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Wednesday, September 29, 2010

5-Day Hands-on Workshop on Molecular Biotechnology and Bioinformatics

A 5-day workshop with hands-on training involving the following topics from molecular biology and bioinformatics. The workshop aims to equip its participants with the right kind of knowledge and tools required to practice 21st century biology.
The biology and bioinformatics contents are interwoven in such a manner that would help a molecular biologist to find solutions to real time problems in a lab and a bioinformatician to understand the laboratory aspects of bioinformatics.

Workshop Dates


17th - 21st May 2010
24th - 28th May 2010
14th -18th June 2010
26th - 30th July 2010
23rd - 27th Aug 2010
10th - 14th Jan 2011
16th - 20th May 2011


Topics
  • Recombinant DNA Technology: Cutting & pasting of DNA molecules (i.e. restriction digestion, ligation, DNA gel eectrophoresis, and gel extraction.) Bioinfo part: Bioinformatics of DNA database / SequenceAnalysis: Pairwise sequence alignment, Multiple sequence alignment, Pattern search.Tools: BLAST, CLUSTALW/X, CLC Bio Main Workbench
  • Genetic Engineering: Transformation and plasmid purification, cloning and sub-cloning, amplification of DNA fragments by polymerase chain reaction (PCR).
    • Bioinfo part:
      • Designing of PCR primers
      • In-silico cloning
      • Searching for homologous and paralogous sequences
    • Tools: CLC Bio Main Workbench, BLAST
  • Genomics Data Visualization: Browsing and comparing human and mouse genomic data with the help of NCBI Genome viewer and UCSC Genome browser.
  • Basic Biostatistics for Molecular Biologist:
    • Data visualization and summarization techniques
    • Univariate and Bivariate data analysis
Fees

Rs. 6000/- (includes tea and food for 5 days). Oncampus accommodation charges extra @ Rs. 400/- per day per person. 
Please click here to register online or download the registration form from here.
    Do do want to know more?


    Monday, September 27, 2010

    Novel Chromosome 6 Locus for LOAD, Genetic Evidence for Folate-Pathway Abnormalities

    Genome-wide association studies (GWAS) of late-onset Alzheimer disease (LOAD) have consistently observed strong evidence of association with polymorphisms in APOE. However, until recently, variants at few other loci with statistically significant associations have replicated across studies. The present study combines data on 483,399 single nucleotide polymorphisms (SNPs) from a previously reported GWAS of 492 LOAD cases and 496 controls and from an independent set of 439 LOAD cases and 608 controls to strengthen power to identify novel genetic association signals. 

    Studies looking for genetic variants across the genome that affect late-onset Alzheimer disease (LOAD) have had little success identifying genes other than APOE. Here, we use an expanded set of AD cases and controls to improve our power to detect genetic variants driving LOAD risk. Analyzing 483,399 genetic variants across the genome in a discovery dataset of 931 cases and 1,104 controls, we found a strong association to the marker rs11754661 on chromosome 6 in the gene MTHFD1L, in addition to the highly replicated chromosome 19 APOE association. We genotyped adjacent variants on chromosome 6 in these same cases and controls and found these variants were also associated with LOAD. We replicated the association with rs11754661 and additional SNPs in MTHFD1L in a combined dataset of cases and controls from our laboratory and from publicly available datasets. This finding is important because the gene is known to be involved in biological pathways influencing levels of homocysteine, a significant risk factor for AD.

    Thursday, September 23, 2010

    Professional (P2), CEM Research Informatics @ Pfizer

    Opportunity: Professional (P2), CEM Research Informatics @ Pfizer--San Francisco, CA (US)

    BACKGROUND:
    Pfizer Inc: Working together for a healthier world

    Founded in 1849, Pfizer is the world's premier biopharmaceutical company taking new approaches to better health. We discover, develop, manufacture and deliver quality, safe and effective prescription medicines to treat and help prevent disease for both people and animals. We also partner with healthcare providers, governments and local communities around the world to expand access to our medicines and to provide better quality health care and health system support. At Pfizer, colleagues in more than 90 countries work every day to help people stay happier and healthier longer and to reduce the human and economic burden of disease worldwide.

