Articles tagged with 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.
Bowling Green State University biology undergraduates will contribute to the Microbial Genome Annotation research program, analyzing microorganisms' genomes and gaining skills in genomics and bioinformatics. The project aims to sequence the genomes of all cultured bacteria and archaea, with BGSU students providing valuable input.
The UC Irvine Institute for Genomics and Bioinformatics has received a $5.6 million grant to expand its Biomedical Informatics Training program, which trains graduate students in the intersection of life sciences and computational technologies. The program, one of only 18 nationwide, provides specialized training in molecular biology, ...
Nicholas Tan Xue-Wei, an 18-year-old Singaporean student, will present his research paper on stem cells at two international conferences in the US and UK. He was nominated for a Best Paper Award at WCE 2007 for his work on growing Mesenchymal Stem Cells in a serum-free medium.
Researchers at UC San Diego and University of Hawaii will analyze avian flu genomes using bioinformatics software and a computational grid. The project aims to combat emerging bird flu pandemic threats using reverse genetics techniques and promotes global cooperation in case of a flu pandemic.
Researchers have developed a new classification system for Rickettsia bacteria, highlighting the importance of plasmids in virulence traits and host recognition. The study provides insight into the evolutionary origin of rickettsiae and has implications for the development of diagnostics and vaccines.
Researchers have discovered that two alphaproteobacteria lack the universal extra guanylate nucleotide typically found in transfer RNA molecule tRNAHis, which assists in incorporating amino acid histidine into new proteins. This finding suggests a radical departure from previously known identity rules for histidine-carrying tRNAs.
Scientists from IRB Barcelona have published a dynamic map of protein behavior, enabling the prediction of protein structures and interactions. The study, part of the MoDel project, aims to establish a 'fourth dimension' for protein structures, facilitating the design of new drugs and understanding of protein functions.
A Medical College of Georgia bioinformatics expert has received a $15 million NIH grant to continue operating the Coordinating and Bioinformatics Unit. The grant will support the development of animal models for diabetic complications, including cardiovascular disease and kidney damage.
Researchers developed a detailed computational model to simulate AZT metabolism in mitochondria, exploring potential mechanisms of toxicity. The model may help minimize or eliminate toxic side effects of AZT in HIV-infected patients.
The study demonstrates an extremely high rate of prediction accuracy (95%) in a very complex pathogen, the vaccinia virus. Bioinformatics was able to reveal the vast majority of epitopes that trigger an effective immune response against the virus.
FELICS, a unique electronic infrastructure project funded by the European Union, offers unrestricted access to prominent biological databases. This initiative provides critical support for BRENDA and CheBI, facilitating navigation of the biological knowledge space for scientists.
Researchers at VBI will utilize the database to identify key genes involved in tomato metabolism and apply RNA interference technology. The project aims to enhance tomato cultivation and expand its application in biotechnology research programs.
A computer scientist has developed a system to analyze proposed drug names and rank them in terms of confusability, using techniques from linguistics and bioinformatics. The system, created in collaboration with the FDA, can identify sound-alike and look-alike drug names with great accuracy, reducing the risk of prescription errors.
Mohamad Halawi, a UH graduate, has been awarded multiple scholarships and a prestigious NIH fellowship to pursue his passion in cancer genomics research. With these honors, he aims to become a physician-scientist practicing in oncology.
A new XML-based architecture could improve access to chemical information in biomedical literature, reducing errors and increasing publication efficiency. The proposed system would link to open databases like PubChem, enabling readers to easily identify compounds mentioned in articles.
The University of Houston is developing DNA probes to detect emerging pathogens using advanced genomic computations and bioinformatics. The goal is to rapidly identify microorganisms and viruses that could be used in bioterrorism attacks.
The NIH has funded two new bioinformatics resources at UT Southwestern to improve drug discovery and vaccine development. The BioHealthBase will focus on understanding how microbes establish infections, while the ImmPort system will integrate data from different biomedical research areas to identify disease-causing genes and proteins.
PathPort is a life sciences interoperability framework providing access to biological characterizations of known pathogens and their near relatives. The project aims to aid in detection, identification, and analysis of high-priority pathogens using its analytical tools and data models.
A $18 million bioinformatics center will provide a single web-based entry point for infectious disease researchers to access data on hundreds of deadly microorganisms. The center aims to accelerate research into the biology and evolution of these pathogens, with a focus on eight key species.
A study published in Physical Review E found that a loss of just 2% of US power grid substations can cause catastrophic failure. Researchers identified high-load transmission substations as critical points, emphasizing the need for increased redundancy and distributed generation.
Researchers at Universitat Autonoma de Barcelona have developed the PDA web service, allowing scientists to analyze genetic diversity in different individuals and species. The server enables the search for small variations in genomes, providing valuable information for studying illnesses with a genetic origin.
The Virginia Tech National Bioinformatics Resource Center will focus on Brucella, Caliciviruses, hepatitis A, Rabiesvirus, and Coxiella burnetii/Rickettsias. The center will enable researchers to access, analyze, and study molecular data for these infectious diseases.