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 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.
Researchers developed PASTE, a method to analyze spatial transcriptomics data in three dimensions, enabling biologists to better understand cell environments and identify rare cell types. The technique can integrate information from multiple tissue slices, providing a more complete picture of gene expression within tissues.
An international team led by BGI-Research has produced the first spatiotemporal maps of cellular dynamics in mice, Drosophila, zebrafish, and Arabidopsis using Stereo-seq technology. This breakthrough enables scientists to analyze the distribution and placement of molecules and cells in situ and over time.
The study provides a single-cell transcriptome map of 45 tissues and organs from long-tailed macaque monkeys, identifying 113 major cell types. This will improve the ability to pinpoint how to develop potential treatments for human diseases with greater precision.
A UT Dallas team analyzes how pain is generated by nociceptors in human dorsal root ganglia neurons using spatial transcriptomics. This provides neuroscientists with a better understanding of which genes are expressed in DRG neurons, helping to clarify why proposed treatments struggle to produce results in humans.
Researchers will use transcriptomics and chemogenetics to identify molecular targets for pain management. The project aims to advance knowledge on pain mechanisms and develop novel therapeutic strategies.
Researchers have revealed mechanisms by which polyps develop into colorectal cancer, setting the stage for improved surveillance utilizing precision medicine. The study found that serrated polyps derive from metaplasia, an abnormal change of cells into non-native tissue.
Researchers found hundreds of genes awaken in human one-cell embryos, remaining active until the four-to-eight cell stage. The study's findings could illuminate events that initiate cancer and provide new diagnostic opportunities.
A study found that spaceflight alters liver gene expression and reduces antioxidant capacity in mice, leading to increased oxidative stress. However, exposure to artificial gravity can mitigate some of these effects, suggesting potential for dietary supplementation to offset changes during spaceflight.
A team of researchers has reconstructed the evolutionary history of dragonflies and damselflies, determining when they first emerged around 200 million years ago. The study provides the most comprehensive divergence time estimates for Odonata to date.
Researchers create maps of senescence in heart and lung cells, comparing different types of senescent cells across the lifespan. The goal is to understand how senescent cells contribute to age-related diseases and develop therapies called senolytics.
Researchers at University of Pittsburgh and Prairie View A&M University developed an algorithm to repurpose cancer drugs for pulmonary hypertension, a devastating lung disease. Two compounds improved human cells and rodent markers, supporting broader drug-repurposing platform use.
Researchers at Karolinska Institutet discovered three different subtypes of mature fat cells in white adipose tissue, with only one subtype, Adipo PLIN, responding to insulin. The study suggests that changes in this specific subtype may contribute to metabolic diseases like Type 2 diabetes.
A comprehensive molecular map of lung squamous cell carcinoma has identified potential new drug targets, including the gene NSD3, and highlighted immune regulation pathways that could help cancer evade immunotherapies. The study's findings have also revealed metabolic dysregulation and crosstalk between different cellular processes.
Researchers mapped the molecular mechanisms of primate hippocampal aging, identifying key cell types and molecules affected by age. The study provides a valuable resource for diagnostic biomarkers and therapeutic targets for neurodegenerative diseases.
Researchers identified microglia as key cell type responsible for brain changes in OUD, revealing a critical role for neuroinflammation in driving pathological alterations. The study also uncovered new mechanisms by which opioids alter brain structure and function, leading to behavioral changes.
Researchers discovered RNA editing events in lung adenocarcinoma and identified a new molecular subtype EC3 with the poorest prognosis. A simplified prediction model using eight RNA editing sites accurately distinguishes this subtype, which is associated with sensitivity to specific chemotherapy drugs.
The conference aims to share experience in developing and applying bioinformatics algorithms, with topics including sequencing technologies, molecular sequence analysis, and genome assembly. Selected abstracts will be published as part of the BiATA 2021 BMC Bioinformatics supplement.
A new method called ACME has revolutionized single-cell transcriptomic technologies by enabling accurate cell fixation and dissociation without causing cell stress. This allows scientists to study thousands of individual cells from living organisms, one-by-one, and sequence each cell's genetic material.
Researchers at OIST Graduate University have identified previously unknown sections of DNA that are silenced by epigenetic regulation in plant cells. The study reveals a crucial role of these sites in suppressing the activity of disruptive 'jumping genes' called transposons, which can threaten genome integrity.
A study reveals the three-dimensional genomic structure of male germ cells, showing a fine-tuned balance between chromatin remodelling and architectural proteins. This structure determines gene expression in these cells, which are essential for reproduction.
A new study compared traditional Illumina platforms to an alternative BGISEQ-500 short-read sequencing platform for single-cell transcriptomics. The authors found that BGISEQ-500 was highly comparable in sensitivity, accuracy, and reproducibility of detected RNA molecules.
The ATS Foundation/Boehringer Ingelheim Pharmaceuticals, Inc. Research Fellowship in Idiopathic Pulmonary Fibrosis aims to advance understanding of the disease through single cell transcriptomic analysis.
Researchers at EPFL discovered that different TFs vary greatly in their ability to scan the genome, with some being highly efficient while others are less effective. The study found that TFs that associate with mitotic chromosomes are more efficient in finding specific binding sites and regulating gene expression.
Researchers from the Luxembourg Institute of Health uncover distinct microglial signatures in response to acute inflammation, highlighting potential benefits for resolving inflammation. Their single-cell transcriptomic study provides new resources for understanding brain disorders and developing novel therapeutic strategies.
The Biogerontology Research Foundation and collaborators announce the development of a novel approach to analyzing transcriptomic data sets, titled iPANDA. The system applies deep learning algorithms to identify patient-specific pathway signatures associated with breast cancer patients.
Researchers at Gladstone Institutes found that three transcription factors -- NKX2-5, TBX5, and GATA4 -- must interact for proper heart development. Without these interactions, severe congenital heart defects occur. The study revealed the proteins' genomic and physical interactions, providing new insights into treating heart disease.
The MD Anderson Cancer Center has been selected as a Genome Characterization Center to analyze patient samples from multiple NCI programs. The center will focus on functional proteomics, enabling the study of protein expression and modification in cancer tumors.
Researchers developed a novel approach to deciphering gene regulation networks by leveraging biological knowledge and computational algorithms. They found that combining laboratory experiments with motif information can accurately predict DNA-binding behavior of transcription factors.
Scientists have discovered a new role for Dicer in preventing genome damage caused by collisions during DNA replication. The protein helps free transcription machinery from DNA, preserving the integrity of the genome. This discovery may help explain why mutations in Dicer are associated with increased risk of cancer and aging.
Researchers have developed a protocol for collecting saliva and stool samples for genomic and transcriptomic analyses, eliminating the need for specialized personnel and facilities. This method provides critical insight into the genetic makeup of the microbiome and its association with diseases such as celiac disease, oral cancer, and ...
Bing Ren has been awarded the distinction of Fellow by the American Association for the Advancement of Science (AAAS) for his outstanding contributions to genome-wide analysis and understanding of human disease. He is a member of the Ludwig Institute for Cancer Research and has directed various projects, including the Roadmap Epigenome...