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Fully funded PhDs from across the Norwich Research Park http://bit.ly/1SeguOA


Originally shared by Earlham Institute (EI)

Fully funded PhDs from across the Norwich Research Park http://bit.ly/1SeguOA

Great article on the additional bioinformatics cost of sequencing.

Great article on the additional bioinformatics cost of sequencing.
http://massgenomics.org/2015/10/ngs-analysis-not-free.html

PhD Studentship: Class-seq: Detection of infectious agents in animal disease from whole genome sequencing data

Originally shared by Earlham Institute (EI)

PhD Studentship: Class-seq: Detection of infectious agents in animal disease from whole genome sequencing data
http://www.jobs.ac.uk/job/AMD335/competition-funded-studentship-class-seq-detection-of-infectious-agents-in-animal-disease-from-whole-genome-sequencing-data-cooper_u16hdtp/

Another great data visualisation from The Guardian .

Another great data visualisation from The Guardian .
http://www.theguardian.com/society/ng-interactive/2015/sep/02/unaffordable-country-where-can-you-afford-to-buy-a-house

This is a really well written article about common analytical problems in science.

This is a really well written article about common analytical problems in science. I not sure concious p-hacking occurs as much as the author insists and I would have thought they would have mentioned multiple testing corrections. I really don't like the idea of using a large number of different methodologies and taking the aggregation of them as the result.
http://fivethirtyeight.com/features/science-isnt-broken

A blog I wrote recently for The Genome Analysis Centre (TGAC) summarising an interesting article on telomere length...

A blog I wrote recently for The Genome Analysis Centre (TGAC)  summarising an interesting article on telomere length and cancer.

http://blog.tgac.ac.uk/diagnosing-cancer-earlier-with-telomeres/
http://blog.tgac.ac.uk/diagnosing-cancer-earlier-with-telomeres

Human genome sequencing at 30X available for £800 from Edinburgh genomics .. wow!

Human genome sequencing at 30X available for £800 from Edinburgh genomics .. wow!
https://biomickwatson.wordpress.com/2015/06/14/complete-genomics-revolocity-and-the-future-of-genome-sequencing

Details of a talk I hosted recently at Norwich by Matt Parker.

Details of a talk I hosted recently at Norwich by Matt Parker.

Bad photo of me but hey ho.
http://www.tgac.ac.uk/news/204/68/10-000-human-genomes-to-help-fight-cancer-and-rare-disease/?utm_source=twitter&utm_medium=bitly&utm_content=matt-parker-seminar&utm_campaign=news

List of R packages for data manipulation

List of R packages for data manipulation

This is a great list of packages for mucking about with data in R. I picked up on readxl for opening Excel files by the excellent Hadley Wickham (Hadley Wickham ) and openxlsx for writing them.
http://www.computerworld.com/article/2921176/business-intelligence/great-r-packages-for-data-import-wrangling-visualization.html

At Biology of Genomes 2015 conference.

At Biology of Genomes 2015 conference. Just finished my talk on multifocal prostate cancer. Someone kindly posted a summary picture on Twitter. #bog15
http://pic.twitter.com/sawWumrXMm

Translational Bioinformatics Year In Review

Translational Bioinformatics Year In Review

Russ Altman gave his "Translational Bioinformatics: The Year in Review" presentation at the close of the AMIA Joint Summit on Translational Bioinformatics in San Francisco on March 26th.
http://www.gettinggeneticsdone.com/2015/04/translational-bioinformatics-year-in.html

More press I missed on our Nature genetics paper

More press I missed on our Nature genetics paper
http://www.eveningnews24.co.uk/mobile/news/uea_research_on_prostate_cancer_cells_1_3976590

More press I missed on our Nature genetics paper

More press I missed on our Nature genetics paper
http://www.healthcanal.com/cancers/prostate-cancer/60817-healthy-looking-prostate-cells-mask-cancer-causing-mutations.html

Some press I missed on our Nature genetics paper

Some press I missed on our Nature genetics paper
http://www.businessweekly.co.uk/news/academia-research/genomics-research-aids-fight-against-prostate-cancer

CRUK has a great blog entry on the metastatic paper.

