The Genome Innovation Hub continually develops a number of protocols and procedures while undertaking our collaborative projects. Below are a selection of detailed developments useful to researchers undertaking Single-cell and Short read sequencing procedures in the laboratory.

Developments

Featured projects Duration
Ribosomal profiling with cellular specificity
Genome Innovation Hub Collaborative Project (UQ infrastructure)
2023
High-throughput sequencing of protein variant libraries
Genome Innovation Hub Collaborative Project (UQ infrastructure)
2023
Proximity ligation sequencing of mixed bacterial communities
Genome Innovation Hub Collaborative Project (UQ infrastructure)
2023
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
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
Understanding host-pathogen interactions through development of new co-transcriptomic single cell RNA sequencing technologies
Genome Innovation Hub Collaborative Project (UQ infrastructure)
2020

Pages

 

Publications & pre-prints

Global Analysis of Transcription Start Sites and Enhancers in Endometrial Stromal Cells and Differences Associated with Endometriosis

Sushma Marla, Sally Mortlock, Sohye Yoon, Joanna Crawford, Stacey Andersen, Michael D. Mueller, Brett McKinnon, Quan Nguyen, Grant W. Montgomery

Cells, Volume 12, Issue 13 (2023); https://doi.org/10.3390/cells12131736

 

Genotype-free demultiplexing of pooled single-cell RNA-seq

Jun Xu, Caitlin Falconer, Quan Nguyen, Joanna Crawford, Brett D. McKinnon, Sally Mortlock, Anne Senabouth, Stacey Andersen, Han Sheng Chiu, Longda Jiang, Nathan J. Palpant, Jian Yang, Michael D. Mueller, Alex W. Hewitt, Alice Pébay, Grant W. Montgomery, Joseph E. Powell & Lachlan J.M Coin

Genome Biology volume 20, Article number: 290 (2019)

 

A Deep Learning Model for Molecular Label Transfer that Enables Cancer Cell Identification from Histopathology Images

Andrew Su, HoJoon Lee, Xiao Tan, Carlos J. Suarez, Noemi Andor, Quan Nguyen, Hanlee P. Ji

bioRxiv 2021.03.18.436004; doi: https://doi.org/10.1101/2021.03.18.436004

 

Spatially resolved transcriptome profiles of mammalian kidneys illustrate the molecular complexity of functional nephron segments, cell-to-cell interactions and genetic variants

Arti M. Raghubar, Duy T. Pham, Xiao Tan, Laura F. Grice, Joanna Crawford, Pui Yeng Lam, Stacey B. AndersenSohye Yoon, Monica S.Y. Ng, Siok Min Teoh, Samuel E. Holland, Anne Stewart, Leo Francis, Alexander N. Combes, Andrew J. Kassianos, Helen Healy, Quan Nguyen, Andrew J. Mallett

bioRxiv 2020.09.29.317917; doi: https://doi.org/10.1101/2020.09.29.317917

 

Spatial analysis of ligand-receptor interactions in skin cancer at genome-wide and single-cell resolution.

M Tran, S Yoon, M Teoh, S Andersen, PY Lam, P Purdue, A Raghubar, SJ Hanson, K Devitt, K Jones, S Walters, ZK Tuong, A Kulasinghe, J Monkman, HP Soyer, I Frazer, Q Nguyen. 

https://doi.org/10.1101/2020.09.10.290833

 

stLearn: integrating spatial location, tissue morphology and gene expression to find cell types, cell-cell interactions and spatial trajectories within undissociated tissues

Duy Pham, Xiao Tan, Jun Xu, Laura F. Grice, Pui Yeng Lam, Arti Raghubar, Jana Vukovic, Marc J. Ruitenberg, Quan Nguyen
bioRxiv 2020.05.31.125658; doi: https://doi.org/10.1101/2020.05.31.125658

 

SpaCell: integrating tissue morphology and spatial gene expression to predict disease cells.

Xiao Tan, Andrew Su, Minh Tran, Quan Nguyen
Bioinformatics, Volume 36, Issue 7, 1 April 2020, Pages 2293–2294

  • Adam

    Dr Adam Hagg

    Research Officer
    School of Biomedical Sciences, Faculty of Medicine
  • Stacey Andersen

    Stacey Andersen

    Operations Manager
    Genome Innovation Hub
  • Dr Tim Bruxner

    Dr Tim Bruxner

    Sequencing Specialist
    Institute for Molecular Bioscience
  • Joanna Crawford

    Joanna Crawford

    Senior Research Assistant
    Institute for Molecular Bioscience
  • Dr Elizabeth Dun

    Dr Elizabeth Dun

    UQ Amplify Associate Lecturer
    School of Biological Sciences, Faculty of Science
  • Dr Emily Goodall

    Dr Emily Goodall

    Research Officer
    Institute for Molecular Bioscience
  • Professor Ian Henderson

    Professor Ian Henderson

    Director
    Institute for Molecular Bioscience
    Affiliate Professor
    UQ Centre for Clinical Research, Faculty of Medicine
    Affiliate Professor
    School of Chemistry and Molecular Biosciences, Faculty of Science
  • Jazmine Lee Humphreys

    PhD candidate
    School of Biological Sciences, Faculty of Science
  • Dr Ronan Kapetanovic

    Dr Ronan Kapetanovic

    Research Fellow
    Friedrich Miescher Institute for Biomedical Research, Basel Switzerland
  • Dr Denuja Karunakaran

    Dr Denuja Karunakaran

    IMB Fellow
    Institute for Molecular Bioscience
  • Professor Grant Montgomery

    Professor Grant Montgomery

    Professorial Research Fellow - GL
    Institute for Molecular Biosciences (IMB)
    Affiliate Professorial Research Fellow
    Queensland Brain Institute (QBI)
    Affiliate Professorial Research Fellow
    Office of the Pro-Vice-Chancellor (Research Infrastructure)
    Former Director
    Genome Innovation Hub (GIH)
  • Valentine Murigneux

    Valentine Murigneux

    Computational biologist
    Genome Innovation Hub
    Bioinformatician
    QCIF Facility for Advanced Bioinformatics
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    Dr Minh-Duy Phan

    Research Fellow
    Institute for Molecular Bioscience
  • Dr Divya Ramnath

    Dr Divya Ramnath

    Research Officer
    Institute for Molecular Bioscience
  • Dr Elizabeth Ross

    Dr Elizabeth Ross

    Research Fellow
    Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation
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    Dr Rebecca San Gil

    FightMND Research Fellow
    Queensland Brain Institute
  • Professor Matt Sweet

    Professor Matt Sweet

    Professorial Research Fellow - GL
    Institute for Molecular Bioscience
    Affiliated Professor
    School of Chemistry and Molecular Biosciences
  • Dr Milos Tanurdzic

    Dr Milos Tanurdzic

    Senior Lecturer
    School of Biological Sciences, Faculty of Science
  • Jessica von Pein

    Jessica von Pein

    PhD candidate
    Institute for Molecular Bioscience
  • Dr Adam Walker

    Dr Adam Walker

    Ross Maclean Fellow
    Queensland Brain Institute
  • Shivangi Wani

    Shivangi Wani

    Research Specialist - Genomics
    Genome innovation Hub
    Senior Research Assistant
    UQ Sequencing Facility
  • Isabel Warner

    Isabel Warner

    PhD candidate
    Institute for Molecular Bioscience
  • Dr Qiongyi Zhao

    Dr Qiongyi Zhao

    Research Fellow
    Queensland Brain Institute