Genome Innovation Hub

Dr Sohye Yoon

Research Specialist - Genomics
Genome innovation Hub
Dr Sohye Yoon

Expertise

  • Short read sequencing
  • Microscopic Imaging analysis
  • Spatial genomics technologies

Researcher biography

Sohye Yoon joined the Genome Innovation Hub in 2018 after 7 years at the Scottish Fish Immunology Research Centre (SFIRC) at University of Aberdeen, UK. At the SFIRC, she attained comprehensive knowledge in immunology and utilised a wide variety of methods in the areas of molecular biology, Antibody engineering and cell biology to perform the necessary assays for her PhD and 2 post-doctoral projects. In addition to a strong record of collaboration with industries/academic researchers, she also supervised master/PhD student research projects during this time.

Since coming to the GIH, she has expanded her research capabilities into the genomics area with her strong competence in molecular biology. Sohye contributed to the development several SOPs and protocols and published literature in peer-revied journals. Her research interests also include spatial multi-omics technologies and long-read sequencing.

Featured projects Duration
Combining novel scSLAM-seq technology with 10x Genomics Chromium to track microchanges in newly synthesised RNA
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2020
Simultaneous identification of RNA-chromatin interactions and transcriptomes in single cells
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2020
Optimised bioinformatics and validation pipeline for genome-wide CRISPR screening data
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2021
Developing new "spatial omics" capabilities
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2021
Enabling population scale epigenomics for crop improvement
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2021
Using nanopore sequencing to test mRNA vaccine quality.
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2022
Division-based single-cell-sequencing
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2022
Adaptive sequencing for metagenomic sequencing of low biomass samples
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2022
Improving CRISPR workflows in plants
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2023
Nanopore sequencing of DNA from extracellular vesicles
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2023
Ribosomal profiling with cellular specificity
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2023
Quantitative transcriptome analysis (CAGE)
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2019
Proximity ligation sequencing of mixed bacterial communities
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2023
Spatial genomics technologies to study cancer and genetic diseases in tissue contexts
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2019
Automated single cell quantitative in situ gene expression in cells and tissues (AutoMerFISH)
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2019
Understanding host-pathogen interactions through development of new co-transcriptomic single cell RNA sequencing technologies
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2020
Single-cell transcriptome and chromatin profiling in plant cells
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2020

Publications

Journal Articles (12)
Conference Papers (10)
Thesis (1)

