??RBC-GEM: Genomic Metabolic Model Tool, ???SCEMENT for scRNA-Seq Integration, ??BeeR: New Protein for Drug Delivery??
Bioinformer Weekly Roundup
Stay Updated with the Latest in Bioinformatics!
Issue: 78 | Date: 21 March 2025
?? 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 are a seasoned researcher, a student, or simply curious about the intersection of biology and data science, we have got you covered. Subscribe now to stay ahead in the exciting realm of Bioinformatics!
?? Featured Research
This study presents the largest mRNA expression atlas for ducks, covering 1,257 tissue samples across 30 tissue types. It identifies co-expression network clusters and 27 housekeeping genes and explores sex-biased gene expression patterns and specific profiles in meat-type and egg-type ducks. The findings provide valuable insights into the genetic basis of duck productivity.?
This study introduces?RegionIndel, a pipeline for detecting large indel structural variants (SVs) in region-based phased diploid assemblies using linked-reads. Appling to sample HG002,?it is claimed that RegionIndel?demonstrated high accuracy in identifying deletions and insertions, outperforming other SV callers. The phased diploid contigs enable detailed investigation of SVs alongside nearby SNPs and small indels.?
This study investigates the role of the immune molecule TGFβ in linking SARS-CoV-2 infection to multisystem inflammatory syndrome in children (MIS-C). The research reveals that TGFβ weakens immune defences against latent viruses, leading to the reactivation of Epstein-Barr virus (EBV). This mechanism contributes to the severe inflammatory response observed in MIS-C, providing insights that could inform therapeutic strategies.?
Prior knowledge on context-driven DNA fragmentation probabilities can improve de novo genome assembly algorithms | bioRxiv
This study explores how prior knowledge of context-driven DNA fragmentation probabilities can enhance de novo genome assembly algorithms. By parameterizing k-mer?assigned breakage probabilities, the approach improves assembly accuracy for highly degraded DNA samples and ultrashort sequencing reads. These findings could advance algorithms for cell-free, ancient, and forensic DNA research.?
This study introduces?NicheCompass, a graph-based deep learning method for identifying and characterizing cell niches in spatial omics data. It models cellular communication to derive interpretable embeddings, enabling the analysis of tissue architecture and?tumour?niches. The method integrates spatial multi-omics data and constructs a spatial atlas of 8.4 million cells, demonstrating scalability and cross-technology compatibility.?
The research explores the effects of amino acid insertions and deletions (indels) on protein stability and function using deep indel mutagenesis. It highlights the variability of indel impacts across proteins and introduces?INDELi, a predictive model combining substitution effects and structural data. The study also examines indels' roles in protein-protein interactions and their potential as gain-of-function variants.?
This work evaluates the feasibility of achieving species-level resolution using short-read sequencing of multiple 16S rRNA variable regions. Employing a new sequencing kit and bioinformatics pipeline, the study demonstrates accurate species identification and reproducibility. It also assesses the impact of sample collection methods on microbiome analysis outcomes.
The study investigates the genetic link between moderate to severe asthma and early-stage lung adenocarcinoma (LUAD) using bioinformatic methods. It employs weighted gene co-expression network analysis and protein-protein interaction network analysis to identify hub genes. Gene ontology and pathway-enrichment analyses are conducted to detect biological functions related to these genes. Receiver operating characteristic (ROC) curves are used to confirm the diagnostic value of the identified hub genes.
Staphylococcus aureus ST764-SCCmecII high-risk clone in bloodstream infections revealed through national genomic surveillance integrating clinical data | Nature Communications
The study focuses on the national genomic surveillance of methicillin-resistant Staphylococcus aureus (MRSA) in Japan, integrating clinical data from bloodstream infections. Researchers performed genome sequencing and antimicrobial susceptibility testing on 580 S. aureus isolates collected between 2019 and 2020. The study highlights the emergence of the high-risk MRSA clone ST764-SCCmecII.
The study presents a method for tracking gene transfer in microbial communities using a universal RNA barcoding system. Researchers developed a synthetic catalytic RNA to barcode ribosomal RNA (rRNA) within living cells. This technique allows for the monitoring of gene transfer across diverse microbial species without disrupting their natural environment. The method leverages 16S rRNA sequencing to identify different bacterial species and track the acquisition of foreign DNA, providing insights into gene transfer dynamics.
