Articles tagged with Transcriptomics
Comprehensive exploration of living organisms, biological systems, and life processes across all scales from molecules to ecosystems. Encompasses cutting-edge research in biology, genetics, molecular biology, ecology, biochemistry, microbiology, botany, zoology, evolutionary biology, genomics, and biotechnology. Investigates cellular mechanisms, organism development, genetic inheritance, biodiversity conservation, metabolic processes, protein synthesis, DNA sequencing, CRISPR gene editing, stem cell research, and the fundamental principles governing all forms of life on Earth.
Comprehensive medical research, clinical studies, and healthcare sciences focused on disease prevention, diagnosis, and treatment. Encompasses clinical medicine, public health, pharmacology, epidemiology, medical specialties, disease mechanisms, therapeutic interventions, healthcare innovation, precision medicine, telemedicine, medical devices, drug development, clinical trials, patient care, mental health, nutrition science, health policy, and the application of medical science to improve human health, wellbeing, and quality of life across diverse populations.
Comprehensive investigation of human society, behavior, relationships, and social structures through systematic research and analysis. Encompasses psychology, sociology, anthropology, economics, political science, linguistics, education, demography, communications, and social research methodologies. Examines human cognition, social interactions, cultural phenomena, economic systems, political institutions, language and communication, educational processes, population dynamics, and the complex social, cultural, economic, and political forces shaping human societies, communities, and civilizations throughout history and across the contemporary world.
Fundamental study of the non-living natural world, matter, energy, and physical phenomena governing the universe. Encompasses physics, chemistry, earth sciences, atmospheric sciences, oceanography, materials science, and the investigation of physical laws, chemical reactions, geological processes, climate systems, and planetary dynamics. Explores everything from subatomic particles and quantum mechanics to planetary systems and cosmic phenomena, including energy transformations, molecular interactions, elemental properties, weather patterns, tectonic activity, and the fundamental forces and principles underlying the physical nature of reality.
Practical application of scientific knowledge and engineering principles to solve real-world problems and develop innovative technologies. Encompasses all engineering disciplines, technology development, computer science, artificial intelligence, environmental sciences, agriculture, materials applications, energy systems, and industrial innovation. Bridges theoretical research with tangible solutions for infrastructure, manufacturing, computing, communications, transportation, construction, sustainable development, and emerging technologies that advance human capabilities, improve quality of life, and address societal challenges through scientific innovation and technological progress.
Study of the practice, culture, infrastructure, and social dimensions of science itself. Addresses how science is conducted, organized, communicated, and integrated into society. Encompasses research funding mechanisms, scientific publishing systems, peer review processes, academic ethics, science policy, research institutions, scientific collaboration networks, science education, career development, research programs, scientific methods, science communication, and the sociology of scientific discovery. Examines the human, institutional, and cultural aspects of scientific enterprise, knowledge production, and the translation of research into societal benefit.
Comprehensive study of the universe beyond Earth, encompassing celestial objects, cosmic phenomena, and space exploration. Includes astronomy, astrophysics, planetary science, cosmology, space physics, astrobiology, and space technology. Investigates stars, galaxies, planets, moons, asteroids, comets, black holes, nebulae, exoplanets, dark matter, dark energy, cosmic microwave background, stellar evolution, planetary formation, space weather, solar system dynamics, the search for extraterrestrial life, and humanity's efforts to explore, understand, and unlock the mysteries of the cosmos through observation, theory, and space missions.
Comprehensive examination of tools, techniques, methodologies, and approaches used across scientific disciplines to conduct research, collect data, and analyze results. Encompasses experimental procedures, analytical methods, measurement techniques, instrumentation, imaging technologies, spectroscopic methods, laboratory protocols, observational studies, statistical analysis, computational methods, data visualization, quality control, and methodological innovations. Addresses the practical techniques and theoretical frameworks enabling scientists to investigate phenomena, test hypotheses, gather evidence, ensure reproducibility, and generate reliable knowledge through systematic, rigorous investigation across all areas of scientific inquiry.
Study of abstract structures, patterns, quantities, relationships, and logical reasoning through pure and applied mathematical disciplines. Encompasses algebra, calculus, geometry, topology, number theory, analysis, discrete mathematics, mathematical logic, set theory, probability, statistics, and computational mathematics. Investigates mathematical structures, theorems, proofs, algorithms, functions, equations, and the rigorous logical frameworks underlying quantitative reasoning. Provides the foundational language and tools for all scientific fields, enabling precise description of natural phenomena, modeling of complex systems, and the development of technologies across physics, engineering, computer science, economics, and all quantitative sciences.
Researchers mapped dental pulp and periodontal ligament stem cells' genomes, revealing significant differences in their differentiation potential. The study identifies the genetic composition and mechanisms of differentiation, paving the way for targeted regenerative therapies.
