Bio Saga Headlines

Bio Saga

Wednesday, December 16, 2009

GlaxoSmithKline to Buy Stake in Intercell AG

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.

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Friday, December 11, 2009

World's fastest growing Semantic discovery & Expert Curated Knowledgebase platform crosses 500,000 biomedical facts now

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 specific biological entities of interest via the “Watch List” feature.

The Highlights

Semantic Search: The first of its kind highly advanced search feature, where in one could query the XTractor Premium Knowledgebase using multiple ontologies. This would enable you to narrow down on your targets at ease.

Concept Linking: Our advanced query feature would enable you to make assumptions from multiple abstracts, and discover facts, which are hitherto not published.

Bibliographic search: Search based on author, organization, affiliation or country.

Save Export and Visualize: Save and export the data in user-friendly formats, also XTractor Premium is made compatible with CytoScape - so one can visualize the networks rendered using a in-house CytoScape plug-in.

Web based and onsite installation available

To know more about the advantages of the XTractor Premium and to register for a free trial account and a webex demo please visit XTractor Premium portal www.xtractor.in/premium.

About XTractor Premium Knowledgebase
XTractor knowledgebase currently contains 503,985 relationships on biomarkers, clinical trials, pathways, knockout studies, mutations, drug interactions, toxicity, pharmacokinetics, disease mechanisms. It is the Only Knowledgebase that gets updated everyday with manually annotated relationships from the latest PubMed publications and contains more than more than 1,269 Unique Drugs, 3,602 Unique Diseases, 11,407 Unique Proteins, and 3,266 Unique Biological Processes. Hence in no time one gets to access one of the largest and the most current manually annotated datasets across the world.

About Molecular Connections
Molecular Connections is a pioneering In silico Discovery Services Company. It provides high quality, cost effective curation, literature informatics solutions and annotation services as well as products. Dr. Limsoon Wong is the Chairman of Molecular Connections. Customers of Molecular Connections include leading pharmaceutical and biotechnology, drug discovery, genomics, proteomics, medical technology, equipment companies and academic institutions spanning across the globe. In addition, Molecular Connections has powerful tool development, database integration, effective data visualization capabilities, specific expertise in building knowledge bases for rapidly growing needs in, ADME Tox, clinical, drugs, chemistry and patent industries. For more information write to us at xtractorpremium@molecularconnections.com

Recent Awards
Deloitte Technology Fast 50 India Winners |Deloitte Technology Fast 500 APAC Winners |CNBC - ICICI Emerging India Awards ‘Small Enterprise of the Year’



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Thursday, December 10, 2009

Bangalore unveils new BT policy

In effort to make Karnataka Biotechnology Capital of Asia, the State government, on Wednesday, launched ‘Millennium Biotech policy II’ a successor to Biotech Policy issued of 2001.


Releasing the policy, Principal Secretary IT, BT S&T Ashok Kumar Manoli said the new policy will provide all fiscal incentives and concessions under Karnataka Industry policy 2009-14 to bio technology industry and the R&D centres.

Biotech organisations will get incentives including a subsidy of 50 per cent for setting up effluent treatment plants. The financial incentives includes assistance for patent tracking and patent registration.

According to the new policy biotech will be treated as special industrial consumers and provided with dedicated power lines that are exempt from power cuts. It also assures power connection to biotech companies within 10 days of applications. Bioinforamtics companies that use up to 50 KVA power will be permitted to be established without any local restrictions. The Biotech unit will be exempted from electricity duty of 100 per cent.

The government also express its commitment and importance of creating a start up ecosystem and the government will encourage setting up of venture capital funds for biotech industries called KBIO-Ven fund of Rs 50 crore. Companies with focused area on transgenics, stem cell biology, bio manufacturing and other social relevance will be eligible for funding.

A separate fund of Rs 15-20 crore will be used to issue grants in the range of Rs 10-20 lakh for firms that translate research to commercial projects. The government will also offer tillable agricultural land of 15-20 acres of land and solely for agriculture related bio tech field trials and experiments for a period of 35 years. All R&D labs will be automatically come under the green category, and omitted from pollution control board permission for setting up labs.

