Articles tagged with Bioinformatics
A team of UConn researchers, without lab experience, published the first chromosome-level genome of a desert hairy scorpion. The study sheds light on arachnid evolution and advances comparative genomics research.
Researchers challenge single-origin theory of root nodule symbiosis, identifying multiple origins and ideal experimental systems to better understand symbiotic relationships. The findings suggest a lesser role for shared genetic machinery in genetically engineering crop plants to work with nitrogen-fixing bacteria.
Researchers found that zebrafish synchronize movements by taking turns to move and responding to neighbors' timing, a two-way process known as reciprocity. Virtual reality experiments confirmed the principle, enabling the recreation of natural schooling behavior in fish and virtual conspecifics.
The DIProT toolkit leverages a non-autoregressive deep generative model to tackle the protein inverse folding problem. It allows users to specify target structures and preserve fixed sequences, improving protein design efficiency through a virtual design loop.
A study utilizing RNA-Seq and single-cell RNA-Seq data identified key transposable elements (TEs) linked to myocarditis. These findings reveal a significant role for TEs in modulating immune responses, providing new insights into cardiomyopathy's pathogenesis.
Researchers have generated complete genome data for four filamentous 'star algae' species, revealing overabundances of signalling genes and environmental response factors that underpin molecular mechanisms shaping plant bodies. The findings provide insights into the origins of land plants and their ability to adapt to environments.
A mysterious plasmid, pBI143, found in 90% of human intestines, could be used to identify faecal contamination and offer insights into intestinal diseases. The discovery also highlights the prevalence of 'cryptic' plasmids in human gut microbiota.
Researchers at Hiroshima University identified 14 genes that are up-regulated and eight genes that are down-regulated when responding to five specific abiotic stresses, including drought, salinity, and cold. These findings provide new insights into the molecular mechanisms underlying plant responses to environmental stressors.
Researchers identified a small set of proteins governing anaplastic large cell lymphoma (ALCL) identity and found that drugs targeting the STAT family of proteins already exist for treatment. The study provides insight into potential vulnerabilities in ALCL cells.
A team of scientists discovered new fusion sites in protein evolution that enable faster and more targeted drug development. By combining evolutionary processes with synthetic biology, they created customized biological drugs with improved therapeutic properties.
A competition among researchers predicted B. pertussis vaccine responses based on a simple correlation between calendar age and antibody responses. The result highlights the need for further research to understand variability in vaccination outcomes.
A new study confirms that giraffes have extensive gene flow among their lineages, indicating a 'reticulated' network of evolutionary history. This challenges the traditional view that high genetic differentiation is a sure sign of speciation.
A study published in Environmental DNA analyzed seawater samples from the Ogasawara Islands, detecting 124 unique fish species and 38 coral genera. The research highlights the importance of monitoring biodiversity in remote regions using efficient methods like eDNA sequencing.
Researchers have published novel spatial omics algorithms and tools in GigaScience and GigaByte journals to analyze biological data-based spatial information. These new methods enable the discovery of spatial domains, improvement of data quality, and better clustering of cells.
A recent study from Argonne National Laboratory has uncovered new insights into the relationship between genetic ancestry and prostate cancer risk. The research, which included large increases in representation among men of African, Hispanic, and Asian ancestries, found 187 new genetic markers that provide more accuracy in calculating ...
Researchers discovered that reducing cholesterol levels in mice with advanced atherosclerosis leads to a decrease in the number of smooth muscle-derived cells causing plaque growth, while preserving stabilizing cell types. This finding opens up new opportunities for targeted therapies.
A team of scientists has developed a computational model to predict properties of intrinsically disordered proteins, enabling the study of all 28,000 human disordered proteins. This breakthrough provides new insights into their roles in disease and biological functions.
Researchers found XRCC1 to have both positive and negative correlations with prognosis across different tumors. The study also revealed associations between XRCC1 expression and DNA methylation patterns, TMB, MSI, immune cell infiltration levels, and immune checkpoint gene expression.
Researchers at USC Stem Cell lab discovered nearly 40 genes associated with immune cell production, including those related to diseases like myelodysplastic syndrome. The study found that gene activity was linked to specific levels of immune cell production, offering insights for improving bone marrow transplantation strategies.
Researchers identified hundreds of genes subject to recent selection in six Candida species, providing valuable knowledge for developing better treatments. The study also found a potential spread of resistance through mating between susceptible and resistant strains.
