Articles tagged with Bioinformatics
A novel mortality risk prediction method helps tailor treatment decisions and transplant needs for patients based on individual symptoms. The new tool uses a random survival forest algorithm to predict individual mortality risk curves, calculate mortality at any given time, and provide a 95% confidence interval.
QUT researchers developed a new mathematical model to enable faster solutions for complicated problems in agriculture, ecology and medicine. The method improves how to determine the 'best' intervention strategies, balancing benefits and side effects, and can be applied to farming practices and chemotherapy.
A team of researchers analyzed over 31 million iNaturalist records to find that highly active users primarily post observations of plants and insects, while large animals are underdocumented. The study provides insights into urban biodiversity and the distribution of biological data.
A new study using Neanderthal fragments suggests that generation intervals have fluctuated over the past 40,000 years, with human life history changing in response to environmental and cultural factors. The research found that Eurasian populations reproduced at a younger age than those in Europe, indicating a difference of 3-5 years in...
Researchers at the University of Pittsburgh School of Medicine have found that brain tissue inflammation is a key driver of Alzheimer's disease progression. By targeting neuroinflammation, they believe combination therapy could be more effective in reducing amyloid plaque formation and limiting tau fiber spread.
Researchers have identified a novel genetic marker, rs139185008, that distinguishes C9orf72 repeat expansion carriers from non-carriers in large population-based cohorts. This SNP is strongly associated with patients having a clinical diagnosis of FTLD and motor neuron disease ALS.
Researchers at Rice University are developing novel computational approaches to track environmental microbiome dynamics over time, across species and after perturbations. The team will use biofilm-based 'species abundance networks' on scaffolds to observe how they form their own genome-exchange networks.
Scientists have discovered how neurotransmitters and proteins interact to trigger neuronal responses in the brain, with implications for understanding mood disorders and addictions. The study reveals small changes in protein connections control cellular responses, enabling precise regulation of neurotransmitter effects.
Deep Longevity has adapted its blood aging clock to work with saliva samples, improving accuracy from 20.9 years to 4.7 years. The company's solution uses cell-type deconvolution to separate the composition of saliva samples.
A new study introduces K2Taxonomer, a software tool that analyzes high-throughput data to identify novel cell types within tumors and their microenvironments. The analysis of breast tumor-infiltrating lymphocytes revealed a transcriptional signature associated with better survival rates in cancer patients.
Researchers have discovered a huge diversity of alternative splicing combinations in the human brain, allowing for adaptation to specific requirements. New glutamate receptor variants, some with potential new functions, were identified using bioinformatic methods.
The Alvis tool helps bioinformaticians analyze DNA sequence data and reference genome databases for more accurate assembly results. It detects chimeric sequences, which can affect data accuracy, and produces efficient vector images for human interpretation.
Researchers from UNC Charlotte analyzed over 2,000 coronavirus genomes to clarify the origins of human infections. They found that bats are ancestral hosts of SARS-CoV-2, MERS-CoV, and other coronaviruses, with transmission occurring episodically.
Researchers discovered that certain anaerobic bacteria can use citrate synthase to catalyze citrate cleavage without consuming ATP, requiring very high CO2 concentrations. The findings suggest that this metabolic pathway may be a relic of early life and have potential applications in biotechnology.
Researchers at Baylor College of Medicine developed guidelines to select the best deconvolution method for RNA-seq data analysis. They evaluated 11 methods and identified their strengths and weaknesses in various scenarios, providing a benchmark for scientists to choose the optimal method for their needs.
A team of bioinformaticians at Saarland University have identified microRNAs as potential biomarkers for Parkinson's disease using artificial intelligence methods. They found that the level of these non-coding RNAs in blood samples can track the course of the disease, particularly in the third decade of life and from around age 70.
New study by Uppsala University researchers identifies ACE2 and integrin beta3 as potential key players in SARS-CoV-2 cell infection. The proteins interact with cellular processes of uptake and disposal, suggesting hijacking during infection.
A new approach to describing shapes uses a network representation called visibility graph, allowing for comparison and reassembly of complex shapes. The tool, GraVis, accurately quantifies shape parameters such as lobe length and cell area.
A study found that a single DNA base-pair change in a specific gene can influence whether a plant is a lark or night owl, affecting its flowering time and ability to withstand climate change. The research could help farmers select plants with clocks best suited to their location.
Researchers from University of Turku developed a new bioinformatics tool to predict microbial sensitivity to glyphosate. The tool classifies 80-90% of microbial species as sensitive or resistant, with 54% of human core gut bacterial species potentially affected.