Researchers identified RBM5 as a key regulator of HOXA9 expression in leukemia cells, revealing its dual function in DNA and RNA handling. Removing RBM5 from cells significantly reduced HOXA9 mRNA levels, suggesting its potential as a therapeutic target for acute myeloid leukemia treatment.
Researchers discovered a previously unreported neuron type with vulnerability in Parkinson's disease, shedding light on the complexity of the disease and potential therapeutic targets. The study identified distinct transcriptomic signatures of this neuron type and found reduced RIT2 expression in Parkinson's disease patients.
Researchers created a single-cell atlas of the human placenta, revealing changes in gene expression patterns among cell types. The study found that cells most affected by labor were in chorioamniotic membranes and generated inflammatory signaling.
A multidisciplinary study has elucidated the structure of the machinery responsible for writing much of our 'dark genome', a 98% unknown biological function. This discovery may lead to novel treatments for autoimmune diseases, cancer and neurodegeneration.
The study maps over 32 million cells in the mouse brain, describing their type, location, and molecular information. This atlas paves the way for a greater understanding of the human brain and development of precision therapeutics for mental and neurological disorders.
Spatial transcriptomics reveals cellular heterogeneity, organizational patterns, and molecular communications foundational to tissue structure and dynamics. The technique has enhanced throughput and resolution, offering a synthesized perspective of biological entities across various levels of detail.
A team has successfully assembled the telomere-to-telomere gap-free reference genome of Vaccinium duclouxii, revealing insights into sugar and acid accumulation, anthocyanin biosynthesis and genetic improvement. The study provides a foundation for understanding the evolution of the Vaccinium genus.
Researchers discuss a new approach integrating genomic, epigenomic, transcriptomic, and machine learning methods to identify functional genetic variants and characterize their mode of action in regulating target genes. This method aims to improve understanding of disease etiology and prioritize causative inherited genetic variants.
Researchers created a comprehensive chromatin map to understand gene regulatory networks contributing to differences between pediatric acute lymphoblastic leukemia subtypes. The study identified key transcription factor footprints and chromatin accessibility patterns, which can predict leukemia subtype with 89% accuracy.
Researchers identified a promising dual-purpose target, KDM1A, using AI analysis of transcriptomic data from 16,740 healthy samples and 11,303 tumors. KDM1A was found to significantly extend lifespan in Caenorhabditis elegans and has anti-cancer activities established in preclinical and clinical studies.
Researchers characterized changes in cognitive behaviors, neuronal morphology and gene expression in a tauopathy mouse model. The study found significant decreases in dendritic arborization and synaptic gene upregulation over time.
Researchers discovered BMAL1 is significantly upregulated in senescent cells and modulates the senescence program through AP-1. The study highlights a previously unappreciated role of BMAL1 in regulating cellular senescence and circadian clock components.
Researchers at Memorial Sloan Kettering Cancer Center developed an open-source computational method, Spectra, to analyze single-cell transcriptomic data. The algorithm identifies functionally relevant gene expression programs and is well-suited for studying large patient cohorts.
The study aims to identify genetic and molecular factors associated with susceptibility and progression of liver disease in Hispanics/Latinos. Researchers will collect data from 300 participants, including those with metabolic-associated fatty liver disease and healthy controls.
Researchers analyzed over 2 million cells from 400 postmortem brain samples to identify cellular pathways that could become new drug targets for Alzheimer's treatments. They found impairments in mitochondrial function, synaptic signaling, and protein complexes, as well as disrupted lipid metabolism.
The Keck School of Medicine of USC has launched a five-year, $50.3 million multi-omics study to better understand the causes and prevention of various diseases, including NAFLD, in underrepresented racial and ethnic groups.
Researchers identified four novel receptors potentially linking endometrial cancer with polycystic ovary syndrome, highlighting a major pathway involved in the increased EC risk in PCOS. The PI3K-AKT signaling pathway is consistent with a link between PCOS and EC.
Research finds that immune cells in older adults are similar to those in newborns and children, but less effective at recognizing infected cells. The study, published in Nature Immunology, suggests that tailored vaccines and therapies could be developed for different age groups based on the unique characteristics of killer T cells.
A study published in eBioMedicine identified 9 sets of biomarkers, both metagenomic and transcriptomic, associated with 30-day mortality in patients with severe community-acquired pneumonia. The biomarkers were validated with an accuracy of 85%, significantly higher than existing clinical prediction models.
Researchers have identified a neoplastic fusion transcript RAD51AP1-DYRK4 in luminal B breast cancer, associated with higher ki67 expression and aggressive clinical characteristics. MEK inhibitor trametinib may be effective in blocking the MEK-ERK signaling driven by this fusion.
