Masters Research Projects
Many Master of Science (Bioinformatics) students have undertaken their research projects under the direct supervision of Melbourne Bioinformatics researchers, putting them in an enviable position for entry into industry, research or a PhD.
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Student Supervisors Thesis topic Year completed Matthew Brown Michael Stumpf; Grace Hall Network inference methods for gene regulatory networks, using Baysian models current Lingyun Ding Chol-hee Jung; Steven Morgan Mutation interaction analysis tool in R current Ching-Yi Peng A/Prof Bernie Pope; Jessica Chung Quantifying the Differences Between Poly-A Selection and Ribo-Depletion in RNA-Seq current Ruixin Cai Tom Harrop Techniques for cross-species RNA seq analysis 2023 Sangzhe Gu Chol-hee Jung Assessing the effects of incorrect metadata to the analysis of DNA methylation with the focus on the sex-labelling 2023 Dafei Lin A/Prof Bernie Pope Assessing the effect of pseudogenes on DNA sequencing alignment and variant calling in human cancer 2021 Jiayi Liu Chol-hee Jung Comprehensive survey of sex status of public DNA methylation datasets 2021 Jiayu Wang A/Prof Bernie Pope Assessing the quality of structural variants in the context of DNA read alignments 2021 Tianyi Lu A/Prof Daniel Park; Khalid Mahmood Towards cost-efficient HLA sequencing screening 2019 -
Student Supervisors Thesis topic Year completed Zizhen Huang Grace Hall; Prof Christopher Hovens; A/Prof Bernie Pope Brain Metastases: Uncovering the role of lipid-biosynthesis pathways in tumor metastatic potential & proliferation current Tzer Ray Su A/Prof Daniel Park; Khalid Mahmood An exploration of cancer biology via The Cancer Genome Atlas current Alexander Nathan Thomas A/Prof Daniel Park; Khalid Mahmood An exploration of cancer biology via The Cancer Genome Atlas current Bibo Zhao A/Prof Daniel Park; Khalid Mahmood An exploration of cancer biology via The Cancer Genome Atlas current Jean Ho A/Prof Bernie Pope Exploring rare brain mets genome somatic variant structure with common brain mets 2024 Ran Li A/Prof Bernie Pope Search for spatial patterns in the somatic mutations (SNVs, INDELs, CNVs and SVs) in ~200 prostate cancer genomes 2024 Difei Huang A/Prof Bernie Pope Can tumour-in-normal contamination detect circulating tumour DNA and does it relate to cancer outcomes? 2023 Senyang Xue A/Prof Daniel Park; Khalid Mahmood Tumour microenvironment and cancer outcomes 2022 Kewei Yuan A/Prof Bernie Pope Assessing the effect of somatic mutations in cancer using reverse phase protein arrays 2022 Patrick Hawkins A/Prof Daniel Park; Khalid Mahmood Cancer Outcomes Related to Viral Agents, the Immune System, and the Tumour Microenvironment 2021 Dongyu Li Chol-hee Jung Exploration of multi-omics prostate cancer data 2021 Mailie Gall A/Prof Paul James; A/Prof Bernie Pope Copy number variation in Familial Colorectal Cancer Type X 2019 Muhammad Kamran Dilmir Khalid Mahmood A framework for prioritizing genomic variants and disease genes in lobular breast cancer 2017 Yu Wan Chol-hee Jung Breast cancer epigenome-wide association study 2014 -
Student Supervisors Thesis topic Year completed Aoxiao Gao Allison van de Meene; Luke Gandolfo Identifying cell wall biosynthetic enzymes in grasses current Yunan Gao Allison van de Meene; Luke Gandolfo Identifying cell wall biosynthetic enzymes in grasses current Wenyuan He Allison van de Meene; Luke Gandolfo Identifying cell wall biosynthetic enzymes in grasses current Ruxin Wang Chol-hee Jung Characterisation of nuclear genome encoded mitochondrial genes (MITIOME) current Wenyu Yang A/Prof Simon Murray; Steven Morgan Signalling Pathways in Oligodendrocytes current -
