Bio Saga Blog - A Chronicle of Life Sciences & Informatics

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Dako today said that the US Food and Drug Administration has approved two assays for use as companion diagnostics for a Genentech drug targeting HER2-positive metastatic breast cancer. FDA simultaneously approved Dako's HercepTest and HER2 IQFISH pharmDx assays and Genentech's drug Kadcyla (ado-trastuzumab emtansine). Kadcyla is for patients with HER2-positive metastatic breast cancer who have been previously treated with Genentech's Herceptin (trastuzumab) and a taxane chemotherapy. Dako, an Agilent company, and Genentech, a Roche company, have been collaborating on the development of companion diagnostics for Genentech's drugs for a few years. In May 2012 the two firms inked a pact to collaborate on the FDA submission of Dako's assays for Kadcyla. A month later the HercepTest and HER2 FISH pharmDx were approved by FDA as companion diagnostics for Genentech's breast cancer drug Perjeta (pertuzumab). In late 2011, FDA gave the thumbs up to Dako's H...

Scientists have discovered a new physical form of proteins that could drastically improve treatments for cancer and other diseases, as well as overcome some of the largest challenges in therapeutics. The protein formulation strategy, developed by researchers at The University of Texas at Austin, is unprecedented and offers a new and universal approach to drug delivery one that could revolutionize treatment of cancer, arthritis and infectious disease. “We believe this discovery of a new highly concentrated form of proteins – clusters of individual protein molecules – is a disruptive innovation that could transform how we fight diseases,” Keith P. Johnston, a chemical engineering professor and member of the National Academy Engineering, said. “It required integration of challenging contributions in fundamental science and engineering from three of our chemical engineering research groups,” he said. Johnston, Chemical Engineering Professor Thomas M. Truskett and Assistant Professor Jennif...

Aileron Therapeutics and Roche announced today that they have entered into a collaboration to discover, develop and commercialise a new class of drugs called Stapled Peptide Therapeutics. As part of this agreement, Roche will work with Aileron to develop drug candidates against up to five undisclosed targets selected from Roche’s key therapeutic areas, which include oncology, virology, inflammation, metabolism and CNS. Stapled Peptide Therapeutics are a result of Aileron’s breakthrough peptide stabilization technology, and are a potential solution to drug as-yet intractable disease targets, including those originating from long sought-after intracellular protein-protein interactions. Under the terms of the agreement, Roche will provide Aileron guaranteed funding of at least $25 million in technology access fees and R&D support. Aileron is eligible to receive up to $1.1 billion in payments upon the achievement of discovery, development, regulatory and commercialisation milesto...

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Sandoz has signed a definitive agreement to acquire Oriel Therapeutics, a privately held US pharmaceuticals company, gaining exclusive rights to a portfolio of generic drug candidates and related technologies targeting medicines in the inhalable respiratory drug market. Terms of the deal were not disclosed. The latter focuses on developing respiratory products with known pathways as generic alternatives to patented drugs for asthma and chronic obstructive pulmonary disease (COPD). The acquisition provides the former with three development projects targeting leading medicines in this field. Regulatory approvals of these medicines, if achieved, would enable the former to increase access to affordable, quality therapeutic alternatives for these increasingly prevalent diseases. Details of the latter's development programs, including anticipated timing of future regulatory submissions, are not disclosed for competitive reasons. The acquisition of the latter, which will be integrated as ...

Sandoz has signed a definitive agreement to acquire Oriel Therapeutics, a privately held US pharmaceuticals company, gaining exclusive rights to a portfolio of generic drug candidates and related technologies targeting medicines in the inhalable respiratory drug market. Terms of the deal were not disclosed. The latter focuses on developing respiratory products with known pathways as generic alternatives to patented drugs for asthma and chronic obstructive pulmonary disease (COPD). The acquisition provides the former with three development projects targeting leading medicines in this field. Regulatory approvals of these medicines, if achieved, would enable the former to increase access to affordable, quality therapeutic alternatives for these increasingly prevalent diseases. Details of the latter's development programs, including anticipated timing of future regulatory submissions, are not disclosed for competitive reasons. The acquisition of the latter, which will be integrated as ...

- GSK becomes first company to freely share chemical structures on 13,500 molecules from its compound library - Alliances formed with leading scientific research communities from private industry and public-domain data provider courtesy CDD Blog GlaxoSmithKline (GSK) had teamed up with leading public-domain data providers European Bioinformatics Institute (EMBL-EBI), the U.S. National Library of Medicine (NLM) and the US-based informatics service provider Collaborative Drug Discovery (CDD) to make freely available key scientific information on more than 13,500 compounds that could ultimately lead to new treatments for malaria. The release of this data marks the first time that a pharmaceutical company has made available the structures of so many compounds and is made possible through the collaboration of the web hosts and their specialist research tools, which will be available at no cost to researchers. The information, which is hosted on websites regularly used by researchers, incl...