CRUK has a great blog entry on the metastatic paper.
http://scienceblog.cancerresearchuk.org/2015/04/01/migration-settlement-and-more-migration-how-prostate-cancers-spread

The Daily Mail article on our recently released paper - The evolutionary history of lethal metastatic prostate cancer

The Daily Mail article on our recently released paper - The evolutionary history of lethal metastatic prostate cancer
http://www.dailymail.co.uk/health/article-3021800/Prostate-cancer-breakthrough-scientists-discover-disease-spreads-paving-way-better-treatments.html

Prof Ros Eeles is interviewed about our recently released paper - The evolutionary history of lethal metastatic...

Prof Ros Eeles is interviewed about our recently released paper - The evolutionary history of lethal metastatic prostate cancer
https://vimeo.com/123286732

The evolutionary history of lethal metastatic prostate cancer - press releases

The evolutionary history of lethal metastatic prostate cancer - press releases

Daniel Brewer from Norwich Medical School at UEA and The Genome Analysis Centre (TGAC) said: “Prostate cancer becomes lethal once it spreads from the prostate and this study has given us a unique insight into the way this occurs.”
“Contrary to the established simple view of one ‘seed’ of cancer moving from the prostate to other organs, we have firmly established that the process is much more complex and dynamic. Cancer cells are continuously interchanged between all organs where cancer has been established and new sites are established both from the prostate and other organs. This step will help scientist develop new approaches in tackling this wide-spread disease.”

* https://www.uea.ac.uk/about/-/scientists-drill-down-to-genetic-root-of-prostate-tumour-development
* http://www.cancerresearchuk.org/about-us/cancer-news/press-release/2015-04-01-scientists-drill-down-to-genetic-root-of-prostate-tumour-development
* http://www.icr.ac.uk/news-archive/scientists-drill-down-to-genetic-root-of-prostate-tumour-development
https://www.uea.ac.uk/about/-/scientists-drill-down-to-genetic-root-of-prostate-tumour-development

Cancer: The complex seeds of metastasis - Michael M. Shen

Cancer: The complex seeds of metastasis - Michael M. Shen

This is a "News & Views" article on ours and another groups recent work on mets in prostate cancer.
http://dx.doi.org/10.1038/nature14377

The evolutionary history of lethal metastatic prostate cancer

The evolutionary history of lethal metastatic prostate cancer

One of our papers is out today and it's in Nature.  It is a genomic study that looks at the sequence of samples from multiple sites where cancer has invaded in prostate cancer patients.  From this we have been able to elucidate the genetic evolution of the cancer when it spreads from the prostate. Pretty amazing stuff.
http://dx.doi.org/10.1038/nature14347

This is worth considering when trying to transfer genomic findings into a clinical test.

This is worth considering when trying to transfer genomic findings into a clinical test. Unfortunately no solution is provided.
http://simplystatistics.org/2015/03/19/a-surprisingly-tricky-issue-when-using-genomic-signatures-for-personalized-medicine/

Some unusual science for the day: Using modern computer science to understand just where Rock n' Roll came from.

Originally shared by Yonatan Zunger

Some unusual science for the day: Using modern computer science to understand just where Rock n' Roll came from. Normally, people who talk about the history of music break it down into genres which have a lot to do with marketing, country of origin, and so on, and talk about individual bands as historical influences on each other. But these boundaries can be quite arbitrary: for example, "gospel" and "rock" are considered very far apart, but if you go back to the 1950's, rock was so influenced by gospel that it was hard to tell them apart at times.

