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 The Kids Research Institute Australia, 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.
-
Appointments
Date Position Institution name 2022 - ongoing Postdoctoral Bioinformatician Telethon Kids Institute 2020 - 2022 Bioinformatician University of Adelaide 2014 - 2020 Co-ordinator, Bioinformatics Hub University of Adelaide -
Education
Date Institution name Country Title 2008 - 2018 University of Adelaide Australia PhD 2006 - 2007 University of Adelaide Australia B Ma & Comp Sc (Hons) 2002 - 2005 University of Adelaide Australia B Sc 1989 - 1991 University of Adelaide Australia B Mus -
Research Interests
Cardiac, Respiratory and Vascular Health Immunology and Infection Indigenous and Disadvantaged Health Translational Health Outcomes Aboriginal and Torres Strait Islander biomedical and clinical sciences Applied Statistics Bioinformatics Cardiology (incl. cardiovascular diseases) Gene Expression Gene expression (incl. microarray and other genome-wide approaches) Genetics Genomics Systems Biology
-
Journals
Year Citation 2024 Lardelli, M., Baer, L., Hin, N., Allen, A., Pederson, S. M., & Barthelson, K. (2024). The Use of Zebrafish in Transcriptome Analysis of the Early Effects of Mutations Causing Early Onset Familial Alzheimer's Disease and Other Inherited Neurodegenerative Conditions. Journal of Alzheimer's Disease, 99(s2), S367-S381.
Scopus2 Europe PMC12024 Hosseinzadeh, L., Kikhtyak, Z., Laven-Law, G., Pederson, S. M., Puiu, C. G., D'Santos, C. S., . . . Hickey, T. E. (2024). The androgen receptor interacts with GATA3 to transcriptionally regulate a luminal epithelial cell phenotype in breast cancer. Genome Biol, 25(1), 44-1-44-28.
Scopus3 Europe PMC22024 Baer, L., Barthelson, K., Postlethwait, J. H., Adelson, D. L., Pederson, S. M., & Lardelli, M. (2024). Differential allelic representation (DAR) identifies candidate eQTLs and improves transcriptome analysis. PLoS Computational Biology, 20(2 February), 27 pages.
2023 Abbott, C. A., Freimayer, E. L., Tyllis, T. S., Norton, T. S., Alsharifi, M., H S Heng, A., . . . Comerford, I. (2023). Determination of Tr1 cell populations correlating with distinct activation states in acute IAV infection. Mucosal Immunology, 16(5), 606-623.
Scopus3 Europe PMC32023 Sung, J., Barratt, K. R., Pederson, S. M., Chenu, C., Reichert, I., Atkins, G. J., . . . Smitham, P. J. (2023). Unbiased gene expression analysis of the delayed fracture healing observed in Zucker diabetic fatty rats. Bone and Joint Research, 12(10), 657-666.
2023 Baer, L., Barthelson, K., Postlethwait, J., Adelson, D., Pederson, S., & Lardelli, M. (2023). Differential allelic representation (DAR) identifies candidate eQTLs and improves transcriptome analysis. bioRxiv.
2023 Wong, Y. Y., Harbison, J. E., Hope, C. M., Gundsambuu, B., Brown, K. A., Wong, S. W., . . . Barry, S. C. (2023). Parallel recovery of chromatin accessibility and gene expression dynamics from frozen human regulatory T cells. Scientific reports, 13(1), 5506-1-5506-15.
Scopus2 Europe PMC22022 Abbott, C., Freimayer, E., Tyllis, T., Norton, T., Alsharifi, M., Heng, A., . . . Comerford, I. (2022). Novel populations of Tr1 cells contribute to the resolution of acute influenza A virus infection.
2022 Bersten, D. C., Sullivan, A. E., McDougal, D., Breen, J., Fitzsimmons, R. L., Muscat, G. E. O., . . . Whitelaw, M. L. (2022). Core and Flanking bHLH-PAS:DNA interactions mediate specificity and drive obesity.
2022 Bogias, J., Pederson, S., Leemaqz, S., Smith, M., McAninch, D., Jankovic-Karasoulos, T., . . . Roberts, C. (2022). Placental transcription profiling in 6-23 weeks’ gestation reveals differential transcript usage in early development.
