FindCSV for Structural Variant ??, sylph: Metagenome Profiler???, START: Brain Mapping??, Nectar Production in Monocot and Dicot??
Bioinformer Weekly Roundup
Stay Updated with the Latest in Bioinformatics!
Issue: 57 | Date: 11 October 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
This study used CRISPR-Cas9 screening to identify 24 gene knockouts that enhance neural stem cell activation and neuron production in old mice. The key target identified is Slc2a4, which codes for the GLUT4 glucose transporter.
In this study a novel cell death signature (CDS) was developed using multiple datasets and machine learning to predict prognosis and immunotherapy benefits in bladder cancer. The CDS, constructed by?StepCox[backward]?+?Ridge algorithms, showed strong performance in predicting overall survival. Low CDS scores were linked to better prognosis and higher immunotherapy benefits.
Evolution of phenotypic plasticity leads to tumor heterogeneity with implications for therapy | PLOS Computational Biology? This study examines the roles of phenotypic plasticity and somatic evolution in tumour heterogeneity within glioblastoma. It identifies that cells at the tumour edge are more likely to migrate, while those in the tumour bulk tend to proliferate.
This recent study talks about PAIP1s role in regulating?alternative splicing of cancer pathway genes, including VEGFA. It suggests that binding with pre-mRNA influences gene expression and tumour development. This sheds light on PAIP1's mechanisms in cancer progression, highlighting its potential as a therapeutic target.?
In this study, researchers have refined a method for flow sorting and sequencing single nuclei from archived tissues, crucial for high-definition genomics in personalized cancer treatments. Despite challenges with low intact cell yield and variable DNA quality, this protocol ensures intact nuclei for?snDNA-seq?and includes quality control for sample prep and selection.
This study combined bulk RNA-seq and scRNA-seq to explore the molecular mechanisms of myocardial infarction (MI). The study says that MI leads to a reduction in endothelial cells and an increase in macrophages and monocytes. Endothelial cells showed higher expression of apoptosis and ferroptosis-related genes. It highlights the significant changes in the transcriptomic landscape of cardiac cells during MI.?
This study looked at how nectar is produced in two different plants: the monocot Ananas comosus (pineapple) and the dicot Nicotiana tabacum (tobacco). The study identifies that nectar production mechanisms differ between these two types of plants.?
Researchers have isolated and immortalized human pancreatic islets-derived mesenchymal stromal cells (hPD-MSCs), confirming their MSC characteristics and differentiation abilities. Transcriptomic analysis revealed unique gene expression profiles, distinguishing?hPD-MSCs from other mesenchymal cells and linking them to pancreatic function and neural development.
This study explored the role of the protein LDB1 in paediatric?T-cell acute lymphoblastic leukaemia (T-ALL). The study establishes function of LDB1 in the tumorigenesis and shows?LDB1 modulates the expression of the MYB gene through enhancer looping, highlighting its significant role in T-ALL progression.?
This study examined how seasonal changes affect miRNA expression in extracellular vesicles (EVs) within the ovarian follicular fluid of horses. It found that different seasons influence the miRNA content in these EVs, which in turn affects follicle development and ovulation.?
This study identified VWF as a key regulator in the metastasis of breast cancer exacerbated by anthracycline-based chemotherapy. The researchers found that chemotherapy drug doxorubicin increases VWF expression, which promotes cancer cell migration and evasion. Berberine, an inhibitor of VWF, effectively reduced these effects, suggesting a potential therapeutic approach to counteract chemotherapy-induced metastasis.?
??? Latest Tools
Luo’s Optimization Categorization Curve (LOCC) is an innovative tool to visualize and score continuous variables against dichotomous outcomes.??It helps select optimal cutoffs, identify survival-related variables, and rank predictors. When combined with GSEA, it can reveal key physiological pathways, enhancing our understanding of prognosis and survival.
Source code is available here.
