Interviste(3): Pierre Lindenbaum dell’Universita’ di Nantes

Pubblichiamo oggi un nuovo articolo per la sezione “interviste” inaugurata qualche tempo fa. Oggi intervistiamo Pierre Lindenbaum, postdoc in genetica presso l’Universita’ di Nantes (Francia) e curatore del blog Yokofakun.

Who are you and where you work at?

I’m Pierre Lindenbaum. I got my PHD in virology in 2000 (I studied theprotein-protein interactions between the rotavirus and the host cell). During my PhD , I needed a program to quickly find the best subcloning strategies using a set of restriction enzymes. I wrote the program in ‘C’ ( and, as I had much fun in doing this, I decided to move my career to bioinformatics.
I now work as a postdoctoral researcher in UMR915/Nantes ( )

Which subjects do you study and research?

We”re working on the genetics of the cardiomyopathies. Using next-generation sequencing,  we’re trying to find what are the common genes involved in a cardiac disease.

Briefly describe your career

1996-2000: PhD at National Institute for Agronomic Research. protein-proteininteractions between the Rotavirus and the host cell
2000-2002: PostDoc at National Center of Genotyping (CNG ). Iwrote a program to find the best strategies for genotyping using mass-spectrometry.
2002-2008: Worked as a Bioinformatician at Integragen ( ). I wrote the programs/databases dedicated to our business.
2008-2009: I worked at the CEPH ( on a biological database based on the key/value datastore berkeleydb.
2010- : post doc in Nantes

What is it like in your university?

I’m working in a new building close to the “Hotel-Dieu hospital”
( ) and facing the “Loire” ( )
We’re also close to a heliport, so it often smells the gazoline.

What is it like in your research lab?

There is a really good atmosphereand people are nice. We counted 14 king ‘s cakes in January for celebrating the epiphany.  😛
There a large number of phd students as well as some physicians: so we’re closeto the patients and their problems.
Some views of my desk & my lab here:

What is it like in your country?

Right now, it’s raining.

Are you plannin’ and go elsewhere to work in the future?

Ask my wife, she decides all 😛

How did it come to your mind to open a bioinformatics blog?

I was in a very bad mood.
The day I started my blog, I told people about but they did notcare. Furthermore I was asked something like “Can you blast the Genome vs itself to see if there is something interesting ? Can we have the result tomorrow in a nice Excel spreadsheet”.  So I started my blog to tell the world about the things I like.

Which are the most important functionalities of it?

It’s my notebook. I can use it to see how I solved a problem some months ago. It also reflects my skills an my interests.

Which advantages did you get durin’ your career for havin’ it?

Thanks to my blog I got an invitation to scifoo2007 ( ) and two invitations to attend the BioHackathons in Japan

D’you think bioinformatics blog are too few around?

At least for French bioinformaticians, I can say they are rare. Why ? I don’t know.

D’you think bioinformaticians should get more in contact thru the web?

Not necessarily, if people come to work with their usual professional network. In my case, I had some nice experiences with FriendFeed
–  After a discussion about RDF
( , I got an invitation to be one of the authors of a chapter  of “Beautiful Data”

– Andrew Su (  asked for a bioinformatician to help
him with the GeneWiki effort ( ). At the end, I was the second author of an article published in an issue of Nucleic Acids Research.

Which bioinformatics organizations are you a member?


Do you visit and want to signal some other bioinformatics blog or website? is currently one of my favorite destination because some of the questions asked  here can be very challenging, fun  and it gives an overview of the other’s problems.
For the blogs, you will find the usual suspects at:



Ringraziamo Pierre per la sua disponibilita’!

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