    RESPONSIBILITIES:
    This role is responsible for supporting computational research operations at Rinat, interfacing with customers and BT partners to deliver IT related support and services.

    Primary Responsibilities:
    - Working with customers from senior leadership to bench scientists to identify and address key information systems needs, including data capture, data analysis and scientific decision making systems
    - Work with Research BT teams to define and deliver solutions to meet the needs of Rinat scientists.
    - Provide training and guidance to research scientists in the use of existing tools.
    - Ensure alignment of any purchased or in-house systems to overall R&D BT Strategy.

    REQUIREMENTS:
    - MS/BS in Computational Sciences, Bioinformatics or related discipline
    - Bioinformatics: at least 2 years experience using common bioinformatics applications, e.g. sequence similarity,   multiple sequence alignment
    - Software Development: At least 4 years experience developing scientific applications
    - Demonstrated excellent interpersonal and communication skills, both verbal and written.
    - Proven ability to operate in an independent manner.
    - Knowledge of pharmaceutical industry and computational sciences

    PREFERENCES:
    - Biological training a plus.

    COMPENSATION:
    Salary commensurate with experience.

    At Pfizer, we've long recognized that our colleagues are our most important asset. We value our colleagues, recognize their talent, encourage their growth and reward their performance. It's a terrific environment that enables people to contribute, to do their best, and to achieve their potential.

    Throughout our history, a legacy of caring for others has been at the heart of everything we do at Pfizer. This commitment is no less important when it comes to our employees.

    When you choose a Pfizer career, we provide the resources to help you develop and succeed both in your career and your personal life. One way we can achieve this is through our comprehensive benefits program, which offers employees and their eligible dependents the variety and flexibility to help address their needs at different stages in life.

    HOW TO APPLY: 
    Please copy and paste the following URL into your browser address bar:
    http://posttrak.arbita.net/cgi-bin/PostTrak.cgi?RefCode=R6871477508962

    DEADLINE: October 22, 2010

    Strategy to build a complete catalogue of human proteins could put China in a leading position

    First the genome; now the proteome. China has already established a leading position in DNA sequencing through the work of the BGI in Shenzhen (formerly the Beijing Genomics Institute), which has been generating eye-catching genomics discoveries for the past few years (see Nature 464, 22–24; 2010). This week, Chinese researchers are set to announce initiatives that could put them at the forefront of international efforts to catalogue and characterize all proteins in the human body. Inspired by the Human Genome Project, protein researchers worldwide have been seeking funds to build a full catalogue of human proteins — a proteome — which, they say, will explain how the information encoded in our genomes can give rise to normal and diseased states.

    his January, the Human Proteome Organization (HUPO) in Montreal, Canada, took the first steps towards an international effort. It set up the Human Proteome Project (HPP) working group to coordinate researchers who are characterizing the products of the 21,000 or so protein-coding genes in the human genome (see Nature 452, 920–921; 2008). But funding agencies worldwide have yet to show full support for the scheme, which is likely to carry a multi billion-dollar price tag. There is also uncertainty over the scope of the project — each human protein can be modified in an as-yet-unspecified number of ways — and over how well data from different labs can be compared (A. W. Bell et al. Nature Methods 6, 423–430; 2009).

    However, this week, Chinese researchers travelled to HUPO's annual congress in Sydney, Australia, to announce plans that defy such scepticism. The Beijing Proteome Research Center, directed by biochemist He Fuchu, has received average grants of roughly 200 million renminbi (US$30 million) per year as one of several institutes involved in HUPO's Human Liver Proteome Project (seeNature 425, 441; 2003). That budget, He says, is soon set to double as the initiative — now renamed the Chinese Human Proteome Project — expands to cover proteins in the blood, brain, lungs, skin and other organs. The Chinese government also plans to invest 1.2 billion renminbi in a national laboratory called the Pilot Hub of Encyclopedical proteomIX (PHOENIX), which has been several years in the planning.