2022 Bogias, K. J., Pederson, S. M., Leemaqz, S., Smith, M. D., McAninch, D., Jankovic-Karasoulos, T., . . . Roberts, C. T. (2022). Placental Transcription Profiling in 6–23 Weeks’ Gestation Reveals Differential Transcript Usage in Early Development. International Journal of Molecular Sciences, 23(9), 17 pages.
Scopus2 WoS3 Europe PMC32022 Casey, A., Liu, W., Hein, L., Sargeant, T., Pederson, S., & Mäkinen, V. -P. (2022). Transcriptional targets of senataxin and E2 promoter binding factors are associated with neuro-degenerative pathways during increased autophagic flux.
2022 Liu, N., Sadlon, T., Wong, Y. Y., Pederson, S., Breen, J., & Barry, S. C. (2022). 3DFAACTS-SNP: using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of type 1 diabetes (T1D) risk. Epigenetics and Chromatin, 15(1), 1-21.
Scopus2 WoS1 Europe PMC32022 Wong, Y., Harbison, J., Hope, C., Gundsambuu, B., Brown, K., Wong, S., . . . Barry, S. (2022). Parallel recovery of chromatin accessibility and gene expression dynamics from frozen human Regulatory T cells.
2022 Casey, A. E., Liu, W., Hein, L. K., Sargeant, T. J., Pederson, S. M., & Mäkinen, V. P. (2022). Transcriptional targets of senataxin and E2 promoter binding factors are associated with neuro-degenerative pathways during increased autophagic flux. Scientific Reports, 12(1), 12 pages.
Scopus2 Europe PMC22022 Jarred, E. G., Qu, Z., Tsai, T., Oberin, R., Petautschnig, S., Bildsoe, H., . . . Western, P. S. (2022). Transient Polycomb activity represses developmental genes in growing oocytes. Clinical Epigenetics, 14(1), 183-1-183-18.
Scopus3 Europe PMC22021 Barthelson, K., Pederson, S. M., Newman, M., Jiang, H., & Lardelli, M. (2021). In-Frame and Frameshift Mutations in Zebrafish Presenilin 2 Affect Different Cellular Functions in Young Adult Brains. Journal of Alzheimer's Disease Reports, 5(1), 395-404.
Scopus7 WoS5 Europe PMC62021 Fabres, P. J., Anand, L., Sai, N., Pederson, S., Zheng, F., Stewart, A. A., . . . David, R. (2021). Tissue and regional expression patterns of dicistronic tRNA-mRNA transcripts in grapevine (Vitis vinifera) and their evolutionary co-appearance with vasculature in land plants. Horticultural Reviews, 8(1), 137-1-137-15.
Scopus3 WoS3 Europe PMC12021 Barthelson, K., Baer, L., Dong, Y., Hand, M., Pujic, Z., Newman, M., . . . Lardelli, M. (2021). Zebrafish Chromosome 14 Gene Differential Expression in the fmr1hu2787 Model of Fragile X Syndrome. Frontiers in Genetics, 12, 1-11.
Scopus3 Europe PMC42021 Liu, N., Low, W. Y., Alinejad-Rokny, H., Pederson, S., Sadlon, T., Barry, S., & Breen, J. (2021). Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C. Epigenetics & chromatin, 14(1), 1-17.
Scopus2 Europe PMC22021 Shue, B., Chiramel, A. I., Cerikan, B., To, T. -H., Frolich, S., Pederson, S. M., . . . Beard, M. R. (2021). Genome-wide CRISPR screen identifies RACK1 as a critical host factor for flavivirus replication. Journal of Virology, 95(24), e00596-21-1-e00596-21-18.
Scopus23 WoS11 Europe PMC202021 Hin, N., Newman, M., Pederson, S., & Lardelli, M. (2021). Iron responsive element-mediated responses to iron dyshomeostasis in Alzheimer's disease. Journal of Alzheimers Disease, 84(4), 1-34.
Scopus14 WoS6 Europe PMC172021 Liu, N., Sadlon, T., Wong, Y. Y., Pederson, S. M., Breen, J., & Barry, S. (2021). 3DFAACTS-SNP: Using Regulatory T Cell-specific Epigenomics Data to Uncover Candidate Mechanisms of Type-1 Diabetes (T1D) risk.
