“Sage Bionetworks Awarded New Center for Cancer Systems Biology - Genetic Engineering News” plus 3 more

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• Sage Bionetworks Awarded New Center for Cancer Systems Biology - Genetic Engineering News
• Helicos BioSciences Featured at Advances in Genome Biology and ... - Consumer Electronics Net
• Successful genome sequencing of pea aphid is a breakthrough for ... - EurekAlert
• Sage Bionetworks Snaps Up $6.7M Grant to Train Young Network ... - Xconomy

Sage Bionetworks Awarded New Center for Cancer Systems Biology - Genetic Engineering News Posted: 23 Feb 2010 07:58 AM PST Message from fivefilters.org: If you can, please donate to the full-text RSS service so we can continue developing it. Email Print Share More News Feb 23 2010, 11:00 AM EST Sage Bionetworks Awarded New Center for Cancer Systems Biology News source: Business Wire Sage Bionetworks has been selected by the National Cancer Institute (NCI) Integrative Cancer Biology Program (ICBP) to establish a new interdisciplinary research and training center. "We are thrilled to receive the strong support from NCI and to join the other Centers for Cancer Systems Biology (CCSB)," said Stephen Friend, Sage Bionetworks President. "We are particularly pleased that they share our view on the critical importance of training." The grant entitled "Integrating Cancer Datasets for Predictive Model Development and Training" will provide a baseline of $6.7m to support the Center's operation and the training of four postdoctoral researchers each year. Dr. Dan Gallahan, the Director of the NCI Integrative Cancer Biology Program said, "Sage Bionetworks' training and research program as well as the developing Sage Commons platform bring a new dimension and I am excited to have their participation in the NCI ICBP centers program." "This prestigious grant is a wonderful endorsement for our young organization and validates our vision to establish a contributor-based integrative genomics and network biology resource to accelerate drug development," Dr. Friend added. "Advanced predictive models of cancer, built through a network analysis of complex molecular and clinical datasets, are increasingly poised to inform drug development and clinical care decisions." Sage Bionetworks is a new nonprofit medical research organization established in 2009 to establish a novel research community Commons. "Sage was established based on three themes; biomedical research, integrative genomics platform building and training. These three tenets establish a foundation for a Commons that will ultimately enable the sharing of large comprehensive datasets and models among scientists," said Dr. Jonathan Derry, Sage's Research Director and the Center's administrative leader. "This new NCI Center represents the first component of our training mission." "Interdisciplinary bridges are essential for the development and use of genomic technologies. For this reason we have chosen to train paired mathematicians/physicists and biologist/clinicians so that they can cross-fertilize each other's thinking." Dr. Friend added. "Such interactions often form the spark of innovation." Prof. Bert Vogelstein, Director of the Ludwig Center for Cancer Genetics & Therapeutics at Johns Hopkins University, commented, "We are delighted to be a part of this novel collaborative center and to provide our comprehensive cancer analysis data as part of the foundation for the Commons platform." He added, "High throughput integrative genomics will strengthen our understanding of cancer and our ability to predict clinical outcomes based on molecular data." Sage Bionetworks will collaborate with the Fred Hutchinson Cancer Research Center, The Johns Hopkins University, The Dana Farber Cancer Institute, The University of Hong Kong and the Netherlands Cancer Institute as well as with the other ICBP Centers. The research projects will initially focus on breast, colon, liver and pancreatic cancer. The resultant computational models will be validated in the laboratory to test their accuracy as well as to help refine and improve the models. About the ICBP Program: The National Cancer Institute (NCI) Integrative Cancer Biology Program (ICBP) supports eleven Centers for Cancer Systems Biology (CCSBs) distributed across the US. Begun in 2004, the current participants include Sloan-Kettering, MIT, Broad Institute, Caritas St. Elizabeth, Methodist Hospital, Georgetown, Ohio State, Vanderbilt, Stanford and Lawrence Berkeley. The Centers are highly interactive and collaborate with other NCI programs and grantees. ICBP is an interdisciplinary program bringing together talented researchers from experimental biology, medicine, math, physics, information technology, imaging and computer science. Viewing cancer as a complex biological system, ICBP's central theme is the development of computational models related to cancer prevention diagnosis and therapeutics. A key feature of the program is the focus on building predictive models of cancer rather than just analyzing data. There is a further pragmatic emphasis on testing the models to validate the usefulness in research, drug development and health care. For more information go to: www.icbp.nci.nih.gov About Sage Bionetworks: Sage Bionetworks is a new nonprofit medical research organization established to revolutionize how researchers approach the complexity of human biological information and the treatment of disease. Sage works with academic and commercial partners on comprehensive molecular and clinical datasets in order to create validated disease models that improve the speed and efficiency of therapeutic drug development. Sage's vision is to create an open access, integrative bionetwork evolved by contributor scientists working to eliminate human disease. For more information visit: www.sagebase.org. Email Print Share More News Five Filters featured article: Chilcot Inquiry. Available tools: PDF Newspaper, Full Text RSS, Term Extraction.