The government will set up ten BT finishing school selected by vision group. The government will provide financial support to the schools to set up lab instruments and other technology related gadgets to train students. It will also provide specific infrastructure for the development of biotechnology. This includes promoting of Hi-tech bio tech park in the state. A 106 acre Biotech park Bangalore Helix is coming up in Electronic City. A Bio-IT park in a 100 acre plant in Ramanagaram is also planned.


Click here for the Policy. Note: File size - 18 mb




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Friday, November 20, 2009

Cutting edge HPC applications for bioinformatics

Canadian-based GPU maker Tycrid Platform Technologies has just announced the launch of the Prometheus Alliance, a collaborative effort aimed at developing cutting edge HPC applications for bioinformatics, with a specific emphasis on next-gen sequencing data and personalized genomics.

Chris Heier, President of Tycrid Platform Technologies, stated in a release that "Alliance is being established to address a specific challenge that continues to impede the progress of scientific discovery – the lack of scalable, purpose-built appliances. I feel this is critical as we can virtually eliminate the need for scientists to become computer scientists. Our goal is to take a fresh, innovative approach to developing HPC solutions that do one thing really well – address specific computational challenges for bioinformatics.”



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Wednesday, November 11, 2009

Vacancy for a Computing Officer - Web Applications and Data Management - University of Oxford

The Oxford University Image Bioinformatics Research Group wishes to appoint a Computing Officer – Web Applications and Data Management to work on the JISC-funded ADMIRAL Project - A Data Management Infrastructure for Research Across the Life Sciences. This will involve interactive working with researchers to improve the management, archiving and Web Publication of their biological research data, undertaking Web application development, and system evaluation and maintenance of the data management infrastructure.

Applicants should have a good B.Sc. or higher degree, probably in maths or science, and show evidence of creativity and research competence. Good programming and data management skills are required, as is familiarity with the standards and principles of modern Web application development. Experience with agile development techniques, Javascript, JQuery, Java, Python and RDF, and competence in Linux computer systems administration would be desirable.
Further details about this post can be found at: http://www.zoo.ox.ac.uk/jobs/adverts/at09035.pdf. The closing date for receipt of applications is Monday 30 November 2009.

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Wednesday, November 4, 2009

NIH Awards $67M in EUREKA Grants

The National Institutes of Health has granted $67.4 million in funding for trailblazing research that could reap great benefits but which are not guaranteeing immediate results, including genomics and proteomics studies, NIH said Monday.

The Exceptional, Unconventional Research Enabling Knowledge Acceleration (EUREKA) program grants $200,000 per year for up to four years for researchers that test unconventional ideas or "tackle major methodological or technical challenges," according to NIH. Of the 56 grants, 10 researchers will receive a total of $10.6 million for two-year awards through the American Recovery and Reinvestment Act of 2009.

"EUREKA awards reflect NIH's continued commitment to funding transformative research, even if it carries more than the usual degree of scientific risk," NIH Director Francis Collins said in a statement. "The grants seek to elicit those 'eureka moments' when scientists make major theoretical or technical advances."

"The research supported by EUREKA could provide us with new concepts, tools and approaches that have a profound impact on our understanding of biology — from fundamental life processes to human diseases and behavior," said Jeremy Berg, Director of the National Institute of General Medical Sciences, which led development of the program.

The grants include support for a study at Arizona State University, Tempe, titled "Working Backwards from the Proteome"; development for a genome-wide RNAi screening platform for the common lab at Scripps Research Institute; a study at the University of Miami of the genome, transcriptome, and proteome interaction in the human cortex, or the human 'brainome'; and a study of single-cell functional genomics at Yeshiva University, among others.

The EUREKA program was developed with collaboration from the National Cancer Institute, the National Institute on Aging, the National Institute of Mental Health, the National Institute on Drug Abuse, the National Institute on Neurological Disorders and Stroke, and the National Library of Medicine.