2021 Barthelson, K., Pederson, S. M., Newman, M., & Lardelli, M. (2021). Brain transcriptome analysis of a protein-truncating mutation in sortilin-related receptor 1 associated with early-onset familial alzheimer's disease indicates early effects on mitochondrial and ribosome function. Journal of Alzheimer's Disease, 79(3), 1105-1119.
Scopus7 WoS4 Europe PMC62021 Donnellan, S. C., Catalano, S. R., Pederson, S., Mitchell, K. J., Suhendran, A., Price, L. C., . . . Richards, S. J. (2021). Revision of the Litoria watjulumensis (Anura: Pelodryadidae) group from the Australian monsoonal tropics, including the resurrection of L. spaldingi. Zootaxa, 4933(2), 211-240.
Scopus5 WoS42021 Dong, Y., Newman, M., Pederson, S. M., Barthelson, K., Hin, N., & Lardelli, M. (2021). Transcriptome analyses of 7-day-old zebrafish larvae possessing a familial Alzheimer’s disease-like mutation in psen1 indicate effects on oxidative phosphorylation, ECM and MCM functions, and iron homeostasis. BMC Genomics, 22(1), 211-1-211-16.
Scopus9 WoS6 Europe PMC52021 Hin, N., Newman, M., Pederson, S., & Lardelli, M. (2021). Iron Responsive Element (IRE)-mediated responses to iron dyshomeostasis in Alzheimer's disease. Journal of Alzheimer's Disease, 84(4), 1597-1630.
2020 Jiang, H., Pederson, S. M., Newman, M., Dong, Y., & Lardelli, M. (2020). Transcriptome analysis indicates dominant effects on ribosome and mitochondrial function of a premature termination codon mutation in the zebrafish gene<i>psen2</i>.
2020 Whyte, C. E., Osman, M., Kara, E. E., Abbott, C., Foeng, J., McKenzie, D. R., . . . McColl, S. R. (2020). ACKR4 restrains antitumor immunity by regulating CCL21. Journal of Experimental Medicine, 217(6), 1-S4.
Scopus25 WoS18 Europe PMC202020 Schwensow, N., Pederson, S., Peacock, D., Cooke, B., & Cassey, P. (2020). Adaptive changes in the genomes of wild rabbits after 16 years of viral epidemics. Molecular Ecology, 29(19), 3777-3794.
Scopus4 WoS3 Europe PMC12020 Jiang, H., Pederson, S. M., Newman, M., Dong, Y., Barthelson, K., & Lardelli, M. (2020). Transcriptome analysis indicates dominant effects on ribosome and mitochondrial function of a premature termination codon mutation in the zebrafish gene psen2. PLoS One, 15(7), e0232559-1-e0232559-25.
Scopus6 WoS3 Europe PMC42020 Breen, J., McAninch, D., Jankovic-Karasoulos, T., McCullough, D., Smith, M., Bogias, K. J., . . . Roberts, C. (2020). Temporal placental genome wide expression profiles reflect three phases of utero-placental blood flow during early to mid human gestation.
2020 Brown, C. Y., Sadlon, T., Hope, C. M., Wong, Y. Y., Wong, S., Liu, N., . . . Barry, S. C. (2020). Molecular Insights Into Regulatory T-Cell Adaptation to Self, Environment, and Host Tissues: Plasticity or Loss of Function in Autoimmune Disease. Frontiers in Immunology, 11(September), 1-17.
Scopus14 WoS9 Europe PMC122020 Barthelson, K., Pederson, S. M., Newman, M., & Lardelli, M. (2020). Brain transcriptome analysis reveals subtle effects on mitochondrial function and iron homeostasis of mutations in the SORL1 gene implicated in early onset familial Alzheimer's disease.. Molecular brain, 13(1), 142.
Scopus22 WoS14 Europe PMC152020 Barthelson, K., Pederson, S., Newman, M., & Lardelli, M. (2020). Transcriptome analysis of a protein-truncating mutation in sortilin-related receptor 1 associated with early-onset familial Alzheimer’s disease indicates effects on mitochondrial and ribosome function in young-adult zebrafish brains. biorxiv.
2020 Liu, N., Sadlon, T., Wong, Y. Y., Pederson, S., Breen, J., & Barry, S. C. (2020). 3DFAACTS-SNP: Using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of Type-1 Diabetes (T1D) risk. biorxiv.
