Career, Science

It’s always good to hear the Boss say nice things …

In case you couldn’t get enough of this Future Leader buzz … here is the official Cancer Research UK blog about it:

http://www.cancerresearchuk.org/funding-for-researchers/research-features/2016-11-15-future-leaders-and-a-lifetime-in-drug-development-our-research-prizes

And this is Simon Tavare, the director of my Institute, nominating me while carefully avoiding to say my name.

Maybe the people who did the interview thought it might save money and time should someone else with a very similar profile ever  be nominated by Simon in the future and they could just reuse the video:

THANK YOU, Simon!

Florian

Creativity

Team building? Piece of cake … and a dancing Sir Bruce Ponder

The highlight of every Institute Retreat is the team building challenge. And my lab is pretty good at it; we’ve won it several times.

See for example the marble run we built in 2014.

We are so good at it, actually, that for the last two years the official announcement of the team building challenge included the statement: “The goal of this exercise is to make sure the Markowetz lab doesn’t win again.”

Last year, we had succumbed to the mounting pressure: When asked to build a life-like animal from paper and cardboard we produced what even optimistically can only be called a ‘roadkill turtle‘. No wonder we came last in the competition. No photographic evidence survives (we made sure of that).

This year was comeback time!

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Career, Science

Look what I got for my birthday: a plastic C. Thank you, CRUK!

Last week was my birthday.

Thank you! Very kind of you.

No, I don’t mind you asking: I turned 29.

Yes, 29.

Yes … just like last year.

Yes … and the year before that.

How about we change the subject, if you don’t mind. Any other questions?

What did I  get for my birthday?

Well, books mostly.

I always get books.

I got so many this time, it will be hard to read them all before my next birthday.

Yes,  that will also be my 29th. Stop asking!

Anything else? Oh, yes, now that you mention it. I also got a plastic C.

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Science

A visual summary of my keynote at #scidata16

I gave my talk on 5 selfish reasons to work reproducibly as a rabble-rousing conference opener at Publishing Better Science through Better Data 2016 (#scidata16) on Wednesday.

Throughout the talk cartoonist Royston Robertson was scribbling away on a huge sheet of paper to visually summarize our key statements.

keynote1.jpg

Hmmm, interesting to have this record what I said.

“Long CVs is what science is all about,” true and sad at the same time.

From now on, I want a personal cartoonist for every talk I give.

Florian

Duty Calls, Science

Science is devoid of significant human and social elements, they say I said.

Every citation is a good citation, right? So I was pleased to see that even the little pamphlet I wrote about my lab last year has a couple of citations now (ok, one is a self citation, please don’t tell anyone).

“You are not working for me; I am working with you” is what I said back then.

And my paper got cited here: “Are Leadership and Management Essential for Good Research? An Interview Study of Genetic Researchers” by Alison L. Antes, Adelina Mart and James M. DuBois in the Journal of Empirical Research on Human Research Ethics.

Leadership in Science – a topic I am definitely interested in.

Let’s see where and how they cite me ..

So exciting!

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Science

Measuring cancer evolution from the genome

Trevor and Andrea just published a really nice review in the Journal of Pathology:

Measuring cancer evolution from the genome
http://dx.doi.org/10.1002/path.4821

In this review, we describe how a cancer’s genome can be analysed to reveal the temporal history of mutation and selection, and discuss why both selective and neutral evolution feature prominently in carcinogenesis. We argue that selection in cancer can only be properly studied once we have a handle on what the absence of selection looks like. We review the data describing punctuated evolution in cancer, and reason that punctuated phenotype evolution is consistent with both gradual and punctuated genome evolution.

Even Hopeful Monsters make an appearance – I predict they are the next big thing in cancer research!

Florian

Career, Science

Making peer review more transparent … and earning bragging rights!

How do you procrastinate? In my case, when deadlines loom, I suddenly feel the urge to upload all my personal information to some randomly selected web-service that promises to make me rich and famous … or at least a better human being or scientist.

The latest thing I went for is called Publons.

Publons works with the world’s top publishers so you can effortlessly track, verify and showcase your peer review contributions across the world’s journals.

And who wouldn’t want to work with the world’s top publishers?

