Articles tagged with Bioinformatics
The special issue of Applications in Plant Sciences explores bioinformatic methods to analyze plant morphology. Researchers successfully applied automated classification and identification techniques, geometric morphometrics, and skeleton networks to examine plant form.
Researchers at A*STAR's Institute of Medical Biology have identified a biomarker, Lgr5, to detect ovarian cancer earlier. Bioinformatics analysis has also revealed genes whose mutation status can be used for prognosis and development of personalized treatment.
Researchers discovered a significant difference in the contents and distribution of mobile DNA elements between fruit fly populations on opposite sides of Evolution Canyon. The study found that these repetitive sequences are increasingly recognized as agents of adaptive change, influencing stress resistance and mating.
Researchers identified distinct genetic underpinnings for different manifestations of preeclampsia, including early vs. late timing and high severity levels. The study found unique sets of genes involved from both mother and fetus, suggesting specific biological contributions to the condition.
Researchers at Virginia Tech and MIT have developed a computer-aided design tool called GenoCAD to create genetic languages for designing biological systems. The tool helps capture biological rules to engineer organisms that produce useful products or healthcare solutions from inexpensive materials. GenoCAD enables the standardization ...
A team of scientists from Harvard University and Virginia Tech has established a reliable set of human genotypes to benchmark human genome sequencing. This will help researchers gain traction against human disease by refining genomic data. The findings are available online, enabling real-time benchmarking of DNA-sequencing methods.
Researchers have developed software that can learn from a patient's normal and seizure electrical activity to predict when another seizure may occur. This allows for an early warning system, potentially enabling people with epilepsy to live safer lives by avoiding hazardous situations before a seizure begins.
Professor Speed has developed tools to help biologists analyze and explain their results, making it possible to look at hundreds of genes in a DNA sequence at once to understand genetic changes involved in complicated diseases. He is also working on determining the genetic traits that make normal and cancerous cells different.
Researchers investigate protein diversity, finding that many small changes have no impact, but some can significantly affect functionality. The study suggests that the wide functional spectrum of proteins plays a key role in evolution, and may hold the key to personalized medicine.
A new bioinformatics software tool, DrGaP, has been developed to identify genetic mutations responsible for cancers. The tool combines statistical methods and bioinformatics tools to distinguish between driver mutations and passenger mutations, leading to a more complete identification of altered genes and signaling pathways in cancer.
The $11 million investment will support large-scale applied and small-scale innovative projects to develop new tools and methodologies. These innovations aim to improve cancer treatments, response to infectious disease outbreaks, food production, and more.
Researchers analyzed over 858,717 grant and contract summaries to identify potential instances of duplicate funding. They found strong evidence that tens of millions of dollars may have been spent on grants where at least a portion was already being funded.
The FASEB MARC Program has awarded $3,700 to two students and their faculty mentors at the ISCB Rocky 2012 meeting. The program aims to increase diversity in biomedical research by promoting participation of underrepresented minority students and scientists.
A new $2 million grant will support a pan-continental bioinformatics research network in Africa. The H3ABioNet project aims to aggregate and analyze large datasets, establish collaborations among preexisting centers, and train African students and scientists in bioinformatics.
A new approach combines pupillography with blinking assessment to measure alertness, sidestepping subjective assessment by healthcare workers. The method has been successfully tested on two groups of volunteers and links blink, pupillary indices and subjective sleepiness.
The National Science Foundation has awarded funding to the Gramene project for a 5-year period, supporting the development of a Plant Reactome. This will increase the functionality of Gramene, which already provides valuable comparisons across and within sequenced plant genomes.
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.
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.
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.
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.
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.
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.
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.