2020 Barthelson, K., Pederson, S. M., Newman, M., Jiang, H., & Lardelli, M. (2020). Frameshift and frame-preserving mutations in zebrafish presenilin 2 affect different cellular functions in young adult brains.
2020 Liu, N., Low, W. Y., Alinejad-Rokny, H., Pederson, S., Sadlon, T., Barry, S., & Breen, J. (2020). Seeing the forest through the trees: Identifying functional interactions from Hi-C. biorxiv.
2020 Barthelson, K., Pederson, S. M., Newman, M., & Lardelli, M. (2020). Brain transcriptome analysis reveals subtle effects on mitochondrial function and iron homeostasis of mutations in the SORL1 gene implicated in early onset familial Alzheimer’s disease. biorxiv.
2020 Dong, Y., Newman, M., Pederson, S., Hin, N., & Lardelli, M. (2020). Transcriptome analyses of 7-day-old zebrafish larvae possessing a familial Alzheimer’s disease-like mutation in psen1 indicate effects on oxidative phosphorylation, mcm functions, and iron homeostasis. biorxiv.
2020 Ward, C. M., To, T. -H., & Pederson, S. M. (2020). ngsReports: A Bioconductor package for managing FastQC reports and other NGS related log files.. Bioinformatics, 36(8), 2587-2588.
Scopus58 WoS41 Europe PMC362020 Singhal, G., Morgan, J., Jawahar, M. C., Corrigan, F., Jaehne, E. J., Toben, C., . . . Baune, B. T. (2020). Effects of aging on the motor, cognitive and affective behaviors, neuroimmune responses and hippocampal gene expression. Behavioural Brain Research, 383(6), 112501-1-112501-16.
Scopus21 WoS15 Europe PMC132020 Hin, N., Newman, M., Kaslin, J., Douek, A. M., Lumsden, A., Moussavi Nik, S. H., . . . Lardelli, M. (2020). Accelerated brain aging towards transcriptional inversion in a zebrafish model of the K115fs mutation of human PSEN2. PloS one, 15(1), e0227258.
Scopus22 WoS17 Europe PMC162020 Sanyal, S., Brugger, J., Etschmann, B., Pederson, S., Delport, J., Dixon, R., . . . Shuster, J. (2020). Metal resistant bacteria on gold particles: Implications of how anthropogenic contaminants could affect natural gold biogeochemical cycling. Science of the Total Environment, 727, 138698-1-138698-14.
Scopus10 WoS62020 Fabres, P. J., Anand, L., Sai, N., Pederson, S., Zheng, F., Stewart, A., . . . David, R. (2020). Tissue and regional expression patterns of dicistronic tRNA-mRNA transcripts in grapevine (<i>Vitis vinifera</i>) and their evolutionary co-appearance with vasculature in land plants.
2019 Morgan, J. A., Singhal, G., Corrigan, F., Jaehne, E. J., Jawahar, M. C., Breen, J., . . . Baune, B. T. (2019). Ceasing exercise induces depression-like, anxiety-like, and impaired cognitive-like behaviours and altered hippocampal gene expression. Brain Research Bulletin, 148, 118-130.
Scopus18 WoS17 Europe PMC112019 Wan, Q., Yiner-Lee Leemaqz, S., Pederson, S. M., McCullough, D., McAninch, D. C., Jankovic-Karasoulos, T., . . . Bianco-Miotto, T. (2019). Quality control measures for placental sample purity in DNA methylation array analyses.. Placenta, 88, 8-11.
Scopus2 WoS1 Europe PMC22019 To, T. -H., & Pederson, S. (2019). strandCheckR: An R package for quantifying and removing double strand sequences for strand-specific RNA-seq. Journal of Open Source Software, 4(34), 1145.
2019 Singhal, G., Morgan, J., Jawahar, M. C., Corrigan, F., Jaehne, E. J., Toben, C., . . . Baune, B. T. (2019). The effects of short-term and long-term environmental enrichment on locomotion, mood-like behavior, cognition and hippocampal gene expression. Behavioural Brain Research, 368, 111917-1-111917-10.
Scopus25 WoS18 Europe PMC142019 Newman, M., Hin, N., Pederson, S., & Lardelli, M. (2019). Brain transcriptome analysis of a familial Alzheimer's disease-like mutation in the zebrafish presenilin 1 gene implies effects on energy production. Molecular Brain, 12(1), 1-5.
