Category Archives: BioInformatics

June 27, 2017 For more information, contact: Nicole Fawcett, nfawcett@umich.edu 734-764-2220 For immediate release Grant establishes proteogenomics center at U-M Combining study of protein and genes will help researchers understand molecular basis of cancer Newswise ANN ARBOR, Michigan Researchers at the University of Michigan will lead one of five nationally funded centers dedicated to accelerating research into understanding the molecular basis of cancer and sharing resources with the scientific community. U-M researchers received a grant from the National Cancer Institute to establish a Proteogenomic Data Analysis Center. The center will comprehensively characterize cancer tumor samples to integrate and analyze proteogenomic data to improve researchers ability to develop more targeted cancer therapies. Proteogenomics reflects proteomics the study of proteins with an understanding of genomics. The investment in proteomics on the part of NCI through this consortium shows importance of proteomics and proteogenomics research, says principal investigator Alexey I. Nesvizhskii, Ph.D., associate professor of pathology and of computational medicine and bioinformatics at the University of Michigan. Proteomics provides complementary information not apparent from the analysis of genomic and transcriptomic data alone. U-M is uniquely positioned to implement advanced bioinformatics infrastructure to address these challenges, he adds. The program intends to leverage recent … Continue reading →

The Office of Cancer Clinical Proteomics Research announced today its multi-institutional program to further the convergence of proteomics with genomics, or proteogenomics, to better understand the molecular basis of cancer and accelerate research in these areas by spreading research resources within the scientific community. Among these participating Proteogenomic Translational Research Centers (PTRCs) is the Lester and Sue Smith Breast Center, part of the NCI-designated Dan L Duncan Comprehensive Cancer Center at Baylor College of Medicine, the only site executing these tasks in the South. Bringing centers together under CPTAC The announcement of the PTRCs builds on the recently launched Proteome Characterization Centers (PCCs) and Proteogenomic Data Analysis Centers (PGDACs), which comprehensively characterize biospecimens and integrate/analyze resulting proteogenomic data to extrapolate cancer knowledge. Baylor also has been awarded as a PGDAC site. These three variations of proteogenomic centers of excellence (PCCs, PGDACs, and PTRCs) form the interdisciplinary pillars of the NCIs Clinical Proteomic Tumor Analysis Consortium (CPTAC), which centers on using the analysis of genomic and proteomic data to eventually help solve clinically relevant cancer questions, such as drug response and drug sensitivity. This is an emerging method of collaboration, said Dr. Bing Zhang, professor in the Lester and Sue Smith … Continue reading →

By Kelsey M. Mackin | June 27, 2017 When it comes to food safety,being able to identify traits of what is considered normal for a food ingredient, helps producers detect when something is abnormal. IBM and Cornell University will be collaborating to help keep the global milk supply safe. Specifically, next-generation genetic sequencing combined with bioinformatics analytics, will help reduce the chances of safety breaches impacting dairy. The teaching dairy barn at Cornell University will provide real-world conditions for researchers. Lindsay France/University Photography Researchers will collect genetic data from the microbiome of raw milk samples in a real-world scenario at a Cornell farm and the Cornell Dairy Processing Plant in Ithaca. Cornells resources are unique in that they represent the full dairy supply chain from farm to processing to consumer, according to a news release from the university. This initial data collection will form a raw-milk baseline and be used to expand IBMs Consortium for Sequencing the Food Supply Chain bioinformatic analytical tools. Cornell University is the most recent addition to the Consortium.The food safety initiative was launched in January 2015 by IBM Research and Mars Inc. A year later Bio-rad Laboratories Inc. joined. The Consortium is conducting the largest-ever … Continue reading →

Cambridge-based PetaGene software addresses challenges caused by growing volumes of genomics data. Initially part of a project exploring new storage and compression approaches in collaboration with the European Bioinformatics Institute, it achieves up to a 5x reduction in both storage costs and data transfer times (compared to gzipped FASTQ and BAM files), and integrates with existing storage infrastructure and bioinformatics pipelines. PetaGene started life as Project PetaGene, a research project by a group of PhD graduates from the University of Cambridge, who worked in collaboration with the European Bioninformatics Institute to try to solve the problem of genomic data storage from a new angle. PetaGene was a member of London-based incubator Entrepreneur Firsts sixth cohort, from which it graduated in 2016. Co-Founder and Business Development Manager, Vaughan Wittorff (pictured) is a Cambridge University PhD with significant experience in inventing technology and commercialising it in the private sector. He was formerly a Senior Lecturer in Electrical Engineering at Curtin University of Technology, and long-term Visiting Fellow at Cambridge University in Computer Science and Technology. petagene.com More here: PetaGene - Business Weekly … Continue reading →

article Dr. Francis Beaudry, University of Montreal, demonstrates the idea that HPLCOrbitrap can be used to detect specific peptide biomarkers in the digested gelatin, and food samples and that this method can be an effective strategy to detect gelatin adulteration. Sponsored by Thermo Fisher Scientific, the webinar sawFrancis present a strategy to detect specific peptide biomarkers in the digested gelatin and food samples using HPLCQqOrbitrap. He further demonstrated that this method can be an effective strategy to detect gelatine adulteration. Since June 2009, Francis has supervised or co-supervised 19 MSc and PhD students and is the author or co-author of 93 peer reviewed manuscripts and 90 research abstracts. In February 2017 he received The Faculty of veterinary medicine of the Universit de Montral / Zoetis award for excellence in research. In this article Francis selects a few of his favourite questions from the audience, and provides his answers: Typically, we homogenize 100mg (0. 1 g) of gelatin in an ammonium bicarbonate buffer (pH 8. 5) in a ratio of 1:5. The digestion can be performed directly with trypsin at this point but we do obtain better results when we perform an ethanol precipitation and re-dissolve the protein pellets in 100mM … Continue reading →

