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Anatomical distance has been identified as a key factor in the organizational principles of the human brain. On the other hand, criticality was proposed to accommodate the multiscale properties of human brain ...
Citation: BMC Bioinformatics 2021 22:32
Driven by deep learning, inter-residue contact/distance prediction has been significantly improved and substantially enhanced ab initio protein structure prediction. Currently, most of the distance prediction ...
Citation: BMC Bioinformatics 2021 22:30
Due to continued advances in sequencing technology, the limitation in understanding biological systems through an “-omics” lens is no longer the generation of data, but the ability to analyze it. Importantly, ...
Citation: BMC Bioinformatics 2021 22:29
Drug repositioning is an emerging approach in pharmaceutical research for identifying novel therapeutic potentials for approved drugs and discover therapies for untreated diseases. Due to its time and cost eff...
Citation: BMC Bioinformatics 2021 22:28
Currently, large-scale gene expression profiling has been successfully applied to the discovery of functional connections among diseases, genetic perturbation, and drug action. To address the cost of an ever-e...
Citation: BMC Bioinformatics 2021 22:27
Brain Computer Interfaces (BCIs) translate the activity of the nervous system to a control signal which is interpretable for an external device. Using continuous motor BCIs, the user will be able to control a ...
Citation: BMC Bioinformatics 2021 22:26
Diverse microbiome communities drive biogeochemical processes and evolution of animals in their ecosystems. Many microbiome projects have demonstrated the power of using metagenomics to understand the structur...
Citation: BMC Bioinformatics 2021 22:25
Long non-coding RNAs (lncRNAs) regulate diverse biological processes via interactions with proteins. Since the experimental methods to identify these interactions are expensive and time-consuming, many computa...
Citation: BMC Bioinformatics 2021 22:24
Copy number alterations (CNAs), due to their large impact on the genome, have been an important contributing factor to oncogenesis and metastasis. Detecting genomic alterations from the shallow-sequencing data...
Citation: BMC Bioinformatics 2021 22:23
In this study, we demonstrate that our modified Gene Set Enrichment Analysis (GSEA) method, drug perturbation GSEA (dpGSEA), can detect phenotypically relevant drug targets through a unique transcriptomic enri...
Citation: BMC Bioinformatics 2021 22:22
Computational modelling of cell biological processes is a frequently used technique to analyse the underlying mechanisms and to generally understand the behaviour of these processes in the context of a pathway...
Citation: BMC Bioinformatics 2021 22:21
Next generation sequencing (NGS) technologies have improved the study of hereditary diseases. Since the evaluation of bioinformatics pipelines is not straightforward, NGS demands effective strategies to analyz...
Citation: BMC Bioinformatics 2021 22:20
Circular RNAs (circRNAs) are widely expressed in cells and tissues and are involved in biological processes and human diseases. Recent studies have demonstrated that circRNAs can interact with RNA-binding prot...
Citation: BMC Bioinformatics 2021 22:19
The ongoing global COVID-19 pandemic is caused by SARS-CoV-2, a novel coronavirus first discovered at the end of 2019. It has led to more than 50 million confirmed cases and more than 1 million deaths across 2...
Citation: BMC Bioinformatics 2021 22:18
Querying drug-induced gene expression profiles with machine learning method is an effective way for revealing drug mechanism of actions (MOAs), which is strongly supported by the growth of large scale and high...
Citation: BMC Bioinformatics 2021 22:17
Three-way data started to gain popularity due to their increasing capacity to describe inherently multivariate and temporal events, such as biological responses, social interactions along time, urban dynamics,...
Citation: BMC Bioinformatics 2021 22:16
One of the current directions of precision medicine is the use of computational methods to aid in the diagnosis, prognosis, and treatment of disease based on data driven approaches. For instance, in oncology, ...
Citation: BMC Bioinformatics 2021 22:15
With the development of deep learning (DL), more and more methods based on deep learning are proposed and achieve state-of-the-art performance in biomedical image segmentation. However, these methods are usual...
Citation: BMC Bioinformatics 2021 22:14
Predicting the drug response of the cancer diseases through the cellular perturbation signatures under the action of specific compounds is very important in personalized medicine. In the process of testing dru...
