Articles tagged with Bioinformatics
Researchers from Jena University used Einstein's equation to calculate the optimal value of hematocrit, finding that it is around 40% in humans and many other vertebrates. This value may explain why similar levels of hemoglobin are found across species.
The journal Fundamenta Informaticae publishes a special issue commemorating Alan Turing's work on reaction-diffusion theory, which is considered a foundation of chaos theory and theoretical biology. The issue explores the applications of mathematical theories inspired by Turing's work to natural phenomena.
Researchers at the University of Saskatchewan have developed a powerful new tool for analyzing kinases, which are enzymes involved in various cellular processes. The software promises to improve data accuracy and understanding of biology, representing important treatment targets for diseases.
The study confirms that studying genes shared with other animals is a viable means of extrapolating information about human biology. Researchers analyzed 400,000 pairs of genes and found only a weak decrease in functional similarity between orthologs.
Researchers confirmed long-held belief that studying shared genes with other species is useful. They analyzed 400,000 gene pairs and found that studying orthologs is more relevant to understanding human biology than previously thought.
A study found that a simple genetic test can predict the aggressiveness of rhabdomyosarcoma tumours in children, allowing for tailored treatment and improved survival rates. The test identified a panel of genes whose altered activity levels could be used to predict patient response to treatment.
A study published in Clinical Nutrition found that patients with mild to moderate Crohn's disease showed significant improvement when taking supplementary CLA. The natural fatty acid has anti-inflammatory properties and may offer a safer alternative to synthetic drugs.
A new community resource, DGRP, provides the highest-resolution view to date of genome structure and variation in a population of fruit flies with diverse traits. The study has far-reaching effects on animal breeding, pesticide development, and personalized medicine.
Researchers at University of Oxford and Harvard Stem Cell Institute have developed a common standard to describe and integrate large datasets from various fields, enabling better coordination of findings. The ISA Commons platform allows small research groups to store laboratory data without dedicated bioinformatics support.
Despite efforts to identify and retract plagiarized papers, a significant percentage remain untagged, raising concerns about the prevalence of scientific plagiarism. Researchers like Harold Garner have called for improved detection systems to address this growing issue.
Researchers have developed a software package called PoPoolation2 to compare population data, facilitating the study of evolution and adaptation. The tool uses next-generation sequencing methods to determine allele frequencies between populations, providing insights into evolutionary processes.
A study using Quebec's BALSAC population database found that families on the edge of migration waves had more children and contributed more to the contemporary population's genetics. This phenomenon, known as 'gene surfing', may explain the elevated frequency of genetic diseases in certain regions.
Researchers analyzed genealogies of over one million individuals in Quebec to show that pioneers on the edge of colonization waves had a selective advantage. This advantage led to increased fertility and reproductive success, as well as a desire for exploration and colonization.
The Minimum Information about a Bioactive Entity (MIABE) standard aims to capture more information about bioactive compounds, enabling better analysis and design. By adopting this standard, researchers can analyze large datasets from various drug discovery programs, leading to improved understanding of successful drugs.
The new NSF grant will leverage Convey's hybrid-core platform and technologies to process vast amounts of biological data. Researchers can extract meaningful information from this environment using cutting-edge tools, leading to incredible breakthroughs in the biosciences.
The National Institutes of Health has renewed funding for a research project at Virginia Tech to develop computational models to assist policymakers and researchers in making better-informed decisions about emerging infectious diseases. The project aims to refine existing models to provide software tools that can help public health off...
Ralph Roskies, PSC's scientific co-director, has been appointed to the National Library of Medicine's Board of Regents for a four-year term. He brings expertise in bioinformatics and high-performance computing to the role.
Researchers in Germany sequenced and analyzed a draft genome sequence of an E. coli O104:H4 strain from the 2011 outbreak, identifying a new progenitor strain. The study's rapid sequencing technique has immediate implications for surveillance, diagnostics, and future therapies.
The open-source software, GenPlay, is designed to help biologists visualize, analyze and transform raw genomic data. Biologists can now analyze their own data using a user-friendly tool that provides continuous visual feedback, making it easier to make sense of the avalanche of new data.
A recent study suggests that successful genetic blueprints for mesodermal development are recycled by evolution, rather than being invented anew in different species. The researchers found highly conserved transcription factor binding sites across six fruit fly species, indicating a shared regulatory program.