Scopus20 WoS18 Europe PMC152019 Hope, C. M., Welch, J., Mohandas, A., Pederson, S., Hill, D., Gundsambuu, B., . . . Barry, S. C. (2019). Peptidase inhibitor 16 identifies a human regulatory T-cell subset with reduced FOXP3 expression over the first year of recent onset type 1 diabetes. European Journal of Immunology, 49(8), 1235-1250.
Scopus20 WoS14 Europe PMC172019 Singhal, G., Morgan, J., Jawahar, M. C., Corrigan, F., Jaehne, E. J., Toben, C., . . . Baune, B. T. (2019). Short-term environmental enrichment, and not physical exercise, alleviate cognitive decline and anxiety from middle age onwards without affecting hippocampal gene expression. Cognitive, Affective and Behavioral Neuroscience, 19(5), 1143-1169.
Scopus16 WoS14 Europe PMC122019 Newman, M., Hin, N., Pederson, S., & Lardelli, M. (2019). A familial Alzheimer's disease-like mutation in the zebrafish presenilin 1 gene affects brain energy production.
2018 Konaté, M., Wilkinson, M. J., Mayne, B. T., Pederson, S. M., Scott, E. S., Berger, B., & Rodriguez Lopez, C. M. (2018). Salt Stress Induces Non-CG Methylation in Coding Regions of Barley Seedlings (Hordeum vulgare). Epigenomes, 2(2), 12.
2018 Ward, C., To, H., & Pederson, S. (2018). ngsReports: An R Package for managing FastQC reports and other NGS related log files.
2018 Sadlon, T., Brown, C. Y., Bandara, V., Hope, C. M., Schjenken, J. E., Pederson, S. M., . . . Barry, S. C. (2018). Unravelling the molecular basis for regulatory T-cell plasticity and loss of function in disease. Clinical and Translational Immunology, 7(2), e1011-1-e1011-15.
Scopus25 WoS16 Europe PMC152018 Delacroix, S., Chokka, R. G., Nelson, A. J., Wong, D. T., Pederson, S., Nimmo, J., . . . Worthley, S. G. (2018). Effects of renal sympathetic denervation on myocardial structure, function and perfusion: A serial CMR study. Atherosclerosis, 272, 207-215.
Scopus4 WoS5 Europe PMC22018 Yang, D., Wijenayaka, A., Solomon, L., Pederson, S., Findlay, D., Kidd, S., & Atkins, G. (2018). Novel insights into Staphylococcus aureus deep bone infections: the involvement of osteocytes. mBio, 9(2), e00415-18-1-e00415-18-10.
Scopus124 WoS92 Europe PMC762018 Zeng, L., Pederson, S., Cao, D., Qu, Z., Hu, Z., Adelson, D., & Wei, C. (2018). Genome-Wide Analysis of the Association of Transposable Elements with Gene Regulation Suggests that Alu Elements Have the Largest Overall Regulatory Impact. Journal of Computational Biology, 25(6), 1-12.
Scopus12 WoS10 Europe PMC82018 Hin, N., Newman, M., Kaslin, J., Douek, A. M., Lumsden, A., Zhou, X., . . . Lardelli, M. (2018). Accelerated brain aging towards transcriptional inversion in a zebrafish model of familial Alzheimer's disease. BioRxiv, OnlinePubl.
2018 Homan, C., Pederson, S., To, T. -H., Tan, C., Piltz, S., Corbett, M., . . . Gecz, J. (2018). PCDH19 regulation of neural progenitor cell differentiation suggests asynchrony of neurogenesis as a mechanism contributing to PCDH19 Girls Clustering Epilepsy. Neurobiology of Disease, 116, 106-119.
Scopus43 WoS28 Europe PMC272018 Maung, K. Z. Y., Leo, P. J., Bassal, M., Casolari, D. A., Gray, J. X., Bray, S. C., . . . Gonda, T. J. (2018). Rare variants in Fanconi anemia genes are enriched in acute myeloid leukemia. Blood Cancer Journal, 8(6), 50-1-50-5.
