Articles tagged with Bioinformatics
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.
BU researcher Avrum Spira recognized for his work on early detection of lung cancer using Percepta RNA biomarker, as well as development of new drugs for chronic obstructive pulmonary disease (COPD). His research has made a direct impact on diagnosis and daily care of patients with lung cancer and COPD in the past 20 years.
Researchers have developed a new tool called ModelFinder to study the evolution of proteins. The program allows for more accurate scientific estimates of evolutionary processes, which will help unravel the mysteries behind life's diversity on Earth.
Researchers applied bioinformatics to develop and evaluate boron-containing compounds for treating cancer and infectious diseases. Computational approaches facilitate pharmacochemical analysis, revealing essential parameters of the boron atom and its effects on biological systems.
Researchers identified molecules as potential biomarkers for early detection of type 2 diabetes, up to nine years before diagnosis. SIB's role in IMIDIA project demonstrates its unique value and capabilities as a competence center in large-scale health-data projects.
Researchers discovered molecular mechanisms of how post-translational protein modifications influence apoptosis, a process of programmed cell death. This process is crucial for maintaining tissue homeostasis and preventing diseases such as Alzheimer's and Parkinson's.
A team of scientists has conducted the largest genome-wide association study on proteomics to date, revealing 539 associations between protein levels and genetic variants in complex diseases. The study found these associations overlap with risk genes for 42 complex conditions, such as cardiovascular disease and Alzheimer's disease.
A new bioinformatics tool called IMP has been developed to increase the transparency and reproducibility of biological experiments. It preserves computer programs in a frozen state, allowing for easy reprocessing and analysis of complex data.
EDGE brings genomics expertise to everyone with a user-friendly web-based platform that integrates cutting-edge tools and reduces data analysis times from days to minutes. The platform has already helped streamline data analysis for groups worldwide, including those in Thailand, Georgia, Peru, and Egypt.
Researchers can now analyze biological signaling pathways with unprecedented accuracy thanks to OmniPath, combining 27 public databases on signalling interactions. The tool provides a comprehensive and unified collection of literature-curated signalling pathways based on an analysis of 41,000 scientific papers.
VirusDetect is a free, open-source bioinformatics pipeline that analyzes small RNA datasets to identify both known and novel viruses. Researchers can predict the presence of RNA viruses, DNA viruses, and viroids using an antiviral defense system called RNA interference (RNAi).
The sequencing of the tobacco hornworm moth's genome has opened new avenues for research, including understanding insect physiology, biochemistry, and molecular biology. The study identified over 600 genes involved in defense against pathogens, highlighting the potential for genetic insights into this important agricultural pest.
Researchers have developed a bioinformatics tool that can analyze 40,000 proteins per minute to predict the effect of cancer-associated mutations. The tool combines protein sequences, functional motifs, and cancer mutations to identify potential targets for studying disease development.
Researchers created a comprehensive metabolic model of C. elegans, linking over 2,000 processes to identify genes contributing to lifespan extension. The 'ElegCyc' model enables analysis of large datasets and will aid in understanding human diseases and microbiome interactions.
A team of scientists at TSRI has created a data-harvesting platform to automatically import and update genetic data from public databases. This allows researchers to focus on their own work instead of manually searching through large datasets.
The Werner Siemens Foundation has donated 11.5 million euros to support the launch of Synthetic Biotechnology at the Technical University of Munich (TUM). This new focus integrates research approaches from biochemistry, bioinformatics, and industrial biotechnology.
A new study suggests that neurons often co-express functionally distinct alternative products from the same gene, facilitating acquisition of complex shapes and functions. Co-expression of alternative variants is essential for proper development of axons and dendrites in mice.
An international research team is developing new molecular treatment methods for asthma and high blood pressure. The goal is to prevent further complications and reduce the risk of subsequent illnesses.
Researchers created accurate 'maps' of gene networks across 400 human cell types, describing hundreds of thousands of regulatory interactions. This global view provides new insights into disease mechanisms, pinpointing affected genes and tissues in complex diseases.
A study published in Genome Biology and Evolution sequenced the genome of Metaseiulus occidentalis, a predatory mite widely used to control plant pests. The research revealed completely atomized Hox genes and superdynamic intron evolution, highlighting the unique biology of this agriculturally important predator.
The new software, SIFT 4G, accelerates genome analysis by preparing predictions at a much higher speed, reducing processing time from 25 days to just three days on a single GPU. This enables researchers to analyze genomes in five minutes, advancing science and developing technology that can benefit human health.
A bioinformatics error affected the results, overestimating the genetic impact. The corrected study reveals extensive Eurasian admixture only in Eastern Africa.
The deer tick's genome provides insights into its ability to transmit diseases like Lyme disease and human granulocytic anaplasmosis. The sequence revealed proteins involved in transmission, saliva composition, and blood digestion mechanisms, offering potential targets for control programs.