??Nanogripper to Grab Virus, ??Hetian Sheep: Hair Follicle Transcriptome, ??S. anginosus in Gastric Cancer, ??COCONUT 2.0: Natural Products Database??
Bioinformer Weekly Roundup
Stay Updated with the Latest in Bioinformatics!
Issue: 64 | Date: 29 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
The article analyses variants of uncertain significance (VUSs) in genomic data using bioinformatics tools. It classifies and interprets VUSs, providing insights into their potential pathogenicity and implications for genetic research and clinical practice. The study highlights the challenges and advancements in understanding VUSs.?
This article investigates the relationship between COVID-19 severity and T cell receptor diversity. It finds correlations between T cell receptor diversity and disease severity, suggesting potential biomarkers for predicting COVID-19 outcomes. These findings could help in developing targeted therapies for severe cases.?
The article identifies genetic loci affecting the main stem node number (MSN) in soybeans using QTL mapping across multiple environments. It highlights several QTLs, including a major QTL on chromosome 6, which influence MSN and could aid in soybean breeding programs.?
The article refines the understanding of SARS-CoV-2 intra-host variation by analysing large-scale sequencing data. It enhances the detection of intra-host single nucleotide variants (iSNVs), offering understanding about viral adaptation mechanisms. This detection is useful for predicting and mitigating future viral threats.
The article studies the transcriptome of hair follicles in Hetian sheep during different growth periods. It identifies differentially expressed genes and lncRNAs, giving details about hair follicle development and potential improvements in wool quality. These findings contribute to the understanding of genetic regulation in sheep.?
Regulatory Element Analysis and Comparative Genomics Study of Heavy Metal-Resistant Genes in the Complete Genome of Cupriavidus gilardii CR3 | Sage Journals ?
A recent study?analysed?the complete genome of?Cupriavidus?gilardii?CR3?to identify and compare regulatory elements and heavy metal-resistant genes. The research revealed specific genetic mechanisms that enable the bacterium to resist heavy metals, providing info about potential bioremediation applications. This study enhances our understanding of bacterial resistance and could inform future environmental and industrial strategies.?
The article identifies three key autophagy-related genes (CCL2, LAMP2, CTSB) linked to advanced carotid atherosclerosis. These genes are potential diagnostic markers and therapeutic targets for the disease. This study underscores the importance of autophagy in the progression of atherosclerosis and its potential for clinical applications.?
Characterization of the landscape of the intratumoral microbiota reveals that Streptococcus anginosus increases the risk of gastric cancer initiation and progression | Cell Discovery?
Recent research has identified Streptococcus?anginosus?within?tumour?tissues as a significant factor that increases the risk of initiating and progressing gastric cancer. This bacterium has been found to encourage?tumour?cell growth and spread, while also suppressing the immune system. These discoveries suggest that targeting Streptococcus?anginosus?could be crucial in diagnosing and treating gastric cancer.?
??? Latest Tools
This web resource offers enhanced tools for studying mammalian genomes. Recent updates include expanded annotations for long non-coding RNAs (lncRNAs) and transcribed cis-regulatory elements (CREs), accessible via platforms like ZENBU-Reports and fanta.bio.
It is openly accessible here.
COCONUT 2.0 is an updated version of the COCONUT database, a major resource for natural product data. It includes chemical structures, species and organism parts, geographic information, and literature references. The latest version features a rewritten web application, newly assembled and curated data, and supports user submissions and community curation.
It is freely accessible here.
REDIportal is a specialized database for A-to-I RNA editing. It integrates data from the TCGA project and connects with resources like Ensembl and UniProt. The latest version includes information on RNA editing in double-stranded RNAs and an extended catalog of recoding events.
REDIportal is available here.
This new C toolkit is designed for alignment-free analysis of multi-FASTA data, ideal for large viral genome datasets. It identifies patterns and temporal dynamics in sequences, filtering low-quality data automatically. AltaiR supports multithreading as well.
The toolkit is freely available here.
Repun is a haplotype-aware variant-alignment unification algorithm. It harmonizes variant representation across different sequencing platforms. It aligns variants with sequencing data before variant calling. Repun uses phasing to match haplotypes, claiming over 99.99% precision and 99.5% recall in evaluations.
Repun is open-source and available here.