While this is very encouraging what's going to be it's impact on the industry on proprietary database vendors? More & more of open database consortia and open curation models are on the offing, with high level of participation from both the academia and the Industry. The European Molecular Biology Laboratory's European Bioinformatics Institute has launched a "vast online database" of genomic-based drug and small molecule information available in an open access format for researchers seeking new therapeutics, according to EMBL-EBI. The ChEMBLdb holds translational information on more than 520,000 small molecules, including data on target binding, the affect these compounds have on cells and organisms, and information about the molecules' absorption, distribution, metabolism, excretion, and toxicity. "The data lie at the heart of translating information from the human genome into successful new drugs in the clinic," EMBL-EBI said this week. EMB...

GlaxoSmithKline Plc will buy a stake in Austria’s Intercell AG in a move that analysts said underscores drugmakers’ growing interest in vaccines. Glaxo will pay 33.6 million euros ($49.5 million) as part of the alliance to develop and market Intercell’s needle-free, patch-based immunizations for traveler’s diarrhea and pandemic influenza. The London-based drugmaker also will buy as much as 5 percent of Intercell for up to 84 million euros via a staggered shareholding option, the companies said in a statement today. XTractor Premium - A Platform for discovery , knowledge sharing, analysis and modelling of published biomedical facts. The only Knowledgebase which provides "manually" annotated facts from PubMed on a weekly basis Innovative Features like Semantic Search , Concept Linking , Bibliographic search , Save, Export and Visualize Only Knowledgebase with daily updations from PubMed XTractor Premium now at an Special Introductory Offer. Subscribe now and save! Re...

Indian Life Sciences Informatics Company, Molecular Connections announced today, that their XTractor Premium platform now has more that 503,985 " Expert " annotated biomedical facts from literature and is the fastest growing knowledgebase currently. XTractor Premium platform is Fast Becoming the definitive Semantic Knowledge discovery & Expert curated Knowledgebase for Life Science Researchers. The XTractor Premium Knowledgebase in addition to more than 503,985 relationships on proteins, drugs, biological process and diseases has advanced semantic search, concept linking analytics for effective knowledge discovery and modeling. XTractor Premium provides Precision based mining of the most relevant facts. Compared to natural language processing engines, manual annotation approach reduces false positives rate by 12-35%. XTractor premium serves as a platform to stay current with weekly updates from PubMed. Provides “Topic Tracking” with email alerts on spe...

Entrez gene is the most widely used data resource for Gene based information worldwide. To enable researchers to obtain high quality manually annotated information from XTractor when they search for a Gene on Entrez Gene, we are now providing direct links from Entrez Gene records to corresponding Gene Reports in XTractor. To use this outlinked option- when in Entrez Gene, for any human gene select the “Link Out” option from the Display menu in Entrez Gene and click on the XTractor link. You will be taken directly to the XTractor graphical report for the Gene of interest and also manually annotated facts on the associated Diseases, Drugs and the Biological Processes for the Gene. http://www.xtractor.in/ncbiSearch.do?xid=XT_15377&symbol=BRCA1 XTractor Premium - A Platform for discovery , knowledge sharing, analysis and modelling of published biomedical facts. The only Knowledgebase which provides "manually" annotated facts from PubMed on a weekly basis Innovati...

Mutations in the protein tyrosine kinase gene ERBB4 contribute to — and may provide hints about treating — a subset of melanoma, according to a paper by researchers from the National Institutes of Health and Johns Hopkins University that appeared in the advanced, online edition of Nature Genetics this week. The team sequenced protein tyrosine kinase or PTK genes in 29 individuals with melanoma. Their search uncovered dozens of somatic mutations affecting the kinase domain of 19 different PTK genes. When they looked at the same 19 genes in another 79 melanoma patients, the researchers found that almost a fifth of those tested harbored mutations in ERBB4 . And, they reported, knocking down the mutated form of ERBB4 or using a drug that targeted the gene slowed the growth of melanoma cell lines, suggesting it might be useful to evaluate ERBB4 status in melanoma patients. Researchers at the NIH Intramural Sequencing Center sequenced all 86 PTK family genes in tumor samples from 29 ...