Helicos BioSciences Featured at Advances in Genome Biology and ... - Consumer Electronics Net Posted: 23 Feb 2010 04:37 AM PST Message from fivefilters.org: If you can, please donate to the full-text RSS service so we can continue developing it.   February 23, 2010 -- CAMBRIDGE, Mass., BUSINESS WIRE -- Helicos BioSciences (NASDAQ:HLCS) and it's collaborators will deliver presentations featured at the Advances in Genome Biology and Technology (AGBT) meeting in Marco Island, Florida, from February 24-27, 2010. The presentations demonstrate the unique attributes of single molecule sequencing available for customers using the Helicos Genetic Analysis System, and highlight the suitability of the technology for answering difficult and previously intractable questions in biology and medicine. Dr. Timothy Triche, MD, PhD, University of Southern California on behalf of the Children's Oncology Group will discuss recent collaborative studies undertaken with Helicos in a talk entitled 'Unraveling the Complexity of Primary and Metastatic Ewing's Sarcoma Using Helicos Single Molecule Sequencing'. Using a Helicos Genetic Analysis System, the group performed a comprehensive and quantitative survey of a cancer patient's genome and transcriptome to identify changes responsible for tumor metastasis and drug resistance. In a talk entitled 'A True Unbiased View of Genome Biology: Helicos Single Molecule Sequencing' Patrice Milos, PhD, Vice President and Chief Scientific Officer, of Helicos will present the technology's unique ability to perform Direct RNA Sequencing and Direct Chromatin Immunoprecipitation Sequencing (ChIP-Seq), providing unbiased quantitation and sequence information. The unparalleled quantitative accuracy of Helicos' direct measurement will be demonstrated relative to 2nd Generation, amplification-based technologies. In addition, John Thompson, PhD, Helicos's Senior Director of Genomic Sciences, will give a poster presentation entitled 'Single Molecule Sequencing of DNA Invisible to Other Technologies' describing Helicos' unique ability to sequence DNA from samples other technologies can't. These include samples that are highly degraded, contaminated or of very ancient origin. The Helicos Genetic Analysis System is the world's first and only commercially available technology capable of True Single Molecule Sequencing (tSMS)TM. Unlike amplification-based technologies, the Helicos approach is free from the biases and artifacts associated with amplification, and provides a direct view of biological samples, enabling applications that can revolutionize biology, diagnostics and medicine. About Helicos BioSciences: Helicos BioSciences is a life science company focused on innovative genetic analysis technologies for the research, drug discovery, and diagnostic markets. Helicos' proprietary True Single Molecule Sequencing, tSMS(TM), technology allows direct measurement of billions of strands of DNA enabling scientists to perform experiments and ask questions never before possible. Helicos is a recipient of two $1,000 genome grants and committed to providing scientists the tools to unlock the era of genomic medicine. The company's corporate headquarters are located at One Kendall Square, Building 700, Cambridge, MA 02139, and its telephone number is (617) 264-1800. For more information, please visit www.helicosbio.com. Certain statements made in this press release that are not based on historical information are forward-looking statements which are made pursuant to the safe harbor provisions of the Private Securities Litigation Reform Act of 1995. This press release contains express or implied forward-looking statements relating to, among other things, the prospective value of the unique attributes of single molecule sequencing as discussed in this press release and the presentations at the AGBT meeting, and management's plans, objectives and strategies. These statements are neither promises nor guarantees, but are subject to a variety of risks and uncertainties, many of which are beyond Helicos' control, which could cause actual results to differ materially from those contemplated in these forward-looking statements. In particular, the risks and uncertainties include, among other things, our ability to successfully complete and/or scale the manufacturing and commercialization process for the Helicos Genetic Analysis System; our history of operating losses and ability to achieve profitability; our ability to sustain and scale our manufacturing capabilities; the research and development spending levels of academic, clinical and governmental research institutions and pharmaceutical, biotechnology and agriculture companies who may purchase our Helicos Genetic Analysis System; our reliance on third-party suppliers; competition; changing technology and customer requirements; our ability to operate in an emerging market; market acceptance of our technology; the length of our sales and implementation cycles; our dependence on large contracts for the sale and implementation of our Helicos Genetic Analysis System; failure of our technology and products; our ability to maintain customer relationships and contracts; ethical, legal and social concerns surrounding the use of genetic information; our ability to retain our personnel and hire additional skilled personnel; our ability to manage our growth while operating with limited resources; our ability to control our operating expenses; general economic and business conditions; our ability to obtain capital when desired on favorable terms; and the volatility of the market price of our common stock. Existing and prospective investors are cautioned not to place undue reliance on these forward-looking statements, which speak only as of the date hereof. Helicos undertakes no obligation to update or revise the information contained in this press release, whether as a result of new information, future events or circumstances or otherwise. For additional disclosure regarding these and other risks faced by Helicos, see the disclosure contained in Helicos' public filings with the Securities and Exchange Commission. Five Filters featured article: Chilcot Inquiry. Available tools: PDF Newspaper, Full Text RSS, Term Extraction.