A combination of 11 proteins can predict long-term disability outcomes in multiple sclerosis, making it possible to tailor treatments to individual patients. The study identified a specific protein, neurofilament light chain, as a reliable biomarker for disease activity.
The study reveals that hepatoblasts along the portal vein receive Notch signaling and differentiate into bile duct epithelial cells. Hematopoietic cells fail to transmit signals, resulting in the failure of differentiation. This discovery provides molecular biological support for mathematical analysis results.
Researchers at IRB Barcelona developed BioExcel-CV19, a repository of Molecular Dynamics simulations to understand SARS-CoV-2 infection. The database provides over 10,000 trajectories for key proteins and facilitates community-wide analysis.
Researchers developed a pipeline to evaluate the risk of infections by aquatic animals. The study found no evidence of human-associated viruses in aquatic animal transcriptomes, confirming their safety as protein sources. However, proper handling and storage are crucial to controlling SARS-CoV-2 spread through cold-chain food.
A new algorithm, SIMSEF, significantly speeds up and simplifies the identification of chemicals in tissues, enabling researchers to confidently recognize and visualize their distribution in organs. This development has great implications for medical diagnosis and treatment outcomes.
Researchers at La Jolla Institute for Immunology found that most T cells can still target epitopes on the new Pirola variant, suggesting people may be able to mount a response against it. The study's findings provide positive news in the fight against SARS-CoV-2, emphasizing the importance of vaccination with updated vaccines.
A team of researchers successfully synthesized a 1.5-million-year-old antibiotic called paleomycin, which displays potent properties against human pathogens. By tracing the evolutionary path of glycopeptide antibiotics, the team gained insights into the development of new drugs and uncovered a common precursor molecule.
Researchers examined venom genes in bees and other hymenopteran taxa using comparative genomics. They found that 12 'families' of peptides and proteins were present in all analyzed hymenopterans, indicating a common ancestor possessed these genes. This suggests that Hymenoptera insects are venomous as an entire group.
Researchers at La Jolla Institute for Immunology and Massachusetts General Hospital mapped the genome to understand how IKAROS controls healthy B cell development. They found that IKAROS solves a big problem in B cell development by bringing together far-away genes through looping, leading to proper expression and antibody production.
This special collection in SLAS Discovery highlights the significant impact of high-content imaging in basic and translational research. Researchers have made advancements in cell painting and phenotypic profiling, offering new therapeutic approaches for diseases such as Gaucher's.
Regenstrief researchers and experts will address key issues in medical informatics at the 2023 AMIA Annual Symposium. The event features a wide range of scientific sessions on topics such as translational bioinformatics, clinical research informatics, and public health informatics.
The A3D-MOBD is a comprehensive database for studying protein aggregation in twelve model organisms. It contains over half a million predictions of protein regions prone to forming aggregates, providing insights into the basis of this phenomenon.
Researchers observed a satellite bacteriophage consistently attaching to a helper bacteriophage at its neck, revealing a new viral relationship. The discovery suggests that this system may be more common than previously thought and could have significant implications for understanding the evolution of viruses.
Novel vaccine candidates using Computationally Optimized Broadly Reactive Antigens (COBRAs) protect against multiple influenza B strains, including those from different lineages. These vaccines show long-lasting protection, potentially reducing the need for yearly updates.
The Cumming Global Centre for Pandemic Therapeutics is offering global grants of up to $200,000 per annum for three years to develop novel therapeutics for pathogens of pandemic potential. Researchers are invited to submit expressions of interest for Round Two of the Foundation Grants program.
Researchers developed the DANGER analysis tool to overcome challenges in CRISPR gene editing. The tool assesses on- and off-target effects without a reference genome, quantifying phenotypic risk at the gene ontology level. This breakthrough enables safer strategies for genome editing in various organisms.
The study reveals that approximately half of examined transcription factors possess distinct binding sequences for specific cell types. MOCCS profiles also predict the effect of single nucleotide polymorphisms on DNA binding of transcription factors.
OmicsSuite is a desktop suite that integrates statistics and multi-omics analysis and visualization, enabling users to analyze large volumes of biological data in multiple formats. The suite provides step-by-step workflows for horticultural plant breeding and molecular mechanism studies.
Researchers at UMC Utrecht developed a deep-learning algorithm that can identify brain tumor types within 20-40 minutes, allowing neurosurgeons to adjust surgical strategies on the spot. This technology has shown promising results and is already being used in clinical practice.
Researchers used AI to predict 3D shapes of over 215 million proteins, providing insights into their functions and evolution. The Protein Universe Atlas offers a valuable resource for scientists to explore protein diversity.
