In progress
Source codes of my doctoral thesis in Latex.
This repository might be beneficial as a template that complies with ETH Zurich's thesis formatting requirement. Please adapt accordingly.
I used the Latex workshop in visual studio code with an automatic build run of pdflatex (default command). My latex distribution is MacTex on MacOS.
To build this project please invoke command below.
It will generate two pdf versions of the thesis for an online (main_online.pdf) and a print (main_print.pdf) version.
./compile.sh
My PhD work is mainly in developing and using variation-aware genome graphs as reference genome in cattle population. I showed that the use of graphs instead of linear genome lead to a more accurate and unbiased genetic variants discovery. Additionally, the use of graphs facilitate genetic investigation on the region intractable with a single linear reference genome.
The dissertation is divided into 5 parts:
- Chapter 1: General introduction of cattle genomics, pangenomics, and variation-aware graphs
- Chapter 2: Construction and analysis of cattle cohort-specific graphs. Based on this paper published in Genetics Selection and Evolution:
Crysnanto D., C. Wurmser, and H. Pausch, 2019.Accurate sequence variant genotyping in cattle using variation-aware genome graphs. Genet. Sel. Evol. 51.
- Chapter 3: Variant prioritization into cattle graphs and construction of cattle whole genome graphs that enable elimination of reference bias. Based on the paper published in Genome Biology
Crysnanto D., and H. Pausch, 2020 Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery. Genome Biol. 21.
- Chapter 4: Construction and analysis of bovine multi-assembly pangenome graphs. I developed methods to extract and analyze non-reference sequences from graphs unified from collection of genome assemblies. I found that substansial amount of sequences absent in the reference genome are functionally relevant. Based on this Preprint and by (2/04/2021) accepted in PNAS (Proceedings of the National Academy of Sciences of the USA).
Crysnanto D., A. S. Leonard, Z. Fang, and H. Pausch, 2021 Novel functional sequences uncovered through a bovine multi-assembly graph. Accepted PNAS.
- Chapter 5: General discussion and future directions