Rna Sequencing
Articles tagged with Rna Sequencing
Novel tool enables high-precision, low-cost pediatric leukemia diagnostics
Study may help predict response to chemotherapy in triple-negative breast cancer
Liquid biopsy predicts response to breast cancer immunotherapy
A new liquid biopsy method has been developed to predict the response to immunotherapy in high-risk breast cancers. The study found that repeated blood sampling can assess and predict the evolving antitumor immune response to therapy, offering a potential tool for guiding immunotherapy decision-making.
Self‑replicating circular RNA persists in extreme environments: Insights from hot spring microbiomes
A novel circular RNA replicon was identified in a high-temperature hot spring ecosystem, showing profound divergence from previously known circular RNAs. The discovery reveals diverse self-replicating RNAs exist even in extreme environments, broadening the ecological scope of RNA-based replication systems.
Giving a voice to vocal fold regeneration
A team of researchers from Kyoto University has identified multiple types of stromal and secretory cells in the larynx, revealing new insights into vocal fold regeneration. The study's findings provide potential stem cells for treating vocal cord dysfunction and other voice disorders.
New sequencing method exposes hidden gaps in immune signaling
Researchers have developed a new single-cell technology called CIPHER-seq that captures the timing of cytokine activity with greater accuracy. This allows for a clearer view of immune cell behavior and strengthens the foundation for understanding cancer, inflammation, and treatment resistance.
Gut microbiomes of elephants altered by livestock in shared spaces
Research conducted by San Diego Zoo Wildlife Alliance and Save the Elephants found that elephants' gut microbiomes shifted significantly when sharing habitat with livestock. Microbes commonly found in livestock became more abundant, while beneficial microbes decreased.
Cellular ‘atlas’ of prostate cancer opens new avenues for earlier detection
Scientists have identified a new cell type and discovered that many normal-looking prostate cells harbor cancer-related changes. The study's findings could lead to new risk factors, earlier detection methods, and more targeted therapies for patients at high risk of aggressive disease.
New study maps cellular mechanisms driving fibrosis in Crohn's Disease
Researchers have uncovered unusual clustering of endothelial cells around immune cells, signaling the start of excessive collagen production and scarring. This discovery could lead to new treatments for fibrosis, a common complication in Crohn's Disease affecting 10-20% of patients.
Researchers uncover distinct tumor “neighborhoods”, with each cell subtype playing a specific role, in aggressive childhood brain cancer
New research reveals that tumor cells in supratentorial ependymomas cluster into distinct neighborhoods, each with a specific role, such as proliferating or invading. Understanding these cell subtypes could help predict treatment response and inform targeted therapies for this aggressive childhood brain cancer.
Groundbreaking study maps complex interplay between cells, metabolism, and immunity in breast cancer lymph node metastasis
Researchers developed an integrative analysis of single-cell sequencing and spatial mapping to reveal novel mechanisms driving breast cancer metastasis. The study identifies key drivers of metastasis, including early disseminated cancer cells with enhanced invasive capabilities.
Upcycling genes: New platform breathes life into underperforming genetic parts
A research team has developed a 'SUPER' platform that utilizes synthetic small RNAs as add-on controllers for genetic switches. This technology enhances the performance and stability of gene regulatory devices by addressing the issue of 'leakage', where genes continue to express at low levels even in the 'OFF' state.
University of Tennessee shows viral impact on ocean oxygen
A new study by the University of Tennessee shows that virus infection of cyanobacteria releases nutrients, fueling microbial growth and contributing to enhanced oxygen levels in the ocean. The findings suggest a direct link between viral activity and ecosystem functioning below the surface.
How stressors during pregnancy impact the developing fetal brain
A new study maps the impact of stressors during pregnancy on the developing fetal brain, revealing a cell atlas and identifying key immune pathways. The research sheds light on how maternal gut-immune disruptions can shape neurodevelopmental disorders in children.
Study captures how cancer cells hide from brain immune cells, shows that removing their “don’t eat me” signals stops their escape
Researchers have identified two proteins that allow cancer cells to evade destruction by brain immune cells, known as microglia. By removing these proteins, microglia play a key role in eliminating cancer cells during the early stage of their arrival in the brain.
Georgia State brain researchers draw cellular blueprint for how we think, feel
A breakthrough study from Georgia State University links brain biology to behavior, revealing the long-sought bridge between micro- and macro-level brain organization. The research team uncovered a detailed biological map connecting different levels of the brain, shedding light on how molecular features influence cognition.
