Articles tagged with Transcriptomics
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...
The ENCODE project has published a series of articles annotating the functional elements in the human genome, revealing new information on pseudogenes and regulatory elements. The study's findings are now freely available online as part of BioMed Central's open access policy.
Scientists have identified how E. coli O157:H7 colonizes fresh-cut lettuce, providing new insights for food safety. The bacteria breaks down leaf cells, releasing carbohydrates and antimicrobial compounds that can be used as energy sources.
Researchers at UCSD have made a breakthrough discovery that enables the experimental annotation of genomes. By combining multiple genome-scale measurements, they can identify the location and use of genomic elements with precision. This innovation has significant implications for metabolic engineering, disease research, and drug design.
The FANTOM4 consortium has published several milestone papers in Nature Genetics and BioMed Central journals, providing new data on genomic regulatory blocks and chromatin conformation signatures. These findings have the potential to revolutionize our understanding of gene regulation and cell differentiation.
The launch of BioMed Central's Genome Medicine journal marks a significant milestone in the field of personalized medicine. The journal will focus on the latest technologies and findings impacting human health and disease, covering topics such as genomics, epigenetics, and computational approaches to disease management.
Researchers discovered a positive role for gene recruitment to the nuclear periphery, with significant implications for cell polarity and development. The study's findings suggest a complex interplay between nuclear organization and transcriptional regulation.
The study reveals that antisense transcripts (SATs) are widely expressed in various mouse tissues and cell cultures, exhibiting tissue-specific expression patterns. SATs tend to be poly(A)-negative and enriched in the nucleus, suggesting a functional role in gene regulation.
The Neisseria meningitidis genome contains hundreds of repetitive elements that facilitate genome fluidity and antigenic variation. The most abundant element is the neisserial DNA uptake sequence, which enables transformation among different species.
Dr. Julie R. Korenberg's comprehensive map integrates three ways of looking at the human genome, marking critical points with fluorescent signposts for rapid translation of clinical problems into genome-based solutions. The guide has significant practical applications in cancer treatment and genetic diagnosis.
A recent University of Georgia study suggests that retroviruses, including HIV, may have an ancient origin. Researchers analyzed the genome of a worm called Caenorhabditis elegans and found evidence of retroviral-like elements in its DNA. This finding challenges previous assumptions about the evolution of complex retroviruses.