?? REDalign for RNA Structural Alignment, ?? Quaqc: ATAC-seq quality control, ?? S. Canis in Companion Animals??, ADLF for Precision Agriculture??
Bioinformer Weekly Roundup
Stay Updated with the Latest in Bioinformatics!
Issue: 61 | Date: 08 November 2024
?? Welcome to the Bioinformer Weekly Roundup!
In this newsletter, we curate and bring you the most captivating stories, developments, and breakthroughs from the world of bioinformatics. Whether you're a seasoned researcher, a student, or simply curious about the intersection of biology and data science, we've got you covered. Subscribe now to stay ahead in the exciting realm of bioinformatics!
?? Featured Research
Streptococcus canis transcriptomic modifications in host cell entry environments of human keratinocytes | BMC Genomics
This study investigates how?Streptococcus canis?adapts its gene expression when entering human keratinocytes, a possible infection site in humans. Findings says that S.canis downregulates metabolism-related genes and upregulates transcriptional activity, potentially supporting latent infection in human cells.?
This study examines the role of MPP2 expression and DNA methylation in colorectal cancer prognosis. It suggests that low DNA methylation leads to high MPP2 expression, which is associated with poorer outcomes and impacts immune cell activity. The study also says that MPP2 may serve as potential biomarkers, with knockdown experiments showing reduced cell proliferation via the mTOR pathway.?
Intestinal commensal bacteria promote Bactrocera dorsalis larval development through the vitamin B6 synthesis pathway | Microbiome?
This study explores how gut bacteria aid the growth of?Bactrocera?dorsalis larvae under poor dietary conditions. The research highlights that certain bacterium, especially Enterobacteriaceae, enhance larval development through the vitamin B6 synthesis pathway. The findings suggest that vitamin B6 supplementation can rescue larval growth, offering insights into microbial contributions to insect development.?
The article discusses the development of the?Agro?Deep Learning Framework (ADLF) to enhance precision agriculture. By leveraging deep learning technologies, the framework processes extensive datasets, including soil moisture, temperature, and humidity, to improve decision-making and crop management.
The article explores a method for rapid bacterial identification using Volatile Organic Compounds (VOCs) analysis combined with deep learning algorithms. The study achieved high accuracy rates, with?AlexNet?producing the best results, reaching an average accuracy of 99.24% for single bacterial culture classification. This approach aims to enhance clinical diagnostics by enabling quick and precise bacterial identification, potentially reducing antimicrobial resistance.
The article discusses the creation of ultra-precise 3D maps of cancer cells, which provide detailed insights into?tumour?growth and development. These maps, developed by the Human?Tumour?Atlas Network, allow researchers to study cancer at single-cell resolution, revealing how different regions within the same?tumour?can respond differently to treatments.
This research provides a comprehensive genomic and transcriptomic analysis of 117 gastrointestinal stromal?tumours?(GISTs), revealing significant genetic heterogeneity and identifying four distinct molecular subtypes. The study highlights the role of complex genomic alterations, such as?chromothripsis?and?kataegis, in aggressive GISTs and identifies YLPM1 as a potential?tumour?suppressor gene.
This research delves into the molecular mechanisms of diabetic nephropathy (DN) using bioinformatics and meta-analysis techniques on datasets from the Gene Expression Omnibus (GEO). The study identified 911 differential gene expressions (DGEs) and highlighted 12 novel protein-coding genes related to DN. Notably, Fc Receptor-Like 6 (FCRL6) was identified as a potential biomarker, linked to poor immunoregulation in the diabetic kidney.
The study investigated the salivary microbiomes of 63 Nepali individuals representing a spectrum of lifestyles revealed how the "oral microbiome" differs from nomadic hunter gatherers to farmers to industrialized groups. The study found that lifestyle, as well as specific lifestyle factors like smoking, can shape the microbiome of individuals.
The study demonstrated that diet could influence host-microbiome interaction related to multiple sclerosis (MS), an autoimmune disease. The researchers found that β-hydroxybutyrate (βHB) and gut bacterium derived indole lactic acid (ILA) metabolite attenuated the autoimmune disease.
The study finds that almost all reprogrammed neurons are derived from the neural crest (NC) lineage. Additionally, researchers observed a large reduction in the number of reprogrammed neurons when rare proliferating NC precursors are selectively removed. The findings refute the popular theory in cellular reprogramming that, via the infusion of transcription factors, developed cell can be induced to switch its identity to a completely unrelated cell type.
The study applied Markov fields (MFs) approach to explain vaccine efficacy and immune correlations via multivariate network paths, without requiring large numbers of samples relative to multivariate features. The model approach integrated multiple data nodes and removes spurious connections between the data nodes.