Scopus15 WoS14 Europe PMC112018 Brown, C. Y., Dayan, S., Wong, S. W., Kaczmarek, A. K., Hope, C. M., Pederson, S. M., . . . Barry, S. C. (2018). FOXP3 and miR-155 cooperate to control the invasive potential of human breast cancer cells by down regulating ZEB2 independently of ZEB1. Oncotarget, 9(45), 27708-27727.
Scopus19 Europe PMC152018 Zeng, L., Pederson, S., Kortschak, R., & Adelson, D. (2018). Transposable elements and gene expression during the evolution of amniotes. Mobile DNA, 9(1), 17-1-17-9.
Scopus14 WoS15 Europe PMC92018 Konate, M., Wilkinson, M., Mayne, B., Pederson, S., Scott, E., Berger, B., & Rodriguez Lopez, C. (2018). Salt Stress Induces Non-CG Methylation in Coding Regions of Barley Seedlings (Hordeum vulgare). Epigenomes, 2(2), 12.
Scopus21 WoS162018 Tikhomirova, A., Trappetti, C., Standish, A., Zhou, Y., Breen, J., Pederson, S., . . . Kidd, S. (2018). Specific growth conditions induce a Streptococcus pneumoniae non-mucoidal, small colony variant and determine the outcome of its co-culture with Haemophilus influenzae. Pathogens and disease, 76(7), 11 pages.
Scopus8 WoS7 Europe PMC52018 Zeng, L., Pederson, S., Kortschak, D., & Adelson, D. (2018). Transposable elements and gene expression during the evolution of amniotes.
2017 Delacroix, S., Chokka, R., Nelson, A. J., Wong, D. T., Sidharta, S., Pederson, S. M., . . . Worthley, S. G. (2017). Renal sympathetic denervation increases renal blood volume per cardiac cycle: A serial magnetic resonance imaging study in resistant hypertension. International Journal of Nephrology and Renovascular Disease, 10, 243-249.
Scopus3 WoS2 Europe PMC32017 Wilson, R., Leemaqz, S., Goh, Z., McAninch, D., Jankovic-Karasoulos, T., Leghi, G., . . . Roberts, C. (2017). Zinc is a critical regulator of placental morphogenesis and maternal hemodynamics during pregnancy in mice. Scientific Reports, 7(1), 15137-1-15137-14.
Scopus33 WoS22 Europe PMC182017 Schwensow, N. I., Detering, H., Pederson, S., Mazzoni, C., Sinclair, R., Peacock, D., . . . Sommer, S. (2017). Resistance to RHD virus in wild Australian rabbits: Comparison of susceptible and resistant individuals using a genomewide approach. Molecular Ecology, 26(17), 4551-4561.
Scopus13 WoS12 Europe PMC62012 Hill, D., Eastaff-Leung, N., Bresatz-Atkins, S., Warner, N., Ruitenberg, J., Krumbiegel, D., . . . Barry, S. (2012). Inhibition of activation induced CD154 on CD4⁺ CD25⁻ cells: a valid surrogate for human Treg suppressor function. Immunology and Cell Biology, 90(8), 812-821.
Scopus13 WoS10 Europe PMC102012 McInnes, N., Sadlon, T., Brown, C., Pederson, S., Beyer, M., Schultze, J., . . . Barry, S. (2012). FOXP3 and FOXP3-regulated microRNAs suppress SATB1 in breast cancer cells. Oncogene, 31(8), 1045-1054.
Scopus91 WoS82 Europe PMC672010 Sadlon, T., Wilkinson, B., Pederson, S., Brown, C., Bresatz, S., Gargett, T., . . . Barry, S. (2010). Genome-wide identification of human FOXP3 target genes in natural regulatory T cells. Journal of Immunology, 185(2), 1071-1081.
Scopus118 WoS109 Europe PMC91- Liu, W., Mäkinen, V. -P., Tilley, W. D., & Pederson, S. M. (n.d.). sSNAPPY: an R/Bioconductor package for single-sample directional pathway perturbation analysis. F1000Research, 13, 628.