TPepPro is a Transformer-based model designed for predicting peptide-protein interactions (PepPIs). It combines local protein sequence and global protein structure feature extraction, optimizing the neural network architecture to reduce computational resource requirements.
The source code is available here.
SAMP is an ensemble learning model for predicting antimicrobial peptides (AMPs) using a new feature called proportionalized split amino acid composition (PSAAC). It captures residue patterns and sequence order information, outperforming existing methods in accuracy and other metrics. SAMP is claimed to be scalable for large-scale AMP identification.
It is available as a Python package here.
MoAGL-SA is an adaptive multi-omics integration method that uses graph learning and self-attention to improve cancer subtype classification. It generates patient relationship graphs, extracts omics-specific embeddings with graph convolutional networks, and uses self-attention for integration. MoAGL-SA identifies key biomarkers for various cancers.
MoAGL-SA is implemented in Python and is available on GitHub here.
CHARMER is an end-to-end pipeline for chromatin conformation capture (CCC) assays like Hi-C and Capture Hi-C (CHiC). It is reported that it generates statistically significant, harmonized chromatin interactions in a consistent BED-like format across various cell and tissue types.
CHARMER is freely available here.
TreeWave is a command-line tool designed for alignment-free phylogeny reconstruction using graphical representation of DNA sequences and genomic signal processing. It leverages Frequency Chaos Game Representation (FCGR) and Discrete Wavelet Transform (DWT) to analyse large genomic datasets, providing phylogenetic trees with reduced computational time comparatively.
TreeWave is available here.
?? Community News
Researchers have used high-resolution cryo-electron microscopy to uncover new details about the action of DNA gyrase, a crucial bacterial enzyme. This enzyme, which helps in supercoiling DNA, is a key target for antibiotics. The study provides insights that could aid in developing new antibiotics to combat resistant bacterial strains.?
Researchers have developed a nanorobotic hand made of DNA, called the NanoGripper, which can detect and block viruses. The NanoGripper can rapidly identify viruses like COVID-19 by grabbing them, aiding in diagnostics. It can also prevent viruses from entering cells, serving as a preventive measure. The device could be adapted for other viruses and used for targeted drug delivery. This advancement highlights the potential of DNA-based nanotechnology in medical applications.
Researchers have mapped the activity of repair proteins in individual human cells, revealing how these proteins collaborate in "hubs" to repair DNA damage. These hubs function like "repair cafés," where multiple damaged DNA regions are brought together for efficient repair. The study highlights the importance of these hubs in maintaining genomic integrity and could lead to treatments for diseases involving DNA damage, such as cancer.
Wobble Genomics Developing Breast Cancer Dx Based on Sensitive RNA Detection Tech | Wobble Genomics?
Wobble Genomics is developing a diagnostic platform for breast cancer using predictive RNA biomarkers. Their technology captures rare and low-abundance RNA transcripts, enabling early detection of the disease. The platform includes methods like Level-Up for normalizing low-abundance RNA molecules and TAMA for identifying novel RNA signals.?
?? Upcoming Events
This interactive workshop aims to discuss the professional roles and competencies required to implement AI in research infrastructures (RIs) and Core Facilities (CFs), identify training gaps, and share current actions addressing these needs. Attendees will engage in discussions, group work, and presentations to explore how different organizations support AI for research, the essential roles and competencies needed, and the main training challenges and needs. The workshop aims to enhance participants’ understanding of AI implementation in research contexts.
?? Educational Corner
The web resource offers a tutorial on amplicon analysis using QIIME2. The topic covers examining the quality of the dataset, selecting sequence variant using Dada2 and Deblur. In addition, the tutorial includes taxonomic analysis, abundant analysis, Gneiss analysis and phylogenetic tree generation are being covered.?
This blog discusses the widely used text editors VI and VIM and explores the fundamentals of using them to edit text files on Linux systems.
This blog delves into various platforms for deploying R Shiny apps, examining the most common options along with their advantages and disadvantages.?It focuses on five key aspects for comparison: authentication requirements, security requirements, scaling requirements, operation management overhead tolerance, and investment.?
The blog introduces readers to key statistical concepts such as?effect size, statistical power, significance level, and sample size. The analysis is being done in python.?
This blog demonstrates various methods for comparing strings in R, offering different examples and an exercise.?
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