README.Rmd

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# My PhD thesis

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## From gene expression to pathway and transcription factor activities to study chronic liver diseases

This thesis is based on three manuscripts each forming a separate chapter. An online version of this thesis can be accessed at [Netlify](https://christianholland-thesis.netlify.app).

### Chapter 1

Transfer of regulatory knowledge from human to mouse for functional genomics analysis ([Publication](https://doi.org/10.1016/j.bbagrm.2019.194431), [GitHub repository](https://github.com/saezlab/ConservedFootprints)).

### Chapter 2

Robustness and applicability of transcription factor and pathway analysis tools 
on single-cell RNA-seq data ([Publication](https://doi.org/10.1186/s13059-020-1949-z), [GitHub repository](https://github.com/saezlab/FootprintMethods_on_scRNAseq)).

### Chapter 3

Transcriptomic cross-species analysis of chronic liver disease reveals consistent regulation between humans and mice ([Publication](https://doi.org/10.1002/hep4.1797), [GitHub repository](https://github.com/saezlab/liver-disease-atlas)).