Student Supervisors Thesis topic Year completed Dania Al Istwani Vicky Perreau; Steven Morgan Use of public single cell RNAseq datasets to explore expression of NTRK2 transcript variants in different CNS cell types current Chorpaka Chankaew Vicky Perreau Using public data to explore expression of GFAP transcript variants in disease and Injury current Sally Beard Matt Wakefield Investigation of pregnancy complications: bioinformatics for therapeutic development 2020 Yuchuan Liu Prof Judy Savige; Khalid Mahmood The genetics of inherited renGenetics of fibrillary glomerulonephritis 2019 Steven Morgan Tara Karnezis; A/Prof Bernie Pope; A/Prof Daniel Park Identification of genetic variants associated with Lipodema project 2019 Jianan Wang Prof Judy Savige; A/Prof Daniel Park Identification of novel genes for inherited causes of kidney failures 2018 Jonathan Reich Juan Nunez-Iglesias; Torsten Seemann Accelerating the reconstruction of brain circuits with big image analysis 2017 -
Student Supervisors Thesis topic Year completed Xin Wang A/Prof Daniel Park; Khalid Mahmood Resistance mechanisms to immunotherapy in melanoma current Ruofei Jiang A/Prof Daniel Park; Khalid Mahmood Exploring the relationship between neoantigens and immune microenvironment in cutaneous melanoma 2023 Shijia Tang A/Prof Daniel Park; Khalid Mahmood Anti-PD1 IT in melanoma outcomes 2023 Farjana Akhter A/Prof Daniel Park; Khalid Mahmood Immune involvement in ductal and lobular breast cancer 2022 Yizhe Mao A/Prof Daniel Park; Khalid Mahmood TCGA and Immune system 2021 Alexander Barnett A/Prof Daniel Park; Khalid Mahmood Towards personalized cancer vaccines: modeling HLA:neoepitope binding 2020 Peizi Chen A/Prof Daniel Park; Khalid Mahmood Somatic mutations in mismatch repair genes: an investigation using TCGA 2020 Himanshi Arora Vicky Perreau Use of transcriptomic data and interaction networks to gain insight into addiction pathways for the prospect of future personalised medicine strategies. 2019 -
Student Supervisors Thesis topic Year completed Lechuan Ren Gayle Philip; Vinicius Werneck Salazar Comparative genomics of ocean microbial communities current Raquel Cooper Dieter Bulach Establishment of in silico virulence factor assays for use in Public Health Microbiology 2022 Qiwei Hu Dieter Bulach Metagenomics approaches to the detection of bacterial antimicrobial resistance genes 2020 Priyanka Pillai A/Prof Sepehr Tabrizi; Dieter Bulach A Whole Metagenome Sequencing approach for the investigation of the onset of bacterial vaginosis 2016 Agnes Tan A/Prof Sepehr Tabrizi; Gayle Philip Changes in microbial communities upon onset of Bacterial Vaginosis 2015 Serene Siah Torsten Seemann Genomic analysis of a novel marine mycobacterium 2014 -
Student Supervisors Thesis topic Year completed Andrew Harrison A/Prof Daniel Park; Khalid Mahmood Assessing the role of protein conformations in protein variant effect prediction on protein function current Jessica Sun A/Prof Daniel Park; Khalid Mahmood Protein structural data augmentation current Yuanjie Wang A/Prof Daniel Park; Khalid Mahmood Protein structural features for variant effect prediction current Pengan Zhang A/Prof Daniel Park; Khalid Mahmood Protein structures data augmentation current Chuyi Wang A/Prof Daniel Park; Khalid Mahmood Protein structure features for variant effect prediction 2024 Maria Orlovskaya A/Prof Daniel Park; Khalid Mahmood Mutation effect prediction for clinical diagnostics and disease gene discovery 2021 Emma Darling A/Prof Daniel Park; Khalid Mahmood Improved mutation effect prediction via functional datasets 2020