    "The investment is impressive and unprecedented," says Ruedi Aebersold, a proteomics expert at the Swiss Federal Institute of Technology in Zurich and a member of the HPP working group. "The launch of a large project in China would give the whole HPP project a significant boost. "The PHOENIX project will include a doubling of facilities for nuclear magnetic resonance imaging at Peking University, already the largest facility for structure determination in China but heavily oversubscribed. Tsinghua University's electron microscope facility will be expanded, and there will be more capacity for protein-structure studies at the Institute of Biophysics of the Chinese Academy of Sciences in Beijing.

    But the core of the project, and half the budget, will go to He's new mass spectroscopy centre, to be built near the Beijing Proteome Research Center. The cash will buy 20 new mass spectrometers, bringing the total number in the centre to 29. They will be integrated with a robotic pipeline for high-throughput processing of proteins, including bioinformatic analysis. It will be the "first laboratory in the world to reach that level of integration", says He.
    China's human proteome project will build on the success of He's liver project, which he says produced the largest human organ proteome to date, encompassing nearly 7,000 proteins (A. Sun et al. J. Proteome Res. 9, 50–58; 2010). At the Sydney meeting, He plans to discuss unpublished work that maps protein–protein interactions and their localization. "It's a real, comprehensive demonstration for other organs," he says.

    Tuesday, September 21, 2010

    Conference on Semantics in Healthcare and Life Sciences (CSHALS)

    CSHALS is the premier annual event focused on the use of semantic technologies in the pharmaceutical industry, including hospitals/healthcare institutions and academic research labs.

    Rather than a Semantic Web conference, CSHALS focuses on specific applications of semantic technologies. Attendees will gain a better understanding of where the field is headed and be prepared to advance with the field.


    Themes of past CSHALS conferences:
    • Clinical Information Management
    • Discovery Information Integration
    • Integrated Healthcare and Semantics in Electronic Health Records
    • Translational Medicine / Safety
    • Search and Document Management/Business Intelligence/Text Mining
    • Text Mining/ Information Extraction
    For further details visit 

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    Monday, September 20, 2010

    e-LICO multi-omics prediction challenge


    We present a biological data-mining problem that poses a number of significant challenges: The available data are of high dimensionality but of extre...

    Time Left: 90 days
    Teams: 84
    Prize: 2500 EUR

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    DBT-Research Associateship 2011 Biotechnology & Life Sciences

    DBT-Research Associateship 2011 Biotechnology & Life Sciences

    Applications are invited from Indian nationals for the award of "DBT-Research Associateship" 2011 for pursuing research in frontier areas of Biotechnology and applied biology. The Associateship is tenable in Research Institution/Universities including non-profit R & D Institutions within India. The Associateships are awarded under a program sponsored by the Department of' Biotechnology, Ministry of Science and Technology, Government of India.

    Eligibility-:
    The applicants should hold a Ph.D. degree in Science, Engineering or M.D. or M.S. degree in any area of medicine with research interests in Biotechnology and Life Sciences and a good academic record. The Associateship can be availed within 3 years of the award of Ph.D./M.D./M.S. degree; however, may be relaxable in case of women (by 2 years) and in-service candidates. Those who have already submitted the Ph.D./M.D./M.S. thesis are also eligible to apply. The applicants should preferably be below the age of 40 years and 45 years in case of women candidates.

    Persons already employed are also eligible to apply. However, their applications should be routed through their employers.

    Details of the Award-:
    The Research Associateship is a purely temporary assignment and is tenable for a period of 2 years. In exceptional cases, depending upon the progress of the research, the Associateship may be extended upto 5 years. Each fellow would be entitled to a stipend in the range of Rs.22,000-24,000 per month and a research contingency grant of Rs.50,000 per year, payable to the host Institution.

    Candidates who are yet to be awarded the Ph.D./M.D./M.S. degree, if selected, will be paid Rs.18,000 per month till the award of the degree. The associate would also be entitled to HRA and other benefits as per the DST guidelines applicable to Research Associateship. The Associateships normally are not availed at the same Institution where candidates have earned their Ph.D./M.D./M.S. degree.