Successful genome sequencing of pea aphid is a breakthrough for ... - EurekAlert Posted: 23 Feb 2010 07:29 AM PST Message from fivefilters.org: If you can, please donate to the full-text RSS service so we can continue developing it. Public release date: 23-Feb-2010 [ | E-mail | Share ] Contact: Ben Norman Lifesciencenews@wiley.com 44-012-437-70375 Wiley-Blackwell A special issue of Insect Molecular Biology reports the detailed analyses of specific aspects of the genome of the important plant pest, the Pea Aphid. The analyses are based on the publication of the aphid genome sequence in PLoS Biology and is a major step in enhancing our understanding of insect ecology and evolution with important implications for controlling these significant plant pests. The sequencing of the Pea Aphid, Acyrthosiphon pisum, genome is a major milestone for insect scientists. To date all insect genomes that have been sequenced have been holometabolus species, such as flies, bees, ants, butterflies and wasps. The Pea Aphid is a member of a group of insects that are more ancient than flies and bees etc. and are closely related to the wingless insects which are thought to have evolved more directly from the first insects. This unique position of the Pea Aphid within the insect tree of life will provide important keys to understanding insect biology and evolution. "Aphids are economically very important insects as they contain a host of agricultural and forestry pests as well as some medically important species," said Professor Charles Godfrey from the University of Oxford, in the editorial of the special issue. "The pea aphid is, as the name would suggest, a pest of peas and other legumes though does not cause the major economic damage of related species such as the peach-potato aphid." The Pea Aphid is of particular interest to ecologists as aphid populations can develop to specialise in different food plants. When a population selects a new plant to colonise the association with the plant leads to balanced gene flow which prevents further divergence and speciation to occur in the aphid population. This process of specialisation means the Pea Aphid has become a model organism for evolutionists studying specialisation and ecological speciation with the sequencing of the genome now allowing new testing of speciation theories and models. The sequencing also allows scientists studying the spread of agricultural diseases to further understand the relationship between a virus, the host insect and the plant. Aphids are also major vectors of viral plant disease, which cause severe economic damage for agriculture. Some viruses have evolved to facilitate their transmission by aphids and the newly published genome sequence will allow scientists to understand the physiological, genetic and molecular basis of this critical interaction. Aphids feed on plant juices which they obtain from the phloem tissue of leaves and stems using long piercing mouthparts. Phloem is rich in carbohydrates, but low in the nitrogenous compounds which complex organisms need to make proteins to survive. Aphids have a highly developed gut and the genome sequence reveals many genes for sugar transporter proteins but oddly are missing common genes involved in making some amino acids. Remarkably, symbiotic bacteria living inside the aphid provide these missing proteins. One of the most curious findings of this sequencing project is the absence of many genes involved in defending the insect from pathogens, parasites and predators. A large part of the typical insect immune system which is well studied in other insects, is absent from the Pea Aphid. This is surprising as Pea Aphids are attacked by a variety of natural enemies ranging from fungal diseases to parasitoid wasps. "It is likely that aphids are selected for extremely high rates of reproduction, they have to colonise a plant and produce offspring before their enemies find and exterminate them," said Godfrey. "We know there are tradeoffs between defence and other fitness components and in Aphids natural selection may have favoured reproduction over defence." "Biologists working on the pea aphid now have a valuable new set of tools to attack novel questions," concludes Godfrey. "Studies on the pea aphid will inform our understanding of aphid biology and of insects more generally, with clear economic benefits at a time of increasing food security." "At some point, perhaps in the near future, the publication of another insect genome may not warrant special notice, and this, no doubt, will be a reflection of how advanced our technical capabilities as molecular biologists have become," said journal editors David O'Brochta and Lin Field. "Presently, at least for Insect Molecular Biology, a new insect genome remains an exciting and significant event in which we are pleased to play a small role." [ | E-mail | Share ]   Five Filters featured article: Chilcot Inquiry. Available tools: PDF Newspaper, Full Text RSS, Term Extraction.

