Articles tagged with Bioinformatics
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.
Researchers developed a novel, more accurate classification system for gliomas using molecular profiles of 1122 cells. The study identified seven categories for tumor progression assessment, providing a more precise way to predict patient outcomes and treatment responses.
A recent study found that mildly deleterious mutations evolve as neutral during early human migrations out of Africa, while very harmful mutations are found at similar frequencies globally. This suggests a maximum threshold for human tolerance to genetic damage.
The book 'Video Bioinformatics: From Live Imaging to Knowledge' bridges the gap between life sciences and computer science. It provides breakthrough capabilities in understanding continuous life processes through intelligent analysis of live imaging data.
The researchers have developed a new model that allows atomic-level simulations of DNA dynamics, achieving extraordinary accuracy in just 5 years of work. The data is stored in a public website with over 4 Terabytes of information.
The Genome Analysis Centre has achieved a major milestone in wheat research by assembling the genome into larger and more complete chunks. This breakthrough, made possible by improved sequencing technology, will enable researchers to develop new insights into wheat genes and breeding programmes.
Researchers have developed methods to overcome technical limitations in studying the immune system, allowing for investigation of interdependent components and their impact on functions at the systems level. The new book provides valuable insights into team science and the application of computational tools to model immunity.
Researchers developed computational models to study cancer cells' genome structure, improving understanding of genetic changes. The approach uses statistical methods to reconstruct chaotic genomes and identify structural changes in tumour DNA.
Dr. Prerna Dua, associate professor of health informatics and information management at Louisiana Tech University, has been honored with the AHIMA Triumph Award for her research expertise in healthcare and decision support. The award recognizes her dedication to enriching the field of health information management.
Two NIH grants will support Cathy Wu's work on protein ontology and big data analysis to improve understanding of human disease and identify potential diagnostic targets. Researchers will use natural language processing tools to retrieve targeted therapy information from scientific literature and clinical trials.
A group of scientists from seven international laboratories failed to replicate the STAP study, which claimed to turn ordinary cells into pluripotent stem cells. Computational analysis revealed significant genomic inconsistencies, including different genders and mixtures of embryonic and placental stem cells in some experiments.
The UK10K project analyzed nearly 10,000 individuals to understand the contribution of rare genetic variants to various diseases. The study identified new genetic variants and genes underlying disease risk, increasing the resolution of genetic discoveries.
An international team of researchers identified key opportunities in nutrition science to close a major gap between available and projected food by 2050. The researchers proposed eight axes of research, including sustainability, food safety, and big data analysis, to improve nutrition as a science.
A new project aims to characterise the genetic diversity of traditional Vietnamese rice varieties using genomic markers for disease resistance and salt tolerance. Bioinformatics capacity will be built in Vietnam through training workshops and data sharing.
A new bioinformatics approach has been developed to identify associations between molecules from vast data sources, resulting in more accurate results than current methods. This technique improves the detection of genes related to lipid metabolism by 15% on a mouse nutritional study.
Researchers at the University of Michigan have identified the genetic blueprint of a bacteria that produces ET-743, a compound extracted from a marine invertebrate. This discovery expands understanding of the microbe and could lead to lab-grown production of the cancer-fighting drug.
A UK-China consortium, funded by the BBSRC, will host training workshops to support scientists in managing and sharing their metabolomics data and analyses. The partnership, involving EMBL-EBI, universities, and GigaScience, aims to improve data sharing in metabolomics, promoting better quality data and efficient research.
A high demand for bioinformatics training is driven by the increasing use of big data in life sciences. The Global Organisation for Bioinformatics Learning, Education & Training (GOBLET) aims to develop a global community-centred training portal with comprehensive resources and courses.
A novel online tool, PolyMarker, has been developed to automate primer design for multiple genome species, significantly reducing turnaround time. This innovation enables the identification of genetic markers associated with desirable traits in crops, such as high yield or disease resistance.
The Aquaria project has created a powerful web resource that simplifies the process of gleaning insight from 3D protein structures. The tool offers around 46 million computer models, allowing users to view additional information such as genetic differences mapped onto 3D structures.
A landmark study published by an international team of over 100 researchers reconstructs the insect tree of life, answering longstanding questions about their origins and evolution. The study reveals that insects originated at the same time as early terrestrial plants and developed wings 400 million years ago.
The University of California, Los Angeles (UCLA) will develop new strategies for mining and understanding complex biomedical data sets. The center's findings will help shape guidelines for future data integration and use.
The new Competence Center for High Performance Computing in the Natural Sciences will facilitate interdisciplinary collaborations and provide improved HPC services. The center will focus on research and application optimization, with a strong emphasis on Big Data and hardware accelerators.