So I signed up for it. Check out my profile here.

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Science

Why are those ugly devils not dead yet?

Devil facial tumour disease (DFTD) is a transmissable cancer that affects Tasmanian devils and has substantially depleted their population, rasing concern that the species faces extinction. However, a new study offers some hope. Epstein et al. report that three populations of Tasmanian devil are exhibiting immune-modulated resistance to DFTD owing to modifications in certain genomic regions that may overcome immune suppression (which is how DFTD spreads between individuals). The selective pressure imposed by DFTD may therefore be encouraging its own undoing.

writes Gemma Alderton in Nature Reviews Cancer to highlight a study in Nat Comm by Epstein et al. The evolution of cancer in Tasmanian devils is really interesting, because it is not intra-tumour evolution, like the rest of the stuff I write about, but the evolution of a transmissible cancer from one devil to the next. It seems they like to bite each others faces. And that spreads the cancer.

Now … if transmissible face cancer is what floats your boat, make sure you also read Dan Graur’s take on it: “All #Hype, No Evidence: Have #TasmanianDevils Evolved Resistance to Facial Tumor Disease? Who knows?

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Science

Systems Genetics of Cancer 2016

I spent the last days of the British summer this week at Lucy-Cavendish College in Cambridge, where Peter van Loo and I had invited 20 equally opinionated researchers from all over the world to discuss what is new and hot in cancer research.

The workshop was called Systems Genetics of Cancer 2016 (and if you click this link to the workshop webpage you will find an impressive list of participants). And because we like to be special, we did not allow any Powerpoint slides. All talks were chalk talks – or rather pen on flip-chart. Among many advantages, this allowed us to take full advantage of the college garden.

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Books, Creativity

Who else likes a Goblin? The daughter and I do.

As the offspring of two bona fide bibliomaniacs, my toddler daughter continuously demands to have books read to her.

Some of the books she likes I find boring (but as a dutiful father soldier on reading them to her) and some of them I quite enjoy (like everything Donaldson and Scheffler cook up).

But now for the first time we seem to have found an age-appropriate book that Daddy might even be more enthusiastic about than the daughter: Nobody Likes a Goblin by Ben Hatke.

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Uncategorized

Pioneering Research: CRUK’s annual research publication

I made it into CRUK’s annual glossy research publication with some quotes about data sharing:

“In genomics the situation’s quite simple,” says Dr Florian Markowetz, group leader at the CRUK Cambridge Institute. “We have the infrastructure, and we’re all required to deposit all our genomics data in the databases to be able to publish. It’s second nature. And that has really demonstrated its value. Pretty much every dataset that I might want to access, I’m able to.”

While genomics has been blazing trails, pioneering technology and standards and developing a mature culture of data sharing, other fields of cancer research have struggled to overcome some of the barriers. Florian is exasperated by what he sees as excuses for not sharing data, but he is also mindful of the real challenges that need to be addressed.

Yeah, when I am quoted for official publications I tend to have very balanced opinions…

It’s good they didn’t ask me what I thought of the New Effing England Effing Journal Of Effing Medicine … I might not have been half as balanced or polite.

Read the whole interview here.

Florian

Science

Understanding genetic interaction networks

Here is a video of a talk I gave at the Newton Institute in Cambridge on Understanding genetic interaction networks as part of a Programme on Theoretical Foundations for Statistical Network Analysis.

I would have liked to embed the video, but wordpress didn’t let me. So click here please:

http://sms.cam.ac.uk/media/2284116/embed

At the end is a surprisingly long Q&A about what type of analysis did and did not go into the iconic Figure 1 of Costanzo et al 2010. I need to learn the magic words “What a great question! Let’s discuss it offline…”

Florian

Science

Research Highlight: Computing tumor trees from single cells

Edith‘s OncoNEM paper made it into the Genome Biology Special Issue on Single-Cell Omics, together with a paper on a tree inference method called SCITE by Niko Beerenwinkel’s group.

If you need any more evidence that our two papers were -at least in my totally unbiased opinion- the obvious highlights of the whole Special Issue, just observe that Alexander Davis and Nick Navin chose us to write a Research Highlight about. They conclude:

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