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Antibiotic resistance has become an increasingly serious problem in the past decades. As an alternative choice, antimicrobial peptides (AMPs) have attracted lots of attention. To identify new AMPs, machine lea...
Natural products are the source of various functional materials such as medicines, and understanding their biosynthetic pathways can provide information that is helpful for their effective production through t...
The Drug Ontology (DrOn) is a modular, extensible ontology of drug products, their ingredients, and their biological activity created to enable comparative effectiveness and health services researchers to quer...
This article is part of a Supplement: Volume 20 Supplement 21
Use of medication can cause adverse drug reactions (ADRs), unwanted or unexpected events, which are a major safety concern. Drug labels, or prescribing information or package inserts, describe ADRs. Therefore,...
This article is part of a Supplement: Volume 20 Supplement 21
In the United States and parts of the world, the human papillomavirus vaccine uptake is below the prescribed coverage rate for the population. Some research have noted that dialogue that communicates the risks...
This article is part of a Supplement: Volume 20 Supplement 21
Different human responses to the same vaccine were frequently observed. For example, independent studies identified overlapping but different transcriptomic gene expression profiles in Yellow Fever vaccine 17D...
This article is part of a Supplement: Volume 20 Supplement 21
Adenosine-to-inosine RNA editing can markedly diversify the transcriptome, leading to a variety of critical molecular and biological processes in mammals. Over the past several years, researchers have develope...
This article is part of a Supplement: Volume 20 Supplement 24
Following publication of the original article [1], the author reported that an incorrect figure has been published as Figure 2. The correct Figure 2 is shown below.
The original article was published in BMC Bioinformatics 2019 20:205
Emerging evidence suggests retroviruses play a role in the pathophysiology of amyotrophic lateral sclerosis (ALS). Specifically, activation of ancient viral genes embedded in the human genome is theorized to l...
This article is part of a Supplement: Volume 20 Supplement 24
RNA sequencing technologies have allowed researchers to gain a better understanding of how the transcriptome affects disease. However, sequencing technologies often unintentionally introduce experimental error...
This article is part of a Supplement: Volume 20 Supplement 24
Ribosome profiling brings insight to the process of translation. A basic step in profile construction at transcript level is to map Ribo-seq data to transcripts, and then assign a huge number of multiple-mappe...
This article is part of a Supplement: Volume 20 Supplement 24
Signal peptides play an important role in protein sorting, which is the mechanism whereby proteins are transported to their destination. Recognition of signal peptides is an important first step in determining...
This article is part of a Supplement: Volume 20 Supplement 24
Between June 9–11, 2019, the International Conference on Intelligent Biology and Medicine (ICIBM 2019) was held in Columbus, Ohio, USA. The conference included 12 scientific sessions, five tutorials or worksho...
This article is part of a Supplement: Volume 20 Supplement 24
The Correction to this article has been published in BMC Bioinformatics 2020 21:148
Gene expression profiling experiments with few replicates lead to great variability in the estimates of gene variances. Toward this end, several moderated t-test methods have been developed to reduce this vari...
This article is part of a Supplement: Volume 20 Supplement 24
Computational prediction of a phenotypic response upon the chemical perturbation on a biological system plays an important role in drug discovery, and many other applications. Chemical fingerprints are a widel...
This article is part of a Supplement: Volume 20 Supplement 24
With the rise of metabolomics, the development of methods to address analytical challenges in the analysis of metabolomics data is of great importance. Missing values (MVs) are pervasive, yet the treatment of ...
This article is part of a Supplement: Volume 20 Supplement 24
Various statistical models have been developed to model the single cell RNA-seq expression profiles, capture its multimodality, and conduct differential gene expression test. However, for expression data gener...
This article is part of a Supplement: Volume 20 Supplement 24
Short tandem repeats (STRs) serve as genetic markers in forensic scenes due to their high polymorphism in eukaryotic genomes. A variety of STRs profiling systems have been developed for species including human...
This article is part of a Supplement: Volume 20 Supplement 24
RNA sequencing has become an increasingly affordable way to profile gene expression patterns. Here we introduce a workflow implementing several open-source softwares that can be run on a high performance compu...
This article is part of a Supplement: Volume 20 Supplement 24
Proteomic measurements, which closely reflect phenotypes, provide insights into gene expression regulations and mechanisms underlying altered phenotypes. Further, integration of data on proteome and transcript...
This article is part of a Supplement: Volume 20 Supplement 24
Skewness is an under-utilized statistical measure that captures the degree of asymmetry in the distribution of any dataset. This study applied a new metric based on skewness to identify regulators or genes tha...
This article is part of a Supplement: Volume 20 Supplement 24
Current approaches to identifying drug-drug interactions (DDIs), include safety studies during drug development and post-marketing surveillance after approval, offer important opportunities to identify potenti...
Macrophages show versatile functions in innate immunity, infectious diseases, and progression of cancers and cardiovascular diseases. These versatile functions of macrophages are conducted by different macroph...
Quantitative areas is of great measurement of wound significance in clinical trials, wound pathological analysis, and daily patient care. 2D methods cannot solve the problems caused by human body curvatures an...