Citation: BMC Bioinformatics 2021 22:13
Multi-locus genotype data are widely used in population genetics and disease studies. In evaluating the utility of multi-locus data, the independence of markers is commonly considered in many genomic assessmen...
Citation: BMC Bioinformatics 2021 22:12
High-throughput sequencing has increased the number of available microbial genomes recovered from isolates, single cells, and metagenomes. Accordingly, fast and comprehensive functional gene annotation pipelin...
Citation: BMC Bioinformatics 2021 22:11
Circular RNA (circRNA) is a novel type of RNA with a closed-loop structure. Increasing numbers of circRNAs are being identified in plants and animals, and recent studies have shown that circRNAs play an import...
Citation: BMC Bioinformatics 2021 22:10
Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent hi...
Citation: BMC Bioinformatics 2021 22:9
Protein inter-residue contact and distance prediction are two key intermediate steps essential to accurate protein structure prediction. Distance prediction comes in two forms: real-valued distances and ‘binne...
Citation: BMC Bioinformatics 2021 22:8
Accurate prediction of binding between class I human leukocyte antigen (HLA) and neoepitope is critical for target identification within personalized T-cell based immunotherapy. Many recent prediction tools de...
Citation: BMC Bioinformatics 2021 22:7
Multi-omics experimental approaches are becoming common practice in biological and medical sciences underlining the need to design new integrative techniques and applications to enable the multi-scale characte...
Citation: BMC Bioinformatics 2021 22:6
Single-cell RNA sequencing (scRNA-seq) enables the possibility of many in-depth transcriptomic analyses at a single-cell resolution. It’s already widely used for exploring the dynamic development process of li...
Citation: BMC Bioinformatics 2021 22:5
Statistical potentials, also named knowledge-based potentials, are scoring functions derived from empirical data that can be used to evaluate the quality of protein folds and protein–protein interaction (PPI) ...
Citation: BMC Bioinformatics 2021 22:4
Hydrogen cross-feeding microbes form a functionally important subset of the human colonic microbiota. The three major hydrogenotrophic functional groups of the colon: sulphate-reducing bacteria (SRB), methanog...
Citation: BMC Bioinformatics 2021 22:3
The relentless continuing emergence of new genomic sequencing protocols and the resulting generation of ever larger datasets continue to challenge the meaningful summarization and visualization of the underlyi...
Citation: BMC Bioinformatics 2021 22:2
Protein–peptide interactions play a fundamental role in a wide variety of biological processes, such as cell signaling, regulatory networks, immune responses, and enzyme inhibition. Peptides are characterized ...
Citation: BMC Bioinformatics 2021 22:1
As the number of RNA-seq datasets that become available to explore transcriptome diversity increases, so does the need for easy-to-use comprehensive computational workflows. Many available tools facilitate ana...
Citation: BMC Bioinformatics 2020 21(Suppl 18):578
This article is part of a Supplement: Volume 21 Supplement 18
Addiction to drugs and alcohol constitutes one of the significant factors underlying the decline in life expectancy in the US. Several context-specific reasons influence drug use and recovery. In particular em...
Citation: BMC Bioinformatics 2020 21(Suppl 18):554
This article is part of a Supplement: Volume 21 Supplement 18
Personalized cancer vaccines are emerging as one of the most promising approaches to immunotherapy of advanced cancers. However, only a small proportion of the neoepitopes generated by somatic DNA mutations in...
Citation: BMC Bioinformatics 2020 21(Suppl 18):498
This article is part of a Supplement: Volume 21 Supplement 18
Drug resistance is a critical problem limiting effective antiviral therapy for HIV/AIDS. Computational techniques for predicting drug resistance profiles from genomic data can accelerate the appropriate choice...
Citation: BMC Bioinformatics 2020 21(Suppl 18):497
This article is part of a Supplement: Volume 21 Supplement 18
In recent years, to investigate challenging bioinformatics problems, the utilization of multiple genomic and proteomic sources has become immensely popular among researchers. One such issue is feature or gene ...
