RNA-Seq with pathlinkR ??, ST-GEARS: Spatial 3D Downstream Research ??, scBubbletree for scRNA-seq Data ??, genAIRR in V(D)J Recombination???
Bioinformer Weekly Roundup
Stay Updated with the Latest in Bioinformatics!
Issue: 55 | Date: 20 September 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 study investigates the RAD51C gene, crucial for DNA repair, using saturation genome editing to map its functional regions. Researchers identified over 3,000 genetic variants that could increase the risk of breast and ovarian cancers, highlighting the importance of these findings for better risk assessment and personalized care. This comprehensive mapping provides valuable insights for future genetic research and clinical applications.?
The study examines the use of SGLT2 inhibitors in patients with type 2 diabetes and their potential to reduce the risk of dementia and Parkinson’s disease. Researchers found that these medications are associated with a significantly lower incidence of these neurodegenerative diseases.?
The study characterizes a new class of peptide–nucleobase hybrid natural products with a?pyrimidine?motif, derived from a?ribosomally?synthesized and post-translationally modified (RiPP) biosynthetic pathway. Researchers identified the enzymatic steps involved in forming these hybrids, expanding the chemical diversity of?RiPP?natural products.?This discovery opens avenues for creating artificial biohybrid molecules with potential applications in biotechnology and medicine.?
The study uses comprehensive bioinformatic analysis to identify pivotal genes and pathways involved in Chorea-acanthocytosis (ChAc), a rare neurodegenerative disorder. Researchers identified 27 genes linked to?ChAc, with 15 selected for further analysis. Key pathways include neuron development and ion transmembrane transport.?The findings highlight potential therapeutic targets and provide a foundation for future research.?
The study presents a graph-based method for comparing DNA sequences in closed cotton species, using weighted loop digraphs and distance measures like Cosine, Correlation, and Jaccard. This approach helps identify genetic connections and similarities without alignment, offering a new tool for bioinformatics.?The method was tested on ten cotton species, showing promising results for future optimizations.?
The study investigates the expression profiles of nearby and non-nested genes in the human genome, revealing that such genes tend to have more similar genotype tissue expression. Researchers found that gene pairs within a certain distance exhibit high expression similarity, while nested genes in opposite orientations show lower similarity.?These findings provide insights into gene regulation and expression patterns.?
The study reveals that nickel tolerance in fungi is mediated through the C-4 methyl sterol oxidase Erg25 in the sterol biosynthesis pathway. Researchers found that overexpression of Erg25 enhances nickel tolerance, while mutations in its binding pocket reduce this tolerance.?These findings highlight the critical role of Erg25 in managing nickel toxicity and suggest potential applications in biotechnology and medicine.?
The study proposes a new lineage nomenclature for dengue virus to improve genomic surveillance. It introduces two sub-genotypic levels, major and minor lineages, which are stable across phylogenetic studies. This system aims to enhance the tracking and classification of dengue virus diversity, aiding regional and global epidemiological efforts. The new nomenclature could facilitate better understanding and management of dengue outbreaks.?
??? Latest Tools
The article presents ST-GEARS, a 3D spatial transcriptomics recovery system aimed at addressing spatial distortions and improving tissue reconstruction accuracy. ST-GEARS uses Distributive Constraints and elastic fields to retrieve precise cross-sectional mappings. The system was evaluated on multiple datasets, showing structural consistency and reliable tissue regionalization.
Source code is available here.
This study introduces pathlinkR, an R package designed to streamline the analysis and interpretation of differentially expressed genes from RNA-Seq data. It integrates pathway enrichment and network-based analyses, producing publication-quality figures to help users efficiently interpret their findings and extract biological meaning from large datasets.
Source code is available?here.
This study introduces a novel approach to predict antibiotic resistance mechanisms using?ProteinBERT, a deep learning-based protein language?model. The?article highlights the tool's ability to offer enhanced interpretability by identifying biologically relevant features such as conserved amino acid residues and antibiotic target binding sites. The approach provides valuable insights into the molecular mechanisms of antibiotic resistance.?
scBubbletree?is a scalable method for visualizing?scRNA-seq data by representing cell clusters as "bubbles" at the tips of dendrograms, facilitating quantitative summaries of cell properties and relationships. It maintains expressiveness with large datasets and integrates additional information such as marker gene expression or?multiomics?data. While it provides robust quantitative assessments, the tool requires familiarity with clustering concepts and can present computational challenges for datasets with millions of cells.?
CREME is an in-silico perturbation toolkit designed to interpret the regulatory rules learned by genomic deep neural networks (DNNs). It identifies cis-regulatory elements that enhance or silence gene expression and analyzes their complex interactions. Applied to the?Enformer?DNN, CREME offers high-resolution insights into gene regulation, translating DNN predictions into mechanistic understandings of genomic regulatory architecture.?
