Top Research Papers on Bioinformatics

A comprehensive review comparing Venn diagram generators and application tools to assist users in selecting suitable tools for analyzing and visualizing user-defined datasets is performed.

Recent key developments in ensemble deep learning are shared and a look is looked at at how their contribution has benefited a wide range of bioinformatics research from basic sequence analysis to systems biology.

The Bio3D‐eddm package supports both experimental and theoretical simulation‐generated structures, is integrated with other methods for dissecting sequence‐structure–function relationships, and can be used in a highly automated and reproducible manner.

Nanopore sequencing is being applied in genome assembly, full-length transcript detection and base modification detection and in more specialized areas, such as rapid clinical diagnoses and outbreak surveillance.

This review collected about 100 circRNA-associated bioinformatics tools and summarized their current attributes and capabilities and performed network analysis and text mining on circRNA tool publications in order to reveal trends in their ongoing development.

The state of fully homomorphic encryption for privacy-preserving techniques in machine learning and bioinformatics is reviewed, along with descriptions of how these methods can be implemented in the encrypted domain.

Abstract Artificial intelligence (AI) systems utilizing deep neural networks and machine learning (ML) algorithms are widely used for solving critical problems in bioinformatics, biomedical informatics and precision medicine. However, complex ML models that are often perceived as opaque and black-box methods make it difficult to understand the reasoning behind their decisions. This lack of transparency can be a challenge for both end-users and decision-makers, as well as AI developers. In sensitive areas such as healthcare, explainability and accountability are not only desirable properties bu...

An historical chronicle of how R became what it is today is provided, describing all its current features and capabilities, and the role of R in science in general as a driver for reproducibility is discussed.

The challenges posed for machine learning, and, in particular, deep learning in biomedicine, are outlined, and unique opportunities for machinelearning techniques integrated with established bioinformatics approaches are suggested to overcome some of these challenges.

Detailed information is provided on utilizing the three most widely accessed tools within the MPI Bioinformatics Toolkit: HHpred for the detection of homologs, HHpred in conjunction with MODELLER for structure prediction and homology modeling, and CLANS for the visualization of relationships in large sequence datasets.

This study aimed to use bioinformatic methods to identify the key biomarkers and immune infiltration in osteoarthritis using the ConsensusClusterPlus package in R software using a consistent clustering approach.

The PyMod project is designed to act as a fully integrated interface between the popular molecular graphics viewer PyMOL, and some of the most frequently used tools for structural bioinformatics, e.g. BLAST, HMMER, Clustal, MUSCLE, PSIPRED, DOPE and MODELLER.

This work provides a comprehensive survey of emerging graph representation learning algorithms and their applications in bioinformatics from molecular level to genomics, pharmaceutical and healthcare systems level and categorize and analyze both graph embedding methods and graph neural networks.

Augur is a bioinformatics toolkit designed for phylogenetic analyses of human pathogens that must scale rapidly with the number of samples and be flexible enough to adapt to a variety of questions and organisms.

Key developments of transformer-based language models are introduced by describing the detailed structure of transformers and the common challenges, including heterogeneity of training data, computational expense and model interpretability, and opportunities in the context of bioinformatics research are identified.

The CK/PCr system acts as a dynamic biosensor based on chemo-mechanical energy transduction, which might explain why dysregulation in Cr metabolism contributes to a wide range of diseases besides the mitigating effect that Cr supplementation may have in some of these disease states.

Tools, rules and incentives are buckling under the flood of coronavirus genome sequences — to help control the pandemic, researchers need new approaches. Tools, rules and incentives are buckling under the flood of coronavirus genome sequences — to help control the pandemic, researchers need new approaches.

This review introduces bioinformatics software and tools designed for mass spectrometry-based protein identification and quantification, and then reviews the different statistical and machine learning methods that have been developed to perform comprehensive analysis in proteomics studies.

A website platform that provides interactive customizable analysis tools, including various kinds of correlation analyses, pathway enrichment analysis, weighted correlation network analysis, and other common tools and functions, and provides users with rich sources of bioinformatics analysis courses, offering a platform for researchers to share and exchange knowledge.

Cilagicin’s ability to sequester two distinct, indispensable undecaprenyl phosphates used in cell wall biosynthesis, together with the absence of detectable resistance in laboratory tests and among multidrug-resistant clinical isolates, makes it an appealing candidate for combating antibiotic-resistant pathogens.

The new version of Expasy provides an up-to-date and accurate description of high-quality resources based on a standardised ontology, allowing to connect functionally-related resources.

