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R

Tidyverse

Python

Git

Docker

Bash

HPC (IBM LSF)



Highly experienced in designing and maintaining bioinformatic pipeline for large scale whole genome sequencing data


Disclaimer

Created with the R package pagedown.

Source code available at github/danangcrysnanto/cv.

Last updated on 2019-11-27.

Main

Danang Crysnanto

Interested in the bioinformatics of the large-scale whole-genome sequencing data. Current work first to propose the transition from linear to more representative, graph-based reference genome for unbiased sequence variant analysis.

Education

PhD Candidate in Computational Animal Genomics

Zurich Switzerland

Swiss Federal Institute of Technology (ETH Zurich)

Current - 2018

  • Research project: Bovine PAN-genomic graphs
  • Skills learned: Graph analytics, Bioinformatics pipeline management

Msc in Quantitative Genetics and Genome Analysis

Edinburgh United Kingdom

The University of Edinburgh

2017 - 2016

  • Thesis: Widespread gene duplication in Drosophila RNAi pathways
  • Skills learned: Pylogenetic analysis, Bayesian statistics
  • The best master thesis with distinction (average marks > 85)

Selected Publications

Accurate sequence variant genotyping in cattle using variation-aware genome graphs

Genetic Selection Evolution

N/A

2019

  • Published within the first year of PhD
  • First work of using graphs for sequence variant discovery in livestock

Widespread gene duplication and adaptive evolution in the RNA-interference pathways of the Drosophila obscura group

BMC Evolutionary Biology

N/A

2019

  • Published from Master’s work
  • Identified massive gene amplifications from analysis >30 Drosophila genome

Selected awards

Sir Kenneth Mather Memorial Prize

N/A

The Genetics Society

2018

  • Rewards a BSc, MSc or PhD student of any UK University or Research Institution who has shown outstanding performance in the area of population genomics or quantitative genetics.

The Douglas Falconer Prize

N/A

The University of Edinburgh

2017

  • Awarded as the best Master’s thesis in the area of Quantitative Genetics and Genome Analysis

Bronze Medalist 21st International Biology Olympiad (IBO)

Changwon South Korea

International Biology Olympiad

2010

  • International biology competition for high school students from 60 countries, who are winners of their respective National Biology Olympiad.

Selected conference and talks

Plant and Animal Genome (PAG) Conference – Selected Speaker

San Diego USA

N/A

2020

  • Talk title: Mapping sequencing read to bovine genome graph

Computational PANgenomics – Selected Participant

Oeiras Portugal

Gulbekian Training Program in Bioinformatics

2019

  • Training with mini-hackaton on graph genomics

Genome Informatics and Livestock Genomics Conference – Selected Speaker

Cambridge United Kingdom

Wellcome Genome Cambridge

2018

  • Talk title: Assessment of the graph-based genotyping with bovine short-read data

Population Genetics Group Conference – Award winner Speaker

Oxford United Kingdom

The Genetics Society

2018

  • Talk title:Widespread gene duplication in Drosophila immune pathways

Selected training

Nextflow for reproducible genomics

Tubingen Germany

Quantitative Biology Center (QBIC)

2019

  • Workshop on implementation of reproducible genomics

R packages

Swiss Institute of Bioinformatics

University of Zurich

2019

  • Training on creating R packages using devtools

Basic Tensorflow

Lausanne Switzerland

Google Zurich

2019

  • Training on basic machine learning in Swiss Applied Machine Learning Days

Docker for reproducible computational research

Swiss Institute of Bioinformatics

University of Bern

2018

  • Training on reproducibility genomic analysis using Docker

Bioinformatics of Long-Range Sequencing

Swiss Institute of Bioinformatics

University of Zurich

2018

  • Training on long-read (Pacbio and Nanopore) data analysis

Python for Life Science

Edinburgh United Kingdom

Edinburgh Genomics

2017

  • Using Python data science stack (e.g., Pandas, Jupyter) for genomics data analysis

High performance computing for genomics application

Scientific IT Services

ETH Zurich

2017

  • Training on best practice of using ETH big data cluster for genomic analysis

GATK Best Practice for Genomic Data Analysis

Broad Institute

Harvard MA USA

2017

  • Training on the best practice variant discovery with Genomic analysis toolkit (GATK)