??? Latest Tools
ViralPrimer is a web server designed to assist in primer design and monitoring for viral nucleic acid amplification tests, particularly for SARS-CoV-2 and Mpox. The server provides a comprehensive primer database and tools for mutation analysis. Its user-friendly interface allows for easy adaptation to monitor other rapidly mutating pathogens. ViralPrimer aims to enhance diagnostic accuracy by keeping primer sequences up to date with evolving viral genomes.
The server is freely accessible here.
MAGqual?is a pipeline designed to assess the quality of metagenome-assembled genomes (MAGs) using the MIMAG standards. Developed by researchers at the University of York, it automates the evaluation of MAG quality by analyzing completeness, contamination, and the presence of rRNA and tRNA genes. MAGqual is implemented in Snakemake, ensuring scalability and ease of use.?
The tool is open-source and available here.
InterLabelGO+ is a hybrid tool developed for improved protein function prediction by integrating deep learning and alignment-based methods. It addresses label dependency and imbalance with a novel loss function, enhancing performance through dynamic weighting. InterLabelGO+ achieved a notable 6th place in the CAFA5 challenge. The tool supports Linux and macOS systems, implemented in Python and PyTorch.
The source code and datasets are available here.
quaqc is a tool for performing ATAC-seq-specific quality control and read filtering of next-generation sequencing (NGS) data with minimal processing time and memory overhead. Developed by researchers at the Centre for Research in Agricultural Genomics, it can handle various use cases, from individual samples on personal laptops to thousands of samples in parallel on compute clusters. The accompanying R package, quaqcr, allows for interactive execution and result exploration.
Source code and documentation are available here.
CompariPSSM is a tool designed to quantify the similarity between motif binding determinants using sliding window PSSM-PSSM comparison and a randomisation-based probabilistic framework. Developed by researchers at the Institute of Cancer Research, it has been benchmarked on curated data from the Eukaryotic Linear Motif (ELM) database and experimental Proteomic Phage Display (ProP-PD) data. CompariPSSM can be used for peptide classification, clustering, and benchmarking experimental motif discovery methods.
The tool is available here.
REDalign is a novel deep learning-based tool designed for RNA secondary structural alignment, utilizing a residual encoder-decoder network. This approach captures consensus structures and optimizes alignments efficiently, significantly reducing computational complexity compared to traditional Sankoff-style algorithms. REDalign excels in handling complex RNA structures, including pseudoknots, and has demonstrated superior accuracy and computational efficiency in extensive evaluations.
The web server is available here.
BASE (Binding Affinity Similarity Explorer) is a web service developed to provide datasets for compound-protein binding affinity prediction with reduced similarity bias. This tool helps mitigate the influence of protein similarity on prediction models, promoting a more balanced use of compound, protein, and interaction features. Researchers can access bias-reduced datasets, potentially enhancing the accuracy and robustness of drug-target affinity predictions.
BASE is available online here.
?? Community News
Cyclone is a novel immunotherapy monitoring tool used in cancer related studies to measure large, diverse waves of T cell response after treatment for different time period. The tool could help clinicians to monitor and understand T cell responses over time in immunotherapy response studies.
This post discusses the newly released ChatGPT Search by OpenAI, which enables ChatGPT to search the web for information when responding to user questions. Unlike before, where it was restricted to knowledge available at the time of training, ChatGPT can now access current information from the web and provide links to its sources.
This post discusses the release of PostgreSQL 17, the newest version of the widely used open-source database. The update emphasizes performance enhancements, featuring a new memory management system for vacuum processes, optimized storage access, and improvements for handling high-concurrency workloads.
?? Educational Corner
This blog post guides readers through the process of creating interactive tables in R. It covers various packages and techniques that enable users to build dynamic and user-friendly tables, enhancing data presentation and analysis.?
This article is part of a series that provides a guide to running Nextflow community pipelines on the Seqera platform. This post covers the steps to execute and visualize protein predictions using the nf-core proteinfold pipeline on Seqera.
This article discusses methods for comparing spatial patterns in categorical raster data across overlapping regions using R. It highlights tools and techniques that facilitate the analysis and visualization of categorical spatial data, focusing on identifying patterns and differences.?
This blog post is the first part of a series focused on modernizing the Nextflow developer experience. It discusses the features of the Nextflow VS Code extension that enhance workflow development and improve the productivity of Nextflow developers.
This blog provides a step-by-step guide on how to install an R package from a private Git repository within a Dockerfile. It includes practical examples and best practices to ensure a smooth installation process.?
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