Bioinformatician, MDU-PHL, The University of Melbourne
Oct, 2023 - Present
Developing and maintaining bioinformatics pipelines for the analysis of genomic data from bacterial pathogens
pipeline-validation and development
microbial bioinformatics
Himal Shrestha
Bioinformatician
Background
About
About
A PhD graduate in Bioinformatics with expertise in computational and mathematical modelling. I am passionate about using data to predict, prevent, and eliminate infectious diseases. Currently, I work as a bioinformatician in the MDU-PHL, University of Melbourne. My research at La Trobe University involved studying the transmission of parasitic disease, called river blindness, by integrating genomic, environmental, and epidemiological data with a variety of modelling and analytical approaches.
Work Experience
Work Experience
Post-doctoral researcher (Bioinformatics/infectious disease modelling), Nematode and Vector Genomics Lab, La Trobe University
Apr, 2023 - Oct, 20236 months
Formulating empirical and/or mechanistic transmission models utilising genomic, environmental and epidemiological data and supervise students working on related research.
landscape genetics
spatial modelling
Casual academic, La Trobe University
Feb, 2020 - Oct, 20222 years 8 months
Demonstrating and tutoring masters and undergraduate students.
BIO5INF (Bioinformatics)
BIO1MGC (Molecules, Genes and Cells)
BIO1EEB (Ecology, Evolution and Biodiversity)
Skills
Skills
- Bioinformatics
Genomics
Public Health
Epidemiology
Geospatial modelling
Infectious disease modelling
Education
Education
New tools for onchocerciasis elimination in Africa: the role of spatially explicit models in informing decisions., PhD in Bioinformatics, La Trobe University
Aug, 2019 - Mar, 2023
Data Driven Mathematical Modelling
Helminth Bioinformatics
Hierarchical Modelling of Species Communities
Deep Learning
Dynamic processes spreading on Networks
Random Fields: Mathematical theory and application in spatial statistics
Thesis: Analysis of ivermectin action on adult female <i>Onchocerca volvulus</i> from embryogram data: evidence for reproductive periodicity and the basis for the embryostatic phenotype., Master of Biotechnology and Bioinformatics, La Trobe University
Jul, 2017 - Mar, 2019
Bioinformatics
Proteomics and Genomics
Scientific Communication Skills
Biobusiness management
Practical Biotechnology
Thesis: Assessment of C-Reactive Protein/Albumin ratio for predicting outcome in critically ill patients with various underlying diseases., Bachelor of Science in Human Biology, Kathmandu University
Aug, 2012 - May, 2016
Human Anatomy
Human Physiology
Biochemistry
Microbiology
Immunology
Molecular Biology
Certificates
Certificates
GitHub actions, LinkedIn Learning
Issued on: Jan 16, 2025
JSON essentials, LinkedIn Learning
Issued on: Jan 27, 2025
Awards
Awards
Best poster prize , Asia Pacific Consortium of Mathematics for Industry (APCMfI)
Awarded on: Jul 21, 2021
Awarded for the poster presentation on 'Parameterising vector movement in an onchocerciasis transmission model with population genetic data' which included a month-long research visit to the ICIAM conference in Tokyo and Kyushu University in Fukuoka, Japan.
Volunteer Work
Volunteer Work
Co-founder and Director, Anka Analytica
Aug, 2022 - Mar, 2024
Started organisation to facilitate research activities between students and researchers in the field of bioinformatics and biotechnology in LMICs and HICs.
Organised Python workshops for Master's in Bioinformatics student at Pokhara University, Nepal
Helped with development of projects with Internation Vaccine Institue (IVI), South Korea
Support Trainer, MDU-PHL
Jan, 2025 - Feb, 2025
Support trainer for the bioinformatics training session with the Aus Awards Fellowships. Assisted with the training on mapping and variant calling, exploring the function/impact of mutations, and galaxy activity.
Publications
Publications
Synthesizing environmental, epidemiological and vector and parasite genetic data to assist decision making for disease elimination , Molecular Ecology
Published on: Apr 29, 2024
This article presents a framework for mapping and analyzing the transmission of vector-borne diseases, specifically onchocerciasis, by integrating environmental, epidemiological, and genetic data of vectors and parasites1. The study focuses on the ecological transition zone in Ghana, highlighting the importance of coordinated disease intervention efforts over large geographic areas to eliminate transmission of onchocerciasis.
Interests
Interests
Bioinformatics
Microbial bioinformaticsParasite genomicsPipeline developmentPipeline validationEpidemiology
Geospatial modellingInfectious disease modellingPublic health genomicsLandscape genomics