SARS-CoV-2's nucleocapsid protein (N) uses human body temperature to replicate, binding to RNA motifs at specific spatial folds. The study reveals new functions and potential targets for antiviral drugs.
Researchers at Carnegie Mellon University have developed a new AI method that uses transformer models to analyze images of human cells. The technology, called subcellular spatial transcriptomics cell segmentation (SCS), accurately identifies individual cells and their constituent parts, revealing critical information about cellular org...
A team of scientists at Harvard Medical School has identified six chemical cocktails that can restore cellular aging and rejuvenate human cells. The study builds upon the discovery of Yamanaka factors, which can convert adult cells into induced pluripotent stem cells, raising hopes for treating age-related diseases and injuries. The im...
Researchers at Nara Institute of Science and Technology identified the WOX13 gene as a key negative regulator of shoot regeneration in plants. The study found that WOX13 inhibits a subset of shoot meristem regulators while directly activating cell wall modifier genes involved in cell expansion and differentiation.
A new study by CNIC researchers reveals that low-grade systemic inflammation triggered by subclinical atherosclerosis accelerates epigenetic aging in otherwise healthy young individuals. The study found a strong association between atherosclerosis progression and accelerated biological age, with potential reversibility through lifestyl...
Researchers developed Precious1GPT, a multimodal transformer-based approach for aging clock development and feature importance analysis. The model utilizes methylation and transcriptomic data to predict biological age and identify disease-related genes, providing a pathway for therapeutic drug discovery.
Researchers developed a non-invasive diagnostic method that analyzes sebum for biomarkers of early-onset atopic dermatitis in infants. The study revealed distinct gene expression profiles associated with AD, allowing for early detection and potential treatment monitoring.
A new computer-modeling system, scDesign3, has been developed to generate realistic synthetic data for analyzing genetic makeup of cells. The system can help researchers evaluate and validate computational methods for tasks such as gene expression analysis and cell trajectory modeling.
Researchers at USC Norris Comprehensive Cancer Center have identified a biomarker, CX3CR1, that can predict which patients with non-small cell lung cancer will respond well to chemoimmunotherapy. Elevated levels of the biomarker in T-cells after six to nine weeks of treatment indicate long-term benefits from the combination therapy.
Coral reef fish larvae undergo significant physiological changes as they transition from open ocean swimming to settling on the reef floor. The study found that gene activity changes play a crucial role in adapting to hypoxic environments at night, allowing the fish to survive and thrive.
SpaceMarkers, a new machine learning software, can identify molecular interactions among distinct cell types in and around tumors. By analyzing spatial transcriptomics data, it reveals genes overexpressed due to cell-to-cell interactions, providing new avenues for understanding cancer progression and treatment responses.
Researchers from the ALFA Score Consortium explore how nutrition and physical exercise can positively impact the aging process by modifying epigenetic changes. They find that healthy aging is associated with more tightly condensed chromatin, fewer histone post-translational modifications, and greater regulation by non-coding RNAs.
West Virginia University is leading a $20 million project to elevate neuroscience research, diversify the workforce, and enhance education. The initiative aims to study synaptic plasticity, expand data science education, and promote participation from underrepresented groups.
Researchers developed NetBID2 to analyze multi-omics data and find hidden druggable targets in cancer. The tool successfully identified previously unappreciated roles for genes like MYC and NOTCH1 in adult lung cancer and pediatric leukemia, highlighting its potential for accelerating clinical trials.
Researchers identified over 1,000 genes with age-related methylation changes in human sperm. These changes are associated with increased offspring disease susceptibility for neurodevelopmental disorders. The study found no correlation between paternal BMI or semen quality and age-related methylation changes.
Researchers estimate transcription error rates in human cells and identify genetic and epigenetic factors responsible for inaccuracies. Inaccurate transcription produces truncated or altered proteins, leading to disease.
Researchers found 270 distinct differentially methylated regions (DMRs) in AD brains compared to normal controls, validating their key findings using an independent cohort. The study offers a novel approach to investigating the relationship between DNA methylation and gene/protein expression.
A study published in Genome Biology and Evolution found a core genetic toolkit for reproductive division of labor in rudimentary insect societies. The authors identified common genes associated with fundamental social divisions in bees and wasps, suggesting a universal molecular 'theme' for cooperation across species.
Researchers at RIKEN Center for Integrative Medical Sciences discover genes and individual variations associated with atrial fibrillation, predicting stroke and mortality risk. They also uncover a potential treatment target, ERRg, involved in the pathogenesis of atrial fibrillation.
