22:135
Significant efforts have been made in building large-scale kinetic models of cellular metabolism in the past two decades. However, most kinetic models published to date, remain focused around central carbon pa...
Citation: BMC Bioinformatics 2021 22:134
Non-coding RNA (ncRNA) and protein interactions play essential roles in various physiological and pathological processes. The experimental methods used for predicting ncRNA–protein interactions are time-consum...
Citation: BMC Bioinformatics 2021 22:133
Historical and updated information provided by time-course data collected during an entire treatment period proves to be more useful than information provided by single-point data. Accurate predictions made us...
Citation: BMC Bioinformatics 2021 22:132
Nowadays, multiple omics data are measured on the same samples in the belief that these different omics datasets represent various aspects of the underlying biological systems. Integrating these omics datasets...
Citation: BMC Bioinformatics 2021 22:131
An increasing number of clinical trials require biomarker-driven patient stratification, especially for revolutionary immune checkpoint blockade therapy. Due to the complicated interaction between a tumor and ...
Citation: BMC Bioinformatics 2021 22:127
Identification of features is a critical task in microbiome studies that is complicated by the fact that microbial data are high dimensional and heterogeneous. Masked by the complexity of the data, the problem...
Citation: BMC Bioinformatics 2021 22:126
Gene co-expression networks (GCNs) are not easily comparable due to their complex structure. In this paper, we propose a tool, Juxtapose, together with similarity measures that can be utilized for comparative ...
Citation: BMC Bioinformatics 2021 22:125
The analysis of long reads or the assessment of assembly or target capture data often necessitates running alignments against reference genomes or gene sets. The aligner outputs are often parsed automatically ...
Citation: BMC Bioinformatics 2021 22:124
Tissues are often heterogeneous in their single-cell molecular expression, and this can govern the regulation of cell fate. For the understanding of development and disease, it is important to quantify heterog...
Citation: BMC Bioinformatics 2021 22:123
Trauma-induced coagulopathy (TIC) is a disorder that occurs in one-third of severely injured trauma patients, manifesting as increased bleeding and a 4X risk of mortality. Understanding the mechanisms driving ...
Citation: BMC Bioinformatics 2021 22:122
The identification of protein families is of outstanding practical importance for in silico protein annotation and is at the basis of several bioinformatic resources. Pfam is possibly the most well known prote...
Citation: BMC Bioinformatics 2021 22:121
Recently, copy number variations (CNV) impacting genes involved in oncogenic pathways have attracted an increasing attention to manage disease susceptibility. CNV is one of the most important somatic aberratio...
Citation: BMC Bioinformatics 2021 22:120
Metagenomics is the study of microbial genomes for pathogen detection and discovery in human clinical, animal, and environmental samples via Next-Generation Sequencing (NGS). Metagenome de novo sequence assemb...
Citation: BMC Bioinformatics 2021 22:119
Metagenomics is gaining attention as a powerful tool for identifying how agricultural management practices influence human and animal health, especially in terms of potential to contribute to the spread of ant...
Citation: BMC Bioinformatics 2021 22:117
Correlation network analysis has become an integral tool to study metabolite datasets. Networks are constructed by omitting correlations between metabolites based on two thresholds—namely the r and the associated...
Citation: BMC Bioinformatics 2021 22:116
Today an unprecedented amount of genetic sequence data is stored in publicly available repositories. For decades now, mitochondrial DNA (mtDNA) has been the workhorse of genetic studies, and as a result, there...
Citation: BMC Bioinformatics 2021 22:115
Y-chromosome DNA (Y-DNA) has been used for tracing paternal lineages and offers a clear path from an individual to a known, or likely, direct paternal ancestor. The advance of next-generation sequencing (NGS) ...
Citation: BMC Bioinformatics 2021 22:114
Automated text classification has many important applications in the clinical setting; however, obtaining labelled data for training machine learning and deep learning models is often difficult and expensive. ...
Citation: BMC Bioinformatics 2021 22:113
Manual microscopic examination of Leishman/Giemsa stained thin and thick blood smear is still the “gold standard” for malaria diagnosis. One of the drawbacks of this method is that its accuracy, consistency, a...
Citation: BMC Bioinformatics 2021 22:112
Machine learning involves strategies and algorithms that may assist bioinformatics analyses in terms of data mining and knowledge discovery. In several applications, viz. in Life Sciences, it is often more imp...
Citation: BMC Bioinformatics 2021 22:110
Somatic single nucleotide variants have gained increased attention because of their role in cancer development and the widespread use of high-throughput sequencing techniques. The necessity to accurately ident...
Citation: BMC Bioinformatics 2021 22:109
Knowledge on the molecular targets of diseases and drugs is crucial for elucidating disease pathogenesis and mechanism of action of drugs, and for driving drug discovery and treatment formulation. In this rega...