Ginkgo Datapoints launches the Virtual Cell Pharmacology Initiative to build a community-driven data standard for AI drug discovery
The Virtual Cell Pharmacology Initiative (VCPI) aims to build the first standardized framework for virtual cell modeling in drug discovery. Ginkgo Datapoints is offering free high-throughput RNA profiling via its platform, generating over 12 billion data points and aiming to test at least 100,000 compounds.
Is shaping brain activity a mechanical process? An international research team provides new insights
A recent study published in Nature Communications reveals that the mechanical properties of the developing brain play a significant role in synapse formation and electrical signal emergence. The researchers found that softer regions exhibit higher synapse densities, while stiffer regions show lower densities.
Chatting with your cells
Researchers developed CellWhisperer, an AI method and software tool that links gene expression with descriptive text across millions of biological samples. It provides a virtual AI-based colleague to support biologists in their research, making biomedical data exploration easier and more exciting.
Folate receptor beta found in pediatric tumors may improve fluorescence-guided cancer surgery
Researchers discovered that folate receptor beta is widely expressed in various pediatric and adolescent solid tumors, making it a promising target for improving tumor surgery accuracy. Pafolacianine, a next-generation dye targeting folate receptors, shows promise as a tumor-agnostic imaging strategy for pediatric cancer surgery.
“Molecular bodyguard” helps infections persist
A key molecular player, RfaH, has been identified as a protective shield for bacterial genes, enabling them to survive the hostile environment inside the body. The protein ensures transcription runs to completion, making it an anti-terminator that prevents premature termination of gene expression.
You’ve never seen corn like this before
Researchers at Cold Spring Harbor Laboratory have mapped two known stem cell regulators across thousands of maize and Arabidopsis shoot cells. This discovery reveals new stem cell regulators in both species and links some to size variations in maize.
Tiny fish open new horizons for autism research.
Researchers used zebrafish with a mutation in the ube3a gene to investigate how environmental factors affect social behavior in individuals with autism spectrum disorders. The study found that environmental adjustments could hold therapeutic potential for ASD-related behavioral challenges.
BSC creates a computational method that reveals previously hidden connections between diseases
A study by BSC-CNS analyzed molecular data from over 4,000 patients and 45 diseases using a newly developed computational method. The results show that 64% of medically known connections are related by similarities in gene expression, providing clues about the biological mechanisms linking them.
ISGlobal develops a bioinformaticstool to boost omics data analysis in precision medicine
HTGAnalyzer is an automated tool simplifying complex transcriptomic workflows, enabling clinicians without bioinformatics expertise to perform essential analyses in precision medicine. The tool has been validated using multiple datasets and identified differentially expressed genes linked to cancer diagnosis, treatment, and prognosis.
Study: Sylvester researchers uncover molecular drivers of cellular differentiation
The study uses Rapid Precision Run-On Sequencing (rPRO-seq) to uncover molecular drivers of cellular differentiation, offering a paradigm shift in understanding regenerative therapies. The technique allows doctors to analyze patients' disease states and treatment response in real-time.
New AI tool illuminates “dark side” of the human genome
Researchers at Salk Institute launched a machine learning framework called ShortStop to explore overlooked DNA regions and discover microproteins with potential roles in disease. The tool identified 210 new microprotein candidates in lung cancer data, including one validated target for therapeutic treatment.
Swiss genome of the 1918 influenza virus reconstructed
Researchers from University of Zurich and Basel decode historical specimen to understand how 1918-1920 influenza pandemic evolved in Europe. The Swiss genome reveals three key adaptations that made the virus more resistant to human immunity and more infectious.
Study uncovers how harmful RNA clumps form — and a way to dissolve them
Scientists have discovered that repeat RNAs aggregate inside droplets but can be disassembled with an engineered piece of RNA. The study sheds new light on how these clusters form within biomolecular condensates and presents a potential therapeutic application.
Study led by IGTP reveals correlation between tuberculosis lesion transcriptomics and patients’ clinical parameters
Researchers at IGTP reveal a clear separation between lesional and non-lesional tissue, with high expression of pro-inflammatory genes in lesions. The study identifies 17 differential transcriptomic modules and associates molecular profiles with clinical indicators from the same patients.
