The SARS-CoV-2 virus that causes COVID has the unsettling ability of often generating variants of itself. Other viruses also mutate, but as SARS-CoV-2 quickly spread throughout the entire human population during the pandemic, killing millions, the virus’ dynamic evolution posed a serious problem: it repeatedly challenged our bodies’ immune response fighting the virus and hindered the process of getting updated vaccines ready. Understanding the genetic mechanism fueling SARS-CoV-2’s ability to generate variants can go a long way in keeping COVID at bay. In this study published in Nature M ..read more

In genomics, understanding how genes are expressed in different cell types within their spatial context is a fundamental goal. With the advent of SPADE (SPAtial DEconvolution), a revolutionary method, researchers at the University of Arizona now have a powerful tool to unravel these spatial patterns and gain deeper insights into complex biological systems. SPADE takes a multi-faceted approach by integrating spatial information into the analysis of cell type composition. Leveraging single-cell RNA sequencing, spatial transcriptomics, and histological data, SPADE accurately estimates the propor ..read more

Understanding the function of rare non-coding variants has long been a daunting task. These elusive variants, residing in regions of the genome that do not code for proteins, play a crucial role in regulating gene expression post-transcriptionally. Now, a groundbreaking study by researchers at the University of California, Los Angeles utilizing a screening method called MapUTR has shed light on the function of these rare variants, particularly those found in the 3′ untranslated regions (UTRs) of messenger RNA (mRNA). MapUTR captures functional 3′ UTR variants in known functional motifs a&nb ..read more

Unraveling the mysteries of RNA has always been a challenging task, but recent advancements in technology have opened up new possibilities, allowing scientists to delve deeper into the secrets of RNA molecules. Direct RNA sequencing is a cutting-edge technique that offers a unique advantage: the ability to simultaneously identify both the canonical bases and epitranscriptomic modifications present in each individual RNA molecule. This means that researchers can now explore not only the genetic code encoded in RNA but also the chemical modifications that adorn it. However, despite the potentia ..read more

In a proof-of-concept study, researchers at the National Institutes of Health (NIH) have developed an artificial intelligence (AI) tool that uses data from individual cells inside tumors to predict whether a person’s cancer will respond to a specific drug. Researchers at the National Cancer Institute (NCI), part of NIH, published their work on April 18, 2024, in Nature Cancer, and suggest that such single-cell RNA sequencing data could one day be used to help doctors more precisely match cancer patients with drugs that will be effective for their cancer. Current approaches to matching pa ..read more

The technology used to sequence SARS-CoV-2 at record speed early in the COVID-19 pandemic has been successfully tested as a technique to monitor arboviruses and diseases transmitted mainly by mosquitoes. In an article published in the journal Microbiology Society, researchers affiliated with Pasteur Institute in São Paulo, Brazil, and the University of São Paulo (USP), in collaboration with colleagues at the University of Birmingham in the United Kingdom, describe the use of the technology to sequence viral RNA and DNA from blood-engorged mosquitoes collected in São P ..read more

Understanding how genes behave over time is crucial for unlocking the secrets of development, disease progression, and more. Researchers have long grappled with the challenge of analyzing gene expression patterns at the single-cell level, where cells can exhibit complex and dynamic behaviors. Now, a new statistical method developed by researchers at Xi’an Jiaotong University called TDEseq is poised to revolutionize the way we study temporal gene expression dynamics in single-cell RNA sequencing (scRNA-seq) studies. TDEseq stands for Temporal Dynamics of Expression Sequencing, and it’s not jus ..read more

Understanding how genes are expressed within tissues and their spatial context is crucial for unraveling mysteries in health and disease. Imagine being able to pinpoint not only which genes are active but also where they are active within a tissue sample. This is where spatially resolved transcriptome (SRT) techniques come into play, offering a revolutionary approach that promises to transform various fields of biology. Gene expression profiling, essentially studying which genes are turned on or off in a cell, has traditionally been done without considering the spatial arrangement of cells wi ..read more

Understanding the relationship between a genome’s structure and its function is crucial. Yet, unraveling this relationship has long been a challenge for scientists, particularly when it comes to measuring both the three-dimensional (3D) genome structure and gene expression of individual cells simultaneously. Enter ‘Linking mRNA to Chromatin Architecture (LiMCA)’—a groundbreaking technique that promises to shed new light on the complex interplay between the 3D genome and transcriptome. Developed by a team of researchers at Peking University, LiMCA offers unparalleled sensitivity and the abilit ..read more

The first comprehensive cell atlas of ageing human muscle reveals the intricate genetic and cellular processes behind muscle deterioration and mechanisms to counteract it. How muscle changes with ageing, and tries to fight its effects, is now better understood at the cellular and molecular level with the first comprehensive atlas of ageing muscles in humans. Researchers from the Wellcome Sanger Institute and their collaborators at Sun Yat-sen University, China applied single-cell technologies and advanced imaging to analyse human skeletal muscle samples from 17 individuals across the adult li ..read more