??MethylCallR for Illumina EPICv2 analysis ??, mGPS: AI for Microbiome Population??, PRONA: Patient Outcome Network Analysis??
Bioinformer Weekly Roundup
Stay Updated with the Latest in Bioinformatics!
Issue: 62 | Date: 15 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
This study integrates GWAS data and single-cell RNA sequencing to identify 20 risk genes linked to coronary artery disease (CAD) in smooth muscle cells (SMCs) and SMC-derived cells. Gene perturbation experiments revealed that these genes regulate shared pathways, including contractile functions, cell cycle, NFkappaB, and type I interferon signaling. The research highlights cholesterol-induced signaling as a pro-atherogenic mechanism influenced by GWAS genes, offering insights into potential therapeutic targets for CAD.
This study uses Visium spatial transcriptomics to analyse both medullary and extramedullary environments in acute myeloid leukaemia (AML). It reveals the spatial co-localization of monocytes and granulocyte-monocyte progenitors with leukemic cells in the bone marrow. The research highlights cell-cell communication via the CXCL12-CXCR4 axis and its correlation with PI3K/AKT/mTOR signalling in inflammatory niches.
This study compares 240,000 retinal cells from four species, revealing significant similarities among homologous cell classes. Researchers identified 690 regulons and 10 common cell class-specific regulators. RNA velocity analysis highlighted conserved driver genes in retinal cell differentiation in mice and zebrafish, suggesting functional similarities with invertebrate Ciona intestinalis photoreceptor cells.
This study introduces a general kernel machine regression framework using principal component analysis to jointly evaluate main and interaction effects of genetic or microbial variants on treatment responses. By extracting principal components from an input kernel, the method constructs endogenous kernels for main effects, interaction effects. This approach works without knowing the underlying real variants and detects effects. The framework also includes an omnibus testing extension for multiple input kernels, named OmniK.
The study examines how human Mesenchymal Stem Cells (MSC) interact with Glioblastoma (GBM) in 3D bioprinted models. It says MSCs develop cancer-associated traits and affect GBM treatment responses. Key findings include mitochondrial genes and markers like TREM-1 impacting patient survival. The research underscores the value of 3D models in studying tumour environments and treatments.
The article highlights the role of METTL3 in kidney diseases, emphasizing its involvement in RNA methylation. The article says that METTL3 affects the onset, progression, and treatment response of renal conditions, making it a promising target for diagnosis and therapy.
The study examines the early transmission dynamics of SARS-CoV-2 in Bangladesh during the first COVID-19 wave. By analysing case reports and whole-genome sequences, researchers identified over 50 virus introductions and found that geographical distance and population density influenced virus spread. This research underlines on SARS-CoV-2 transmission in Bangladesh and highlights similarities and differences with other countries based on the data inferred from other sources.
??? Latest Tools
The BindCompare tool has been developed to investigate the interactions between transcription factors (TFs) and RNA binding proteins (RBPs). It allows researchers to analyse how various TFs and RBPs work together, identifying both common and unique targets across different organisms with annotated genomes. BindCompare facilitates further analysis, enabling scientists to create testable hypotheses regarding the combinatorial regulation of target genes.
The tool is available as an open source python package and the source code can be found here.
PRONA, an R package for Patient Reported Outcomes Network Analysis, has been created to address the limitations of Network Analysis (NA) in clinical settings for understanding symptom interactions and their impact on patient quality of life. It integrates existing NA tools into a unified analysis pipeline and enables the unsupervised identification of patient subgroups with unique symptom patterns.
The source code, usage and installation details can be found here.
The Analysis of Differential Abundance by Pooling Tobit Models (ADAPT) was developed to address challenges in microbiome differential abundance analysis. It treats zero counts as left-censored observations and uses non-differentially abundant taxa to minimize false discoveries.
The source code and package installation details can be found here. The codes for simulation studies and real data analysis are available here.
The open-source R package MethylCallR tackles preprocessing and integration challenges of the Illumina Methylation EPICv2 by standardizing epigenome-wide association study procedures. It manages duplicated probes and includes a conversion function for various Illumina BeadChips. MethylCallR also facilitates outlier detection and statistical power estimation, helping to identify significant probes.