This study identifies lysine methacrylation (Kmea) sites on a non-histone protein, Cyclophillin A (CypA), and explores their functions using a genetic code expansion approach. The research reveals that Kmea at CypA site 125 regulates cellular redox homeostasis and that HDAC1 is the regulator of Kmea on CypA. Additionally, Kmea can be further methylated to ε-N-methyl-ε-N-methacrylation (Kmemea) in live cells.
This study evaluates VG161, an engineered oncolytic herpes simplex virus, in patients with advanced liver cancer. The phase 1 clinical trial shows VG161 is well-tolerated and effective in reshaping the tumour immune microenvironment and re-sensitizing resistant tumours. The study also develops a gene-based model to predict patient response and overall survival, positioning VG161 as a promising third-line treatment for refractory hepatocellular carcinoma.
This study examines the role of PHF2 in lipid metabolism within adipose tissue and the liver. It finds that PHF2 enhances adipogenesis and lipid storage in adipose tissue but suppresses de novo lipogenesis and tumour progression in liver cancer. The research highlights PHF2's dual role as both an epigenetic regulator and an E3 ubiquitin ligase, impacting lipid metabolism and immune cell infiltration in different tissues.?
This study develops and validates an immune signature-based risk model for prognostic assessment in melanoma. By analysing transcriptomic data, the model identifies nine immune features significantly associated with prognosis. The model effectively stratifies patients into high-risk and low-risk groups with distinct survival outcomes. It also explores the relationship between the risk model and genomic heterogeneity, metabolic pathways, and immune infiltration, providing insights for personalized melanoma treatment.
??? Latest Tools
This study introduces a clinical knowledge graph-based tool designed to prioritize candidate genes for diagnosing Mendelian diseases and rare genetic conditions. The tool integrates diverse data sources to enhance gene prioritization accuracy.
Source Code is available here.
The research presents a tool that applies transfer learning to the accelerated failure time model using microarray data. This tool aims to improve survival time predictions by leveraging knowledge from related datasets.
Source Code is available here.
This study validates a web application tool that uses genetic distance metrics to determine species boundaries and assist in helminth identification. The tool aims to enhance the accuracy and efficiency of species identification.
Source Code is available here.
SCEMENT is a scalable and memory-efficient tool for integrating large-scale single-cell RNA-sequencing data. The study details its approach to data integration, highlighting its efficiency and applicability in single-cell analysis.
Source Code is available here.
This study introduces sciRED, a method for interpretable single-cell factor decomposition. It explains the algorithm and its application in breaking down complex single-cell RNA-sequencing data into understandable factors.
Source Code is available here.
AcImpute is a novel approach for imputing single-cell RNA sequencing data using constraint-enhancing smooth-based techniques. The study outlines the methodology and its effectiveness in addressing missing data issues in single-cell RNA-sequencing.
Source Code is available here.
paraCell is a tool for the interactive analysis and visualization of both standard and dual host-parasite single-cell RNA-seq data. The study highlights its functionalities and applications in understanding complex single-cell interactions.
Source Code is available here.
The paper introduces RBC-GEM, a genome-scale metabolic model tool for the systems biology study of human red blood cells. This tool provides insights into red blood cell metabolism and its implications for health and disease.
Source Code is available here.
This research proposes TphPMF, a tool for imputing missing microbiome data using hierarchical Bayesian Probabilistic Matrix Factorization. The tool addresses data sparsity issues to improve the accuracy of microbiome data analysis.
Source Code is available here.
?? Community News
Researchers at the University of Houston found that Tunnelling Nanotube-Like Structures (TNTLs) are crucial for heart formation. TNTLs enable communication between cardiomyocytes and endocardial cells, transporting signalling molecules and proteins essential for ventricular wall development.?
Researchers at Rice University have uncovered new insights into the molecular mechanisms of ADAR1, a protein that regulates RNA-induced immune responses. Their findings reveal how ADAR1's RNA editing activity depends on RNA sequence, duplex length, and mismatches. These insights could lead to novel therapeutic strategies for autoimmune diseases and cancer immunotherapy.?
Researchers at Tianjin Medical University discovered that the NKD2 protein regulates bone cell differentiation. NKD2 enhances osteoblast formation, inhibits adipocyte formation, and suppresses osteoclast activity, offering potential therapeutic targets for osteoporosis.?