Microbial amplicon sequencing studies are an important tool in biological and biomedical research. Widespread 16S rRNA gene microbial surveys have shed light on the structure of many ecosystems inhabited by bacteria, including the human body. However, specialized software and algorithms are needed to convert raw sequencing data into biologically meaningful information (i.e. tables of bacterial counts). While different bioinformatic pipelines are available in a rapidly changing and improving field, users are often unaware of limitations and biases associated with individual pipelines and there ...

This Perspective highlights workflow managers, which are useful for developing and managing complex bioinformatics pipelines, and outlines community-curated pipeline initiatives that enable novice and experienced users to perform complex, best-practice analyses without having to manually assemble workflows.

Abstract The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate &a...

In this review, insights are provided into in silico epitope-based vaccine design and vaccinology procedures used for the development of the next-generation vaccines with high effectiveness.

This review aims to fill the gap that exists among (bio)informaticians, molecular geneticists and clinicians, by presenting a general overview of the NGS technology and workflow, focusing on the two main platforms Illumina and Ion Torrent.

This review summarizes commonly used computational tools for gut microbiome data analysis, which extended the understanding of the gut microbiome in health and diseases.

Food-derived bioactive peptides (FBPs) are gaining interest due to their great potential in agricultural byproduct valorization and high-activity peptide screening. The introduction of bioinformatics into FBP studies further enhances the prospects of this field. This review provides a comprehensive overview and critical insight into the latest advances in bioinformatics-driven FBPs studies. The roles of databases, proteolysis simulation, bioactivity potency evaluation, quantitative structure-activity relationships (QSAR) models, molecular docking, molecular dynamics simulation, and free energy...

The platform consists of three modules, which are pre‐configured bioinformatic pipelines, cloud toolsets, and online omics' courses, which provide a state‐of‐art platform to researchers in interactive communication and knowledge sharing.

To address the growing body of omics data and advances in laboratory techniques, VEuPathDB has added several new data types, searches and features, improved the Galaxy workspace environment, redesigned the MapVEu interface and updated the infrastructure to accommodate these changes.

In vitro experiments showed that KRT5 played the inhibitory effects on melanoma metastasis, and this bioinformatics study provided a deeper understanding of the molecular mechanisms of melan cancer metastasis.

Advanced metastasis of colon cancer makes it more difficult to treat colon cancer. Finding the markers of colon cancer (Colon Cancer) can diagnose the stage of cancer in time and improve the prognosis with timely treatment. This paper uses gene expression profiling data from The Cancer Genome Atlas (TCGA) for the diagnosis of colon cancer and its staging. In this study, we first selected the gene modules with the greatest correlation with cancer by Weighted Gene Co-expression Network Analysis (WGCNA), extracted the characteristic genes for differential expression results using the least absolu...

The meticulous study design is a key step to obtaining meaningful results, and appropriate statistical methods are important for accurate interpretation of microbiome data, and the step-by-step pipelines provide researchers with insights into newly developed bioinformatics analysis methods.

VectorBase (VectorBase.org) is part of the VEuPathDB Bioinformatics Resource Center, providing free online access to multi-omics and population biology data, focusing on arthropod vectors and invertebrates of importance to human health.

Hub genes and candidate drugs involved in OC may improve individualized diagnosis and therapy for OC in future and may produce new insights regarding OC pathogenesis and treatment.

The focus of this review is to comprehend the emerging Bulk RNA-Seq-based analyses, emphasizing less familiar and underused applications and highlighting the power of bulk RNA- Seq in providing biological insights.

This work trained commonly used machine learning classifiers to predict antibacterial or antifungal activity based on features of known natural product biosynthetic gene clusters and identified classifiers that can attain accuracies as high as 80% and that have enabled the identification of biosynthesis enzymes and their corresponding molecular features that are associated with antibiotic activity.

CCL5, CXCR4, GZMA, and CD8A can be used as diagnostic biomarker for RA, and the correlation between immune cells and biomarkers showed that CCL5 was positively correlated with M1 macrophages, CxCR4 was positive correlated with memory activated CD4+ T cells and follicular helper T (Tfh) cells, and GZma was positively correlation with Tfh cells.

It is found that an increased infiltration of moncytes, while NK cells resting infiltrated less may be related to the occurrence of SLE, and IFI27 may be a new candidate molecular marker of the occurrence and progression of Sle.

Drug–gene interactions analysis suggests amsacrine, BRD-K68548958, naproxol, palbociclib and teniposide as the top-scored repurposed drugs.