The Jackson Laboratory on Monday kicked off week-long trainings and lab sessions to bring high school science teachers up to speed on rapidly changing gene research. The Farmington research center brought together more than a dozen teachers from Connecticut and Massachusetts. The focus in the "Teaching the Genome Generation" program is on bioinformatics, the science of collecting and analyzing biological data such as genetic codes, and ethics related to the gathering and use of personal genetic and health information. The professional development program is intended to give teachers training to put in place "modern genetics and genomics" education programs in their schools, said Charles Wray, director of courses and conferences at Jackson Lab. Jackson Lab has trained about 70 Connecticut teachers in the last three years and schools, he said, are using content provided by the Bar Harbor, Maine-based lab. The content includes knowledge, laboratory equipment and other resources. The study of genomics, the part of genetics focused on sequencing and analyzing an organism's genome, or the DNA content within one cell of an organism, is advancing quickly and requires teachers to learn new material, much of it complicated and technical. In addition, students with an interest in biology and … Continue reading →

A genetically modified microorganism (GMM) integrating an antibiotic resistance gene was found in a riboflavin supplement from China aimed at feed use, finds newly published study. Regulators from Germany and Italy, who analyzed a vitamin B2productimported from China three years ago, just released their findings in Food Chemistry. The research was first reported on by Independent Science News . The tests followed the 2014 incident whereby a German enforcement laboratory alerted EU officials to illegal GE bacterial contamination in the imported feedstuff. According to EU biosafety regulations, no GM bacterial strain or any DNA is allowed to be present in commercial food and feed supplements. The officials said they performed tests to characterize the isolated strain. The analysis showed the illegal contaminating strain was not among those the Chinese manufacturer claimed to be using. The differences in the information provided by the Chinese company and the results of the molecular characterization strongly imply that the production strain must have been contaminated or switched before or during production. In 2016, the EU Commissions Food and Veterinary Office (FVO) carried out an audit in China in order to evaluate their control systems for GMO. The review was in response to the detection … Continue reading →

Details WhaTech Channel: Medical Market Research Published: 26 June 2017 Submitted by Research N Reports WhaTech Agency News from Research N Reports Viewed: 13 times The Global Bioinformatics Service Market 2017 examines the performance of the market. It encloses an in-depth judgment of this market state and the competitive landscape globally. Global Bioinformatics Service Market Size, Status and Forecast 2022 This research report thoroughly analyzes the most crucial details of the Global Bioinformatics Service Market with the help of an in-depth and professional analysis. Described in a ground-up manner, the report presents a comprehensive overview of the market based on the factors that are expected to have a substantial and measurable impact on the markets developmental prospects over the forecast period. Download Sample Copy@ http://www.researchnreports.com/request_sample.php?id=91044 Obtaining market-related data is not a very difficult task. Lack of dedicated resources for undertaking focused research that results in the collection of the most fruitful data is one of the most common shortcomings of inbound research activities. The report includes data that can help businesses in handling this issue with ease and provides detailed qualitative and quantitative details pertaining to the market elements that organizations are interested in. With this report, an organization can … Continue reading →

In bioinformatics, sequence clustering algorithms attempt to group biological sequences that are somehow related. The sequences can be either of genomic, "transcriptomic" (ESTs) or protein origin. For proteins, homologous sequences are typically grouped into families. For EST data, clustering is important to group sequences originating from the same gene before the ESTs are assembled to reconstruct the original mRNA. Some clustering algorithms use single-linkage clustering, constructing a transitive closure of sequences with a similarity over a particular threshold. UCLUST[1] and CD-HIT[2] use a greedy algorithm that identifies a representative sequence for each cluster and assigns a new sequence to that cluster if it is sufficiently similar to the representative; if a sequence is not matched then it becomes the representative sequence for a new cluster. The similarity score is often based on sequence alignment. Sequence clustering is often used to make a non-redundant set of representative sequences. Sequence clusters are often synonymous with (but not identical to) protein families. Determining a representative tertiary structure for each sequence cluster is the aim of many structural genomics initiatives. Read more: Sequence clustering - Wikipedia … Continue reading →

on June 24, 2017 at 11:46 am In the modern world, algorithms do much of the digital heavy lifting. Algorithms control the inner-workings of everything from particle accelerators to stock markets. They determine the news you see, what search results you get, how computers learn, and what gets recommended to you on Netflix or Amazon. In short, society couldnt function as-is without algorithms and as we lean on them to run more things, it becomes more important for us to learn what they are and what they do. Todays infographic from Futurism digs into the origins of algorithms, and how they impact our everyday lives. An algorithm is a predetermined set of steps for a computer to accomplish a task. Its basically an instruction manual. And as in life, instruction manuals can be simple (e.g. building an Ikea side table) or extremely complex (e.g. filing a patent). Below is Sorting Out Sorting (1981), a timeless primer on sorting methods. It clearly demonstrates the way computers approach sorting vast quantities of information by following a set of instructions. A famous example of an algorithm is Googles PageRank, which determines the order in which websites appear in Googles search rankings. PageRanks methodology … Continue reading →