Fast and flexible analysis of linked microbiome data with mako
Sam Röttjers and Karoline Faust
In this paper I introduce a framework written in Python to easily integrate microbiome data in Neo4j databases.
Null-model-based network comparison reveals core associations
Sam Röttjers, Doris Vandeputte, Jeroen Raes and Karoline Faust
Here, I present an application developed in Python to compare multiple microbiological networks from different datasets. The application can be used to assess whether networks look more or less similar than we would expect.
Earth microbial co-occurrence network reveals interconnection pattern across microbiomes
Bin Ma, Yiling Wang, Shudi Ye, Shan Liu, Erinne Stirling, Jack A. Gilbert, Karoline Faust, Rob Knight, Janet K. Jansson, Cesar Cardona, Sam Röttjers and Jianming Xu
This paper describes the structure of worldwide microbial networks. I mainly provided feedback on the methodology used in the paper.
manta - a clustering algorithm for weighted ecological networks
Sam Röttjers and Karoline Faust
Here, I describe an algorithm that I wrote to cluster microbial networks. I also evaluate the accuracy of other algorithms on computer-generated data.
From hairballs to hypotheses - biological insights from microbial networks
Sam Röttjers and Karoline Faust
This paper is an in-depth review on microbial networks. It describes the methodology and its pitfalls.