More information regarding the grants can be found here.



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Monday, October 26, 2009

Becton Dickinson Acquires HandyLab

Becton Dickinson has signed a definitive agreement to acquire molecular diagnostics firm HandyLab for an undisclosed sum.

HandyLab sells the Jaguar molecular diagnostics system, which incorporates clinical sample preparation, nucleic acid extraction, microfluidic real-time PCR amplification and detection. The Ann Arbor, Mich.-based firm launched the system in November 2008.

BD said that it plans to place its BD GeneOhm assays for methicillin-resistant Staphylococcus aureus, Clostridium difficile, and vancomycin-resistant Enterococcus on the HandyLab platform and market them as the new BD Max system.

The acquisition follows an alliance between the firms begun earlier this year aimed at placing the GeneOhm tests on the Jaguar system.

"We believe this new platform enables both our healthcare-associated infections offering and future expansion into other molecular opportunities," BD President Vincent Forlenza said in a statement.

BD said that it will provide more information on the acquisition during its fiscal fourth-quarter conference call on Nov. 4.



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Tuesday, October 20, 2009

SAAS product startup from India XTractor

Was going through a recent blog on indiblogger about the NASSCOM Product Conclave. Where this time is themed and focused on SAAS & related services.

In the recent times SAAS or Software as a Service has even captured the attention of Life Science and biomedical community globally. Indian Life Sciences Informatics Company, Molecular Connections' year old SAAS product startup is www.XTractor.in. In July 2008 came of with a commercial version of the product XTractor Premium- expert curated biomedical discovery, analysis and knowledge modeling platform, based on semantic curation and annotation of biomedical facts from PubMed. Has very handy analytics to search and narrow down the most relevant facts, build and discover relationships between biomedical facts check out some of the user CaseStudies.

XTractor Premium knowledgebase currently contains 302,269 relationships categorized on 24 categories Gene-Gene , Gene-Drug , Gene-Disease , Gene-Process , Gene-Mutation/Polymorphism, Drug Disease , Gene Knock-out/RNAi, Gene Pathways , Drug Process , Disease Process , Biomarker/Marker Disease , Prognosis, Diagnosis, Therapeutic or Therapy, Clinical Trials, Drug Bioavailability , Drug clearance , Drug Dosage , Drug-Drug , Disease-Disease , Drug Pharmacokinetics , Drug toxicity , Drug route of administration , Drug pharmacodynamics.

The platform has a recently completed an seamless link-out integration with NCBI EntrezGene.

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Monday, October 19, 2009

DBT invites positions for Directors/Deans

DEPARTMENT OF BIOTECHNOLOGY
Ministry of Science and Technology
Govt of India

TRANSLATIONAL HEALTH SCIENCE AND TECHNOLOGY INSTITUTE
(Autonomous Institute and Part of NCR Bio-medical Science Cluster)
Present location at the National Institute of Immunology
JNU Complex, Aruna Asaf Ali Marg, New Delhi 110 067

EXECUTIVE DIRECTOR AND DEANS

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Thursday, October 15, 2009

Entrez Gene outlink Integration for XTractor

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.

Entrez Outlink
http://www.xtractor.in/ncbiSearch.do?xid=XT_15377&symbol=BRCA1



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Tuesday, October 13, 2009

'Omics Projects Snag More than $625M Worth of NIH Stimulus Grants

The National Institutes of Health has awarded 970 stimulus grants worth more than $625 million — around 14 percent of total NIH stimulus grant funding to date — to projects that fall within the broad family of 'omics disciplines, according to a preliminary analysis of the NIH funding database conducted by GenomeWeb Daily News.

As of Sept. 30, the close of the fiscal year, the National Institutes of Health had awarded a total of $5 billion in stimulus funding — nearly half of the $10 billion appropriation that NIH will disburse over two years under the American Recovery and Reinvestment Act of 2009.