A new technique to use generative AI to design RNA
A new generative AI technique allows for the design of RNA molecules with improved functions, opening up potential for novel therapeutics and diagnostics. The SANDSTORM and GARDN systems enable the prediction and generation of RNA sequences tailored for specific tasks in cells or diagnostic assays.
Chinese researchers reveal core cellular network modulating immune phenotype switching in hepatitis B
This study explored the immune dynamics across different phases of HBV infection, identifying key factors influencing T cell function and liver priming. The research team uncovered distinct types of intrahepatic T lymphocytes and dual roles of DC-SIGN+ macrophages in modulating immune responses.
Estimating complex immune cell structures by AI tools for survival prediction in advanced melanoma
Researchers used AI-driven methods to analyze thousands of digital images of melanoma tumor tissue, identifying key immune cell structures that boost immunotherapy effects. The presence of these structures was linked to significantly better overall survival for patients with advanced melanoma.
Singapore scientists unveil one of world’s largest long-read RNA sequencing datasets to advance disease research
A team of Singaporean scientists has released a comprehensive long-read RNA sequencing dataset, SG-NEx, to accelerate biomarker discovery and precision medicine. The dataset offers deeper biological insights into RNA complexity, enabling researchers to detect clinically relevant biomarkers and develop better treatments.
A legacy unlocked: Mendel-inspired breakthrough that could transform global pea farming
Researchers have mapped the diversity of a globally important pea collection, revealing secrets behind Mendel's famous traits and uncovering agriculturally useful genetic diversity. The new set of gene bank and genomic resources could revolutionize pea breeding and research.
RNA pseudouridine emerges as a novel diagnostic target for colorectal cancer: High-resolution pseudouridine sequencing reveals correlation with clinical markers, offering new avenues for early detection and treatment.
Researchers have discovered RNA pseudouridine as a novel diagnostic target for colorectal cancer. The study found correlations between pseudouridine modifications and clinical markers, enabling potential non-invasive diagnosis. The findings provide a molecular framework for RNA epigenetics-based stratification and targeted interventions.
Novel roles of nucleic acid G-quadruplex mediated by helicase DHX36 during mammalian oocyte growth and early embryo development.
Research reveals DHX36 plays a crucial role in normal chromatin architecture and rRNA homeostasis during oocyte growth. DHX36 deficiency impairs meiotic maturation, post-fertilization embryonic development, and disrupts ribosome assembly.
Pinning down the process of West Nile virus transmission
A project aims to understand how temperature, light pollution, and bird abundance affect West Nile virus transmission in mosquitoes. The goal is to advise health departments on the best time to kill bugs and limit transmission.
Researchers link exosomes to blood-brain barrier dysfunction in pediatric obstructive sleep apnea
A new study found that exosomes from children with pediatric obstructive sleep apnea (OSA) disrupted blood-brain barrier integrity, leading to cognitive impairments. The research suggests a broader impact on barrier function and identifies potential biomarkers for OSA-related neurocognitive dysfunction.
Developing software for easy estimation of 3D gene expression distribution
Researchers developed tomoseqr, a user-friendly software to estimate 3D spatial gene expression distribution. The software successfully reproduced known gene expression patterns and mapped the 3D spatial distribution of genes in zebrafish and planarians.
Spotiphy integrative analysis tool turns spatial RNA sequencing into imager
Researchers have developed a computational tool, Spotiphy, that uses generative AI to enhance the resolution of sequencing-based spatial transcriptomics without sacrificing gene coverage. This breakthrough enables single-cell resolution in tissue imaging while maintaining full transcriptome coverage.
Disruption of a single amino acid in a cellular protein makes breast cancer cells behave like stem cells
A team of researchers at Queen Mary University of London discovered that disrupting a single amino acid in the vimentin protein makes breast cancer cells behave like stem cells. This mutation promotes tumour growth and increases cancer stemness in an oestrogen-independent manner.
Advances and applications in single-cell and spatial genomics
This review highlights the transformative capabilities of single-cell and spatial genomics, providing critical insights into disease mechanisms and developing innovative therapies. The technologies enable comprehensive cell atlases, tracing the evolution of sequencing methods and incorporating multi-omics approaches, which significantl...
St. Jude scientists create scalable solution for analyzing single-cell data
Researchers at St. Jude Children's Research Hospital developed a machine-learning algorithm capable of scaling with single-cell data repositories to deliver more accurate results. The new method, called CSI-GEP, uses unsupervised machine learning to remove bias from analyses, producing better results than existing methods.
