??DIAMOND2GO: Rapid Gene Ontology, ?FaSTPACE for Fast Peptide Alignment, ??Long Non-Coding RNAs in Drosophila Development
Bioinformer Weekly Roundup
Stay Updated with the Latest in Bioinformatics!
Issue: 51 | Date: 23 August 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
Researchers analysed the GSE200117 dataset to pinpoint key genes and pathways in cardiac arrest (CA). They identified 844 differentially expressed genes and highlighted significant pathways related to metabolism, stimulus response, translation, and the immune system. They also identified ten hub genes, along with miRNAs and transcription factors targeting them.
Researchers analysed 120 cortical follicles from children and adults, identifying two main follicle types and noting similar transcriptional changes during growth. Variations were found in extracellular matrix, theca cells, and miRNA profiles. Cyclophosphamide dose correlated with interferon signalling in child follicles.
Using direct nanopore RNA sequencing, this research uncovers various RNA species in umbra-like virus-infected plants. The study identifies long non-coding RNAs, specific cleavage sites, and temporal- and tissue-specific RNA profiles, providing insights into viral infection mechanisms.
This study examines how long noncoding RNAs (lncRNAs) influence alternative splicing (AS) in glioblastoma multiforme (GBM), a severe brain tumour with limited treatment options. It explores the role of lncRNA-mediated AS in affecting cellular pathways, contributing to cancer malignancy and therapeutic resistance in GBM.
This study shows that next-generation sequencing (NGS) can effectively assess small or flat urothelial lesions, even with low tumour content and DNA yield. It distinguished between urothelial atypia and urothelial carcinoma by identifying mutations consistent with urothelial carcinoma in all cases.
This article explores the role of long non-coding RNAs (lncRNAs) in the development and regeneration of Drosophila imaginal discs. It identifies specific lncRNAs, such as CR40469, which are upregulated during tissue repair and are crucial for proper wing regeneration. The findings highlight the importance of lncRNAs in regulating gene expression and tissue regeneration.
This research used single-cell transcriptomics to investigate the roles of fetal membrane layers and maternal decidua in pregnancy outcomes like preterm birth (PTB) and preterm prelabour rupture of membranes (PPROM). Analysis of 18,815 genes from 13 patients identified four gene clusters linked to specific tissue layers, with key pathways including kinase activation and inflammation.
??? Latest Tools
MMINT (Metabolic Modelling Interactive Network Tool) is designed to simplify the exploration and comparison of genome-scale metabolic models (GEMs). It creates interactive visualizations of metabolic networks, derived from techniques like Flux Balance Analysis, allowing users to easily compare flux solutions and identify key metabolic drivers of phenotypes.
Tool is available here.
CCLONE (Cancer Cell Labelling On Noisy Expression) is a tool designed to address the challenges of uncertainty and sparsity in SNVs identified from scRNA-seq data. It simultaneously identifies cancer clonal populations and their associated variants.
Source code is available here.
SpatialOne is a pipeline designed for analysing 10x Visium data, utilizing advanced methods to segment, deconvolve, and quantify spatial information. It facilitates the large-scale analysis of reproducible spatial data.
Source code is available here.
cypress is an open-source R/Bioconductor package designed to perform power analysis for the cell-type-specific data. It calculates FDR, FDC, and power, under various study design parameters, including but not limited to sample size, and effect size. It takes the input of a SummarizeExperimental(SE) object with observed mixture data (feature by sample matrix), and the cell-type mixture proportions (sample by cell-type matrix).
Package is available here.
DIAMOND2GO (D2GO) is a toolset to rapidly assign Gene Ontology (GO) terms to genes or proteins based on sequence similarity searches. It also features the ability to perform enrichment analysis between subsets of data, thereby allowing rapid assignment and detection of over-represented GO-terms in novel sets of sequences.
Source code is available here.
FaSTPACE is a computational tool for aligning short peptides and extracting specificity determinants. It iteratively updates global similarity matrices until convergence, then extracts an alignment and consensus motif. It supports custom weighting for input peptides and shows improved performance on curated and high-throughput peptide datasets.
Source code is available here.
领英推荐
The tool ‘retriever’ was developed to match transcriptional signatures to drug response data, focusing on triple-negative breast cancer (TNBC). By analyzing 152 drug response profiles and 11,476 drug combinations, the combination of kinase inhibitors QL-XII-47 and GSK-690693 was identified as a promising candidate for TNBC treatment.
Tool is available here.
UnigeneFinder enhances de novo transcriptome assembly by reducing redundancy without a reference genome. It integrates clustering methods to produce accurate transcript, coding region, and protein sequences. This tool is suitable for both high-performance and personal computers.
Source code is available here.
?? Community News
Researchers from the labs of César de la Fuente and Ami S. Bhatt have explored the human gut microbiome, analysing samples from nearly 2,000 individuals. Their study, published in Cell, identified dozens of potential new antibiotics. By leveraging algorithms to decode biological information, the team aims to accelerate the discovery of antibiotics that could combat drug-resistant bacteria.
A study in Nature Medicine used the AI model ‘Surreal-GAN’ to analyse brain aging patterns in individuals aged 20-97. It is reported that this approach identified individualized brain changes, aiding in the understanding of neuroanatomical variations and early detection of neurodegenerative diseases like Alzheimer’s.
A new clinical trial will test a "paradoxical intervention" in cancer treatment, aiming to overstimulate and stress tumour cells into self-destruction. This approach, involving the drug LB-100 and WEE1 inhibitors, has been reported to show promise in preclinical studies and will be tested on patients with advanced colorectal cancer.
Using spatial transcriptomics and single-cell RNA-sequencing technologies, the researchers have discovered key insights into malaria's liver stage for understanding the disease's progression. This research uncovers the cellular mechanisms at play during the parasite's development in the liver, offering new potential targets for therapeutic intervention.
?? Upcoming Events
This webinar explores the latest techniques for analyzing gene expression in its spatial context, highlighting both the advantages and pitfalls. It provides insights into cellular interactions and tissue structure. It also explains the assumptions and modelling principles behind the computational models used for spatially resolved transcriptomics data.
?? Educational Corner
This blog from 10x Genomics discusses the importance of data normalization in single-cell RNA-seq analysis in mitigating technical variations and preserving biological signals. The post introduces several popular methods like SCTransform, BASiCS, and Scran. It outlines the key features of each method, helping readers choose the most suitable approach for their analysis.
In this post, the author explores the creation of interactive ridge plots using React and D3 for visualizing data distributions. The tutorial walks through the process of building the plot, including data transformation, SVG container setup, drawing ridge lines, and adding interactivity with tooltips and animations. The post emphasizes the utility of ridge plots in identifying patterns and trends in large datasets.
In sequencing, accuracy is a key topic, especially when comparing long-read technologies from PacBio and Oxford Nanopore (ONT). The blog post discusses how the term "accuracy" can be used interchangeably to describe different aspects of sequencing performance. It outlines the three main types of accuracy in sequencing, providing clarity on how each type is defined and measured.
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