The study analyzed a microarray dataset to identify differentially expressed genes in dilated cardiomyopathy, revealing 172 genes involved in various biological processes. The authors identified hub protein modules and key genes, including DLD and UQCRC2, which suggest potential therapeutic targets for the disease.
A University of Illinois study tracks the evolution of SARS-CoV-2 virus mutations, finding stabilization in key proteins that could improve COVID-19 treatments. The research suggests these stabilizations may help increase viral infectivity and shed light on vaccine development.
Klimov is developing a computational platform to design antibody-antigen interfaces based on DNA origami. The goal is to predict high-affinity peptide sequences that bind to tetanus toxin, targeting structured or unstructured antigen regions.
A new bioinformatics tool called DrBioRight has been developed to enable biomedical researchers to conduct routine analyses of large datasets without specialized expertise in bioinformatics or programming languages. The tool uses a natural-language interface to allow users to ask questions and receive intuitive analysis results.
Researchers developed a new software tool called WhatsHap polyphase to phase plant genomes in high resolution and with low error margins. The tool solves the problem using a two-phase process and is now available for polyploid organisms, including plants.
Researchers developed a mathematical model to predict crop performance and quality, accelerating the process of creating new plant varieties. The model was applied to soybeans and analyzed key traits such as plant height, seed yield, and oil content.
The Medical University of South Carolina (MUSC) rapidly adapted telehealth technologies to meet patients' needs during the pandemic. The hospital's four-pronged response ensured continuity of care for COVID-19 patients and continued outpatient care.
Mason researchers are providing biostatistics and bioinformatic analysis for integrating multi-omic data sets from a breast cancer cohort. The study will include correlations between proteomic, metabolomic, genomic, and/or clinical data from patients with triple-negative breast tumors.
A new hybrid signature based on DNA mutation and RNA expression patterns has been developed to predict the mutation status and survival of colorectal cancer (CRC) patients. The model achieved high accuracy and was found to be prognostic for CRC patients.
Two major microbial groups, Patescibacteria and DPANN, lack the ability to breathe, instead relying on fermentation to synthesize ATP. These microbes, found in Earth's subsurface, may be remnants of ancient forms of life that predate the evolution of respiration.
A web-based database, Archaeal Proteome Project (ArcPP), collects and makes available datasets to further research on archaea, a domain of microorganisms. The platform provides easily accessible data and expertise for analyzing proteomics studies, yielding significant new insights into archaeal biology.
Researchers at MDC developed Janggu, a universal programming tool converting genomics data into a format compatible with deep learning models. This allows for flexible and efficient analysis of large datasets, enabling the investigation of various biological questions.
Scientists at the University of Würzburg have identified thousands of cryptic HLA peptides in tumor immunopeptidomes using a novel bioinformatics method. These peptides may serve as effective targets for cancer immunotherapies and vaccines against virus-infected cells.
The LCSB researchers are coordinating an international collaboration to build a COVID-19 Disease Map, a comprehensive repository of virus-host interaction mechanisms. The map will support research and improve our understanding of the disease by providing a graphical, interactive representation of the disease mechanisms.
Researchers from CSIRO unveiled a new approach to analyzing the genetic codes of SARS-CoV-2, helping understand how strains evolve and identify new clusters. The findings will aid in tracking the virus's progression and informing vaccine development.
The German Network for Bioinformatics Infrastructure (de.NBI) has secured continued funding of up to 5.3 million euros until the end of 2021. The network, coordinated by Bielefeld University, offers researchers a powerful IT infrastructure and services to analyze large data sets.
Butler simplifies genomic data analysis by constantly collecting health metrics and automating self-healing modules. This reduces large project execution times from years to months, improving researcher productivity and efficiency.
A GW-led consortium has received a $2.2 million grant to develop BioCompute Object Specification Project standards for genomic data analysis, aiming to streamline data exchange between researchers, pharmaceutical companies, and the FDA. The project's goal is to facilitate personalized medicine by comparing and building on genomic data.
Researchers have created EphaGen software to provide a straight answer to whether a patient has a mutation. The new method uses a novel evaluation approach to assess the reliability of 'no mutation' results, enabling doctors to make informed decisions.
A new bioinformatics tool, MHcut, reveals that microhomology-mediated end joining is more common in humans than previously thought. Using this tool and commercial genome-editing technology, researchers created precise gene mutations to model diseases, providing insights into rare and orphan diseases.