Predicting protein function and structure from sequence is one important challenge for computational biology. For 26 years, most state-of-the-art approaches combined machine learning and evolutionary informati...
Following publication of the original article [1], the author explained that Table 2 is displayed incorrectly. The correct Table 2 is given below. The original article has been corrected.
The original article was published in BMC Bioinformatics 2019 20:557
Galled trees are studied as a recombination model in theoretical population genetics. This class of phylogenetic networks has been generalized to tree-child networks and other network classes by relaxing a str...
This article is part of a Supplement: Volume 20 Supplement 20
Many cancer genomes are extensively rearranged with highly aberrant chromosomal karyotypes. Structural and copy number variations in cancer genomes can be determined via abnormal mapping of sequenced reads to ...
This article is part of a Supplement: Volume 20 Supplement 20
It is now well established that eukaryotic coding genes have the ability to produce more than one type of transcript thanks to the mechanisms of alternative splicing and alternative transcription. Because of t...
This article is part of a Supplement: Volume 20 Supplement 20
Reconciliation methods are widely used to explain incongruence between a gene tree and species tree. However, the common approach of inferring maximum parsimony reconciliations (MPRs) relies on user-defined co...
This article is part of a Supplement: Volume 20 Supplement 20
In many fields of biomedical research, it is important to estimate phylogenetic distances between taxa based on low-coverage sequencing reads. Major applications are, for example, phylogeny reconstruction, spe...
This article is part of a Supplement: Volume 20 Supplement 20
Bacterial pathogens exhibit an impressive amount of genomic diversity. This diversity can be informative of evolutionary adaptations, host-pathogen interactions, and disease transmission patterns. However, cap...
This article is part of a Supplement: Volume 20 Supplement 20
Maximum parsimony reconciliation in the duplication-transfer-loss model is widely used in studying the evolutionary histories of genes and species and in studying coevolution of parasites and their hosts and p...
This article is part of a Supplement: Volume 20 Supplement 20
A basic tool for studying the polyploidization history of a genome, especially in plants, is the distribution of duplicate gene similarities in syntenically aligned regions of a genome. This distribution can u...
This article is part of a Supplement: Volume 20 Supplement 20
High-throughput technologies have brought tremendous changes to biological domains, and the resulting high-dimensional data has also posed enormous challenges to computational science. A Bayesian network is a ...
High throughput sequence data has provided in depth means of molecular characterization of populations. When recorded at numerous time steps, such data can reveal the evolutionary dynamics of the population un...
Late-Onset Alzheimer’s Disease (LOAD) is a leading form of dementia. There is no effective cure for LOAD, leaving the treatment efforts to depend on preventive cognitive therapies, which stand to benefit from ...
Development of new drugs is a time-consuming and costly process, and the cost is still increasing in recent years. However, the number of drugs approved by FDA every year per dollar spent on development is dec...
This article is part of a Supplement: Volume 20 Supplement 26
A folding RNA molecule encounters multiple opportunities to form non-native yet energetically favorable pairings of nucleotide sequences. Given this forbidding free-energy landscape, mechanisms have evolved th...
Calling genetic variations from sequence reads is an important problem in genomics. There are many existing methods for calling various types of variations. Recently, Google developed a method for calling sing...
A lack of reproducibility has been repeatedly criticized in computational research. High throughput sequencing (HTS) data analysis is a complex multi-step process. For most of the steps a range of bioinformati...
Circular DNA has recently been identified across different species including human normal and cancerous tissue, but short-read mappers are unable to align many of the reads crossing circle junctions hence limi...
Next generation sequencing instruments are providing new opportunities for comprehensive analyses of cancer genomes. The increasing availability of tumor data allows to research the complexity of cancer diseas...
In short-read DNA sequencing experiments, the read coverage is a key parameter to successfully assemble the reads and reconstruct the sequence of the input DNA. When coverage is very low, the original sequence...
The Correction to this article has been published in BMC Bioinformatics 2020 21:24
Computational compound repositioning has the potential for identifying new uses for existing drugs, and new algorithms and data source aggregation strategies provide ever-improving results via in silico metric...
Multiple Sclerosis (MS) is an immune-mediated inflammatory disease of the Central Nervous System (CNS) which damages the myelin sheath enveloping nerve cells thus causing severe physical disability in patients...
This article is part of a Supplement: Volume 20 Supplement 6
The 2nd Computational Methods for the Immune System function Workshop has been held in Madrid in conjunction with the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2018) in Madrid, Spai...
This article is part of a Supplement: Volume 20 Supplement 6
In recent years, the study of immune response behaviour using bottom up approach, Agent Based Modeling (ABM), has attracted considerable efforts. The ABM approach is a very common technique in the biological d...
This article is part of a Supplement: Volume 20 Supplement 6
Myocarditis is defined as the inflammation of the myocardium, i.e. the cardiac muscle. Among the reasons that lead to this disease, we may include infections caused by a virus, bacteria, protozoa, fungus, and ...
This article is part of a Supplement: Volume 20 Supplement 6
Neutrophils are one of the key players in the human innate immune system (HIIS). In the event of an insult where the body is exposed to inflammation triggering moieties (ITMs), neutrophils are mobilized toward...
This article is part of a Supplement: Volume 20 Supplement 6
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