Citation: BMC Bioinformatics 2020 21(Suppl 18):483
This article is part of a Supplement: Volume 21 Supplement 18
In molecular epidemiology, comparison of intra-host viral variants among infected persons is frequently used for tracing transmissions in human population and detecting viral infection outbreaks. Application o...
Citation: BMC Bioinformatics 2020 21(Suppl 18):482
This article is part of a Supplement: Volume 21 Supplement 18
Proteases are key drivers in many biological processes, in part due to their specificity towards their substrates. However, depending on the family and molecular function, they can also display substrate promi...
Citation: BMC Bioinformatics 2020 21:586
Syntactic analysis, or parsing, is a key task in natural language processing and a required component for many text mining approaches. In recent years, Universal Dependencies (UD) has emerged as the leading fo...
Citation: BMC Bioinformatics 2020 21(Suppl 23):580
This article is part of a Supplement: Volume 21 Supplement 23
Entity normalization is an important information extraction task which has gained renewed attention in the last decade, particularly in the biomedical and life science domains. In these domains, and more gener...
Citation: BMC Bioinformatics 2020 21(Suppl 23):579
This article is part of a Supplement: Volume 21 Supplement 23
An amendment to this paper has been published and can be accessed via the original article.
Citation: BMC Bioinformatics 2020 21:585
The original article was published in BMC Bioinformatics 2020 21:301
The estimation of microbial networks can provide important insight into the ecological relationships among the organisms that comprise the microbiome. However, there are a number of critical statistical challe...
Citation: BMC Bioinformatics 2020 21(Suppl 21):581
This article is part of a Supplement: Volume 21 Supplement 21
Genome assembly is fundamental for de novo genome analysis. Hybrid assembly, utilizing various sequencing technologies increases both contiguity and accuracy. While such approaches require extra costly sequencing...
Citation: BMC Bioinformatics 2020 21(Suppl 21):570
This article is part of a Supplement: Volume 21 Supplement 21
The International Association for Intelligent Biology and Medicine (IAIBM) is a nonprofit organization that promotes intelligent biology and medical science. It hosts an annual International Conference on Inte...
Citation: BMC Bioinformatics 2020 21(Suppl 21):563
This article is part of a Supplement: Volume 21 Supplement 21
In genomics, we often assume that continuous data, such as gene expression, follow a specific kind of distribution. However we rarely stop to question the validity of this assumption, or consider how broadly a...
Citation: BMC Bioinformatics 2020 21(Suppl 21):562
This article is part of a Supplement: Volume 21 Supplement 21
Short tandem repeat (STR), or “microsatellite”, is a tract of DNA in which a specific motif (typically < 10 base pairs) is repeated multiple times. STRs are abundant throughout the human genome, and specific r...
Citation: BMC Bioinformatics 2020 21(Suppl 21):542
This article is part of a Supplement: Volume 21 Supplement 21
Although genetic risk factors and network-level neuroimaging abnormalities have shown effects on cognitive performance and brain atrophy in Alzheimer’s disease (AD), little is understood about how apolipoprote...
Citation: BMC Bioinformatics 2020 21(Suppl 21):535
This article is part of a Supplement: Volume 21 Supplement 21
Cryo-EM data generated by electron tomography (ET) contains images for individual protein particles in different orientations and tilted angles. Individual cryo-EM particles can be aligned to reconstruct a 3D ...
Citation: BMC Bioinformatics 2020 21(Suppl 21):534
This article is part of a Supplement: Volume 21 Supplement 21
Fingerprint biometrics play an essential role in authentication. It remains a challenge to match fingerprints with the minutiae or ridges missing. Many fingerprints failed to match their targets due to the inc...
Citation: BMC Bioinformatics 2020 21(Suppl 21):514
This article is part of a Supplement: Volume 21 Supplement 21
Alzheimer’s disease (AD) is the most common type of dementia, typically characterized by memory loss followed by progressive cognitive decline and functional impairment. Many clinical trials of potential thera...
Citation: BMC Bioinformatics 2020 21(Suppl 21):496
This article is part of a Supplement: Volume 21 Supplement 21
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