The FASEB MARC Program has awarded a travel grant of $1,650 to promote diversity in the field of bioinformatics. The award recognizes Cynthia N. Prudence's poster/platform presentation at the ISCB Great Lakes Bioinformatics Conference.
Bhavnani's research uses advanced visual analytical methods to classify asthma patients, enabling targeted diagnosis and treatments. The study builds on molecular data from multiple institutions, demonstrating the potential of translational bioinformatics.
A rigorous bioinformatic analysis of the strengths and limitations of a screening protocol method recommended by the federal government was conducted, leading to the development of GenoTHREAT. The software tool helps detect the use of synthetic DNA as bioterrorism agents and is being released in an open-source format.
The partnership aims to enhance Taverna's commercial support, benefiting users and developers. Researchers can now access high-quality workflow tools without financial constraints.
A new genetic biomarker indicates an increased risk for developing breast cancer is present in an individual's non-coding DNA, particularly in a repetitive microsatellite sequence. The study found that patients with more than 13 copies of this repeat have a cancer susceptibility rate three times higher than those without.
A new study published in PLOS ONE reveals that full-text analysis is needed to uncover duplicate citations in the scientific literature. The researchers found that most papers are novel, but certain sections like the introduction and methods section frequently have reused content. The study offers hope for developing guidelines on acce...
The Virginia Bioinformatics Institute is developing mathematical models to understand immune responses to gut pathogens, aiming to accelerate disease prevention and treatment. The Center for Modeling Immunity to Enteric Pathogens will generate new hypotheses through computer simulations and experimental research.
The Virginia Bioinformatics Institute's COPASI software package has been made open source, allowing global access and use. The new license agreement enables commercial users to freely use the software, while also enhancing its compatibility with other academic programs.
Researchers at UCLA have developed a microfluidic image cytometry platform that can measure cell-signaling pathways in brain tumor samples at the single-cell level. This technology marks an advance toward predictive and personalized medicine, enabling physicians to predict patient prognosis and guide treatment.
A bioinformatics team from Virginia Tech and ENSIMAG is using federal guidance to detect the misuse of synthetic biology. The team's work will help gene synthesis companies identify potential threats, improving national security.
Researchers are developing methods to protect cacao crops from devastating plant pathogens, targeting two mechanisms critical for pathogen attack. The project aims to improve crop resilience and provide nutrition and income options for smallholder farmers in developing countries.
Matthew Lux, a Virginia Tech Ph.D. student, has been awarded a US Department of Defense SMART scholarship to explore opportunities in synthetic biology for defense applications. His research involves developing intelligent sensors and countermeasures using calibrated genetic parts.
Researchers used high-performance computing to locate small genes missed by scientists, uncovering 380 families of undetected gene families. The study used an ephemeral supercomputer to perform an all-to-all sequence search, reducing the search time from nearly 90 years to just 12 hours.
Researchers have created a global map of human gene expression using data from 163 laboratories worldwide involving 5,372 human samples. The analysis reveals six distinct groups or 'continents' of gene expression activity, providing new insights into the genetic basis of human function and behavior.
Rachel J. Dutton received the Raymond W. Sarber Award for her research on disulfide bond formation pathways across bacterial genomes. Her discovery of an alternative VKOR homologue in Mycobacterium tuberculosis has implications for understanding bacterial protein stability and anticoagulant resistance.
A study by Garvan Institute of Medical Research reveals epigenetic changes in prostate cancer cells, silencing nearly 3% of the genome and targeting tumor suppressor genes, making treatment far more complex than imagined.
A new study using bioinformatics predicts the molecular cause of many inherited genetic diseases by analyzing tens of thousands of mutations. The research led to the creation of a web-based tool available to academic researchers.
Researchers have successfully designed new IDO inhibitors using a docking algorithm, with 50% of in silico designs showing activity against human tumors. The computational tool, EADock, has shown promise for future drug developments in cancer-immunotherapy.
GenoCAD, a web-based Computer Assisted Design environment for synthetic biology, is being developed as an open-source software project. The system will facilitate collaboration among developers from different institutions without intellectual property issues.
The USDA has awarded a two-year grant of $908,280 to Virginia Tech and the University of Minnesota to complete sequencing the genome of the domesticated turkey. The project aims to identify genes and functions in the final genome sequence, providing invaluable information for disease prevention.
