Alexander Marx

Large-scale, interpretable gene regulatory network inference through biologically informed matrix factorization

This paper introduces Giraffe, a matrix factorization method for gene regulatory network inference that estimates signed regulatory effects, showing improved accuracy in distinguishing activating and inhibitory interactions across multiple biological contexts.

Integrative analysis of epigenetics data identifies gene-specific regulatory elements

This paper introduces a new method to identify gene-specific regulatory elements by integrating epigenomics data and demonstrates its application in prioritizing doxorubicin-resistance genes.