    Candidates who are already in regular employment can avail the Associateship during the period of his/her sabbatical/study leave,in a different institute/university  


    Mode of Selection-:
    The candidates will be selected based on their C.V. and performance in the interview. The interview will be held at the Indian Institute of Science, Bangalore, in November 2010 and candidates called for interview will be paid II class railway (non-AC) /bus fare by the shortest route from their home town. If the candidate accepts the Associateship, he/she must join the host Institution/University within a month's time.

    Mode of Application-:
    Candidates may submit their application on plain paper alongwith bio-data, list of publications (attach reprints of 2 important papers), copies of certificates (B.Sc, M.Sc, Ph.D./M.D./M.S.), One page synopsis of Ph.D./M.D./M.S. thesis, 2 letters of recommendation (academic).

    The applicant is advised to propose his/her place of work, name of the supervisor, enclose one page synopsis of proposed research which must be compatible with the on-going research of the proposed supervisor, and his/her consent for availing the Associateship. They should also enclose a declaration stating that if selected for the Associateship, he/she will complete the tenure of the Associateship.

    However, they may be allowed to relinquish the Associateship only if accepting permanent employment in India. Those who had applied previously need not apply.

    Applications should be addressed to:

    The Coordinator,
    DBT-Research Associateship Program,
    Department of Biochemistry,
    Indian Institute of Science Campus,
    Bangalore - 560 012.

    The last date for the same is 15 October, 2010 and the envelope should be clearly marked as "DBT-Research Associateship

    For more information visit-: http://www.iisc.ernet.in/
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    Thursday, September 16, 2010

    Sun Pharmaceutical Announces Expiration of Offer for Taro



    Sun Pharmaceutical Industries Ltd. today announced the expiration of the Tender Offer by Sun’s subsidiary, Alkaloida Chemical Company Exclusive Group Ltd., to purchase all outstanding Ordinary Shares of Taro Pharmaceutical Industries Ltd. for $7.75 per Ordinary Share.


    “Sun is pleased to be able to finally close the Offer,” said Dilip Shanghvi, Chairman and Managing Director of Sun. Transactions contained in an Option Agreement related to the transfer of Taro shares owned or controlled by the Levitts to Sun and its affiliates are to be consummated contemporaneously with the expiration of the Offer. “We will now make every effort to consummate our Option Agreement to purchase the Levitts’ controlling shares of Taro,” he added.


    Sun has been informed by Computershare, the Depositary for the Offer, that as of the expiration of the Offer at midnight, New York City time, on September 14, 2010, a total of 29,382 Ordinary Shares, or approximately 0.07% of Taro’s outstanding Ordinary Shares, had been tendered into the Offer and not withdrawn. No Ordinary Shares were tendered subject to guaranteed delivery. All Ordinary Shares validly tendered and not properly withdrawn prior to the expiration of the Offer have been accepted and Alkaloida will pay for such Ordinary Shares promptly.


    As of 9:00 a.m., New York City time, on September 15, 2010, Alkaloida commenced a subsequent offering period for all remaining Ordinary Shares that have not yet been tendered. Stockholders who tender Ordinary Shares during such period will be paid the same $7.75 per Ordinary Share, net to the seller in cash (subject to applicable withholding taxes), paid during the Offer. Ordinary Shares tendered during the subsequent offering period may not be withdrawn. Alkaloida will immediately accept any Ordinary Shares validly tendered during the subsequent offering period as they are tendered, and will pay for such Ordinary Shares promptly. The subsequent offering period will expire at 12:00 midnight, New York City time, on Tuesday, September 28, 2010.



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    Wednesday, September 15, 2010

    Agorithm from Blood-Based Alzheimer's Biomarkers


    In a study appearing in the newest issue of the Archives of Neurology, members of the Texas Alzheimer's Research Consortium reported that they have identified protein biomarkers in the blood that can be used to distinguish between individuals with and without Alzheimer's disease.
    The researchers compared protein patterns in blood samples from hundreds of individuals with or without Alzheimer's disease and incorporated these potential biomarkers into an algorithm for detecting Alzheimer's cases in a test group. Their results so far suggest this algorithm can accurately classify most Alzheimer's cases — particularly when combined with APOE status and demographic data.
    And, they said, information from the biomarker study is offering clues about possible sub-groups within Alzheimer's. For instance, by looking at some of the proteins that are frequently expressed at different levels in the blood of those with Alzheimer's disease, the team identified a potential subset of individuals with inflammation-related biomarker patterns.