So these researchers tried something else. They analyzed the songs which topped the US charts from 1960 to 2010, about 17,000 in all. For each song, they examined features not of the marketing around the music, but of the music itself: instrumentation, chord changes, timbre, types of harmony. They then used a technique called "k-means" to find the natural clusters into which the songs fell by these measures, and found thirteen natural groupings. To understand these groupings better, they adapted a technique from molecular genetics which is used to understand the functions of genes: they took song tags from last.fm, and did a mathematical analysis to see which song tags were most strongly associated with each cluster. (For example, if one cluster had songs tagged "R&B" far more often than the other clusters did, it's a good sign that this tag describes the cluster) 

They came up with 13 clusters -- what you might call the "purely musical" genres of the music, since they're based entirely on the songs' musical qualities, not on the politics or marketing around them. These ranged from cluster #2 (hip hop / rap / gangsta rap / old school) to #9 (classic rock / country / rock / singer-songwriter) to #8 (dance / new wave / pop / electronic). 

The image you see a bit of below is the history of the popularity of these genres over time, with 1960 at the bottom of the graph and 2010 at the top. You can see the sudden rise of rap (leftmost column), the gradual vanishing of jazz and the blues from the charts (the dwindling figure center-right), and the coming and going of hard rock (the dark blue bubbly thing at the center).

Interestingly, they have answered one important historical question, about the significance of the British Invasion: apparently no, this was not the key catalyst of the revolution in American music; the revolution was already well underway before the Beatles arrived in 1964. (Which shouldn't really surprise people too much, given that this is where rock came from) 

If you look at the bottom of the image, you'll notice a tree structure which the summary on the arXiv blog doesn't talk about; you'll have to read the article itself (http://arxiv.org/pdf/1502.05417v1.pdf) for that. It's basically a genetic tree of these genres of music. This is constructed using the same techniques of "genetic relatedness" which are used to create modern evolutionary trees of species, only instead of being based on DNA snippets, they're based on those underlying musical features like chord changes which were the basis of the clustering. So you can see (for example) that hip-hop comes from a completely different ancestry than all the other observed genres, while pairs like country and classic rock are close relatives.

Why is this interesting? Apart from the obvious fun of studying music history using the methods of molecular biology, it shows the ways in which these techniques can be used to describe a whole host of things. To make this work, what you need is a large sample of items to classify (here, songs); for each item, a large collection of features to measure (a few hundred at least; in this case, things like chord changes and instrumentation); and if you want to be able to describe the function of these features, have functional labels (here, song tags) for at least a good collection of the items you want to classify. Then you can do a "genetic analysis," grouping them into families, observing family trees, and (if you have additional data, like the year of release in this case) understand things like the evolution of these groups over time or space.

What's marvelous is that you can do this sort of analysis with all sorts of things. Do it on news articles, with the features being words, and you'll discover that they cluster into stories, which in turn cluster into subjects. (Why? Because you'll see, say, a bunch of stories with the word "Brezhnev" which also include references to the USSR, and these come and go over time, and at later times start to also include stories about "Andropov," "Chernenko," and "Gorbachev." Depending on how finely you slice these, you can either see the life of a politician, or the history of the Soviet Union.) Do it on a city's road network, with features involving the number of cars on each chunk of the road at a given time, and you'll discover... well, I'm not sure what you'll discover. I don't know if anyone's ever done that analysis. But you could do it and find out.

This is the real magic of data analysis: it gives you new ways to stare at what seem like hopelessly complex piles of data, and see meaningful patterns.
https://medium.com/the-physics-arxiv-blog/genetic-data-tools-reveal-how-pop-music-evolved-in-the-us-48ad60bf495b

Around 7 min mark Prof. Cooper talks about our recently published work.

Around 7 min mark Prof. Cooper talks about our recently published work.
http://www.bbc.co.uk/iplayer/episode/b05398fn/look-east-east-04032015

Our work also appeared in the local Norfolk press.

Our work also appeared in the local Norfolk press.
http://www.edp24.co.uk/news/health/uea_research_on_prostate_cancer_cells_1_3976590

An article on our research in The Times.