Combining long- and short-read sequencing in single cells reveals new mRNAs in neurodegenerative diseases
Researchers at Sanford Burnham Prebys used two sequencing methods to reveal new mRNAs associated with Alzheimer's disease, dementia with Lewy bodies, and Parkinson's disease. The study found vast mRNA isoform diversity in genes related to neurodegenerative diseases.
Breakthrough AI model can translate the language of plant life
A pioneering AI model has been developed to understand the genetic 'language' of plants, allowing for precise predictions about RNA functions and identification of functional patterns. This breakthrough has significant implications for crop improvement and the next generation of AI-based gene design.
RNA modifications in individual cells better understood with new modelling
Researchers developed a new tool called SigRM to analyze single-cell epitranscriptomics data, enabling the study of RNA modifications in individual cells. This can provide valuable insights into gene regulation and its impact on health and disease, particularly in complex conditions like cancer.
NUS and A*STAR researchers discover cell-type-specific link between alternative splicing and autoimmune disease inheritance
Researchers from NUS and A*STAR have discovered a connection between the regulation of alternative splicing in different cell types and the predisposition to autoimmune diseases. The study used a population-scale single-cell gene expression profiling dataset to analyze splicing events specific to particular cell types, revealing ancest...
Delivery mechanism discovery resolves gene expression puzzle
Researchers have shed new light on gene expression by visualizing ribosomes in unprecedented detail. The study reveals a molecular mechanism for mRNA delivery to the ribosome, advancing our understanding of gene expression at the molecular level.
A newly developed algorithm shows how a gene is expressed at microscopic resolution
Researchers developed an algorithm to analyze high-resolution spatial data from Seq-Scope and other technologies, called FICTURE. This enables scientists to see how and where a gene is expressed at microscopic resolution, improving our understanding of gene expression.
Can snake research help explain human digestion?
Researchers from UT Arlington sequenced RNA genes of pythons, discovering conserved pathways in humans that are activated uniquely by these snakes. This knowledge helps explain intestinal regeneration and metabolism changes, offering potential therapeutic targets.
Soil’s secret language: Researchers decode plant-to-fungi communication
Plant roots use a silent molecular 'language' to direct fungi to attach, providing phosphates. Researchers discovered that strigolactone activates fungal genes associated with phosphate metabolism, leading to new strategies for cultivating hardier crops and combatting disease-causing fungi.
Proteomics of bone formation in young-adult and old mice
A new proteomics study explores the relationship between protein and transcript levels in young-adult and old mice bones. The research identifies key targets associated with bone mineral density and aging, shedding light on protein-specific changes that occur with age.
An integral T cell pathway helps regulate female gene expression
A new study reveals a connection between NF-κB signaling pathways and X chromosome inactivation in T cells, which has implications for understanding sex-based immune responses. Researchers found that the maintenance of X chromosome inactivation depends on nuclear factor kappa B (NF-κB), a transcription factor.
How doxycycline for STI prevention affects the gut microbiome
A study found that doxycycline post-exposure prophylaxis (doxy-PEP) did not significantly alter the overall composition of gut bacteria in individuals who took it for six months. However, the researchers noted signs of resistance building against tetracycline, a class of antibiotics to which doxycycline belongs.
Bacteria involved in gum disease linked to increased risk of head and neck cancer
A new study found that over a dozen bacterial species in the oral microbiome are linked to a 30-50% increased chance of developing head and neck squamous cell carcinoma. The research analyzed data from 159,840 Americans and identified key bacteria that may contribute to the disease.
The cell rejuvenation atlas: identifying master regulators of rejuvenation strategies
Researchers developed SINGULAR, a cell rejuvenation atlas that offers a comprehensive systems biology analysis of diverse rejuvenation strategies across multiple organs at single-cell resolution. The study identified master regulators and uncovered common targets across immune cells.
Elevating analysis of genomic data with breakthrough mathematical technique
A new method, scAMF, reduces noise in single-cell RNA sequencing data while preserving crucial biological information. This enables more accurate cell type characterization and clustering. The framework also lays the foundation for constructing high-resolution cell atlases.
Hepatitis C leaves “scars” in immune cells even after successful treatment
Researchers found that the frequency of activated TREG cells remained elevated during treatment and continued to be high even after the virus was eliminated. Inflammatory features, such as increased TNF signaling, were sustained in TREG cells, indicating long-term immune system changes induced by the chronic infection.