Citation: BMC Bioinformatics 2021 22:108
Visual exploration of gene product behavior across multiple omic datasets can pinpoint technical limitations in data and reveal biological trends. Still, such exploration is challenging as there is a need for ...
Citation: BMC Bioinformatics 2021 22:107
VCF formatted files are the lingua franca of next-generation sequencing, whereas HL7 FHIR is emerging as a standard language for electronic health record interoperability. A growing number of FHIR-based clinic...
Citation: BMC Bioinformatics 2021 22:104
Deep learning contributes to uncovering molecular and cellular processes with highly performant algorithms. Convolutional neural networks have become the state-of-the-art tool to provide accurate and fast ima...
Citation: BMC Bioinformatics 2021 22:103
Non-targeted cytotoxics with anticancer activity are often developed through preclinical stages using response criteria observed in cell lines and xenografts. A panel of the NCI-60 cell lines is frequently the...
Citation: BMC Bioinformatics 2021 22:102
The rapid expansion of the CRISPR toolbox through tagging effector domains to either enzymatically inactive Cas9 (dCas9) or Cas9 nickase (nCas9) has led to several promising new gene editing strategies. Recent...
Citation: BMC Bioinformatics 2021 22:101
There have been many recent breakthroughs in processing and analyzing large-scale data sets in biomedical informatics. For example, the CytoGPS algorithm has enabled the use of text-based karyotypes by transfo...
Citation: BMC Bioinformatics 2021 22:100
Tracking dispersal of microbial populations in the environment requires specific detection methods that discriminate between the target strain and all potential natural and artificial interferents, including p...
Citation: BMC Bioinformatics 2021 22:98
The accumulation of various multi-omics data and computational approaches for data integration can accelerate the development of precision medicine. However, the algorithm development for multi-omics data inte...
Citation: BMC Bioinformatics 2021 22:97
microRNAs (miRNAs) have been shown to play essential roles in a wide range of biological processes. Many computational methods have been developed to identify targets of miRNAs. However, the majority of these ...
Citation: BMC Bioinformatics 2021 22:96
Numerous efforts have been poured into annotating the wealth of knowledge contained in biomedical articles. Thanks to such efforts, it is now possible to quantitatively explore relations between these annotati...
Citation: BMC Bioinformatics 2021 22:95
To effectively detect and investigate various cell-related diseases, it is essential to understand cell behaviour. The ability to detection mitotic cells is a fundamental step in diagnosing cell-related diseas...
Citation: BMC Bioinformatics 2021 22:91
Matrix factorization methods are linear models, with limited capability to model complex relations. In our work, we use tropical semiring to introduce non-linearity into matrix factorization models. We propose...
Citation: BMC Bioinformatics 2021 22:89
Prediction of the change in fold stability (ΔΔG) of a protein upon mutation is of major importance to protein engineering and screening of disease-causing variants. Many prediction methods can use 3D structura...
Citation: BMC Bioinformatics 2021 22:88
Microbes perform a fundamental economic, social, and environmental role in our society. Metagenomics makes it possible to investigate microbes in their natural environments (the complex communities) and their ...
Citation: BMC Bioinformatics 2021 22:87
The increasing number of genome-wide association studies (GWAS) has revealed several loci that are associated to multiple distinct phenotypes, suggesting the existence of pleiotropic effects. Highlighting thes...
Citation: BMC Bioinformatics 2021 22:86
Benchmarking the performance of complex analytical pipelines is an essential part of developing Lab Developed Tests (LDT). Reference samples and benchmark calls published by Genome in a Bottle (GIAB) consortiu...
Citation: BMC Bioinformatics 2021 22:85
Single-cell RNA-seq (scRNA-seq) enables the profiling of genome-wide gene expression at the single-cell level and in so doing facilitates insight into and information about cellular heterogeneity within a tiss...
Citation: BMC Bioinformatics 2021 22:83
Immunofluorescent confocal microscopy uses labeled antibodies as probes against specific macromolecules to discriminate between multiple cell types. For images of the developmental mouse lung, these cells are ...
Citation: BMC Bioinformatics 2021 22:82
A wide range of bioactive compounds is produced by enzymes and enzymatic complexes encoded in biosynthetic gene clusters (BGCs). These BGCs can be identified and functionally annotated based on their DNA seque...
Citation: BMC Bioinformatics 2021 22:81
One goal of multi-omic studies is to identify interpretable predictive models for outcomes of interest, with analytes drawn from multiple omes. Such findings could support refined biological insight and hypoth...
Citation: BMC Bioinformatics 2021 22:80
Linkage and linkage disequilibrium (LD) between genome regions cause dependencies among genomic markers. Due to family stratification in populations with non-random mating in livestock or crop, the standard me...
Citation: BMC Bioinformatics 2021 22:79
The rapid identification of pathogen clones is pivotal for effective epidemiological control strategies in hospital settings. High Resolution Melting (HRM) is a molecular biology technique suitable for fast an...
Citation: BMC Bioinformatics 2021 22:76
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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