Journal Articles

Friedman, Clayton E., Cheetham, Seth W., Negi, Sumedha, Mills, Richard J., Ogawa, Masahito, Redd, Meredith A., Chiu, Han Sheng, Shen, Sophie, Sun, Yuliangzi, Mizikovsky, Dalia, Bouveret, Romaric, Chen, Xiaoli, Voges, Holly K., Paterson, Scott, De Angelis, Jessica E., Andersen, Stacey B., Cao, Yuanzhao, Wu, Yang, Jafrani, Yohaann M.A., Yoon, Sohye, Faulkner, Geoffrey J., Smith, Kelly A., Porrello, Enzo, Harvey, Richard P., Hogan, Benjamin M., Nguyen, Quan, Zeng, Jian, Kikuchi, Kazu, Hudson, James E. and Palpant, Nathan J. (2023). HOPX-associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and function. Developmental Cell, 59 (1), 91-107.e1. doi: 10.1016/j.devcel.2023.11.012
Pham, Duy, Tan, Xiao, Balderson, Brad, Xu, Jun, Grice, Laura F., Yoon, Sohye, Willis, Emily F., Tran, Minh, Lam, Pui Yeng, Raghubar, Arti, Kalita-de Croft, Priyakshi, Lakhani, Sunil, Vukovic, Jana, Ruitenberg, Marc J. and Nguyen, Quan H. (2023). Robust mapping of spatiotemporal trajectories and cell–cell interactions in healthy and diseased tissues. Nature Communications, 14 (1) 7739, 1-25. doi: 10.1038/s41467-023-43120-6
Marla, Sushma, Mortlock, Sally, Yoon, Sohye, Crawford, Joanna, Andersen, Stacey, Mueller, Michael D., McKinnon, Brett, Nguyen, Quan and Montgomery, Grant W. (2023). Global analysis of transcription start sites and enhancers in endometrial stromal cells and differences associated with endometriosis. Cells, 12 (13) 1736, 1-22. doi: 10.3390/cells12131736
Tran, M., Yoon, S., Teoh, M., Andersen, S., Lam, PY., Purdue, B. W., Raghubar, A., Hanson, S.J., Devitt, K., Jones, K., Walters, S., Monkman, J., Kulasinghe, A., Tuong, Z.K., Soyer, H.P., Frazer, I. H. and Nguyen, Q. (2022). A robust experimental and computational analysis framework at multiple resolutions, modalities and coverages. Frontiers in Immunology, 13 911873, 911873. doi: 10.3389/fimmu.2022.911873
Raghubar, Arti M., Pham, Duy T., Tan, Xiao, Grice, Laura F., Crawford, Joanna, Lam, Pui Yeng, Andersen, Stacey B., Yoon, Sohye, Teoh, Siok Min, Matigian, Nicholas A., Stewart, Anne, Francis, Leo, Ng, Monica S. Y., Healy, Helen G., Combes, Alexander N., Kassianos, Andrew J., Nguyen, Quan and Mallett, Andrew J. (2022). Spatially resolved transcriptomes of mammalian kidneys illustrate the molecular complexity and interactions of functional nephron segments. Frontiers in Medicine, 9 873923, 873923. doi: 10.3389/fmed.2022.873923
Attaya, Ahmed, Veenstra, Kimberly, Welsh, Michael D., Ahmed, Mukhtar, Torabi-Pour, Nessim, Saffie-Siebert, Suzanne, Yoon, Sohye and Secombes, Christopher J. (2021). In vitro evaluation of novel (nanoparticle) oral delivery systems allow selection of gut immunomodulatory formulations. Fish and Shellfish Immunology, 113, 125-138. doi: 10.1016/j.fsi.2021.03.007
Faber, Marc, Shaw, Sophie, Yoon, Sohye, de Paiva Alves, Eduardo, Wang, Bei, Qi, Zhitao, Okamura, Beth, Hartikainen, Hanna, Secombes, Christopher J. and Holland, Jason W. (2021). Comparative transcriptomics and host-specific parasite gene expression profiles inform on drivers of proliferative kidney disease. Scientific Reports, 11 (1) 2149, 2149. doi: 10.1038/s41598-020-77881-7
Attaya, A., Wang, T., Zou, J., Herath, T., Adams, A., Secombes, C. J. and Yoon, S. (2018). Gene expression analysis of isolated salmonid GALT leucocytes in response to PAMPs and recombinant cytokines. Fish and Shellfish Immunology, 80, 426-436. doi: 10.1016/j.fsi.2018.06.022
Wang, Jun, Liu, Min, Wu, Yang, Yoon, Sohye, Alnabulsi, Abdo, Liu, Fuguo, Fernandez-Alvarez, Clara, Wang, Tiehui, Holland, Jason W., Secombes, Chris J. and Zou, Jun (2018). Immune-modulation of two BATF3 paralogues in rainbow trout Oncorhynchus mykiss. Molecular Immunology, 99, 104-114. doi: 10.1016/j.molimm.2018.04.016
Yoon, Sohye, Alnabulsi, Ayham, Wang, Ting Yu, Lee, Po Tsang, Chen, Tzong-Yueh, Bird, Steve, Zou, Jun and Secombes, Christopher J. (2016). Analysis of interferon gamma protein expression in zebrafish (Danio rerio). Fish and Shellfish Immunology, 57, 79-86. doi: 10.1016/j.fsi.2016.08.023
Yoon, Sohye, Mitra, Suman, Wyse, Cathy, Alnabulsi, Ayham, Zou, Jun, Weerdenburg, Eveline M., van der Sar, Astrid M., Wang, Difei, Secombes, Christopher J. and Bird, Steve (2015). First demonstration of antigen induced cytokine expression by CD4-1(+) lymphocytes in a poikilotherm: studies in zebrafish (Danio rerio). Plos One, 10 (6). doi: 10.1371/journal.pone.0126378
Kim, Young-Hwa, Jun, Lyu Jin, Park, Shin-Hoo, Yoon, So Hye, Chung, Joon Ki, Kim, Jae Cherl and Do Jeong, Hyun (2007). Prevalence of tet(B) and tet(M) genes among tetracycline-resistant Vibrio spp. in the aquatic environments of Korea. Diseases of Aquatic Organisms, 75 (3), 209-216. doi: 10.3354/dao075209

