Category: papers

The presentation of my PhD defence

news, papers, slideshows, talks4 Comments

That’s it! Last week I defended my PhD thesis!! I have gone through it, and survived to tell!

I don’t feel very different from before, apart from being relieved :-). Now the future is possibly more difficult than before, because I have to look for a job position and finish a lot of things.

While I was preparing the slideshow, I realized that there are not many examples of presentations for a PhD defence online. This is bad, because you need all forms of help to prepare this presentation.The PhD defence is the last thing that you do as a PhD student, so you want to do it perfectly. It is also the moment when you describe many years of your work to the your colleagues and family. Thus, it is bad that there are few examples of slideshows for PhD defence online.

Here is the presentation that I have prepared for my defence. I hope that it will be useful to other people as an example for their defences.

I think that, for this type of presentation, the first slide to make is the “summary of the talk” slide, like the “Topics” slide I have. Usually I don’t like to have such summary slides in my presentation, but for the Thesis defence it is very important, because it gives you a feeling of security when you present. Having a well defined structure allows you to know when you can stop to drink some water or to check if everybody is following, and to know exactly what to say in each slide of the talk.

my attempt at following every possible Best Practice in Bioinformatics

methodology, news, papers10 Comments

I have just uploaded my first paper to arXiv. The title is “Human Genome Variation and the concept of Genotype Networks“, and presents a first, preliminary application of the concept of Genotype Networks to human sequencing data. I know that the title may sound a bit pretentious, but we wanted to  pay a tribute to a great article by John Maynard Smith, to which the work presented is inspired.

Nevertheless, in this blog post I am not going to discuss the contents of the paper, but only on how I did this work. This was a project that I did in my last year of my PhD, and I have made an extra effort in trying to follow every best practice rules I knew.

I started my PhD in the pre-bedtools and pre-vcftools era of bioinformatics, and I saw the evolution of this field, from a spare group of people in nodalpoint to the rise of Biostar and Seqanswers. During this time, I have read and followed a lot of discussions about “what is the best way to do bioinformatics”, from whether to use source control, to testing, and much more. For the last project as a PhD student, I wanted to apply all the practices that I had learn, to determine if it was really worth to spend time learning them.

Premise: dates and times of the project

My PhD fellowship supports a three months stay in another laboratory in Europe. I decided to do it in prof. Andreas Wagner’s group in Zurich.

The decision to go to Wagner’s group was motivated by a book that he had recently published, entitled “The Origins of Evolutionary Innovations”. Previous to the start of this project I had read some articles by Andreas Wagner, and found them very interesting, so the opportunity to stay in his lab was very exciting. However, in light of what I learned during this time, I have admit that before December 2011, I didn’t understand most of the concepts present in the book. Thus, we can say that for this project, I started from zero.

I started thinking of this project in December 2011. I did the first practical implementation in the three months of the stay in Zurich, from May to August 2012. The first preliminary results came in January 2013, and the first manuscript in April 2013. We submitted to ArXiv in August 2013. During this period of time, I have also worked on three other projects, wrote my thesis, and taught at the Programming for Evolutionary Biology workshop in Leipzig.

I started working on this project in December 2011, and finished in August 2013. The log only shows the activity of code changes.
I started working on this project in December 2011, and finished in August 2013. This figure only shows the activity of code changes.

 

Note: this blog article is very long, you may want to download as PDF and read it more comfortably.

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N-Glycosylation – one pathway, two distinct selective constraints

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Our group just published a new paper in BMC Systems Biology. The title is Distribution of events of positive selection and population differentiation in a metabolic pathway: the case of asparagine N-glycosylation. It is already on the journal’s web page.

The pathway of N-Glycosylation can be ideally splitted into two separate parts, one upstream and one downstream of a process known as Calnexin/Calreticulin Cycle, in which an intermediate product of the pathway is involved. In theory, given their function, we can hypothesize that the two parts of the pathway are exposed to different selective constraint, and evolve at different paces among human populations.

The biology and function of the two parts of the pathway are explained in details in the article, but I will try to summarize them here. The upstream part of this pathway is required for this Calnexin/Calreticulin Cycle, a mechanism of folding quality control, so we can expect that all of his genes are conserved among populations. On the other hand, the downstream part of the pathway is involved in host-pathogen interactions, and can be expected to be more variable when comparing populations that adapted to different environments. In the article we have shown that in fact, signatures of population differentiation are more abundant in the downstream part of the pathway.

Unfortunately I don’t have much time to prepare a good presentation to illustrate the paper, but I have uploaded a short resume to slideshare. Have a look at it if you are interested:


You can also check this previous post, where I explained briefly that the main theme of work done in our lab is to study how selective constraints are distributed along the genes of a pathway.

Biostar paper published!

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The Biostar paper has just been published in PLoS Computational Biology. Hurra! 🙂

Biostar is a community for questions/answers for Bioinformatics related queries. It is a good resource to visit if you are a bioinformatician, or if you have a question to ask to a bioinformatician. Browse the site to have an idea of the topics discussed: there it is mostly everything, from ‘What tools/libraries do you use to visualize genomic feature data? ‘ to ‘Where to advertise or find bioinformatics jobs?‘, and much more.

First of all, I would like to thank all the Biostar users. I am very happy of this publication, because this kind of activities (participating to an online technical forum) are very difficult to get acknowledged in the academic world.

Participating to an online forum and help is something that each bioinformatician should do, and that improves the overall quality of scientific research. The discussions on biostar helped hundreds of researchers, and saved time and money to many research projects. However, these types of contributions are very rarely considered by universities when evaluating a curriculum. Writing a 50 upvotes post on Biostar won’t help you at all in getting a faculty position at your university, or in getting a grant, despite the time you may have spent in writing it.

So, let’s hope that the publication of this article will make easier for other resources of the type to be acknowledged in the academic world. I think that between Biostar and other active forums for discussion on Research topic, such as Protocol Online (focused on wet-lab techniques), and SeqAnswers (focused on Next Generation Sequencing), a lot of researchers are getting advantages from this kind of resource. The same fact that the Ten Simple Rules article on Getting Help from Scientific Communities paper that we published a month ago has already gotten almost 5000 visualization, corroborates this fact. Let’s see if the universities and the academic world will learn that contributions to online forums must be encouraged and acknowledged.