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.

Continue reading

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?

Continue reading

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.

Continue reading

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.

Continue reading

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:

Continue reading

Creativity, Science

A 4D Atlas of Cancer

Welcome to the future of cancer research!

I collaborate in a CRUK Grand Challenge application:

Professor Ehud Shapiro from the Weizmann Institute, Israel with collaborators from Israel, the UK and USA will find a way of mapping tumour at the molecular and cellular level. [ Read more ]
And here is how the result will look like:

 

Now we just hope that the nice people of CRUK are kind enough to give us the 20 million quid we need …

Florian

 

Career, Science

3 open positions in Roland Schwarz’ new lab in Berlin

The Max Delbrück Center for Molecular Medicine (Berlin) and the Berlin Institute for Medical Systems Biology (BIMSB) invite applications for

  1. PhD student (10681/2016)
  2. Postdoc (10680/2016)
  3. Scientific Programmer (10682/2016)

in the research group “Evolutionary and cancer genomics” of Dr Roland Schwarz.

The Schwarz lab investigates the relationship between genetic variation and complex phenotypes from an evolutionary perspective. A focus is thereby on the aetiology and functional implications of intra-tumour heterogeneity in human cancers. We are particularly interested in understanding the effect of structural variants and copy-number changes on cancer evolution in-vivo and closely collaborate with clinical partners to achieve this goal.

Send your application to roland.schwarz@mdc-berlin.de and mention the reference number 1068x/2016 where x is in {0,1,2}.

Florian

Duty Calls, Science

If I don’t get it, you should be concerned.

The latest post at Shit My Reviewers Say is “My first concern is that I don’t get it.

And the obvious response is illustrated by a picture saying “Your problems with me are not my problems, those are your problems.

What can you do as an author if the reviewer is just too stupid to understand your ingenuity?

But … and this is a big but … there are areas of research where I would use that reviewer’s comment myself. If, say, you are writing about probabilistic models in cancer genomics and I can’t make any sense of what you are saying, it is your problem, not mine.

Here is an example. The ABSOLUTE paper on “Absolute quantification of somatic DNA alterations in human cancer”.

Continue reading

Science

Ask me anything at PLOS Science Wednesday on May 18

PLOS Science Wednesday is a weekly science communication series featuring live, direct chats with PLOS authors on redditscience (/r/science), the popular online gathering place for researchers, students and others interested in science which has over 8 million registered members. The series provides a forum for PLOS authors to communicate their work and interact directly with fellow researchers and the public.

You can find the complete schedule here.

And on May 18th it’s my turn to answer anything together with my colleague James Brenton.

And when I say ‘anything’ I mean ‘anything about cancer evolution’.

Florian

Science

UAI 2016 Workshop on Machine Learning for Health

Machine Learning for Health: Learning to understand human disease

Machine learning is revolutionizing our understanding of many human health problems from obesity to cancer. With ever increasing amount of data coming from this domain, computational biology and medicine are also transforming the machine learning community by not only providing new applications but also inspiring new modeling frameworks and learning paradigms.

The goal of this workshop is to bring together machine learning scientists and computational biologists. We would like to showcase recent advances in this field and discuss challenges in computational methodology and biomedical application.

Continue reading

Career, Science

Open positions – cancer evolution and networks

I have three open positions in my lab:

  1. A PhD student position for “Single-cell analysis of cancer evolution” http://www.jobs.cam.ac.uk/job/10282/
  2. A postdoc position for “Evolutionary biology in cancer”. This position is ideal for somebody trained in evolutionary biology in model systems to make the transition to biomedical applications in cancer.
  3. And finally a postdoc position broadly advertised as “Computational cancer genomics” but actually having a strong network focus. http://www.jobs.cam.ac.uk/job/10265/

More info here http://www.markowetzlab.org/positions.php

Any questions, just contact me directly.

Florian