CRUSTY is a versatile web platform for high-dimensional flow cytometry (FCM) data analysis, designed to simplify complex computations. It integrates popular algorithms for analyzing FCM data and provides interactive, real-time exploration of results. The tool generates publication-quality figures rapidly, reducing the time from data exploration to manuscript preparation.?
altAFplotter?is a user-friendly web app designed for detecting uniparental?disomies?(UPDs) using panel or exome data in NGS diagnostics, addressing a gap in most standard pipelines. The tool processes VCF files using?bcftools?and?tabix, and provides a quick, sensitive evaluation of UPDs, making it suitable for high-throughput diagnostics.??
Source code is available?here.?
PopMLvis?is an interactive tool designed for analyzing and visualizing population structure using genotype data from genome-wide association studies (GWAS). It supports various algorithms such as principal component analysis, clustering, and outlier detection, allowing researchers to explore genetic similarities across different ancestries. The platform offers features like interactive visualizations, compatibility with diverse input datasets, and dimensionality reduction.?
Source code is available?here.?
领英推荐
HiCMC?(High-Efficiency Contact Matrix Compressor) is a novel tool designed for compressing Hi-C data by leveraging the intrinsic properties of contact matrices, such as compartments and domains.?HiCMC?integrates domain-specific information into compressed bitstreams, enhancing the efficiency of downstream analyses. This platform offers better compression by utilizing the symmetry and hierarchical structures of chromosomal organization, making it optimal for large-scale genomic studies.?
Source code is available?here.?
Virus-Host Interaction Predictor (VHIP)?is a machine learning tool that predicts virus-host interactions using genomic data. Built on the Virus Host Range network (VHRnet), VHIP achieves 87.8% accuracy in identifying virus-host pairs and is unique in predicting multiple interactions, reflecting the complexity of natural ecosystems. This tool enables researchers to study virus-host networks at various scales, offering new insights into viral ecology and microbial interactions.?
Source code is available?here.
?? Community News
Researchers have developed a tool that provides new insights into cause-and-effect relationships between cells and how these change over time. This computational pipeline discovers causal and possibly time-lagged effects from cellular features and cell-cell interactions in live-cell imaging data.
Scientists have discovered the thermodynamic principles underpinning energy use in our cells. They measured how energy is arranged into different wave patterns formed in the cell’s external membrane and its internal structure, or “cytoskeleton”—both components of the cell “cortex.”
Shiny Assistant is a free specialized chatbot interface created to assist with building Shiny apps in both R and Python. Currently, it is a closed beta version, available by invite only.
A recent study reveals that cancer cells metabolize lipids not just for energy but also to evade immune detection. Researchers found that glycosphingolipids in cancer cells suppress immune signals, helping the cells avoid destruction by the immune system. Blocking lipid production using FDA-approved drugs enhances immune responses, showing promise in treating aggressive cancers like those driven by the KRAS gene mutation.
?? Upcoming Events
This workshop delves into the complexities of soil communities and how highly accurate long-read metagenome assembly can help in understanding them. It will cover the latest techniques and technologies used in metagenome assembly.
This training session focuses on the integration of spatial multi-omics, specifically how metabolites interact with RNA. It aims to provide participants with a comprehensive understanding of the latest methods and applications in spatial multi-omics, enhancing their research capabilities in this cutting-edge field.
?? Educational Corner
This is a short tutorial showing users how to convert the row name or row index of a Pandas dataframe into a column by using use Pandas reset_index() function.
This blog offers a step-by-step guide to convert FASTA files into CSV format, enabling easy integration with other metadata, quick visualization, and seamless use in machine learning applications.?
This blog discusses using the?summarytools?package in R to simplify data exploration, generate comprehensive summaries with minimal code, and enhance data understanding for better predictive modeling and production deployment.?
This article presents a Python code snippet to extract data from .CEL files, which store microarray data, and convert it into a?DataFrame. It includes a log transformation for variance stabilization, aiding in effective preprocessing for machine learning tasks such as feature selection and model training.?
The blog explains how V(D)J recombination creates diverse antigen receptors and how affinity maturation?improves antibody affinity. It also introduces?GenAIRR, a tool for analyzing these immune processes.?
This guide helps biologists deploy computational pipelines on HPC clusters, focusing on the?Slurm?resource management system. It explains the architecture of HPC clusters, including frontend, computing, and storage nodes, and how they work together to perform complex computations.?
?? Connect with Us
Stay connected and engage with us on social media for daily updates, discussions, and more!
?? Subscribe
Don't miss an issue! Subscribe to the Bioinformer Weekly Roundup and receive the latest insights directly in your inbox.
We hope you enjoyed this week's edition of the Bioinformer Weekly Roundup. Feel free to share it with your colleagues and friends who share your passion for bioinformatics!
Disclaimer: The information provided in this newsletter is for educational and informational purposes only and does not constitute professional advice.
Contact: [email protected]
Copyright ? 2024, Bioinformer Weekly Roundup. All rights reserved.