Natural historians can now share and manage their data using the Scratchpads platform, which serves over 1100 users across 100 sites. The system allows users to create virtual workbenches to study aspects of organisms, promoting biodiversity informatics approaches.
The National Institute of Allergy and Infectious Diseases has awarded a $15.7 million contract to develop an open-access national online database and analysis resource center for viral pathogens. The database will contain information on viruses such as herpes, hepatitis C, and smallpox, as well as newly emerging pathogenic viruses.
The M.D. Anderson team will use a systems biology approach to analyze multi-gene pathways and combinations of pathways in cancer. The goal is to generate molecular portraits of cancers to personalize therapy choices and improve cancer risk assessment.
Virginia Tech's CyberInfrastructure Group receives funding to integrate pathogen data, provide key resources and tools, and analyze genomic and proteomic data. The Pathogen Portal will serve as a centralized gateway for biomedical researchers.
A three-year, $2.4 million grant will develop a systems biology approach to combat the effects of drought on staple food crops like maize, wheat, and rice. The project aims to identify key regulatory genes and signaling pathways that can improve drought resistance.
The National Science Foundation has awarded a grant to develop GenoCAD, a web-based Computer Assisted Design environment for synthetic biology. The platform allows users to design complex DNA sequences in minutes and will support teams of undergraduate students enrolled in iGEM.
Researchers demonstrate that Affymetrix Gene platform can analyze differential splicing activity, comparable to Exon arrays, providing added value to existing data. The new statistical method, FIRMAGene, uses adjacent poorly fitting probes to calculate differential expression.
Researchers developed AssociationViewer to analyze genetic differences and uncover new genetic markers for diseases. The software displays SNPs on a large scale, enabling scientists to visualize significant variations in the genomic context.
The University of Southern California will be the central clearing house for a national project to collect and integrate biomedical data, facilitating access to physicians and researchers. BIRNCC aims to create a nationwide computer network that accelerates collaborative biomedical research and translates basic science into treatments.
Researchers Edgar de Graaf and Jeroen De Knijf analyzed patterns in web surfing behavior to reduce the number of results and improve efficiency in data mining. They developed methods to detect relevant patterns quickly and effectively within large quantities of semi-structured data.
Researchers at Virginia Tech will develop high-performance computer modeling tools to design efficient wireless spectrum markets. The goal is to create a robust, economically viable and efficient Dynamic Spectrum Access architecture for cellular networks.
The Swiss Institute of Bioinformatics has produced an encyclopaedic knowledge capturing the functions and interactions of human proteins. The dataset covers 20,325 human proteins and will speed up scientific work aimed at improving quality of life, particularly in combating genetic-based diseases.
Dr. Joseph DeRisi receives the Heinz Award for his pioneering work in viral detection platforms, including the ViroChip that detects new viruses and characterizes malaria parasites' life cycles. His open access approach to science enables free sharing of research and software.
A new approach, MisPred, uses five principles to identify suspect proteins with abnormal or incomplete annotations in public databases. The majority of errors are attributed to the absence of expected signal peptides and domain integrity violations.
The MIBBI initiative brings together grassroots standardisation groups to create a unified framework for high-throughput biology. By sharing minimal information standards, researchers can increase data reproducibility and analysis power.
Researchers at Virginia Tech developed guidelines for designing and managing next-generation databases of biological parts. The study identified key needs for improvement, including standardization of DNA clones and quality control measures.
Researchers used metabolomics to identify groups of relevant biomarkers of disease in healthy and diabetic mice. The study found that the ratios between certain metabolite concentrations were more informative than their absolute concentrations.
A team of undergraduate students from UC San Diego has developed a new area of bioinformatics called comparative proteogenomics, which analyzes multiple genomes and proteomes simultaneously. This approach improves genomic and proteomic annotations, unlocking biological mysteries and addressing difficult problems in the field.
A new EC-funded project aims to unite Europe's biological data resources into a sustainable, integrative network for life sciences research. The European Life-science Infrastructure for Biological Information (ELIXIR) project will provide a secure funding mechanism and protect valuable data from insecure or short-term funding.
The study provides a global analysis of human proteins interacting with viral and bacterial proteins, revealing possible intervention points for future therapeutics. Pathogens preferentially target high-impact human proteins called hubs and bottlenecks, which are involved in cancer pathways.