Budi Permana, PhD

Budi Permana, PhD

Microbial Genomics | Bioinformatics | Data Visualisation

I am a bioinformatician by training with focus in microbial genomics research, and web-based visualisation tool or pipeline development. My research revolves around the genomic epidemiology of multi-drug resistant bacteria in healthcare settings. I am confortable working with a large-scale bacterial genome datasets and analysis using various bioinformatics tools and pipelines. I am also incredibly passionate in web-based software design, and have been enjoying to design and implement web user interface (UI) using various Javascript frameworks and libraries. As a bioinformatician, I also comfortable with High-Performance Computing, Unix commands, R, and Python programming.

Career history

Postdoctoral Research Fellow
UQ Institute for Molecular Biosciences (January 2024 - Present)

With Dr Brian Forde, I continue my research journey to investigate the genetic diversity of drug-resistant bacteria from hospitals in Queensland using metagenomics, including bioinformatics and visualisation pipeline development.

Genomic Scientist
Herston Infectious Diseases Institute (HeIDI) (December 2022 - Present)

My responsibilities include:

  • Support the work of HeIDI Fellows and researchers who are conducting research in the area of genomics and bioinformatics.
  • Perform bioinformatic analyses of bacterial next-generation sequencing data, including quality control, assembly, annotation, read-mapping, and phylogenomic analysis.
  • Data analysis and data munging.
  • Use of database systems, including relational database management systems and laboratory information management systems.
  • Work collaboratively with other multidisciplinary researchers (including scientific, clinical and computational researchers) and teams across RBWH and MNHHS, UQ Centre for Clinical Research (UQCCR), Pathology Queensland, Forensic and Scientific Services (FSS), University partners/collaborators, health care consumers.
  • Work with relevant stakeholders to develop genomic education resources.

Bioinformatician
UQ Centre for Clinical Research (May 2022 - December 2023)

I worked as a part-time Bioinformatician at UQ Centre for Clinical Research (UQCCR) under supervision of Dr Brian Forde. My primary responsibility is to carry out large-scale bacterial genome analysis and contribute to developing a web-based application for real-time tracking of drug-resistant bacteria identified from hospitals in Queensland. My research includes but is not limited to analysing population structure, AMR factors, genetic diversity, cluster identification and visualisation tools development. This research and development work aims to improve prevention and control of hospital-acquired infections.

Teaching Assistant
The University of Queensland (Jul 2018 - December 2022)
I have been a teaching assistant for the Advanced Genome Informatics course since 2018. This course is held in 12 weeks and split into four modules: Introduction to Unix, genome assembly and phylogenomics, cancer genomics and metagenomics. My primary responsibilities are supporting lecturers in delivering the lectorials (lecture and tutorial) and answering students’ questions on the online discussion portal.

Overseas Operational Officer
Markany Inc (May 2013 - Dec 2015)
MarkAny is a company providing data security solutions based in South Korea. I worked at its branch in Indonesia and was responsible for supporting an Official Development Assistance (ODA) project between MarkAny, Korea International Cooperation Agency (KOICA) and Indonesia from 2013 to 2015. My primary duties include organizing conferences, assisting knowledge transfer programs and managing the R&D laboratory. At this time, I became interested in computer science and decided to take a Master of Bioinformatics to combine my background in Biology and my passion for computer science.

Education

Doctor of Philosophy
The University of Queensland (Finished 2022)
My PhD focused on genomic epidemiological research of drug-resistant bacteria and concurrently developing visualisation tools for integrating genomic and epidemiological information in healthcare settings. Under supervision of A/Prof Scott Beatson and Dr Brian Forde, I worked on two genomic epidemiological studies of Vancomycin-resistant Enterococcus faecium (VREfm) in hospitals in Queensland. Additionally, I developed two novel visualization tools: HAIviz and GraphSNP. During my PhD, I had the opportunity to learn new skills, present my research at various conferences, and collaborate to publish several scientific papers.

Master of Bioinformatics
The University of Queensland (Finished 2017)
I received a degree of Master of Bioinformatics from The University of Queensland after completing a 24 units postgraduate coursework program. I took nine courses, including Concept and Advanced Bioinformatics, Data Mining, Software Engineering, Introduction to Information Systems, Computational Statistics, Advanced Genome Informatics, Molecular Genetics and Major Research and Seminars. Cumulative GPA (24 units): 6.11/7; Dean’s Commendation for Academic Excellence.

Bachelor of Science (Biology)
Institut Teknologi Bandung (Finished 2013)
I received a Bachelor of Science from the Bandung Institut of Technology (ITB) in 2013 in Indonesia. My undergraduate program specialised in Biology, which delivers a wide range of life science courses, including mathematics, physics, organic chemistry, ecology, microbiology, and research in biology. Cumulative GPA (144 units): 3.44/4; Excellent.