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Membrane proteins are key gates that control various vital cellular functions. Membrane proteins are often detected using transmembrane topology prediction tools. While transmembrane topology prediction tools ...
Citation: BMC Bioinformatics 2020 21(Suppl 19):575
RNA-Seq is an increasing used methodology to study either coding and non-coding RNA expression. There are many software tools available for each phase of the RNA-Seq analysis and each of them uses different al...
Citation: BMC Bioinformatics 2020 21(Suppl 19):574
Coiled-coils are described as stable structural motifs, where two or more helices wind around each other. However, coiled-coils are associated with local mobility and intrinsic disorder. Intrinsically disorder...
Citation: BMC Bioinformatics 2020 21(Suppl 19):573
Finding relevant literature is crucial for many biomedical research activities and in the practice of evidence-based medicine. Search engines such as PubMed provide a means to search and retrieve published lit...
Citation: BMC Bioinformatics 2020 21(Suppl 19):572
Predicting physical interaction between proteins is one of the greatest challenges in computational biology. There are considerable various protein interactions and a huge number of protein sequences and synth...
Citation: BMC Bioinformatics 2020 21:584
The population growth rate is an important characteristic of any cell culture. During sustained experiments, the growth rate may vary due to competition or adaptation. For instance, in presence of a toxin or a...
Citation: BMC Bioinformatics 2020 21:583
Biomedical research projects deal with data management requirements from multiple sources like funding agencies’ guidelines, publisher policies, discipline best practices, and their own users’ needs. We descri...
Citation: BMC Bioinformatics 2020 21:582
Citation: BMC Bioinformatics 2020 21(Suppl 20):567
Protein–protein interaction (PPI) prediction is an important task towards the understanding of many bioinformatics functions and applications, such as predicting protein functions, gene-disease associations an...
Citation: BMC Bioinformatics 2020 21(Suppl 16):560
Millions of people are suffering from cancers, but accurate early diagnosis and effective treatment are still tough for all doctors. Common ways against cancer include surgical operation, radiotherapy and chem...
Citation: BMC Bioinformatics 2020 21(Suppl 16):559
Identification of de novo indels from whole genome or exome sequencing data of parent-offspring trios is a challenging task in human disease studies and clinical practices. Existing computational approaches us...
Citation: BMC Bioinformatics 2020 21(Suppl 16):547
Although biomedical publications and literature are growing rapidly, there still lacks structured knowledge that can be easily processed by computer programs. In order to extract such knowledge from plain text...
Citation: BMC Bioinformatics 2020 21(Suppl 16):543
Single-cell RNA sequencing can be used to fairly determine cell types, which is beneficial to the medical field, especially the many recent studies on COVID-19. Generally, single-cell RNA data analysis pipelin...
Citation: BMC Bioinformatics 2020 21(Suppl 16):540
Protein–protein interactions (PPIs) are of great importance in cellular systems of organisms, since they are the basis of cellular structure and function and many essential cellular processes are related to th...
Citation: BMC Bioinformatics 2020 21(Suppl 16):537
With the rapid development of medical treatment, many patients not only consider the survival time, but also care about the quality of life. Changes in physical, psychological and social functions after and du...
Citation: BMC Bioinformatics 2020 21(Suppl 16):504
Maize (Zea mays ssp. mays L.) is the most widely grown and yield crop in the world, as well as an important model organism for fundamental research of the function of genes. The functions of Maize proteins are an...
Citation: BMC Bioinformatics 2020 21(Suppl 16):420
Gene fusion events are significant sources of somatic variation across adult and pediatric cancers and are some of the most clinically-effective therapeutic targets, yet low consensus of RNA-Seq fusion predict...
Citation: BMC Bioinformatics 2020 21:577
Digital plant images are becoming increasingly important. First, given a large number of images deep learning algorithms can be trained to automatically identify plants. Second, structured image-based observat...