Researchers tracked the disruption of gut microbes after antibiotics, finding that some individuals experienced long-term changes to their microbiome. The study used bioinformatic tools to analyze fecal samples from 30 young adults who received single or triple antibiotic treatments.
The Bacterial and Viral Bioinformatics Resource Center combines two independent resources to support richer scientific data and more powerful analytic tools. The hub will provide rapid access to genomic datasets, computational tools, and artificial intelligence techniques to analyze data and make predictions.
A University of Michigan study found that a high sugar diet depletes key brain metabolites, affecting behavior and potential connections to depression. The researchers compared fasting and fed fruit flies, discovering rapid changes in brain versus body metabolites.
Researchers at the University of Bonn used AI to diagnose rare diseases in 679 patients with 105 different rare diseases. The neural network combines facial analysis with genetic data to improve diagnosis accuracy.
A new bioinformatics tool analyzes CRISPR pooled screen data to identify candidate genes involved in diseases, outperforming existing methods. The web-based tool is quicker and more user-friendly, empowering non-bioinformaticians to analyze data.
A new workflow combines genome annotation with undergraduate education, providing efficient training for both researchers and students. The framework uses a set of logical steps to begin an undergraduate annotation program, resulting in high-quality genome annotations and valuable skills for future careers.
Seven researchers from the University of California, San Diego have been recognized as AAAS Fellows for their groundbreaking work in various fields. Robert Continetti was honored for his novel studies on molecular reaction dynamics, while Farhat Beg received recognition for his contributions to high energy density science.
Researchers created Knomics-Biota to analyze metagenomic data, identifying bacteria types, proportions, and beneficial substances. The platform allows users to visualize results and compare data with thousands of other samples, facilitating international collaborations in microbiome analysis.
Researchers have developed a new method to identify differences between single cells using single nucleotide variants, which can eliminate biases in traditional sequencing methods. This technique uses variant information to retrieve gene expression data, enabling better identification of tumor subpopulations.
Researchers found that children of radar soldiers who were exposed to high doses of radiation had a higher rate of multisite de novo mutations and chromosomal alterations compared to offspring of non-radiation exposed parents. The results support the idea that accumulation of genotype damage by radiation can occur in the next generation.
A new online training platform is being developed to address the lack of bioinformatics and statistics knowledge among researchers in the life sciences. The Galaxy Europe project aims to provide interactive tutorials using real datasets, aiming to improve data science methods use.
Researchers investigated the molecular mechanisms underlying myocardial regenerative ability in newborn mice, identifying fructose-induced glycolysis as a key factor for cardiac muscle cell proliferation. The study provided insights into the loss of regenerative capacity and potential new treatments for heart disease.
EPFL scientists have joined the Human Cell Atlas initiative, a global project mapping every type of cell in the human body. The team developed an automated single-cell analysis pipeline, enabling non-expert labs to engage in high-level genomic research.
A study by McGill University researchers found that complex interactions among roots, fungi, and bacteria drive the degradation of hydrocarbons in polluted soil. This discovery suggests a new approach to phytoremediation, highlighting the importance of interdisciplinary research.
Researchers at UCSF and Stanford University sequence the genome of a mysterious skeleton, nicknamed 'Ata', revealing rare genetic mutations associated with dwarfism and bone growth disorders. The analysis highlights the power of open-source genetic data in enabling precise diagnoses.
The Association for Molecular Pathology publishes consensus recommendations for validating next-generation sequencing bioinformatics pipelines. The guidelines emphasize the critical role of trained molecular laboratory professionals and provide practical advice for laboratories.
SourceData provides a suite of tools to generate, validate and use figure data, making it efficient to find and reuse published results. The platform links figures to other related figures across papers and journals, creating a searchable knowledge graph.
Researchers are developing next-generation computational and bioinformatics tools to quickly assess the risk of synthesized DNA strands posing a threat. Mihai Pop and Todd Treangen are working with Fraunhofer and Signature Science to create a bioinformatics analysis pipeline for identifying potential biological threats.
Researchers found that SMAD4 loss is associated with cetuximab resistance and induction of MAPK/JNK activation in HPV-negative head and neck squamous cell carcinoma (HNSCC) patients. The study suggests that targeting pro-survival pathways may be a novel strategy for overcoming cetuximab resistance.
The Human Cell Atlas is using sequencing technology to redefine every cell in the body. The platform will allow scientists to share and analyze vast amounts of diverse information generated by researchers across academia and industry.