Stephen Pederson

Stephen Pederson

Adelaide Medical School

Faculty of Health and Medical Sciences

Eligible to supervise Masters and PhD - email supervisor to discuss availability.


I am a post-doctoral bioinformatician working within Black Ochre Data Labs at Telethon Kids Institute, as part of the Preventing Renal OPthalmic Heart Events in CommunitY (PROPHECY) study. This is the largest genomic and multi-omics study undertaken into Type 2 Diabetes, Cardiovascular Disease and other complications from T2D within the Indigenous Australian population. As this is a complex multi-mics study, I am primarily responsible for the transccriptomics component, along with the integration across multiple 'omics layers

My background is in genetics and statistics and I possess a high level of fluency in the the language R. I am also an enthusiastic contributor to the Bioconductor community of open source packages for the biological research community. I am a firm advocate of reproducibility in bioinformatics research and use git, snakemake, workflowr and other management tools for all analyses.

My personal interests are primarily focussed on transcriptomics, and I have considerable depth of experience ranging from microarrays to bulk RNA-Seq, along with a growing experience in single-cell data. I have spent a considerable amount of time focussing on data integration across multiple platforms, such as ChIP-Seq across multiple transcription factors, in tandem with HiC-Seq data to ascertain nearby and distant regulatory function, and RNA-Seq data to confirm the associated regulatory changes.

In my first academic appointment (2014-2020) I was the Coordinator of the Bioinformatics Hub and oversaw the growth of this facility from a single person, to several staff with a wide network of collaborators and students across all campuses of the University. We provided support and advice for hundreds of researchers across the university via consultations and delivered training workshops to over 1500 people.

Brain Foundation Analysing the effects of an Alzheimer’s disease-causing mutation at the
level of single cells.,
$25,000 2020
South Australian Health and Medical Research Institute (SAHMRI) Improving T cell homing to solid tumours $100,000 2020
NHMRC Th17 cells, chemokine receptors and control of inflammation $776,432 2019-2022
NHMRC Using the chemokine receptor system to improve immunological memory $675,788 2019-2021

Whilst working in the Bioinformatics Hub, I was one of the primary lecturers and tutors for the subject Biotech7005: Introduction to Bioinformatics and Systems Modelling, from 2015 to 2019. In Semester 1 2020, I developed and delivered the vast majority of the course material for BIOINF3005/7160 Transcriptomics Applications

  • Current Higher Degree by Research Supervision (University of Adelaide)

    Date Role Research Topic Program Degree Type Student Load Student Name
    2023 Co-Supervisor High dimensional chemokine receptor and cell trajectory profiling of single autoreactive T cells in EAE using CITE-Seq technology. Master of Philosophy Master Full Time Miss Megan Rachel Monaghan
    2020 Co-Supervisor Bioinformatics analyses of familial Alzheimer's disease mutation models in zebrafish Doctor of Philosophy Doctorate Full Time Mr Lachlan Warren William Baer
  • Past Higher Degree by Research Supervision (University of Adelaide)

    Date Role Research Topic Program Degree Type Student Load Student Name
    2021 - 2023 Principal Supervisor Unlocking Insights from Complex Transcriptomic Data: Novel Bioinformatics Methods for Neurodegeneration and Cancer Studies Doctor of Philosophy Doctorate Full Time Miss Wenjun Liu
    2019 - 2020 Co-Supervisor Transcriptome Analysis of Zebrafish Genetic Models to Reveal Early Molecular Drivers of Alzheimer's Disease Doctor of Philosophy Doctorate Full Time Miss Nhi Hin
    2019 - 2023 Co-Supervisor Bioinformatic approaches to variant detection and subtype classification in acute lymphoblastic leukaemia Doctor of Philosophy Doctorate Full Time Miss Jacqueline Ann Rehn
  • Other Supervision Activities

    Date Role Research Topic Location Program Supervision Type Student Load Student Name
    2019 - ongoing Co-Supervisor RNA Seq analysis of Early Onset Familial Alzheimer's Disease-like mutations in Zebrafish The University of Adelaide Bachelor of Science Honours Full Time Lachlan Baer
    2019 - ongoing Principal Supervisor scRNA Analysis of Tumour Samples The University of Adelaide Master of Biotechnology (Biomedical Science) Master Full Time Junwei Wang
    2018 - 2018 Principal Supervisor An investigation on library size and analytic methods for RNA Seq data University of Adelaide Bachelor of Science (Summer Research Program) Other Full Time Wenjun Liu
    2018 - ongoing Principal Supervisor Utilizing RNA-Seq to understand the contribution of miR-223 and miR-155 to endometriosis lesion development University of Adelaide Master of Biotechnology (Biomedical Science) Master Full Time Tianzhi Yu
    2018 - 2018 Co-Supervisor Forensic Analysis of Two Unidentified Individuals University of Adelaide Master of Biotechnology Master Full Time Guanchen Li
    2018 - ongoing Co-Supervisor Analysis of HiC Data from Water Buffalo University of Adelaide B.Ma&CompSc (Hons.) Honours Full Time Yan Wang
    2017 - ongoing Co-Supervisor Assembly of the Venom Gland Transcriptome in Tiger Snake University of Adelaide Bachelor of Science Honours Full Time Monique Ahrens
    2017 - ongoing Co-Supervisor Network Analysis of Zebrafish Brains Containing A Familial Altzheimer's Disease Mutation University of Adelaide - Master Full Time Nhi Hin
    2017 - 2017 Co-Supervisor Analysis of DNA Damage Patterns in Ancient Bacterial Samples University of Adelaide Master of Biotechnology (Biomedical Science) Master Full Time Jacqueline Ann Rehn
    2017 - 2017 Principal Supervisor Methylation Analysis of Monzygotic Twins Discordant for Major Depressive Disorder University of Adelaide Master of Biotechnology Master Full Time Yan Ren
    2017 - 2017 Co-Supervisor Integration of Multiple Omics Data from V. Vinefera University of Adelaide - Honours Full Time Konstantinos Justinian Bogias

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