Play with Data

Microbial Advent Calendar – 05 Winter’s black death

For the fifth day of our Microbial Advent Calendar I wanted to start with: Yersinia pestis, the party crasher of 1665 that pretty much ruined Christmas and everything else in London during that year and the following one. Although it did ruin everything, while reading about it I realized it…

AdrienDecember 6, 2017

Bio-informatic [PwD] H. pylori

[Playing with Data] 607 pylori part III: Start digging

Hello Folks, it's been a while! I thought it would be time to continue this big Helicobacter pylori genomes experiment and keep the blog going on. We left with the previous post on preparing the data for our analyses. The main next step will be re-annotating all the genomes in…

AdrienNovember 14, 2017

Bio-informatic [PwD] H. pylori

[Playing with Data] 607 pylori part II: getting the data ready

In the previous post we had a look at some interesting features of Helicobacter pylori. Now it is time to finally get our hands on the data. This post will present the data preparation, how to get everything ready in a comparable way for easy analyses.Now that we know more…

AdrienApril 17, 2017

Bio-informatic [PwD] H. pylori

[Playing with data] 607 pylori part I : the introduction

Every story or study needs an introduction to give some context to what we are look at. When I first started writing the introduction about Helicobacter pylori, I realised quite quickly that my first attempts were massively paraphrasing again and again Wikipedia's summary. Because the Wikipedia article contains most of…

AdrienApril 10, 2017

Bio-informatic [PwD] H. pylori

[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

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

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

Microbial Advent Calendar – 05 Winter’s black death

[Playing with Data] 607 pylori part III: Start digging

[Playing with Data] 607 pylori part II: getting the data ready

[Playing with data] 607 pylori part I : the introduction

[Playing with Data] Comparing Helicobacter pylori genomes

[Playing with Data] Looking at a Fish pathogen genome

[Playing with Data] A network of Pylori

Interesting Publication