Science

Computing Has Changed Biology—Biology Education Must Catch Up

When I opinionated on and on about All Biology being Computational Biology, I was aware that these were not really novel ideas. After all Hallam Stevens had written a whole book about it and my friends inside my intellectual bubble kept on asking why I had spent so much time on writing up something so glaringly obvious.

But what I had missed is that some of my points had already been made very clearly in an excellent piece by Pavel Pevzner and Ron Shamir in Science in 2009 titled “Computing Has Changed Biology—Biology Education Must Catch Up“.

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Science

The Human Cell Atlas needs a pre-registered analysis plan

The Human Cell Atlas preprint came out some days ago on bioRxiv. It describes a project to collect all the cell types in the human body in one big reference map.

Our mission: To create comprehensive reference maps of all human cells—the fundamental units of life—as a basis for both understanding human health and diagnosing, monitoring, and treating disease. [from humancellatlas.org]

The contributors to the project are a Who-is-who of the leaders in single cell genomics and this will be a fantastic data set when it comes out. Because in-depth analysis of resources like this provides the foundation of all biology, as you know.

I enjoyed reading the preprint. It puts the project into a historical perspective and discusses promises as well as limitations. It even references Borges’ `On Rigor in Science’. (I love well-read scientists!) And even if all that means nothing to you, it is still worth reading as a comprehensive summary of the current state-of-the-single-cell-art.

But I kept wondering, with a project like this, how do you know whether it is a success or not? How do you know that your reference map is really comprehensive and covers all (most?) of what it is supposed to find?

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Science

Keep your research group and their science healthy

Have a look at this excellent editorial in Nature: Integrity starts with the health of research groups – Funders should force universities to support laboratories’ research health.

I really like the term ‘research health’, which encompasses both technical aspects of doing research right as well as the well-being of researchers.

[Research health] includes technical robustness of lab practices, assurance of ethical integrity and the psychological health and well-being of group members.

Science is by humans for humans and it is good to see these different aspects being discussed together.

Of course, none of this will be news to keen readers of this blog.

I don’t want to show off, but …

… I emphasized the importance of group leaders to shape the culture of their labs in 5 Selfish Reasons

… and I have highlighted that the quality of people skills is being neglected in current scientific assessment practices, when I argued for continuous leadership support back in 2015.

If these ideas now make it to Nature, there is a actually a chance that scientific culture improves.

The subtitle of the editorial puts the burden on funders, but -honestly- there is no excuse for department heads or individual PIs to neglect their laboratories’ research health no matter what the funders do or say.

Florian

Image: Keith Brofsky/Getty

Duty Calls, Science

All biology is computational biology – 28 days later

Almost a month has passed since I published an opinion piece called “All biology is computational biology” in PLoS Biology.

In my paper, I envisioned a biology that explicitly and clearly acknowledges how much it has changed over the last 20 years, how much its questions have changed, and how much the practice of doing biology has changed. I envisioned a biology that gives credit broadly and fairly to everybody who contributed to key insights – regardless of what tools they used.

As intended, my paper provoked many responses from the community, and in the following you find my thoughts on some particularly interesting comments.

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Duty Calls, Science

Well, that will cause some eye-rolling: All biology is computational biology!

I met Emma Ganley from PLOS Biology at the #scidata16 conference last year, and shortly afterwards she invited me to contribute to the PLOS Biology collection Research Matters:

In this series, we ask leading scientists in their respective fields to explain clearly and engagingly for a lay audience why the research carried out in their laboratories – and those of their collaborators and their colleagues – matters.

It wasn’t immediately clear to me, what I should write about. I tend to label myself a cancer researcher nowadays, but cancer research does not need any explanation why it matters – unfortunate as that is.

At the same time, I am a computational biologist – and here I thought was a much bigger need to explain why it matters. The question is not so much why computational biology and bioinformatics are useful (nobody seems to question that it’s handy to have the geeks around) but why is it biological research, rather than just a support and service activity.

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Science

MEDICC — highly recommended!

It’s good to get feedback now and then. Better still if it is positive.

Ian Holmes highly recommends our paper introducing MEDICC (Minimum Event Distance for Intra-tumor Copy-number Comparisons; more here) at F1000:

High-throughput sequencing of tumors should be informative about the stages of cancer progression. This paper is one of several that exploit the interesting observation that cancer progression is essentially a phylogenetic reconstruction problem. Of course, that should not be surprising since cancer is an evolutionary disease.

This paper looks at copy number variation (CNV) in particular, reducing CNV to an integer vector by considering SNPs in a series of windows along the genome. It addresses both allele phasing and phylogeny.

Most interestingly, from a methodological viewpoint, it does so using techniques from language and automata theory (specifically, context-free grammars and finite-state transducers). These are both tools that have found application in phylogenetics, in fact, as rather advanced tools for modelling the evolution of things like indels and RNA structure.

So, this paper represents an example of the state-of-the-art in one field (phylogenetics) being applied to advance another (computational cancer biology).

Highly recommended!

Thank you. Very appreciated.

Florian

Reference:

  • Schwarz RF, Trinh A, Sipos B, Brenton JD, Goldman N, Markowetz F.
    Phylogenetic quantification of intra-tumour heterogeneity.
    PLoS Comput Biol. 2014 Apr 17;10(4):e1003535.
    doi: 10.1371/journal.pcbi.1003535.  PMID: 24743184;
Career, Science

Come and work with me: Postdoc in Evolutionary biology of cancer

Tired of viruses and fruit flies? Want to work on something really important for a change? Come and help us to figure out cancer evolution!

We are looking for outstanding candidates to work on inferring patterns of tumor evolution from genomics data. We work with a close group of clinical collaborators, both locally and internationally, who will provide multi-sample bulk sequencing and single-cell data sets. We plan to adapt methods from population genetics and phylogenetics to the cancer setting. Key questions will be to compare mutation rates and selection hotspots between the genomes of cancer clones.

This position is ideal for somebody trained in evolutionary biology in model systems to make the transition to biomedical applications in cancer.

The successful applicant will have a PhD in a quantitative field like mathematics, statistics, physics, engineering, bioinformatics, or computer science. A background in evolutionary biology, molecular evolution or population genetics is highly desired. The applicant should have a good biological background and excellent computing skills. The atmosphere at CI is very collaborative and interactive; good communication skills are key.

To apply, please visit http://www.jobs.cam.ac.uk/job/12614/

References

  1. Beerenwinkel et al (2014) Cancer evolution: mathematical models and computational inference, Systematic Biology.
  2. Ross and Markowetz (2016), OncoNEM: Inferring tumour evolution from single-cell sequencing data, Genome Biology, 17:69
  3. Schwarz et al (2015), Spatial and temporal heterogeneity in high-grade serous ovarian cancer: a phylogenetic reconstruction, PLoS Med, 12(2)
  4. Yuan et al (2015), BitPhylogeny: A probabilistic framework for reconstructing intra-tumor phylogenies, Genome Biology, 16:36
Career, Science

#scidata16 follow-up

More publications, more grants, more awesome! Here is my #scidata16 talk on youtube:

And here is Jonathan Page reporting on my talk in Naturejobs:

http://blogs.nature.com/naturejobs/2016/12/02/work-reproducibly-for-the-sake-of-your-career/

The problem lies in the fact that working reproducibly often requires some time investment, something which many scientists working in competitive fields claim they can’t afford. Florian Markowetz from the University of Cambridge counters these claims by saying “not to ask what you can do for reproducibility, but to ask what can reproducibility do for you!”

Indeed I do.

Florian

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

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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