Why I left Harvard and went to Sheffield. The reveal.

Why I left Harvard and went to Sheffield. The reveal..

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Why I left Harvard and went to Sheffield. The reveal.

I explain why I left Harvard in a talk: Inaugural Lecture

Breaking the Human Genome Code – Opening Pandora’s Box?

At the end of the talk (min 47:00)  there is a reveal as to why I recently left Harvard to move to Sheffield.

In a nutshell this is a place where the community is poised, capable and ready to deliver on key aspects of precision medicine. I think that here, it’s ready to bring all the moving parts together to leverage the #100KgP UK 100K genomes project, the NHS, the superb research and clinical data environment, and the highly motivated and focus funded research and research management community. Here we have machine learning, computational modelling, computational biology, clinical records, patients, physicians, basic scientists, all focused on key aspects of the diseases we action.

This is a place I respect, and where I am respected. I am able to impact health directly here as a focused force. Harvard has aspects of what I describe in droves. Its just that here I can work directly with a highly specialised team of collaborators with direct engagement across social sciences, healthcare, data science, government strategy and institutional development.

I’m looking for folks to join the new centre for genome translation we are building here. Doc? Programmer? Research Scientist? Think about a future with us.

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Why I left Harvard – and went to Sheffield

Why I left Harvard – and went to Sheffield.

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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

 

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‘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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