Sage Bionetworks Snaps Up $6.7M Grant to Train Young Network ... - Xconomy Posted: 23 Feb 2010 07:58 AM PST Message from fivefilters.org: If you can, please donate to the full-text RSS service so we can continue developing it. Biotech, Genomics, startups Luke Timmerman 2/23/10 Sage Bionetworks, a fledgling Seattle nonprofit attempting to launch an open-source biology movement, has nabbed a $6.7 million grant from the National Cancer Institute to train young scientists to learn to better use genomic data to help improve drug discovery and patient care. The grant lasts for four years, and it may be supplemented and extended, says Sage Bionetworks founder and president Stephen Friend. Here's how it will work: Each year, the plan is to identify two young postdoctoral physicists who have deep understanding of mathematical models and algorithms, and to pair them with two clinician/scientists at the same stage of their careers, but with deep knowledge of biology, Friend says. The vision is that these pairs will cross-fertilize each others' thinking, so that together, they can use math and computing tools to build predictive models that can show the connections between genomic alterations, the faulty proteins that arise from them, and clinical symptoms of diseases that are the end result. By finding the connections between underlying genotype and the phenotype, so-called network biologists will be able to create the first predictive models of disease—sort of like how engineers build predictive models of an airplane on a computer before it flies. This new kind of network approach could reduce the huge waste of time and money on drugs that fail in development, by weeding out duds early, and someday helping guide personalized treatment decisions for doctors. But if this vision is going to become reality, it will require a culture change in biology, making it more open and less proprietary. The new training program is one key step toward making that happen. "There will be a national competition to identify the winners of these spots in the training program. I can see this becoming like winning a MacArthur fellowship," Friend says. Stephen Friend Sage made its public debut about a year ago when Friend announced he was leaving his high-profile job in charge of cancer research at Merck. Even at a company with as much money and brainpower as Merck, Friend said the problems of biology are too big for any company, and that his next quest would be to apply crowdsourcing or collective brainpower to the challenge. The organization secured $5 million in charitable commitments, and was seeded with data from Merck that represented about $150 million of R&D. Sage has since secured more support from Quintiles, the giant contract research organization, and Pfizer. There are really three main themes Sage is pursuing in its early days, Friend says. It starts with building up its research capability through support from foundations and companies. Then comes the training component that's being supported by the National Cancer Institute. The third theme is building up the Sage platform, in which it creates the public repository for data with common standards and annotations, proper governance, and a user interface that hopefully makes this whole thing user-friendly so a large number of scientists will actually use it. Sage hopes to make progress on that third theme at its first international congress on April 23 and 24 in San Francisco. But as for today's news, it's another significant step for Sage as an organization. The nonprofit now has about 20 people, counting staff and postdocs, and the grant will allow it to grow to about 25 after it adds some more mentors for its aspiring network biologists, Friend says. Sage will now collaborate with the Fred Hutchinson Cancer Research Center in Seattle (where it is physically housed), as well as Johns Hopkins University, the Dana-Farber Cancer Institute, the University of Hong Kong, and the Netherlands Cancer Institute. In the beginning, the research projects will focus on breast, colon, liver, and pancreatic cancer models. Researchers at Sage will build computational models of disease, and then run wet-lab experiments to see how accurate they are, and to refine their methods. The goal, over time, will be to extend this sort of training to many other centers beyond Sage, Friend says. "We want to set up a paradigm for training. If after four years, this is the only place doing this training, it will be too bad," Friend says. Luke Timmerman is the National Biotechnology Editor for Xconomy. You can e-mail him at ltimmerman@xconomy.com, call 206-624-2374, or follow him on Twitter at http://twitter.com/ldtimmerman. Five Filters featured article: Chilcot Inquiry. Available tools: PDF Newspaper, Full Text RSS, Term Extraction.

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