An article on our research in The Times.
http://www.thetimes.co.uk/tto/health/news/article4370164.ece?CMP=OTH-gnws-standard-2015_03_02

Independent article on our Phylogeny prostate cancer paper.

Independent article on our Phylogeny prostate cancer paper.
http://www.independent.co.uk/life-style/health-and-families/health-news/prostate-cancer-sufferers-may-need-healthylooking-cells-treated-too-10081085.html

Professor Ros Eeles briefly talks about our research.

Professor Ros Eeles briefly talks about our research.
https://vimeo.com/121053321

Prostate Cancer Phylogeny paper press releases

Prostate Cancer Phylogeny paper press releases

* UEA: https://www.uea.ac.uk/mac/comm/media/press/2015/mar/colin-cooper-prostate-cells
* Cancer Research UK: http://www.cancerresearchuk.org/about-us/cancer-news/press-release/2015-03-02-healthy-looking-prostate-cells-mask-cancer-causing-mutations
* http://www.icr.ac.uk/news-archive/healthy-looking-prostate-cells-mask-cancer-causing-mutations

Here's my quote from the UEA one:
Co-author Daniel Brewer, from Norwich Medical School and The Genome Analysis Centre (TGAC) at Norwich Research Park, said: “This study has sequenced the whole genetic sequences of multiple samples from the prostate for the first time - both from tumours and apparently normal tissue."

“Surprisingly there were a large number of abnormal genetic changes found in the normal prostate tissue, suggesting that the prostate as a whole is a hot bed of genetic instability and is primed and ready for tumours to develop. This gives us important clues to how prostate cancer develops and has potential consequences to how it is treated.”
https://www.uea.ac.uk/mac/comm/media/press/2015/mar/colin-cooper-prostate-cells

Our work on the front page of Nature Genetics website. Not the best figure to choose, but who am I to complain.


Our work on the front page of Nature Genetics website. Not the best figure to choose, but who am I to complain.

Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in...

Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue

This bit of work has been my main focus for a long time and it is really great that it has finally been published in Nature Genetics. This study, for the first time, has sequenced the whole genetic sequences of multiple samples from the prostate, both from tumours and apparently normal tissue. Surprisingly there were a large number of abnormal genetic changes found in the normal prostate tissue, suggesting that the prostate as a whole is a hot bed of genetic instability and is primed and ready for tumours to develop. This gives us important clues to how prostate cancer develops and has potential consequences to how it is treated.
http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3221.html

This is an interesting finding. Needs more research, but interesting none the less.

This is an interesting finding. Needs more research, but interesting none the less.
http://scienceblog.cancerresearchuk.org/2015/01/27/the-latest-plot-twist-in-the-treatment-of-prostate-cancer/

Mutation detection in formalin-fixed prostate cancer biopsies taken at the time of diagnosis using next-generation...

Mutation detection in formalin-fixed prostate cancer biopsies taken at the time of diagnosis using next-generation DNA sequencing - Manson-Bahr et al. - Journal of Clinical Pathology

This is a methodology paper from us that describes a new technique for obtaining DNA from prostate cancer biopsy tissue stored in FFPE.  We go on to show that the quantity and quality of DNA is good enough for targeted next-generation sequencing to be performed reliably.  This is important because it shows that targeted sequencing can be used as a test in the clinic without changes to the pathology processing that is currently performed in hospitals.
http://jcp.bmj.com/content/early/2015/01/13/jclinpath-2014-202754.abstract

This is a really good summary of the recent paper that was interpreted as suggesting that the majority of cancer was...

This is a really good summary of the recent paper that was interpreted as suggesting that the majority of cancer was down to luck rather than lifestyle. It didn't really say that at all but showed that there was a correlation between average reproduction rates of stem cells and cancer incidence across tissues, not across populations. Which makes a lot of sense.
http://scienceblog.cancerresearchuk.org/2015/01/05/cancer-mainly-bad-luck-an-unfortunate-and-distracting-headline/