blog

I am delighted to announce the publication of our first articles on our preliminary consultation site.  They showcase a range of topics and all offer easy access to the data behind the results.

HIV education campaigns in Africa leaving public vulnerable

Devon Brewer (Director, Interdisciplinary Scientific Research) has submitted an article entitled Knowledge of specific HIV transmission modes in relation to HIV infection in Mozambique pointing out that people in southern Africa who are unaware of blood-borne HIV transmission are at increased risk of HIV infection.  His article somewhat controversially suggests that HIV education campaigns in this region are not addressing blood-borne risks and thus may be leaving the public vulnerable to infection.

Brewer told us his reasons for submitting to F1000 Research:

“Publication contingent on the outcome of peer review often amounts to censorship and is the single greatest obstacle to scientific advancement.  This is particularly true when the evidence or perspective in a manuscript runs counter to the dominant paradigm in a field.” He added: “F1000 Research goes a long way toward removing this obstacle.”

Detecting diagnostically relevant mutations – are we using the wrong tools?

Gavin Oliver (Team Leader, Almac Diagnostics Ltd) examines Considerations for clinical read alignment and mutational profiling using next-generation sequencing, and provides a clear comparison of a range of short read aligners in detecting diagnostically relevant mutations from targeted sequencing.

Oliver comments that researchers working in this area have been known to base their choice of aligner on frequency of citation or availability of a graphical user interface. His article challenges these approaches by suggesting that common choices are often sub-optimal. He points out that by understanding the options available as well as the data being studied, superior accuracy and reliability of results can be achieved. Reliable results are of course always important but especially so when human health is at risk.

His article is supported by 1675 data files totalling almost 3GB, which we have made viewable through a novel widget, developed in conjunction with figshare. The widget enables readers to preview the data files without having to download them, and allows all readers, even those without suitable viewers for these files, to view the datasets in a ‘friendly’ format.

Oliver commented:

“The fields of bioinfomatics, genetics and genomics are advancing more rapidly than ever before, and the need for modern conduits to disseminate scientific results rapidly and widely is well known and increasingly publicized. We believe that F1000 Research‘s novel approach to publication represents a pioneering step toward the future of peer review and sharing of scientific results”.

Personal genomes for the family – what can you learn on a budget?

Finally, Manuel Corpas (Plant and Animal Genomes Project Leader, Genome Analysis Centre, Norwich Research Park) and colleagues have submitted an article on Low-budget analysis of Direct-To-Consumer familial genomic testing data that assesses, perhaps for the first time, how much can be discovered about the personal genomes for a whole family using mainly free software analysis tools and no laboratory equipment. This article is also accompanied by 20 varied datasets and supplementary files, totalling almost 11GB and viewable within the article through the embed widget, that support the results and conclusions of the article.

Corpas said:

“F1000 Research was a suitable place for publishing this article because: a) its innovative editorial process allows the community instant access to our findings, even before the article is wholly reviewed; b) we experienced no limitations in terms of how much supporting data we could submit; and c) F1000 Research‘s wide coverage of biology and medicine means we didn’t have to worry about whether our research would fit in.”

He continued:

“We are very excited about contributing to F1000 Research‘s new approach to reviewing. This approach will provide a lot more context to readers when trying to understand the article, as they may agree or disagree with some of the issues brought by reviewers and will be able to follow our discussions. It clearly has the potential to make the review process more transparent and effective.”

What next?

These three articles are now out for formal peer review and we will hear from our referees within the next couple of weeks. The referees’ identities and their reports will be openly displayed on the site.

As a reader, we also invite you to comment scientifically on any of the articles.

We will publish a number of further articles over the coming weeks and months, so watch this space.  If you have an article you would like to contribute, please just e-mail it into research@f1000.com; author guidelines are available, and submission is free until the end of 2012!