npj Systems Biology and Applications
An online Open Access journal dedicated to publishing the premier research that takes a systems-oriented approach and encourages studies that integrate, or aid the integration of, data, analyses and insight from molecules to organisms and broader systems.
Finding the microbial heroes: Identifying the smallest groups of microbes, capable of executing a desired function, from a large microbial community
Given a large co-operative microbial community, an algorithm to identify the smallest subsets of that community capable of a desired functionality is presented. These subsets, called minimal microbiomes, will contain the keystone species that achieve the required purpose.
The need for predictive biomarkers of tumor hypoxia
In our paper we showcased how to retain low-abundant signals of tumor hypoxia from spatial omics data for biomarker discovery. In this post, we want to emphasize why tumor hypoxia is relevant and why there is still an urgent need for predictive molecular biomarkers.
Inferring patient-specific gene networks from bulk transcriptomics data
While traditionally network inference on bulk transcriptomics data generates an 'average' gene network for the population, single-sample network inference constructs patient-specific gene networks. We evaluated several tools in the context of precision oncology when ‘normal tissue’ is not there.
