?? VarChat: AI Assistant for Variants, ?? iScore: ML-Based drug discovery ???, MPRAVarDB: ???? Database for regulatory effects of Genetic Variants
Bioinformer Weekly Roundup
Stay Updated with the Latest in Bioinformatics!
Issue: 32 | Date: 12 April 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!
?? In the Spotlight
?? Featured Research
This study involves the use of two independent metabolomics platforms and metagenomics. Both 16S rRNA gene and shotgun sequencing were performed for metagenomic analysis. These techniques helped in identifying the variations in the gut microbiota of infants and adults, and the associated shifts in different metabolite classes.
This study examines the algorithms and methods of Seurat and Scanpy, two widely used packages for standard single-cell RNA-sequencing analysis (scRNA-seq). It reveals that these differences are significant and can be compared to the variability introduced by sequencing less than 5% of the reads or analysing less than 20% of the cell population.????????
The study presents a detailed single-cell atlas of full-length RNA isoform regulation across brain regions, cell subtypes, developmental stages, and species. It reveals significant variability in isoform expression, splicing, transcription start and polyadenylation sites, and suggests additional cell-type specificity in the human brain.
The study compares short and long read sequencing for metagenomic analysis. It finds that long read sequencing improves taxonomic classification, assembly quality, and accuracy of abundance estimation, making it a better choice for metagenomic studies.
This article investigates the relationship between COVID-19 and Gastric Cancer (GC). It identifies 209 shared differentially expressed genes (DEGs) and shows that immune-related pathways are involved in both diseases. Ten hub genes and numerous transcription factors and miRNAs are identified. The study also finds ten potential therapeutic agents for GC and COVID-19, providing better insights for treatment research.
??? Latest Tools
The study introduces a new pipeline, fmh-funprofiler, which leverages the FracMinHash k-mer-sketching algorithm in sourmash software for functional profiling of metagenomic samples. When coupled with the KEGG database, it not only replicates fundamental biological insights but also uncovers signals from the Human Microbiome Project datasets.
Source code is available here.
The study introduces AMRomics, a streamlined microbial genomics pipeline designed for large datasets. It addresses the need for a fast and scalable solution for whole genome analysis in microbial genomics, particularly for studying and monitoring antimicrobial resistance strains. AMRomics offers similar results with improved performance.
Software is available here.
VarChat synthesizes complex genomic findings into concise, interpretable summaries, facilitating the translation of extensive genomic datasets into clinically relevant insights. It provides users with a brief description of specific genetic variants and their potential impacts on human health and encourages further research by providing direct links to related scientific sources.
Tool is available here.
lute, a computational tool designed to accurately deconvolute cell types with varying sizes in bulk RNA-sequencing data. It estimates cell type proportions, thereby controlling for cell composition differences across heterogeneous tissue samples. It wraps deconvolution algorithms in a standardized framework and adjusts for differences in cell sizes to improve the accuracy of cell composition estimates.
Software is available here.
MPRAVarDB, an online database and web server for exploring the regulatory effects of genetic variants using Massively Parallel Reporter Assay (MPRA). It contains 18 MPRA experiments, testing a total of 242,818 variants across more than 30 cell lines and 30 human diseases or traits. MPRAVarDB allows queries by genomic region, disease, and cell line, and offers pretrained machine learning models for genome-wide prediction of regulatory variants.
领英推荐
Database is available here.
The study introduces NetMe 2.0, a web-based platform that automatically extracts relevant biomedical entities and their relations from various input texts and models them as a BioMedical Knowledge Graph (BKG). It also implements a Retrieval Augmented Generation module (Graph-RAG) that distills well-formed sentences explaining the content of the BKG.
Software is available here.
A snakemake toolkit with three pipelines (skim2mt, skim2rrna, and gene2phylo) designed to unlock the genomic potential of historical museum specimens using genome skimming. The toolkit can recover mitochondrial and ribosomal genes from poorly preserved museum specimens and perform phylogenetic analysis. The results are consistent with current taxonomic understanding.
The study introduces iScore, a machine learning-based scoring function for predicting the binding affinity of protein-ligand complexes. iScore uses ligand and binding pocket descriptors, avoiding the need for explicit knowledge of protein-ligand interactions and atomic contacts. It employs three ML methodologies: Deep Neural Network (iScore-DNN), Random Forest (iScore-RF), and eXtreme Gradient Boosting (iScore-XGB)
?? Community News
Baylor College of Medicine researchers conducted a study revealing the role of inherited DNA variants on recessive disease traits. They found a correlation between complex genetic disorders and increased levels of consanguinity, providing insights into the effects of shared ancestry on genetic variations.
Scientists from the Medical Research Council (MRC) identified genetic variants in two genes, APBA1 and BSN, that significantly influence obesity risk. The variants in the BSN gene, also known as Bassoon, can increase obesity risk by up to six times and are associated with higher risks of non-alcoholic fatty liver disease and type 2 diabetes. These variants potentially impact about 10,000 people in the U.K.
?? Educational Corner
This course provides a comprehensive understanding of the Ensembl Variant Effect Predictor (VEP) and its functionalities. It guides learners on how to annotate a variation dataset using the VEP tool and interpret its output. The course also teaches how to access variant information in UniProt and evaluate protein structures using PDBe-KB and AlphaFoldDB (AFDB).
Explore how Illumina Connected Annotations is transforming genomic variant annotation, overcoming accuracy and scalability challenges. Integrated into platforms like Emedgene and DRAGEN Secondary Analysis, this tool streamlines annotation processes. Its endorsement by top population studies like All of Us and UK Biobank highlights its credibility, offering potential improvements in research and clinical analyses.
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