Researchers at King's College London discovered a new protein,?BeeR, in soil and human gut bacteria.?BeeR?forms a hollow tubular structure, unlike other actin-like proteins. This discovery could enhance cancer drug delivery by targeting drugs to tumor sites.?
Researchers at the University of Virginia found that COVID-19 damages macrophages, impairing lung healing. They identified peroxisomes as key to macrophage function and suggested an FDA-approved drug to restore peroxisome function, reducing lung inflammation and fibrosis.?
Researchers at Walter and Elizabeth Hall Institute (WEHI) imaged the structure of the Parkinson's disease protein PINK1 bound to mitochondria for the first time. This breakthrough reveals how PINK1 detects and tags damaged mitochondria, offering new therapeutic targets for Parkinson's disease.?
Researchers at Texas A&M University found that targeting the cytokine IL-12 could reduce neuroinflammation and amyloid plaque formation in Alzheimer's disease. This approach may open new pathways for developing Alzheimer's treatments.?
Neuropeptide Y identified as key driver of pancreatic cancer spread | News Medical Life Sciences? Researchers at the Garvan Institute identified Neuropeptide Y (NPY) as a key factor in pancreatic cancer spread. Blocking NPY in mouse models reduced metastasis to the liver. This suggests NPY as a potential target for further research in pancreatic cancer treatment.?
Researchers at Northeastern University found that the antibiotic?teixobactin?is effective against anthrax and shows no detectable resistance.?Teixobactin?binds to a fatty molecule essential for bacterial cell walls, preventing resistance. This discovery suggests?teixobactin?as a potential countermeasure against engineered bioweapons like anthrax.??
Researchers at the Max Planck Institute found that cells with stronger mechanical forces have a survival advantage in cellular competition. This study, published in Nature Materials, shows that these "winner" cells can eliminate weaker "loser" cells, maintaining tissue health. The findings challenge traditional views on cell competition and highlight the importance of mechanical forces in cellular interactions.?
?? Upcoming Events
The virtual RShiny conference hosted by Appsilon will be happening for three days from 9 April 2025 to 12 April 2025. The event planned to run a workshop on the first day followed by main conference on the subsequent days. Registration is open and Interested user are required to register to attend this virtual event.
This virtual webinar is free to attend for participant hosted by Genomics England Biocuration team. This webinar showcases machine learning solution to actively search the scientific literature and helping to save time for experts to evaluate the evidence. Interested readers are recommended to complete the registrations for attending the webinar.
?? Educational Corner
The article introduces the "ellmer" package, designed to integrate Large Language Models (LLMs) with R for scientific workflows. It discusses the package's functionalities, including simplifying LLM usage and facilitating advanced data analysis. Examples and potential applications are provided to showcase how "ellmer" can support researchers in enhancing productivity and handling complex tasks in R.
The article examines trends in Python-related questions on Stack Overflow, analyzing changing patterns in question volume and topics over time. It utilizes statistical and data visualization methods to highlight shifts in user engagement and interests. Key factors influencing these trends and their implications for Python's ecosystem are discussed, supported by data insights.
The article outlines the development of a Nextflow pipeline, "biopy_sra.nf" to automate the access, download, and preprocessing of RNA-seq data from the Sequence Read Archive (SRA). It addresses challenges such as managing large datasets, ensuring reproducibility, and reducing manual intervention. The pipeline integrates tools like Docker for containerization and FastQC for quality control, streamlining genomic data workflows.
The article provides instructions on centering titles, subtitles, and captions in ggplot2 visualizations created in R. It details the necessary adjustments to theme settings and introduces specific coding techniques for achieving alignment. Practical examples demonstrate the process, ensuring users can accurately apply these methods to their data visualizations.
The article explores the concept of "Shift-Left Testing," emphasizing the importance of moving integration testing earlier in the software development cycle. It highlights how Testcontainers can facilitate local integration tests, making them as lightweight as unit tests. The discussion includes benefits such as faster defect detection, reduced late-stage fixes, and improved development velocity, supported by DORA metrics.
The article explores the application of machine learning models to analyze and forecast the future trends of the BIST 100 index. It details the use of various algorithms, including ARIMA, boosted ARIMA, and exponential smoothing, to predict market movements. The study includes data preprocessing, model calibration, and accuracy evaluation to provide insights into the index's potential trajectory.
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