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    Pfizer Postdoctoral Program in Neuroscience

    Pfizer Neuroscience Postdoctoral

    Fellowship Program
    www.pfizerneuroscience.com Based in scenic
    Groton, Connecticut, the Pfizer Neuroscience Fellowship Program provides an
    unparalled opportunity for young scientists interested in understanding
    brain disorders and translating knowledge into innovative medicines. We
    seek motivated and enthusiastic individuals with a demonstrated track record
    in basic or translational neuroscience interested in pursuing an
    academic-style postdoc in an industry setting. Successful candidates will
    come from a range of backgrounds including molecular/cellular biology,
    protein biochemistry, in vitro and in vivo electrophysiology, imaging,
    systems neuroscience, animal models, and behavioral/cognitive neuroscience.

    At Pfizer, there are extensive programs in molecular/cellular neuroscience,
    synapse biology, and pharmacology. Moreover, there is a vibrant in vivo
    electrophysiology program for cognition, extensive behavioral models,
    imaging platforms, and essentially limitless access to chemical biology and
    animal models. In addition, postdocs at Pfizer get exposed to the art and
    science of drug discovery, with first hand ability to interact with programs
    working to develop new medicines.
     


    Applications are accepted throughout the year with reviews and interviews occurring in the fall and spring. For the fall review, applications are due October 1st and interviews will be conducted early in November. Candidates will be contacted by October 15th if they have been selected for an interview. The application deadline for the spring review will be April 1st and interviews will be scheduled in May. Interested candidates should apply at the link below, making sure to submit a resume and a summary of research interests (2-3 pages in length). In addition, please have three letters of recommendation emailed directly to Kate Yannacci at kate.m.yannacci@pfizer.com. Details on the Pfizer Neuroscience Postdoctoral Program can be found at www.pfizerneuroscience.com.


    Apply to the postdoc program:
    Applications are reviewed on a regular basis and top candidates are invited to visit, present their research, and interview at Pfizer's Groton Research Campus. More extended descriptions of the interview process will be provided to the invited candidates at the time of invitation.


    Apply Now


    Monday, September 13, 2010

    PubDNA Finder

    Courtesy: Dr Raghava & Bioclues
    PubDNA Finder is an online repository to link
    PubMed Central manuscripts to the sequences of nucleic acids appearing
    in them. It extends the search capabilities provided by PubMed Central
    by enabling researchers to perform advanced searches involving
    sequences of nucleic acids. This includes, among other features, (1)
    searching for papers mentioning one or more specific sequences of
    nucleic acids and (2) retrieving the genetic sequences appearing in
    different articles.


    These additional query capabilities are provided
    by a searchable index that was created by using the full text of the
    176672 papers available at PubMed Central at the time of writing and
    the sequences of nucleic acids appearing in them.


    To automatically extract the genetic sequences occurring in each paper an
    original method has been developed. The database is updated monthly by
    automatically connecting to the PubMed Central FTP site to retrieve
    and index new manuscripts. Users can query the database via the web
    interface provided. Availability: PubDNA Finder can be freely accessed
    at http://servet.dia.fi.upm.es:8080/pubdnafinder

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    Tuesday, September 7, 2010

    Creating awareness of extremely resistant TB




    I thought you should see these photographs. They're both powerful and moving.  They highlight the awful disease XDR -TB, a new and deadly form of tuberculosis that is threatening to become a global pandemic.


    By viewing and passing on this link we can help to spread awareness, which is the first step to halting the disease. XDRTB.ORG (http://www.xdrtb.org/)


    (As background, the photographs were taken by leading photojournalist James Nachtwey and were 'unveiled' on October 3rd, 2008 in more than 50 cities on seven continents as a deliberate attempt to highlight this new danger faced by the world.)

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    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...

    Tag It