Human genome has gone from What, to Where and When

Today’s Nature has published our article that describes a comprehensive, detailed map of the way genes are active across the major cells and tissues of the human body.

The findings describe the complex networks that govern gene activity – detailing each promotor for each gene, and showing how it is active in each cell type. In parallel we’ve developed a program (CAGExploreR) that allows the detection of how promotor use changes as you go from each type of cell to each other type of cell. This is the clearest picture yet of how human genes are regulated in the vast array of cell types in the body – work that should help people target genes linked to disease.

This means that we can see in detail exactly where genes are initiating their activity in each major cell type in the body. Now we know where to look for genes that may be related to disease in for instance, dendrites, neurons, macrophages, skin cells …

The release is here and the article is here

 

Posted in bioinformatics, Data sharing, expression atlas, Gene regulation, genome data sharing, Genomics, networks, open access, pathways, stem cell bioinformatics, Uncategorized | Leave a comment

‘Occupy Science’: Sage Commons Congress marching to the transformation of attitude to biomedical research

Working on a project with an incredible sense of joy - imagine that?

Bioscience? Well this is a battle of attitude – share your data, attribute contribution by DOI links to the data you deposit, share your methods in real time, attribute the authors through provenance of their contributions, and publish as an ensemble with the software platform supporting interaction and editing of the data you have developed. Its Science Social Innovation writ large.

Real-time drug responses from Citizens? Patients taking control of their own data?

This congress – an eclectic collection of thought leaders, TED style talks and actual hard core biomedical research meeting around a virtual fireplace of a software open data sharing system.

As I write, the founder of Red Hat, Bob Young, talks to us about ‘make things for what people need, not what they want‘.

Most impact is coming from actual studies where crowdsourcing of a problem within a commons results in a spectacular, efficient, result. The Breast Cancer Dream Challenge.

Most useful outcome is the Commons environment “synapse” – where researchers can develop shared systems approaches to interpretation of biomedical phenotype/genomic data on a common platform, using common tools, with remarkably, provenance on the methods and data. “Collaborate for the cure” is the motto, but it reminds me of a BBQ meet so perhaps they should change that.

Health activism – Joep Lange described how he worked with world organisations and pharmcos to make drugs affordable for HIV. That’s now morphing into making drugs affordable for chronic complex diseases in low income countries – where the diseases are most prevalent – and its where most people are sick but have no funds for drugs. I met several groups working on this problem – something I’m asking philanthropic organizations to consider more seriously.

Take home: Disease philanthropic organisations such as the National Brain Tumor Society now want to actively support systems biology approaches to understanding diseases such as glioblastoma – hey – this is great. 

I love this atmosphere. Highlight for me, was a talk by the CEO of Al Jazeera,  Wadah Khanfar, showing us that depth in journalism, and sincerity is of the real value we need:

Impact of conventional wisdom is to rot the soul. Acknowledge the voice of the youth who really know the news

This has been an eye opening experience – I know my science will change from here on. 

Join me

#sagecon

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Commons sharing – buzz at this years Translational Bioinformatics Conference

Our work on a stem cell commons – an as-open-as-you-choose sharing data system for placing stem cell molecular and experimental information into context was shared with the community by Shannan Ho Sui – the program director- at the TBI last week. Tweets #TBI2013 covered it – and tweeted us nicely as they say. Why? because its hard to bring together researchers, their NGS data, the molecular profiles that result and then to combine it in order to find the underlying shared function and meaning and shared interests. The Harvard Stem Cell Institute Stem Cell Commons plans to do just that. Find our presentation here. Genomeweb shout out here.

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The next resignation from an Elsevier Board

Today,  Bart Knols, editor of MalariaWorld and chair of the advisory board followed my resignation with his own decision to resign from the editorial board of Acta Tropica (Elsevier):. MalariaWorld, a project of the Dutch Malaria Foundation, is the world’s scientific and social network for malaria professionals with more than 7300 members from 135 countries. MW promotes Open Access 2.0 (free reading and publishing) to malaria information and publishes the first peer-reviewed OA 2.0 scientific journal: the MalariaWorld Journal.

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Reform is overdue: No longer working for a journal that puts profit over access to research

I resigned today from the board of Genomics, where I have been an associate editor for the last few years. My resignation and my reasons for it are blogged at the UK Guardian.

It is not easy to do this publicly – a good friend heads the board, and I respect him and what the science of the journal seeks to achieve. But now I just think this way of publishing is wrong. Just wrong. My colleagues in South Africa in general don’t have access to the swathe of journals we take for granted in the west. Yet I was working to edit publications that were often written by people who are not in the mainstream western institutions.

How to move forwards?

First and foremost, we need to be able to see everything that our governments have paid us, using our taxes, to research.

Secondly, we need to address the ‘closed shop‘ that is peer review – we need to be able to engage interactively with a larger community, some of which have to be actual experts in the area.

Finally we need to address the tenure issue – High profile publications need to be defined by the actual impact of the work , as opposed to the perceived impact of the journal. These are *different* things.

Posted in African bioinformatics, bioinformatics, Data sharing, genome data sharing, Genomics, open access, open access | 9 Comments

H5N1 surveillance: Shift expertise to where it matters

Jeremy Farrar is someone who “gets it”. He works at the Hospital for Tropical Diseases in Ho Chi Minh City.  He writes in today’s Nature on the need to have expertise at the site of infection. Together with other ‘out there in the real world’ research professionals, he has trained thousands of regional scientists in clinical medicine, epidemiology, microbiology, bioinformatics and other disciplines crucial to monitoring, controlling and understanding infectious diseases and outbreaks. H5N1 is nasty. It kills millions of birds and of course threatens people in pandemic ways as yet unexplored. He makes the hugely important point that  local treatment is impossible when the work requires individuals to fly in and out and to analyse samples in another country. This reflects in the access to flu data – an ongoing debate at several levels. Should new lab-mutated flu strains be published and accessible to all? Should flu data painstakingly generated in Indonesia be used by western labs without recognition of the governments and people who capture it? Flu kills. Its as simple as that. We should stop the bickering about who should and should not access the strain data – and instead concentrate on educating our communities across the world on how better to work together to ensure its control.

Farrar’s model for containing flu is an excellent one. Its robust, cheap and efficient. It trains people locally and it addresses the disease at the site of infection. It needs the support of the global scientific community, not just the Wellcome Trust. We used a similar model for development of approaches to containing public health at the SA National Bioinformatics Institute in South Africa and here. Recognition of the power of these approaches will make a dramatic difference to public health, not only in the developing world, but in the developed world where pandemics are a reality.

Posted in African bioinformatics, bioinformatics, bird flu, Data sharing, genome data sharing, Genomics, influenza, networks, open access, pathways, swine flu | Leave a comment

6 months delayed… but – open access proposed for all US Government funded research

From the GenomeWeb Newsite: – Members of both houses of Congress this week introduced identical bills that would expand public access policies for research funded by taxpayers, such as the one in place at the National Institutes of Health, to include all the major science-funding agencies.

The Federal Research Public Access Act, which has bipartisan sponsors in the US House of Representatives and the US Senate, would require that research funded by federal departments and agencies with annual extramural budgets of $100 million or more be submitted after publication in a peer-reviewed journal.

The bills require that manuscripts be submitted within six months of publication for storage in an accessible repository that would be publicly available online. The poicy will cover  the National Science Foundation, the Department of Agriculture, the Department of Defense, the Department of Energy, and others.

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