Adrien

[Playing with Data] Comparing Helicobacter pylori genomes

With the upcoming gloom of an eventual unemployment period, I decided to fill my non existent free time with a fun little project I've has in mind for a while; as one of my previous post might have indicated. It is time to tackle it! I have been working with…

AdrienMarch 5, 2017

Summary

ISME 2016 – Conference Summary

Few weeks back, I attended the International Society for Microbial Ecology conference in Montreal. Over four days I listened to a series of great talks and I wanted to share a summary of the highlights of this conference and also try to not forget everything as it was quite an…

AdrienSeptember 26, 2016

Bio-informatic Play with Data

[Playing with Data] Looking at a Fish pathogen genome

In this blog note I will use some of the techniques I used in my previous post to look at a recently published dataset. Last year I came across a study by the Institute for Veterinary Pathology, in Zürich, Switzerland describing a bacterial pathogen of fish. Aquaculture is a big…

AdrienSeptember 5, 2016

Summary

ISME 2016 – Sketch compilation

I went in June to the ISME 2016, it was a blast. While I was there I did a series of portrait of the different speakers I have listen to. I have compiled them in the list below

AdrienAugust 27, 2016

Announcement

A story of epibionts in deep sea mussels – My first paper published !

My very first paper : "A specific and widespread association between deep-sea Bathymodiolus mussels and a novel family of Epsilonproteobacteria" is finally available as an Early View on the Environmental Microbiology Reports website. For the past four years, I have been working with deep sea bathymodiolin mussels. They are one…

AdrienAugust 12, 2016

Bio-informatic

Fetching information from NCBI directly from the command line

I recently (re)discovered the edirect software package published on NCBI. As described on the website this "software suite that enables users to use the UNIX command line to directly access NCBI databases, as well as to parse and format the data to create customized downloads". How does it work? Basically…

AdrienJuly 26, 2016

Announcement

Talk at the ISME-2016

I am excited to announce that I will be presenting some of the work I did during my PhD at the ISME conference this year in Montreal. On the 26th of August in the "Oceans of discovery, seas of change" session I will be talking about an alternative pathway for…

AdrienJuly 14, 2016

Bio-informatic [PwD] H. pylori

[Playing with Data] A network of Pylori

So I am playing with the idea of genome comparison and network analysis. And as a small teaser I want to share the above picture. On this figure each dot represent a gene from one of the 83 more or less complete Helicobacter pylori genomes used in the comparison, linked…

AdrienJuly 5, 2016

Announcement

Thesis submitted!

So finally, after 4 years there it is the official Manuscript of my PhD thesis: "Deep Se(a)quencing: A study of deep sea ectosymbioses using next generation sequencing" In there I described my work on characterizing a new epibiont of Bathymodiolus mussels using a wide array of meta- genomics and transcriptomics…

AdrienMay 2, 2016

Bio-informatic

Link dump – Fancy distinct colors

Writing the blog and the thesis at the same time appeared to be harder than expected. I will be back here soon enough ! In the mean time, I was looking to beautify R generated graphs and most of the time I got stuck in having to choose nice but…

AdrienMarch 9, 2016

Interesting Publication