-
Conference Items
Year Citation 2023 Pederson, S. (2023). extraChIPs: Detection and Visualisation of Differential ChIP Signal. Poster session presented at the meeting of BIoc2023. Boston, USA. 2020 Breen, J., Smith, M., McAninch, D., Jankovic-Karasoulos, T., McCullough, D., Pederson, S. M., . . . Roberts, C. (2020). Defining Co-expression Patterns and Molecular Pathways of the Placenta During Early Pregnancy.. Poster session presented at the meeting of REPRODUCTIVE SCIENCES. Vancouver, CANADA: SPRINGER HEIDELBERG. 2020 Wan, Q., Breen, J., Leemaqz, S. Y. -L., Pederson, S. M., Jankovic-Karasoulos, T., McAninch, D. C., . . . Bianco-Miotto, T. (2020). Characterisation of Placental DNA Methylation Across Early Human Gestation.. Poster session presented at the meeting of REPRODUCTIVE SCIENCES. Vancouver, CANADA: SPRINGER HEIDELBERG. 2020 Rehn, J. A., Breen, J., Heatley, S. L., McClure, B. J., Eadie, L. N., Schutz, C. E., . . . White, D. L. (2020). Pseudo-alignment technique for accurate detection of disease-causing variants in acute lymphoblastic leukaemia. Poster session presented at the meeting of Australian Bioinformatics and Computational Biology Society (ABACBS) 2020 National Conference. Canberra, ACT. -
Theses
Year Citation 2018 Pederson, S. M. (2018). BMEA: Bayesian Modelling for Exon Array Data. (PhD Thesis, University of Adelaide). -
Internet Publications
Year Citation 2017 Zeng, L., Pederson, S., Cao, D., Qu, Z., Hu, Z., Adelson, D., & Wei, C. (2017). Genome-wide analysis of the association of transposable elements with gene regulation suggests that<i>Alu</i>elements have the largest overall regulatory impact.
DOI2017 Perry, K. D., Pederson, S. M., & Baxter, S. W. (2017). Genome-wide SNP discovery in field and laboratory colonies of Australian<i>Plutella</i>species.
DOI Europe PMC1 -
Software
Year Citation 2024 Pederson, S. (2024). motifTestR: Perform key tests for binding motifs in sequence data [Computer Software]. Bioconductor.
DOI2024 Pederson, S. (2024). transmogR: Modify a set of reference sequences using a set of variants [Computer Software]. Bioconductor.
DOI2023 Pederson, S. (2023). prepareChIPs (Version 0.1.0) [Computer Software]. Workflow Hub.
DOI2019 Ward, C., To, T. -H., & Pederson, S. M. (2019). ngsReports (Version 1.0.1) [Computer Software]. Bioconductor.
DOI2018 Pederson, S. M., & To, T. -H. (2018). strandCheckR (Version 1.1.2) [Computer Software]. Bioconductor.
DOI2018 Pederson, S. M., & To, T. -H. (2018). strandCheckR (Version 1.1.2) [Computer Software]. Bioconductor.
DOI2017 Sai, N., Rodriguez Lopez, C. M., Bogias, K., Pederson, S., Burgess, A., Breen, J., . . . David, R. (2017). Bioinformatic pipeline to detect di-cistronic RNA transcripts from RNA-sequencing data [Computer Software]. - Pederson, S. (n.d.). BSgenome.Drerio.UCSC.danRer11_0.99.0.tar.gz [Computer Software].
DOI -
Preprint
Year Citation 2022 Jarred, E., Qu, Z., Tsai, T., Oberin, R., Petautschnig, S., Bildsoe, H., . . . Western, P. (2022). Transient Polycomb activity represses developmental genes in growing oocytes.
DOI
| 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 2024 Co-Supervisor Understanding Pathogenic CD4+ T Cell Recruitment to the Inflamed Nervous System Doctor of Philosophy Doctorate 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 Nora 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 Principal Supervisor scRNA Analysis of Tumour Samples The University of Adelaide Master of Biotechnology (Biomedical Science) Master Full Time Junwei Wang 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 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
-
Board Memberships
Date Role Board name Institution name Country 2023 - ongoing Board Member Community Advisory Board Bioconductor United States -
Committee Memberships
Date Role Committee Institution Country 2017 - ongoing Member ABACBS Conference Committee - Australia 2016 - 2016 Member BioinfoSummer 2016 Organising Committee University of Adelaide Australia 2016 - ongoing Member BiocAsia Organising Group - - -
Memberships
Date Role Membership Country 2018 - ongoing Member University of Adelaide Australia 2017 - ongoing Member Australian Bioinformatics And Computational Biology Society (ABACBS) Australia
Connect With Me
External Profiles