One of my recent post discussed the dawn of the new era and new breed of search engines Search Wars . YEBOL a youngling from the the Stanford stable, a new search in the block. Yebol's mission is to build human-like world's knowledge base and provide knowledge based search (semantics) and services. Yebol utilizes a combination of patented algorithms paired with human knowledge to build a Web directory for each query and each user. Instead of the common “listing” of Web search queries, Yebol automatically clusters and categorizes search terms, Web sites, pages and contents. Yebol allows for a multi-dimensional search result instead of the normal one-dimensional search seen by most web search engines today. This provides a more accurate summary of top sites and categories; a wider array of related search terms; a longer and richer expansion for query results; and a deeper base of links and keywords in search result pages. Unlike ...

BioFocus DPI has partnered with the cancer drug candidate and biomarker company Oncodesign to offer an integrated service platform, Galapagos division BioFocus DPI said today. The agreement will create a service that combines BioFocus DPI's target discovery and screening capabilities with Oncodesign's biomarker and pharmacological services to offer target validation and clinical candidate selection services, the company said. BioFocus DPI offers gene-to-drug candidate discovery services, including in vitro and cell-based screening, chemogenomic and informatics offerings , storage, distribution, and other structural biology and medicinal chemistry services. XTractor Premium - A Platform for discovery , knowledge sharing, analysis and modelling of published biomedical facts. The only Knowledgebase which provides "manually" annotated facts from PubMed on a weekly basis Innovative Features like Semantic Search , Concept Linking , Bibliographic search , Save, ...

A not very long time ago, in a galaxy near, very near by.... SEARCH WARS Search, Search engines, While the Search engine big wigs fight for a niche in the search engines landscape .... The Google , Yahoo & now Micorsoft too (with their Bing ) There are the Wolfram | Alpha likes that are forming a separatist and slowly gaining power over the Google order. In fact google has managed to bring balance to both with its Google Squared . While platforms like XTractor , NextBio , Novoseek , GoPubMed , BioMedSearch have specialized in searching biomedical and biological knowledge are even more strengthening the separatists. Now to see and know who is more powerful, the galactic empire or the separatist? I leave it to the 'Republic' i.e. You users! to judge, in the form of your comments and experiences with such tools and searches! you could even voice your opinions here

Life sciences informatics company Molecular Connections , India, has announced the availability of XTractor Premium, a knowledge management platform, for the biomedical research community. The product is projected to provide scientists with new and refined ways to access the latest scientific facts from PubMed. Pharmaceutical companies, researchers and scientists can use the platform to identify, verify and develop predictive relationships from PubMed Literature. Leveraging the ability to transform data to knowledge and to assist experts is seen to be crucial to the success of research investigation today. XTractor Premium offers several enhancements over the beta version in managing large volume of published biomedical data to accelerate decision making. The XTractor knowledgebase currently contains 150,000 relationships on biomarkers, clinical trials, pathways, knockout studies, mutations, drug interactions and disease mechanisms. The knowledgebase is updated everyday with manually a...

XTractor Premium - a platform for discovery, analysis and modelling of published biomedical facts. The application also comes with -XTractor Premium Knowledgebase - the only knowledgebase, which provides "manually" annotated facts from PubMed on a daily basis.The XTractor Premium Knowledgebase now has more than 150000 relationships. TAGS: text mining, manual annotation, data alerts, pubmed, genes, drugs, processes, diseases, free, data mining, tag, drug discovery, web 2.0, natural language processing, data analysis, visualization, concept linking, abstraction, precision, recall, data accuracy, proteins, interactions, index, query, MeSH, NLM, manual curation, protein interactions, abstraction, abstracts, accuracy, accurate, data, annotations, biological process, biomedical literature, categorization, colloborations, concept linking, curate, curation, data accuracy, data alerts, literature, categorization, colloborations, concept linking curate curation data accuracy data ale...

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BANGALORE, Indian Researchers have achieved a breakthrough, identifying a protein pathway that triggers cancer in the human body owing to its erratic behaviour. Researchers at Bangalore’s National Centre for Biological Sciences (NCBS) led by Satyajit Mayor and Neha Vyas have identified what is known as the Hedgehog pathway and the ways in which it forms and leads to cancer. The researchers, who have published their work in the journal, Cell, say this pathway is formed when the proteins (called hedgehog), which are separate, get drawn to each other by electrostatic interactions between amino acids present around the proteins. A small cluster of proteins then gets formed and goes on to form a mega-cluster. This travels to other cells and creates effects that are good or bad — the cluster could be normal and help organ regeneration or tissue repair, or the cluster could get hyperactive and affect other cells, which is the sign that cancer is coming. Simply put, the NCBS research indicates...