Conference Papers

Raghubar, Arti M., Pham, Duy T., Tan, Xiao, Grice, Laura F., Lam, Pui Yeng, Crawford, Joanna, Andersen, Stacey, Yoon, Sohye, Holland, Samuel E., Francis, Leo, Combes, Alexander N., Kassianos, Andrew J., Healy, Helen G., Nguyen, Quan and Mallett, Andrew J. (2020). Spatial Transcriptomics (ST): Integrating Molecular Profiles with Histomorphology in Kidney Tissue Sections. Kidney Week, Online, 19-25 October 2020. Washington, DC United States: American Society of Nephrology. doi: 10.1681/asn.20203110s112b
Mckillen, J., Welsh, M., Gray, D. , Savage, P. , Maxwell, K. , Mooney, M., Monaghan, S.J., Yoon, S. , Secombes, C.J., Adams, A. and Allan, G. (2019). Mucosal nanoparticle immunisation against salmon alphavirus (SAV) in Atlantic salmon (Salmo salar L.). International Conference on Diseases of Fish and Shellfish, Porto, Portugal, 9 - 12 September 2019.
Shahin, Khalid, Monaghan, Sean , Yoon, Sohye , Adams, Alexandra , Secombes, Chris and Herath, Tharangani (2019). Temporal immune responses induced following primary and booster mucosal vaccination regimes against Vibrio anguillarum in rainbow trout (Oncorhynchus mykiss). International Conference on Diseases of Fish and Shellfish, Porto, Portugal, 9 - 12 September 2019.
Attaya, Ahmed, Sohye Yoon, Veenstra, Kimberly, Welsh, Michael D., Torabi-Pour, Nessim, Ahmed, Mukhtar, Siebert, Suzanne R. Saffie and Secombes, Chris (2018). The development of novel nanoparticle based oral vaccines for use in salmonids. Congress of the International Society of Development and Comparative Immunology, Santa Fe, NM, United States, 17 -21 June 2018.
Attaya, Ahmed, Yoon, Sohye, Zou, Jun and Secombes, Chris (2017). Immune reactivity of isolated Atlantic salmon (Salmo salar) gut leucocytes to PAMPs and recombinant cytokines. International Conference on Diseases of Fish and Shellfish, Belfast, United Kingdom, 4 - 8 September 2017.
Yoon, Sohye, Attaya, Ahmed, Wang, Tiehui, Zou, Jun and Secombes, Chris (2016). Immune gene profiling of different gut regions and gut associated lymphoid cells from rainbow trout (Oncorhynchus mykiss). 2nd International Conference of Fish and Shellfish Immunology, Portland, ME, United States, 26-30 June 2016. London, United Kingdom: Academic Press. doi: 10.1016/j.fsi.2016.04.085
Yoon, Sohye, Attaya, Ahmed, Zou, Jun and Secombes, Chris (2016). Immune gene profiling of different gut regions and gut associated lymphoid cells from rainbow trout (Oncorhynchus mykiss) and immune responses following oral vaccination against Yersinia ruckeri. Aquaculture Europe, Edinburgh, United Kingdom, 20 - 23 September 2016.
Yoon, Sohye, Zhitao, Qi, Alnabulsi, Ayham, Secombes, Chris and Holland, Jason (2015). Immune characterization of novel parasite antigen biomarkers for Proliferative Kidney Disease in salmonids. International Conference on Diseases of Fish and Shellfish, Gran Canaria, Spain, 7 - 11 September 2015.
Yoon, S., Bird, S., Zou, J. and Secombes, C. J. (2013). Specific T helper cell immune response of zebrafish (Danio rerio) following immunisation and restimulation. London, United Kingdom: Academic Press. doi: 10.1016/j.fsi.2013.03.362
Yoon, S., Secombes, C. and Zou, J. (2011). Discovery and characterization of CD4(+) cells in zebrafish (Danio rerio). Annual Congress of the British-Society-for-Immunology, Liverpool England, 5-8 December 2011. Chichester, West Sussex, United Kingdom: Wiley-Blackwell.

Thesis

Yoon, Sohye (2014). Studies of adaptive immune responses in zebrafish (Danio rerio), with a focus on the role of CD4+ cells. PhD Thesis, School of Biological Sciences, University of Aberdeen.

Areas of research

Advanced Imaging
Cells
DNA
Long-read
RNA
Single-cell