Genome Innovation Hub

Jun Xu

Computational biologist
Former GIH staff
Jun Xu

Expertise

  • Single cell muli-omics analysis
  • Machine learning applications in genomics
  • Development of biological software tools

Researcher biography

Jon has been working in data analysis for over 15 years. He has experience with a broad range of data analysis and data mining tools such as SAP BI, Oracle BIEE, and SAS.  He is proficient in a variety of different programming languages and has worked on numerous operating systems. Jon worked as a software project manager in industry before he obtained a Master of Bioinformatics from UQ. After that, Jon has been focussing on analysing single cell multi-omics datasets, and has developed a novel bioinformatics tool to demultiplex mixed single cell datasets purely based on the difference in genotypes, using machine learning technology. His main interest lies in using different machine learning models to analyse genomics and epigenomics datasets to uncover biological meaning.

As one of the first members of GIH, Jon has collaborated with multiple groups from IMB, QBI, AIBN, QAAFI and School of Biological Sciences.

Featured projects Duration
Single-cell transcriptome and chromatin profiling in plant cells
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2020
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
RNA velocity quantification of single-cell transcriptomics
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2021
Expanding the scope of multimodal single cell sequencing
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2021
HTS single cell CRISPR technology for experimental validation of population genetics and functional genomics discovery
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2021
Developing new "spatial omics" capabilities
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
Enrichment and analysis of siRNAs for topical RNAi applications.
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2022
Genome-wide CRISPR screening for modifiers of diverse cellular phenotypes
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2019
Spatial genomics technologies to study cancer and genetic diseases in tissue contexts
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

Publications

Journal Articles (5)

Journal Articles

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
Gunter, Helen M., Idrisoglu, Senel, Singh, Swati, Han, Dae Jong, Ariens, Emily, Peters, Jonathan R., Wong, Ted, Cheetham, Seth W., Xu, Jun, Rai, Subash Kumar, Feldman, Robert, Herbert, Andy, Marcellin, Esteban, Tropee, Romain, Munro, Trent and Mercer, Tim R. (2023). mRNA vaccine quality analysis using RNA sequencing. Nature Communications, 14 (1) 5663, 1-12. doi: 10.1038/s41467-023-41354-y
Shim, Woo Jun, Sinniah, Enakshi, Xu, Jun, Vitrinel, Burcu, Alexanian, Michael, Andreoletti, Gaia, Shen, Sophie, Sun, Yuliangzi, Balderson, Brad, Boix, Carles, Peng, Guangdun, Jing, Naihe, Wang, Yuliang, Kellis, Manolis, Tam, Patrick P L, Smith, Aaron, Piper, Michael, Christiaen, Lionel, Nguyen, Quan, Bodén, Mikael and Palpant, Nathan J. (2020). Conserved epigenetic regulatory logic infers genes governing cell identity. Cell Systems, 11 (6), 625-639.e13. doi: 10.1016/j.cels.2020.11.001
Pham, Duy, Tan, Xiao, Xu, Jun, Grice, Laura F., Lam, Pui Yeng, Raghubar, Arti, Vukovic, Jana, Ruitenberg, Marc J. and Nguyen, Quan (2020). stLearn integrating spatial location, tissue morphology and gene expression to find cell types, cell-cell interactions and spatial trajectories within undissociated tissues. Biorxiv, 1-18. doi: 10.1101/2020.05.31.125658v1
Xu, Jun, Falconer, Caitlin, Nguyen, Quan, Crawford, Joanna, McKinnon, Brett D., Mortlock, Sally, Senabouth, Anne, Andersen, Stacey, Chiu, Han Sheng, Jiang, Longda, Palpant, Nathan J., Yang, Jian, Mueller, Michael D., Hewitt, Alex W., Pébay, Alice, Montgomery, Grant W., Powell, Joseph E. and Coin, Lachlan J. M. (2019). Genotype-free demultiplexing of pooled single-cell RNA-seq. Genome Biology, 20 (1) 290, 290. doi: 10.1186/s13059-019-1852-7

Areas of research

Bioinformatics
Genomics