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’!


Interviste (1): Duarte Molha dell’Oxford Gene Technology

Inauguriamo oggi una nuova rubrica del blog: quella delle interviste a scienziati, ricercatori ed esperti in qualche modo legati alla bioinformatica. Oggi intervistiamo Duarte Molha dell’Oxford Gene Technology, curatore del blog dedicato alla bioinformatica What’s Hot on Bioinformatics (

Who are you and where you work at?

Hi my name is Duarte Molha, I am Portuguese and I’m a computational Biologist at Oxford Gene Technology.

Which subjects do you study and research? What about your career?

At Oxford Gene Technology’s (OGT) we provide high throughput genomic services in diverse areas such as CNV detection, methylation, miRNA and Gene Expression studies. We also have developed cytogenetics solutions (aCGH) together with easy tools for visualizing and interpreting results from these types of studies.
We are now moving into the area of clinical diagnosis solutions and have recently announced some important breakthroughs in the diagnosis of prostate cancer by developing  a panel of biomarkers for the diagnosis of prostate cancer that are much better in both sensitivity and specificity to current prostate cancer diagnostic tests.

My work as a computational biologist in OGT consists in supporting our clients in the early stages of microarray design development, optimizing array designs of optimal performance and helping on the development of new analysis methodologies such as our recently developed UPD detection analysis that enables the detection of both chromosomal aberrations and Uniparental disomy using standard aCHG technology.

I was always interested in informatics since a very early age. Nevertheless, my love for Biology was greater and I decided to study Biochemistry back in my home country (Portugal). I specialised in molecular Biology but after completing my studies, I tried to get a job in my area but found very few opportunities in Portugal.

I eventually decided to emigrate to the UK where I knew I skills set would be much more in demand. After working in several labs, I became a bit disenchanted with lab work and my calling for computer science and especially for the growing demand to bioinformatics skills led me to enroll in a Online course in Bioinformatics called S*Start allience.

It was a nice introduction to some of the skills you need to develop to become a proficient bioinformatician and after that I decided to improve my skills by doing a Msc in Bioinformatics.

This gave the the confidence and some of the skills that you require to to become a good bioinformatician, but I have no douth that to succedd in this area more than education, what you need is a hunger to be constantly developing your skills set. The computer revolution in constantly acceleration and if you do not try to keep up with it you will be obsolete before you even realize.

What is it like in your research lab?

Our company has not been affected by the current economical downturn so much as the rest of the UK. I was hired in the peek on the economical collapse in be beginning of 2009 and I have been very happy working here since then. We have a good working environment and I love Oxford. It is a city full of energy and vitality and with a very diverse international community spurred on by the many people that come here to study in one of the best universities in the world.

What is it like in your country?

The UK has been very much affected by the economical collapse of recent years but it is still a good place to live and work (if you do not mind there terrible weather 🙂 ).  The taxes are very high but the salaries reflect your skills and the market is very dinamic and moves very fast. My country of origin Portugal has the good weather, but unfortunately does not reward people with higher skills sets. I would love to be able to go back to my country are contribute to develop their economy. After all, I was given what I consider to be, a world class education and I would like to give back to my country some of what they have invested in me. However, the graduate market is stagnant and Portuguese business owners do not believe in paying wages that would attract the best graduates back to Portugal.
I graduated in Biochemistry back in 2003. Now 7 years have passed and most of my biochemistry colleagues have either emigrated or taken jobs unrelated to their educational background because the market could not incorporate their skills set.

How did it come to your mind to open a bioinformatics blog?
I created a my bioinformatics blog because I was always interested in communicating some of the most amazing breakthroughs that happen almost every day in this field.
To tell you the truth, I have not kept posting as actively as I could because I have been too busy to focus on writing. I find it faster to just tweet about something interesting I find than to write a thoughtful blog post.

Which are the most important functionalities of it?

I love the interaction you are able to achieve with a blog. People you have never meet can read about something to  wrote and provide insightful comments about the post that can greatly improve it.
I hate the fact that some spammers find their way into the comments sections and I find it very tedious to have to be deleting these spam messages. Nevertheless I prefer to have a open comments sections where people I do not know can provide their input that you have a moderated comments system where only approved people can participate.

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

I believe that having a active blog can show to your potential recruiter that you are a person willing to learn and to share knowledge about your field of interest. It also can be used to showcase your technical knowledge that can be difficult to show on a 30 min interview process. If you add your blog to your CV the recruiter can go there are access your knowledge on a variety of subjects and can make a better judgement of you as a potential employee.

D’you think bioinformatics blog are too few around?

D’you think bioinformaticians should get more in contact thru the web?
Which bioinformatics organizations are you a member?

I do not belong to any bioinformatics organizations. I never felt the need to belong to one, and in general, I believe that professional associations are just a unnecessary bureaucracy layer, remnants of a bygone era where you felt you needed show that you where above the mere mortals that where not as good as you because you belong the the select few. Now seriously I think that professional associations only serve to categorize you and encapsulate you in a very rigid definition that cannot be applied to a field as dynamic as Bioinformatics.

Do you visit and want to signal some other bioinformatics blog or website?

I do not normally visit blogs webpages but instead I add the RSS feed to a RSS feed reader. It increases productivity and allow me to focus on the content. My bioinformatics and science RSS bundles can be access here:

Thanx to Duarte Molha!