This study introduces a novel approach using the dynamic waterwheel plant optimization algorithm (DWWPA), a novel feature selection method, to enhance diabetes classification. The DWWPA algorithm is utilized for optimizing KNN classifier parameters.
sylph is a species-level metagenome profiler that estimates genome-to-metagenome containment average nucleotide identity (ANI) through zero-inflated Poisson?k-mer?statistics, enabling ANI-based taxa detection.?
Source code is available here.
NeuroimaGene, an open-source R package, is designed to improve our understanding of disease pathophysiology by attributing neuroimaging derived features to the genetically regulated expression of provided genes or gene-sets.?
Source code is available here.
FindCSV: a long-read based method for detecting complex structural variations | BMC Bioinformatics? ?
FindCSV?is a new method that uses deep learning and consensus sequences to improve the detection of both complex and simple structural variations, which are crucial in genetic diseases and evolution. It shows reasonable accuracy in detecting structural variations in real and simulated data.
Source code is available here.
领英推荐
BioPred?is an R package?that integrates the modified loss function framework with?XGBoost?to identify predictive biomarkers.?BioPred?utilizes Extreme Gradient Boosting (XGBoost), propensity score weighting, and A-learning methods to optimize individualized treatment rules (ITR) and streamline subgroup identification.
Source code is available here.
?? Community News
Researchers have discovered that two genetic variants, APOE4 and TREM2 R47H, together cause a harmful inflammatory response in brain immune cells, particularly in females. This response leads to more severe brain damage, including tau protein clumps, which are linked to Alzheimer’s disease progression.?
Scientists at the Salk Institute have introduced Single Transcriptome Assisted Rabies Tracing (START), a new brain-mapping tool. START combines monosynaptic rabies virus tracing and single-cell transcriptomics to map neuronal connections. This tool identifies connectivity patterns of transcriptomic neuronal subtypes.?
The Nobel Prize in Medicine was awarded to Victor Ambros and Gary Ruvkun for discovering microRNA, a type of genetic switch that regulates gene expression. MicroRNAs act as switches to turn genes on and off, adding a new layer of complexity to gene regulation. This discovery has potential for developing targeted medical treatments and aid in understanding the genetic susceptibilities of diseases as well.?
The study highlights the transformative potential of single-cell genomics in microbiome research.?Researchers at Waseda University have developed a new single-cell genome technique to understand how bacteria interact and exchange genetic material, including antibiotic resistance genes. This approach, which reads information from individual cells, offers insights into microbial diversity and antibiotic resistance.?
?? Upcoming Events
This workshop is about exploring the role of small molecules in biological systems. Participants will gain hands-on experience using EMBL-EBI tools to study drug interactions with macromolecular targets and their impact on biological pathways.
This conference at EMBL Heidelberg, with a virtual attendance option, is all about mechanistic understanding of complex cellular functions through structural knowledge of macromolecules. It will highlight technological advances like cryo-electron microscopy and mass spectrometry-based proteomics, which provide structural information on molecules within intact cells.
This online symposium focuses on advanced screening technologies in drug discovery. Key opinion leaders from around the globe will discuss fragment screening, CRISPR screening, phenotypic screening, target-based approaches, and more.
?? Educational Corner
This blog post discusses how to define and analyse regions in the genome, such as?ChIP-seq peaks, gene locations, and mutation sites, using efficient data structures and tools. It also covers practical applications and methods for handling large-scale genomic data.?
This article introduces the process of mapping query datasets to annotated references using Seurat v4. It demonstrates how to map?scRNA-seq datasets to a multimodal reference, such as a CITE-seq reference, to identify cell states that are difficult to find with unsupervised analysis.??
This post delves into essential Linux commands for a beginner, enhancing understanding and usage of the system.?It also provides examples for each command, making it easy to follow and comprehend.?
This post highlights top 10 R Packages for Exploratory Data Analysis (EDA). These packages help to streamline the?data analysis workflow and gain deeper insights into the datasets.?
This guide is tailored for beginner R programmers looking to merge rows using Base R, the?dplyr?package, and the?data.table?package. Combining rows with identical column values can simplify data, reduce redundancy, and prepare datasets for further analysis.?
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