title: Modelling Cell-cell Communication using Prior Knowledge with Single-cell and Spatially-resolved Omics Data
creator: Dimitrov, Daniel
description: Cell-cell communication (CCC) is a dynamic process which governs and coordinates diverse biological functions. The popularity of single-cell and spatially-resolved transcriptomics has recently sparked an array of computational methods that model CCC to be developed. My thesis describes the development of LIANA+ - an all-in-one framework for the inference of CCC from single-cell and spatial (multi-) omics data. In the first chapter of my thesis, I summarise the current state of the CCC field and state my motivation for the development of LIANA. In the second chapter, I describe the initial study that led to the development of the first iteration of LIANA. I also show that the choice of CCC method and resource can impact biological insights. In the third chapter, I evaluate CCC methods using alternative data modalities, and show that most CCC methods are generally coherent with those. In the final chapter, I summarise the current challenges of the CCC field and I showcase how the modularity of LIANA+ provides a comprehensive answer to those. I further see LIANA+ as a step towards modelling host-microbiome interactions, with already some pilots in place.
date: 2024
type: Dissertation
type: info:eu-repo/semantics/doctoralThesis
type: NonPeerReviewed
format: application/pdf
identifier: https://archiv.ub.uni-heidelberg.de/volltextserverhttps://archiv.ub.uni-heidelberg.de/volltextserver/35089/1/DanielDimitrovPhDThesis.pdf
identifier: DOI:10.11588/heidok.00035089
identifier: urn:nbn:de:bsz:16-heidok-350898
identifier:   Dimitrov, Daniel  (2024) Modelling Cell-cell Communication using Prior Knowledge with Single-cell and Spatially-resolved Omics Data.  [Dissertation]     
relation: https://archiv.ub.uni-heidelberg.de/volltextserver/35089/
relation: info:eu-repo/grantAgreement/EC/FP7/860329
rights: info:eu-repo/semantics/openAccess
rights: Please see front page of the work (Sorry, Dublin Core plugin does not recognise license id)
language: eng