The $5 billion figure includes both grants and contracts, however. For grants alone, NIH had awarded approximately $4.4 billion via 12,789 ARRA grants as of Oct. 7, according to the database.

The 970 grants awarded to 'omics projects comprise 7.5 percent of the stimulus grants awarded so far, but the total funding awarded to these projects makes up 14 percent of NIH ARRA grant funding to date.

The largest share of grants — 194 — went to bioinformatics and computational biology projects, for a total of $92.4 million in funding.

Sequencing projects snagged the most amount of total funding, however, with 88 grants worth $129.8 million.

Those disciplines were followed by:

• projects and centers focused on translational research and systems biology, which garnered 148 grants totaling $100 million;
• proteomics projects — including instrumentation grants for mass spectrometers and nuclear magnetic resonance systems — which were awarded 141 grants totaling $57.2 million;
• projects that involved RNAi, microRNAs, and other non-coding RNAs, which snagged 93 awards worth a total of $29 million;
• pharmacogenomics and personalized medicine projects, which were granted 80 awards worth $45.2 million;
• biochips and microarrays — excluding genome-wide association studies — which netted 63 awards worth $33.3 million;
• GWAS studies, which were awarded 28 grants worth $42.8 million;
• epigenomics projects, which received 38 awards totaling $26.1 million;
• metabolomics studies, which garnered 11 grants worth a total of $5.5 million; and
• metagenomics efforts, which received 8 grants worth $6.9 million.

There were 134 grants, worth a total of $113.6 million, awarded to genomics projects that did not fall into any of the above categories (see below for a breakout of the number of grants and the funding amounts awarded to each discipline).

The research institutes that picked up the lion's share of the 970 'omics awards were the University of Washington, with 27 grants worth $24.3 million; Harvard/Harvard Medical School with 26 grants worth $19.8 million; and the University of Michigan at Ann Arbor and Stanford University with 22 grants each worth $18.7 million and $11.8 million, respectively.

The University of Pennsylvania, Johns Hopkins University, and Brigham and Women's hospital were each awarded 19 'omics grants, worth $22.1 million, $10.7 million, and $12.5 million respectively.

The Broad Institute, which was awarded 14 'omics stimulus grants, snagged the most total funding, with $33 million.

The largest single 'omics stimulus award, worth $12.2 million, went to Eric Boerwinkle at the University of Texas Health Sciences Center for a project entitled, "Building on GWAS for NHLBI-Diseases: The CHARGE Consortium."

Other 'omics awards in the double-digit million range went to Wash U, which received $10 million for "Center for Large-Scale Genome Sequencing and Analysis;" the Broad Institute, which received $10.2 million for "Comprehensive Sequencing and Analysis of Variation in NHLBI Cohorts;" and the University of Washington, which received $11 million for "Northwest Genomics Center."

The average amount for 'omics stimulus awards was $644,807, compared to an average of $340,524 for all NIH ARRA awards.


arra_awards.jpg




arra_funding.jpg

Editor's note: the number of grants and total funding in the subcategories is greater than the 970 grants and $625 million cited in the article due to some grants being counted in more than one category.



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Thursday, October 1, 2009

Obama, Collins Laud $5B in NIH Stimulus Funds, Much for Genomics

The National Institutes of Health has awarded more than 12,000 grants totaling around $5 billion so far under the economic recovery and stimulus package, the White House said today.

President Barack Obama commuted to Bethesda this morning to announce the funding as a milestone, to unveil a $175 million grant for cancer genomics, and to tour the NIH campus.

In late-morning speeches before a crowd of NIH staff, President Obama, Health and Human Services Secretary Kathleen Sebelius, and NIH Director Francis Collins loosely outlined how the $5 billion in grants over two years — nearly half of NIH’s total $10 billion appropriation under the American Recovery and Reinvestment Act — will stimulate research and create jobs.

A number of genomics-focused programs will be funded under the stimulus package, including $175 million over two years for The Cancer Genome Atlas, a joint effort between the National Human Genome Research Institute and the National Cancer Institute, according to a fact sheet released today by the White House.

