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 genomic-related data analysis.

Developments

Featured projects Duration
Deciphering the epitranscriptome machinery using direct native RNA sequencing
Genome Innovation Hub Collaborative Project (UQ infrastructure)
2021
Assessing DNA Replication Dynamics in Cancer
Genome Innovation Hub Collaborative Project (UQ infrastructure)
2021
RNA velocity quantification of single-cell transcriptomics
Genome Innovation Hub Collaborative Project (UQ infrastructure)
2021
Optimised bioinformatics and validation pipeline for genome-wide CRISPR screening data
Genome Innovation Hub Collaborative Project (UQ infrastructure)
2021
Developing a scalable genome browser and repository for complex multi-omic datasets.
Genome Innovation Hub Collaborative Project (UQ infrastructure)
2021
Genome-Phaser: protocol for fully phasing whole genome variants using haplotagging
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
Combining novel scSLAM-seq technology with 10x Genomics Chromium to track microchanges in newly synthesised RNA
Genome Innovation Hub Collaborative Project (UQ infrastructure)
2020
A genomic dissection of metaorganisms: molecular approaches for teasing apart the hologenome
Genome Innovation Hub Collaborative Project (UQ infrastructure)
2020
TraDIS-Vault: an interactive searchable genome browser and repository for TraDIS data
Genome Innovation Hub Collaborative Project (UQ infrastructure)
2020

Pages

Publications & pre-prints

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

 

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 

 

Comparison of long read methods for sequencing and assembly of a plant genome

Valentine Murigneux, Subash Kumar Rai, Agnelo Furtado, Timothy J.C. Bruxner, Wei Tian, Qianyu Ye, Hanmin Wei, Bicheng Yang, Ivon Harliwong, Ellis Anderson, Qing Mao, Radoje Drmanac, Ou Wang, Brock A. Peters, Mengyang Xu, Pei Wu, Bruce Topp, Lachlan J.M. Coin, Robert J. Henry

bioRxiv 2020.03.16.992933

 

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. Andersen, Sohye 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

  • Professor Scott Beatson

    Associate Professor Scott Beatson

    Associate Professor
    School of Chemistry and Molecular Biosciences, Faculty of Science
    Affiliate Associate Professor
    UQ Centre for Clinical Research, Faculty of Medicine
  • Associate Professor Mikael Boden

    Associate Professor Mikael Boden

    Associate Professor
    School of Chemistry and Molecular Biosciences, Faculty of Science
    Affiliate Research Fellow
    Institute for Molecular Bioscience
  • Dr Cheong Xin Chan

    Dr Cheong Xin Chan

    Senior Research Fellow
    School of Chemistry and Molecular Biosciences, Faculty of Science
    Affiliate Research Fellow
    Institute for Molecular Bioscience
  • Dr Adam Ewing

    Dr Adam Ewing

    Honorary Senior Fellow
    Mater Research Institute-UQ, Faculty of Medicine
  • Dr Dom Gorse

    Dr Dom Gorse

    Director, Data Scientist
    QCIF Facility for Advanced Bioinformatics
  • A/Prof Jessica Mar

    Associate Professor Jessica Mar

    ARC Future Fellow
    Australian Institute for Bioengineering and Nanotechnology (AIBN)
    Affiliate Research Fellow
    Institute for Molecular Bioscience (IMB)
  • Valentine Murigneux

    Valentine Murigneux

    Senior research assistant
    Genome Innovation Hub
    Bioinformatician
    QCIF Facility for Advanced Bioinformatics
  • Dr Quan Nguyen

    Dr Quan Nguyen

    Senior Research Fellow - Group Leader
    Institute for Molecular Bioscience
  • Professor Gene Tyson

    ARC Future Fellow
    School of Chemistry and Molecular Biosciences, Faculty of Science
    Deputy Director
    Australian Centre for Ecogenomics (ACE)
  • Jun Xu

    Jun Xu

    Research Assistant
    Genome Innovation Hub