Doctoral Student at ETH Zurich Switzerland
I am a third year PhD student at Animal Genomics ETH Zurich Switzerland.
I have expertise in the computational methods to analyse genomic big data. I have 5 years experience in using data science stacks e.g., R, Tidyverse, Python, Jupyter for genomic analysis.
I am currently working to integrate millions of bovine genetic variants into a single comprehensive graph-based reference representation. My recent work showed that using reference graphs I implemented reduce the genomic sequencing mapping error by more than 30% compared to the current practices that represent reference genome as a linear string.
I am highly experienced in designing bioinformatics pipelines for variant discovery in large-scale population level (scalable to thousands) of whole genome sequencing data. I mostly using Snakemake for pipelines design and management.
Previously I studied MSc in Quantitative Genetics and Genome Analysis at the University of Edinburgh UK, where I received two awards for my master’s project:
- The Douglas Falconer Prize by Institute of Evolutionary of Biology Edinburgh UK for the best Master’s Thesis.
- Sir Kenneth Mather Memorial Prize by the UK Genetics Society for an outstanding work in Population Genomics.
I am a huge supporter for reproducible and open sciences in computational research. I will make efforts to make all papers I published (including codes), posters, and presentations I present in the conferences to be publicly available.
Publications
Danang Crysnanto, Hubert Pausch. Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery. Genome Biology In press. bioRxiv Preprint from 20th December 2019. Github repository.
Danang Crysnanto, Christine Wurmser, Hubert Pausch. 2018. Accurate sequence variant genotyping in cattle using genome graphs. Published in: Genetics Selection Evolution. bioRxiv Preprint from 4th November 2018. Github repository.
Danang Crysnanto, Darren Obbard. 2018. Widespread gene duplication and adaptive evolution in the RNA-interference pathways of the Drosophila obscura group. Published in: BMC Evolutionary Biology. bioRxiv Preprint from 29th September 2018. Github repository.
Hiltpold M, Niu G, Kadri NK, Crysnanto D, Fang Z-H, Spengeler M, et al. (2020) Activation of cryptic splicing in bovine WDR19 is associated with reduced semen quality and male fertility PLoS Genet 16(5) from 14th May 2020.
Bhati M, Kadri NK, Crysnanto D , Pausch H. Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data. BMC Genomics from 16th July 2019.
Adéla Nosková, Christine Wurmser, Danang Crysnanto et. al. Deletion of porcine BOLL causes defective acrosomes and subfertility in Yorkshire boars. bioRxiv from 7th May 2020.
Zih-Hua Fang, Adéla Nosková, Danang Crysnanto et. al. A 63-bp insertion in exon 2 of the porcine KIF21A gene is associated with arthrogryposis multiplex congenita. bioRxiv from 10th April 2020.
Conferences and Talks
Plant and Animal Genomes Conference (PAG). San Diego USA. Mapping sequencing reads to bovine genome graphs. 11-15 Jan 2020. Selected Oral Speaker. Presentation slides and Poster presentation.
Genome Informatics and Cambridge Livestock Genomics Meeting. Wellcome Genome Campus Cambridge UK. Evaluation of genome graph-based variant genotyping in cattle. 21-22 Sept 2018. Selected Oral Presenter, Long talk. Presentation slides.
52nd Population Genetics. Oxford UK. Widespread gene duplications in Drosophila immune system. 3-6 Jan 2019. Invited Award Winner Speaker. Presentation slides.