“This ambitious effort promises to open new windows into the biology of all cancers, transform approaches to cancer research, and raise the curtain on a more personalized era of cancer care,” Collins said in a statement, describing the TCGA funding as “an excellent example of how the Recovery Act is fueling discoveries that will fundamentally change the way we fight disease and improve our lives.

"We are about to see a quantum leap in our understanding of cancer," Collins said.

NCI and NHGRI will also each commit $50 million in non-Recovery Act funds to the Genome Atlas over this two-year period, according to NCI.

"We know that this kind of investment will also lead to new jobs: tens of thousands of jobs conducting research, manufacturing and supplying medical equipment, and building and modernizing laboratories and research facilities," Obama said in a statement.

At the event, Collins told the NIH assembly that the grants "will fund trailblazing research into treating and preventing our most scary diseases.

“Since arriving [at NIH] six weeks ago I’ve spent a lot of time reviewing some of these grants — I wanted to see what was there — and they propose some of the most innovative and creative directions for research that I have ever seen in 16 years at NIH,” the new NIH director told the crowd.

More than $1 billion of the grant funding is dedicated to using technologies developed through the NIH’s genomics programs, specifically through the Human Genome Project, the White House said.

For cancer, heart disease, and many other areas, researchers will use Recovery Act funding for genomics and genetics-based research approaches to pursue knowledge about these diseases.

According to the White House, over the two years of recovery funding NIH stimulus grants will support studies including:

• Seeking to use microRNAs to predict which patients have tumors that will spread throughout the body;

• Conducting genomic sequencing of individuals with autism and their parents in order to find causes for the disease in the genome and in the environment and to develop and test diagnostic screening tools;

• Cataloging genetic changes associated with oral cancer in order to identify and guide treatment of pre-malignant lesions;

• Sequencing the genomes of more than 10,000 individuals with known risk factors for heart disease in order to identify those risk genes;

• Comparing the genomes of individuals with high and low HDL cholesterol levels in order to accelerate development of drugs that reduce the risk of heart attack;

• Examining the genes of more than 7,000 heart failure patients to identify variants that will enable doctors to identify those at risk for heart failure;

• Identifying genetic markers for increased risk of hypertension, obesity, cardiac hypertrophy, and kidney failure in African Americans;

• Finding markers that circulate in the blood that may signal the onset of a plaque rupture or of thrombosis;

• Analyzing biomarker and genetic data from international atrial fibrillation patient pools in search of markers to identify patients that will benefit from statin therapy.


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Search Engines, Genomics, Medical Literature: Tag Clouds come to PubMed via LigerCat

LigerCat is a search tool for NCBI’s PubMed that uses tag clouds to provide an overview of important concepts and trends. LigerCat aggregates multiple articles in PubMed, summing their MeSH descriptors and presenting them in a cloud, weighted by frequency “.

LigerCat is an abbreviation for Literature and Genomics Resource Catalog, which is a free PubMed search tool developed in 2009 as part of the Biology of Aging project at the MBLWHOI Library at the Woods Hole Marine Biological Laboratory.

LigerCat is great news for geneticists or anyone involved in translational research, a fairly effortless means of data mining for dynamic links to a very complex literature.

LigerCat can be used to search in several ways: 1) to locate and select a list of individual journal titles indexed in PubMed, 2) search using terms from the National Library of Medicine’s Medical Subject Heading (MeSH) list, 3) search using keywords, 4) search on Genes found in the NCBI databases.

Do you want to know more?

for more reading:

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Wednesday, September 30, 2009

NIH Grants $45M for Genome Science Centers

The National Institutes of Health has pledged $45 million in grants to establish two new genomics centers at the University of North Carolina at Chapel Hill and at the Medical College of Wisconsin (MCW), as well as to continue funding existing centers at Johns Hopkins University and at the University of Southern California.