The African BioGenome Project's Open Institute hosts widely-attended workshops across Africa, fostering grassroots knowledge exchange and developing biodiversity genomics and bioinformatics curricula. Over 700 participants learned about cutting-edge technologies shaping the biodiversity and genomics field.
The WVU team evaluated Code Interpreter's features, finding it accessible to students but limited for scientists working with biological data. The plugin breaks down barriers for coding, but lacks internet access and parallel processing capabilities.
Researchers used AI to predict Z-DNA fragment locations that overlap with known mutations causing severe hereditary diseases. These fragments can influence traits and body processes, including hair color, height, weight, and cholesterol levels.
Amarda Shehu is leading a collaborative research project at George Mason University, using deep learning and experimentation to generate controlled properties in molecules. The project aims to address challenges in molecular biology, including resistant bacteria, with potential applications in antimicrobial compounds.
Researchers used a mathematical theory called the free energy principle to predict how real neural networks learn and organize themselves. The study successfully mimicked this process in rat embryo neurons grown in a culture dish, demonstrating the principle's guiding force behind biological neural network learning.
A team of bioinformaticians from Heinrich Heine University Düsseldorf developed a new tool called TurNuP to predict enzyme turnover numbers using AI methods. The tool outperforms previous models and can make predictions even for low-sequence similarity enzymes.
The study identifies 1,074 semi-extractable RNAs potentially involved in phase-separated membraneless organelles. These RNAs are enriched in repressed heterochromatin regions and act as hubs for RNA-RNA interactions.
The Biodiversity Knowledge Hub (BKH) is a one-stop portal providing access to FAIR biodiversity data and services. It enables researchers to navigate linked data, tools, and services across the entire biodiversity research cycle.
The USC PRECOG project aims to develop automated screening tools for clinicians using objective neural and physiological signal biomarkers. The team will advance interdisciplinary methods in neuroscience, linguistics, and machine learning to better understand mental health risk factors.
Researchers at Hokkaido University unveil unprecedented carrier protein-mediated ring-forming step in actinopyridazone biosynthesis. The dihydropyridazinone ring is formed through a novel machinery involving Apy3, Apy4, and Apy6 proteins.
Researchers found that viruses can insert genes into bacteria to help them adapt and survive in nutrient-depleted man-made environments. The study also identified novel immune systems against viruses in bacteria and detected antibiotic resistance genes in viruses on human skin and surfaces.
A pioneering device captures single proteins stochastically, detecting them digitally at high concentrations. This breakthrough could lay the foundation for personalized disease prevention and treatment.
Research identifies beneficial changes in immune system during pregnancy, which can lead to new treatment strategies for MS. Women with MS experience a 70% decrease in relapses during the last third of pregnancy, possibly due to epigenetic changes and hormone regulation.
Researchers developed a primer scheme for the human monkeypox virus that can be easily integrated into existing sequencing and bioinformatics infrastructure. This approach enables public health laboratories to rapidly adapt their genomic workflows in response to new outbreaks.
Researchers developed MOVA to evaluate the pathogenicity of missense variants based on their structural position. The new method showed superior performance in predicting pathogenicity, especially for hotspot mutations in ALS-causing genes like TARDBP and FUS.
Seg2Link refines AI predictions with efficient semi-automated corrections to accurately segment cells in 3D images from a stack of 2D images. This solution enables scientists to process large-scale image data more efficiently, accelerating research in fields such as medicine and biology.
Hanna Kokko, a renowned theoretical evolutionary biologist, has been awarded the Alexander von Humboldt Professorship for her groundbreaking research on the interplay between evolutionary and ecological factors. She will receive EUR 3.5 million to establish her research team and obtain necessary equipment and facilities.
Researchers developed six prediction models using machine learning algorithms to distinguish between atopic dermatitis lesions and non-lesions, achieving high AUC values. The models showed a positive correlation between sample quality and SCORAD scores, indicating improved treatment efficacy.
Researchers have developed an automated calling algorithm for determining B and T cell clonality from NGS data with greater sensitivity than previous models. The new model increases the assay's sensitivity in detecting clonality, allowing for more accurate diagnosis and monitoring of lymphoproliferative disorders.
Researchers developed a 'Skeletal Age' metric to assess impact of fractures on mortality, revealing a loss of one to seven years of life depending on gender, age, and bone site. The online calculator measures bone fragility to help doctors and patients understand fracture risks.