The source code, usage and installation details are available here.
p-IgGen is a protein language model designed for generating paired heavy-light chain antibody sequences. The model produces diverse, antibody-like sequences with natural pairing properties. It can be fine-tuned to generate antibodies with specific 3D biophysical properties.
MR Corge is a tool designed for performing sensitivity analysis of Mendelian randomization based on the core gene hypothesis. It identifies putative core instruments with direct biological roles in an exposure to estimate causal effects, reducing the risk of horizontal pleiotropy. The tool's utility is demonstrated through alignment with established biomedical knowledge and results from randomized controlled trials.
VirusHound-II is a computational tool designed to predict viral proteins that evade the host's innate immune response using machine learning techniques. It evaluates a range of machine learning models and employs pseudo amino acid composition as a descriptor. The random forest model showed 92.90% accuracy on independent tests.
?? Community News
This news is about an AI tool, Microbiome Geographic Population Structure (mGPS), which tracks the most recent location a person has visited by pinpointing the geographical origin of microorganisms. The AI model was trained on microbiome samples from urban environments, soil, and marine ecosystems to identify the unique proportions of these fingerprints and link them to geographical coordinates. This tool could potentially aid medicine, epidemiology, and forensics field.
This news article, citing a recent PNAS journal as its source, reports the impact of mental fatigue on individual health and behaviour. The study showed that metabolic exhaustion within certain brain areas affects an individual’s decision-making processes and may result in hostile behaviour in affected individuals.
The news reports on a genomic sequencing technique called metagenomic next-generation sequencing (mNGS) that could rapidly detect pathogen infection in cerebrospinal fluid (CSF). The test identifies the infection by sequencing all the genetic material in CSF followed by computational analysis to separate the human sequences from the sequences of pathogens – bacteria, virus, fungi or parasites.
?? Upcoming Events
The International Mouse Phenotyping Consortium (IMPC) has created knockout lines for 8,901 mouse genes to study their functions and roles in diseases. This webinar will guide through how IMPC data is generated and how it can be used to investigate Mendelian diseases using the PhenoDigm algorithm. Designed for anyone interested in mouse phenotyping data, it requires only a basic biology background.
Polygenic scores (PGS) aggregate the effects of numerous genetic variants to measure genetic predisposition for traits or phenotypes. The PGS Catalog is the largest repository of PGS and relevant metadata, facilitating evaluation and reuse for various research and clinical applications. This webinar will demonstrate the use of the PGS Catalog Calculator (pgsc_calc) to calculate PGS, including adjustments for genetic ancestry. It is designed for researchers, clinicians, and bioinformaticians, with basic knowledge of CLI applications recommended.
?? Educational Corner
This blog discusses how the Smith-Pittman Algorithm enhances community detection in networks by improving the Girvan-Newman algorithm, focusing on both degree centrality and edge-betweenness to identify more accurate and distinct communities.
The blog on automating channel separation in Fiji provides a tutorial for confocal microscope users to automate separating image channels using Fiji (ImageJ) macros. It aids in conservation of time and ensures consistency in image analysis.
The tutorial on Multi-omic Data Integration for Microbiome Research Using scikit-bio teaches how to integrate and analyse various types of omic data for microbiome research using the scikit-bio library. It covers data preprocessing, integration techniques, and visualization methods.
This course material provides an overview of bioinformatics and computational biology, covering key concepts, tools, and techniques used in the field. It includes practical examples and resources for learning and applying these methods to biological data analysis.
This guide provides an overview of how to use CancerModels.Org to identify suitable patient-derived cancer models for research. It covers the platform's features, including search functionalities, data integration, and model selection criteria, helping researchers find the most relevant models for their studies.
This comprehensive guide explains the usage of the tilde operator (~) in R. It details how the operator is used in various contexts, such as in formula notation for statistical models, data manipulation, and other programming tasks. The guide includes practical examples and tips to help users effectively apply the tilde operator in their R scripts.
?? 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.