The two new Centers of Excellence in Genomic Science at UNC and MCW will pursue genomics studies of mental health and gene regulation, respectively.

Under the new grants, MCW will receive around $8 million over three years and UNC will reap around $8.6 million over five years from the National Human Genome Research Institute and the National Institute of Mental Health.

Johns Hopkins' genomics center will receive around $16.8 million over five years to continue epigenetics of disease studies and USC will use around $12 million over the same period to conduct computational and informatics-based research of genetic variation and disease.

"Our aim is to foster the formation of innovative research teams that will develop genomic tools and technologies that help to advance human health," NHGRI's Acting Director, Alan Guttmacher said in a statement. "Each of these centers is in a position to tackle some of the most challenging questions facing biology today."

The grant to UNC will support the Center for Integrated Systems Genetics (CISGen), where scientists will seek to identify genetic and environmental factors that underlie and contribute to psychiatric disorders.

CISGen will use mouse models and computational biology to study genetic and environmental factors of such disorders, and it will develop new mouse strains specifically to study relevant behavioral traits. These models will serve as a resource of genomic studies screening for genetic variants that are linked to human psychiatric disorders.

"We can use the mouse to narrow the search space from billions of possibilities to only hundreds or even dozens," CISGen co-director and UNC Assistant Professor Fernando Pardo-Manuel de Villena said in a statement. "It's like the PowerBall when you know four or five of the six numbers for sure."

"We chose the hardest problems out there, the ones that have been most resistant to scientific inquiry in humans," explained Patrick Sullivan, CISGen's other co-director and a distinguished professor at the UNC School of Medicine. "We chose to study mouse versions of psychiatric traits potentially relevant to autism, depression and anxiety, and antipsychotic drug side effects and response to treatment."

In Wisconsin, the new center is a collaboration between the Medical College of Wisconsin, the University of Wisconsin, Madison, and Marquette University.

The team at MCW will focus on developing tools for analyzing the proteins that bind to particular DNA regions in an effort to understand the relationship between changes in protein-DNA interactions.

"What is needed, and what we will develop in this center, is technology that is able to identify all of the proteins that are interacting with the genome, even if we do not know in advance what their function may be," said the center's co-Director, Michael Oliver, a professor at MCW's Biotechnology and Bioengineering Center and the Human and Molecular Genetics Center.

Other NIH-funded Centers of Excellence in Genomic Science include centers at the California Institute of Technology, Harvard Medical School, Stanford University, Arizona State University, Yale University, and the Dana-Farber Cancer Institute.



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Thursday, September 3, 2009

"Achilles' heel of a sizable share of melanomas" - Mutations That May Improve Skin Cancer Treatmen

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 individuals with melanoma, picking out somatic mutations by comparing the tumor with matched normal tissue.

Overall, the team detected 30 somatic mutations affecting 19 different PTK genes. When the team sequenced the coding regions of these 19 genes in another 79 melanoma patients, they found 99 non-synonymous mutations.

In particular, 19 percent of the individuals had mutations affecting ERBB4 (also known as HER4), while ten percent carried PTK2B or FLT3 mutations.

Of these, the ERBB4 appeared to be the most severely mutated. As such, the team decided to investigate whether mutations in that gene influenced melanoma growth and/or treatment response, focusing on seven different missense mutations in ERBB4.

The researchers found that the growth of melanoma cell lines containing ERBB4 mutations was curbed when they knocked down the mutated form of the gene using small interfering RNA.

The team was also able to slow the growth of the melanoma cell lines by treating them with the ERBB4-inhibiting drug lapatinib, sold as Tykerb by GlaxoSmithKline.

"We have found what appears to be an Achilles' heel of a sizable share of melanomas," senior author Yardena Samuels, a researcher with the National Human Genome Research Institute's Cancer Genetics Branch, said in a statement.

The team plans to do a clinical trial looking at whether lapatinib is effective for treating melanoma in patients who carry ERBB4 mutations. Steven Rosenberg, chief of surgery at the National Cancer Institute and a researcher with the NIH's clinical center will reportedly head the trial.