Researchers found that mice exposed to WTCPM dust exhibit impaired spatial recognition and memory, as well as changes in genes related to immune-inflammatory responses. The study suggests a peripheral-brain immune inflammatory 'cross-talking' mechanism that may increase cognitive decline risk.
Researchers identified 17 clusters of single cells in peripheral blood, showing upregulation of antigen processing and presentation pathways and downregulation of genes involved in ribosome pathways with age. The study also found senescent T cells resistant to apoptosis, potentially targeted for treatment.
A research team at Carnegie Mellon University has developed a machine learning method called SPICEMIX to analyze spatial transcriptomics data. The tool helps identify and understand gene expression patterns in cells, revealing new insights into brain cell types.
A new study has identified distinct patterns of circular RNA expression in human ALS muscle tissue, which display disease-specific gradients and could inform about neuromuscular molecular programs in ALS. The research reveals that specific circRNAs are elevated in ALS muscle biopsies but reduced in spinal cord samples from ALS patients.
UCSF researchers identified glioma's cellular source of recurrent disease, finding cells shift to mesenchymal, radiation-resistant phenotype in response to standard therapy. Paracrine signals from tumor microenvironment drive this transition through AP1 pathway, leading to therapy resistance and tumor recurrence.
A recent study has unveiled how nucleotide excision repair (NER) is controlled at the molecular level, shedding light on its role in cancer treatment. The research revealed that TFIIH uses XPG to stimulate motor activity and locate damaged DNA, licensing XPG nuclease activity to excise it.
A study using spatial single-cell transcriptomics reveals the spatial organization of cancer cells in patient tissues across ages and locations. The research highlights age- and location-dependent differences in tumor biology, suggesting that kids and adults with diffuse midline gliomas may need different treatments.
A new study suggests that a transcriptomic technique can help distinguish between infections and non-infectious causes of complications following knee and hip replacement surgery. The technique uses RNA sequencing to determine which genes are expressed and identifies specific immune cell types involved in the response to infection.
Researchers identify INPP5D as a key player in the inflammation process contributing to Alzheimer's disease, which may offer new potential targets for therapies. The study found that mice with inactivated INPP5D gene had more plaques covered by microglia, suggesting unexpected results when modulating inflammation genes.
A new study explores the value of 'trash data' from cancer genome sequencing, identifying new strategies to uncover previously unexplored information. The researchers found that genomic and transcriptomic data contain relevant information that can help elucidate carcinogenesis and discover putative biomarkers with clinical applications.
Researchers have characterized the functional significance of DDX41 in molecular processes underlying cancer. The study reveals that DDX41 serves crucial functions in transcriptional processes, RNA splicing, and genomic integrity maintenance, which may hold significance in treating hematopoietic malignancies.
Researchers developed a new method to represent cell communication using graph neural networks, which uncovers the effects of tissue niche composition on gene expression. The node-centric expression models (NCEMs) identify cell-cell dependencies and molecular processes underlying cell communication.
Researchers at Osaka University have developed a computational tool called CAPITAL that can carry out accurate comparative analysis of complex single-cell sequencing datasets. The tool uses a pseudotime trajectory approach to align and compare cells along hypothetical paths reflecting their progress through transitional processes.
A team of scientists generated a molecular atlas of the Australian bearded dragon's brain, comparing it to mouse data. The findings suggest that both reptilian and mammalian brains evolved clade-specific neuron types from a common ancestral set, challenging popular views on brain evolution.
Researchers suggest a new approach for regulating genetically engineered (GE) crops by examining the specific characteristics of the crop itself. The '-omics' methods can be used to scan new crop varieties for unexpected DNA changes, eliminating the need for safety testing if the product is substantially equivalent to existing varieties.
Researchers have constructed a comprehensive map of CLL genetic changes, providing a better understanding of the complex malignancy. The study identifies key genes and subtypes with distinct prognoses, paving the way for more accurate diagnoses and personalized treatments.
A new statistical method called Association Plot facilitates the determination and analysis of marker genes in single-cell data. This allows researchers to trace back RNA molecules to their cell of origin, providing insights into cell-type specific genes.
A new study uses gene expression patterns to reconstruct the evolution of the placenta and predict its characteristics in early mammals. The research suggests that the placenta was invasive in the last common ancestor of eutherian mammals, with non-invasive placentas evolving multiple times among mammals.
Researchers found global redistribution of histone H3 modifications with time, particularly in intergenic regions and near transcription start sites. Caloric restriction diet feeding reduced the extent of changes occurring during the first year of life in these genomic regions.
Researchers discovered that ancient retroviruses embedded in human genome can undergo retrotransposition into iPS cells, potentially posing a risk for regenerative medicine. The study found that HERV-K is expressed in SOX2-expressing cells and may cause cancer and neurological diseases by altering gene expression profiles.