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Ben Goldacre recommends

Further reading on drugs, pharmacology and clinical trials, including an excellent book on evidence-based medicine.

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    Why we need easy access to all data from all clinical trials and how to accomplish it

    Peter G√łtzsche
    Trials Journal, 2011

    This is an excellent academic overview of the need for all trials to be published, from an open access journal.

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    Testing Treatments

    Imogen Evans et al.
    Pinter & Martin, 2011

    This is an excellent book on evidence-based medicine, and the problems in it. It is written by eminent scientists and patients working together, and can be downloaded free online (disclosure: I wrote the foreword!).

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    Bad Science

    Ben Goldacre
    Faber & Faber, 2010

    My book Bad Science has a lot on this topic.

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    BadScience.net

    There is also lots on the problem of publication bias at my own website.