"We envision a day when each cancer patient will have therapies tailored to the specific genetic profile of his or her tumor," NHGRI Director Eric Green, said in a statement. "Ultimately, this should lead to more effective and less toxic approaches to cancer care." Green was not directly involved in the current study, but heads the NIH sequencing center that generated the sequence data.



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Tuesday, August 25, 2009

Researcher at Molecular Connections develop a Alzheimer disease Pathways Compendium for inclusion at the Alzforum

This Pathways Compendium provides an index of Alzheimer disease pathway models contributed by researchers and companies.

Probable Interaction Networks Involved in Pathology of Alzheimer Disease: Predicting Targets and Therapeutic Agents - NetPro™ based Study. Developed by researchers at Molecular Connections Private Limited, an in silico discovery services company. Users can click on a specific node (molecule) to get information on all interactions of the molecule in the given network. Click on the interaction arrows for information on the specific interaction.

The Alzheimer Research Forum is a Pioneering Biomedical Web Community. Founded 13 years ago when the Web was still in its infancy, the "Alzforum" has more than 5,000 registered members and is familiar to most Alzheimer scientists in the world.


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Wednesday, August 19, 2009

NIH Program Targets Bioinformatics, Computational Biology Projects

More good news for Bio, more so for Bioinfo & CompBio while the end of Jyly say House Passes Proposed 3 Percent NIH Funding Increase now NIH is really promoting Bio Science research to bring in a economic turn. The best of times is now!

A National Institutes of Health funding program will support exploratory research and development projects in informatics and computational biology that explore a range of areas, including genomics, medical genetics, proteomics, biomedical imaging, and a wide variety of other approaches.

Funded through the National Cancer Institute, the National Human Genome Research Institute, the other centers across NIH, the "Exploratory Innovations in Biomedical Computational Science and Technology" program will be coordinated by the NIH Biomedical Information Science and Technology Initiative committee.

Under the program, NIH will grant up to $275,000 over two years to academic institutes, small businesses, non-profits, state governments, and other groups who will conduct research aimed at rapidly advancing informatics and computational biology goals in database design, querying approaches, data retrieval, visualization, and integration.

Areas of interest include approaches for handling data from genomic sequencing studies, gene expression, proteomics, pathway data, biomedical imaging, and other areas.

NIH said that the program is seeking to fund the development of

  • Tools for data acquisition, archiving, querying, retrieval, visualization, integration and management;
  • Platform-independent translational tools for data exchange and for promoting interoperability;
  • Analytical and statistical tools for interpretation of large data sets;
  • New models or simulations of complex biological processes at single and multiple levels or across multiple scales.

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Tuesday, August 11, 2009

Curated databases and data curation

"There does appear to be a distinction between the way curation is used in the bio-sciences, and elsewhere. In particular, the term "curated database" tends to mean a manually constructed database that links literature to data, curated by experts who provide authority (eg see the Wikipedia definition of Biocurator). The earliest mention of the term "curated database" I can find is in the abstract (and only in the abstract) of Larsen et al (1993)." Chris Rusbridge Digital Curation Blog
Since these database are hand curated by experts (manually curated), they always promise a accuracy & quality better than uncurated or NLP based databases. While NLP based databases follow a automated curation provide quick updates and tend to be large in terms of the quantum of data. While they may trade off in accuracy due to their automated curation process.

While platforms like XTractor Premium follow a unique approach by trying to adopt the best of both worlds. A hybrid approach of a first level of NLP which promises a quick turnaround and large quantum of data followed by expert curation to preserve and maintain the high quality promised by expert curated database. XTractor Premium is a specialized biomedical text mining platform with semantically enriched search (Semantic search) and analytics to that enable discovery, knowledge sharing, analysis and modelling of published biomedical facts.
















Sunday, August 9, 2009

Search Wars Episode II. Yebol a new search!