Citation: BMC Bioinformatics 2020 21:576
The immune checkpoint receptor programmed cell death protein I (PD-1) has been identified as a key target in immunotherapy. PD-1 reduces the risk of autoimmunity by inducing apoptosis in antigen-specific T cel...
Citation: BMC Bioinformatics 2020 21(Suppl 17):557
An effective yellow fever (YF) vaccine has been available since 1937. Nevertheless, questions regarding its use remain poorly understood, such as the ideal dose to confer immunity against the disease, the need...
Citation: BMC Bioinformatics 2020 21(Suppl 17):551
Multiple Sclerosis (MS) represents nowadays in Europe the leading cause of non-traumatic disabilities in young adults, with more than 700,000 EU cases. Although huge strides have been made over the years, MS e...
Citation: BMC Bioinformatics 2020 21(Suppl 17):550
The 3rd edition of the computational methods for the immune system function workshop has been held in San Diego, CA, in conjunction with the IEEE International Conference on Bioinformatics and Biomedicine (BIB...
Citation: BMC Bioinformatics 2020 21(Suppl 17):546
SARS-CoV-2 is a severe respiratory infection that infects humans. Its outburst entitled it as a pandemic emergence. To get a grip on this outbreak, specific preventive and therapeutic interventions are urgentl...
Citation: BMC Bioinformatics 2020 21(Suppl 17):527
The aim of a recent research project was the investigation of the mechanisms involved in the onset of type 2 diabetes in the absence of familiarity. This has led to the development of a computational model tha...
Citation: BMC Bioinformatics 2020 21(Suppl 17):508
We previously introduced PCPS (Proteasome Cleavage Prediction Server), a web-based tool to predict proteasome cleavage sites using n-grams. Here, we evaluated the ability of PCPS immunoproteasome cleavage model t...
Citation: BMC Bioinformatics 2020 21(Suppl 17):484
Prediction of patient outcome in medical intensive care units (ICU) may help for development and investigation of early interventional strategies. Several ICU scoring systems have been developed and are used t...
Citation: BMC Bioinformatics 2020 21(Suppl 17):481
In 2018, about 10 million people were found infected by tuberculosis, with approximately 1.2 million deaths worldwide. Despite these numbers have been relatively stable in recent years, tuberculosis is still c...
Citation: BMC Bioinformatics 2020 21(Suppl 17):458
The STriTuVaD project, funded by Horizon 2020, aims to test through a Phase IIb clinical trial one of the most advanced therapeutic vaccines against tuberculosis. As part of this initiative, we have developed ...
Citation: BMC Bioinformatics 2020 21(Suppl 17):449
At diagnosis tumours are typically composed of a mixture of genomically distinct malignant cell populations. Bulk sequencing of tumour samples coupled with computational deconvolution can be used to identify t...
Citation: BMC Bioinformatics 2020 21:571
Pedigree files are ubiquitously used within bioinformatics and genetics studies to convey critical information about relatedness, sex and affected status of study samples. While the text based format of ped fi...
Citation: BMC Bioinformatics 2020 21:569
Protein phosphoglycerylation, the addition of a 1,3-bisphosphoglyceric acid (1,3-BPG) to a lysine residue of a protein and thus to form a 3-phosphoglyceryl-lysine, is a reversible and non-enzymatic post-transl...
Citation: BMC Bioinformatics 2020 21:568
Drug repositioning has been an important and efficient method for discovering new uses of known drugs. Researchers have been limited to one certain type of collaborative filtering (CF) models for drug repositi...
Citation: BMC Bioinformatics 2020 21:566
RNA sequencing (RNA-seq) is an ever increasingly popular tool for transcriptome profiling. A key point to make the best use of the available data is to provide software tools that are easy to use but still pro...
Citation: BMC Bioinformatics 2020 21:565
A low replication rate has been reported in some scientific areas motivating the creation of resource intensive collaborations to estimate the replication rate by repeating individual studies. The substantial ...