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 current search platforms, Yebol provides hundreds of easily identified and accessibly categorized results in one easily navigable page. The results not only provide users with a rich search experience, but also help them quickly scan the results to find targeted information. In essence, generate a unique “homepage look” for each search query.

Yebol provides a productive experience for both main types of search – general investigation of a topic and specific target search. For users who want to research and explore a topic, Yebol provides rich information from several dimensions. For users who want a specific type of targeted results, they can quickly focus on their category and navigate to the target.

A search for APOE, top most hit (first) gave a expanded definition Apolipoprotein E - on Wikipedia. Followed by link to GHR, wikigenes, gene cards, AD genetics fact sheet form NIA.

It also gives live context sensitive Twitter streaming too.

XTractor Premium - A Platform for discovery, knowledge sharing, analysis and modelling of published biomedical facts.









Thursday, August 6, 2009

BioFocus, Oncodesign Strike Partnership

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.









Wednesday, August 5, 2009

XTractor Premium surpasses 200,000 mark of Expert Annotated PubMed Facts

Indian Life Sciences Informatics Company, Molecular Connections announced today, that their XTractor Premium platform surpasses 200,000 "Expert" annotated facts from PubMed.

XTractor Premium – is a platform for discovery, analysis and modeling of published biomedical facts. The application also comes with - XTractor Premium Knowledgebase - the only knowledgebase, which provides "Expert" annotated facts from PubMed on a daily basis. The XTractor Premium Knowledgebase now has more than 202,847 relationships on proteins, drugs, biological process and diseases and is ever growing with more than 600 relationships being added every single day. XTractor provides manually categorized updates on the latest published facts from PubMed for more than 20 categories which include : Biomarkers, clinical trials, dosage, pathways, toxicology, RNAi studies, mutations, knockouts, diseases mechanisms, protein- drug relationships and much more.

Expert Annotated Facts make XTractor Premium a High Quality Knowledgebase and the vast coverage of all biological entities wrapped with in intuitive and analytical software allows researchers more time for science and eliminates the need to consult BioIT experts.

The entities are out linked to over 30 different public databases such as patent databases, wikipedia, clinical trials, and other protein/drug databases.

With XTractor Premium one can,

· Quickly access relevant, high quality expert annotated biomedical facts

· Understand multiple target preferences for a specific drug

· Track common gene polymorphisms across multiple diseases

· Understand Pharmacologic actions, protein interactions and toxicity studies of drugs

And for more, please visit the case study section.

About XTractor Premium

The Knowledgebase: XTractor knowledgebase currently contains 202,847 relationships on biomarkers, clinical trials, pathways, knockout studies, mutations, drug interactions, toxicity, pharmacokinetics, disease mechanisms. It is the Only Knowledgebase that gets updated everyday with manually annotated relationships from the latest PubMed publications and contains more than 856 Unique Drugs, 2569 Unique Diseases, 9286 Unique Proteins, and 2102 Unique Biological Processes. Hence in no time one gets to access one of the largest and the most current manually annotated datasets across the world.

To know more about the advantages of the XTractor Premium and to register for a free trial account and a webex demo please visit XTractor Premium portal www.xtractor.in/premium.

XTractor Premium - A Platform for discovery, knowledge sharing, analysis and modelling of published biomedical facts.









Saturday, August 1, 2009

List of Cheminformatics Companies & Institutions

Also check out these:


XTractor Premium - A Platform for discovery, knowledge sharing, analysis and modelling of published biomedical facts.









Life Science and Informatics

What is this?
is this a new industry?
or a old wine in a new bottle?

Well Life Sciences and Informatics can be anything form computational biology, all omes and omics, core bioinformatics to curation and literature mining, database creation, in the area of biology, chemistry , bio-chem space.

There are number of companies in India and bangalore is the forefront as a major bio-cluster with 20 to 30 companies in this sphere.

now how good are these companies doing?
how good are they in terms of the international markets and how profitable is their business?
what do they do?
their clients?

These are some interesting things that could be discussed in this blog page...

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