Citation: BMC Bioinformatics 2020 21:564
Cancer progression reconstruction is an important development stemming from the phylogenetics field. In this context, the reconstruction of the phylogeny representing the evolutionary history presents some pec...
Citation: BMC Bioinformatics 2020 21(Suppl 1):413
Automatic segmentation and localization of lesions in mammogram (MG) images are challenging even with employing advanced methods such as deep learning (DL) methods. We developed a new model based on the archit...
Citation: BMC Bioinformatics 2020 21(Suppl 1):192
Identifying one or more biologically-active/native decoys from millions of non-native decoys is one of the major challenges in computational structural biology. The extreme lack of balance in positive and nega...
Citation: BMC Bioinformatics 2020 21(Suppl 1):189
The Damerau-Levenshtein (DL) distance metric has been widely used in the biological science. It tries to identify the similar region of DNA,RNA and protein sequences by transforming one sequence to the another...
Citation: BMC Bioinformatics 2020 21(Suppl 1):4
Partial Least-Squares Discriminant Analysis (PLS-DA) is a popular machine learning tool that is gaining increasing attention as a useful feature selector and classifier. In an effort to understand its strength...
Citation: BMC Bioinformatics 2020 21(Suppl 1):2
Gaining biological insights into molecular responses to treatments or diseases from omics data can be accomplished by gene set or pathway enrichment methods. A plethora of different tools and algorithms have b...
Citation: BMC Bioinformatics 2020 21:561
High resolution 2D whole slide imaging provides rich information about the tissue structure. This information can be a lot richer if these 2D images can be stacked into a 3D tissue volume. A 3D analysis, howev...
Citation: BMC Bioinformatics 2020 21:558
Alternative splicing isoforms have been reported as a new and robust class of diagnostic biomarkers. Over 95% of human genes are estimated to be alternatively spliced as a powerful means of producing functiona...
Citation: BMC Bioinformatics 2020 21(Suppl 9):541
This is an editorial report of the supplements to BMC Bioinformatics that includes 6 papers selected from the BIOCOMP’19—The 2019 International Conference on Bioinformatics and Computational Biology. These art...
Citation: BMC Bioinformatics 2020 21(Suppl 9):538
Cancer is one of the leading causes of morbidity and mortality in the globe. Microbiological infections account for up to 20% of the total global cancer burden. The human microbiota within each organ system is...
Citation: BMC Bioinformatics 2020 21(Suppl 9):523
Evaluating the toxicity of chemical mixture and their possible mechanism of action is still a challenge for humans and other organisms. Microarray classifier analysis has shown promise in the toxicogenomic are...
Citation: BMC Bioinformatics 2020 21(Suppl 9):239
Lung cancer is the number one cancer killer in the world with more than 142,670 deaths estimated in the United States alone in the year 2019. Consequently, there is an overreaching need to identify the key bio...
Citation: BMC Bioinformatics 2020 21(Suppl 9):218
Compositional data refer to the data that lie on a simplex, which are common in many scientific domains such as genomics, geology and economics. As the components in a composition must sum to one, traditional ...
Citation: BMC Bioinformatics 2020 21(Suppl 9):205
Traditional approaches to elucidation of protein structures by Nuclear Magnetic Resonance spectroscopy (NMR) rely on distance restraints also known as Nuclear Overhauser effects (NOEs). The use of NOEs as the ...
Citation: BMC Bioinformatics 2020 21(Suppl 9):204
Data handling in clinical bioinformatics is often inadequate. No freely available tools provide straightforward approaches for consistent, flexible metadata collection and linkage of related experimental data ...
Citation: BMC Bioinformatics 2020 21:556
Accumulating evidence has demonstrated that long non-coding RNAs (lncRNAs) are closely associated with human diseases, and it is useful for the diagnosis and treatment of diseases to get the relationships betw...
Citation: BMC Bioinformatics 2020 21:555
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