Dr Ning Liu
Postdoctoral Research Fellow
South Australian Immunogenomics Cancer Institute
Faculty of Health and Medical Sciences
Eligible to supervise Masters and PhD (as Co-Supervisor) - email supervisor to discuss availability.
I am a trained bioinformatician/computational biologist at the University of Adelaide with experiences in epigenetics and transcriptomics, specialised in computational method development and next-generation sequencing (NGS) data analysis, including ChIP-seq, ATAC-seq, Hi-C, RNA-seq, single cell RNA-seq and spatial transcriptomics data.
I am currently a senior postdoctoral researcher in the Polo group at South Australian immunoGENomics Cancer Institute (SAiGENCI), Adelaide Medical School, and my research aims to develop computational tools and methods to assist the investigation of the human genome in the context of transcriptomics and epigenetics.
My research aims to develop novel computational tools and methods to study the human genome in the context of transcriptomics and epigenomics. Particularly, I'm currently maintaining three Bioconductor software packages: standR, hoodscanR and scider.
The standR package provides a series of functions to assist different stages of the analysis of spatial transcriptomics data generated from the GeoMX DSP platforms, a widely-used spatial transcriptomics/proteomics technology developed by the Nanostring company.
The hoodscanR package provides a novel algorithm for celluar neighborhood detection, allowing user to accurately identify neighborhoods and perform in-depth neighborhood-based analyses with spatial transcriptomics data at single-cell resolution.
The scider package offers functions to model the global density of cells in a slide of spatial transcriptomics data, allowing researches to perform statistical analyses in a density context for spatial transcriptomics data.
I'm also interested in using machine learning and deep learning models in analysing epigenetics and transcriptomics data in the context of developmental biology. In particular, cell fate prediction, gene regulatory network inference, epigenetic state prediction and etc.
I have a strong emphasis on identifying novel biological insights that can translate to medical applications including diagnostics and treatment.
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Appointments
Date Position Institution name 2023 - ongoing Senior Postdoctor Researcher University of Adelaide 2021 - 2023 Research Officer Walter and Eliza Hall Institute of Medical Research -
Language Competencies
Language Competency Chinese (Cantonese) Can read, write, speak, understand spoken and peer review Chinese (Mandarin) Can read, write, speak, understand spoken and peer review English Can read, write, speak, understand spoken and peer review -
Education
Date Institution name Country Title 2017 - 2021 University of Adelaide Australia PhD of Medicine 2015 - 2017 University of Adelaide Australia Master of Biotechnology (Biomedical) 2011 - 2015 Xiamen University China Bachelor of Biotechnology (Biostatistics) -
Research Interests
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Journals
Year Citation 2024 Liu, N., Bhuva, D. D., Mohamed, A., Bokelund, M., Kulasinghe, A., Tan, C. W., & Davis, M. J. (2024). standR: spatial transcriptomic analysis for GeoMx DSP data. Nucleic Acids Research, 52(1), 11 pages.
Scopus3 WoS1 Europe PMC12024 Bhuva, D. D., Tan, C. W., Liu, N., Whitfield, H. J., Papachristos, N., Lee, S. C., . . . Davis, M. J. (2024). vissE: a versatile tool to identify and visualise higher-order molecular phenotypes from functional enrichment analysis. BMC Bioinformatics, 25(1), 22 pages.
2024 Tan, C. W., Chen, J., Liu, N., Bhuva, D. D., Blick, T., Monkman, J., . . . Davis, M. J. (2024). In situ single-cell profiling sheds light on IFI27 localisation during SARS-CoV-2 infection. eBioMedicine, 101, 4 pages.
2023 Aldersey, J. E., Liu, N., Tearle, R., Low, W. Y., Breen, J., Williams, J. L., & Bottema, C. D. K. (2023). Topologically associating domains in the POLLED region are the same for Angus- and Brahman-specific Hi-C reads from F1 hybrid fetal tissue.. Anim Genet, 54(4), 536-543.
Scopus12023 Bhuva, D., Tan, C. W., Marceaux, C., Chen, J., Kharbanda, M., Jin, X., . . . Davis, M. (2023). Library size confounds biology in spatial transcriptomics data.
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), 15 pages.
Scopus2 Europe PMC22023 Sadeghirad, H., Liu, N., Monkman, J., Ma, N., Cheikh, B. B., Jhaveri, N., . . . Kulasinghe, A. (2023). Compartmentalized spatial profiling of the tumor microenvironment in head and neck squamous cell carcinoma identifies immune checkpoint molecules and tumor necrosis factor receptor superfamily members as biomarkers of response to immunotherapy. Frontiers in Immunology, 14, 1-16.
Scopus6 Europe PMC32023 Mohamed, A., Bhuva, D. D., Lee, S., Liu, N., Tan, C. W., & Davis, M. J. (2023). VissE.cloud: A webserver to visualise higher order molecular phenotypes from enrichment analysis. Nucleic Acids Research, 51(W1), W593-W600.
Scopus1 Europe PMC12023 Buckberry, S., Liu, X., Poppe, D., Tan, J. P., Sun, G., Chen, J., . . . Lister, R. (2023). Transient naive reprogramming corrects hiPS cells functionally and epigenetically. Nature, 620(7975), 863-872.
Scopus9 WoS5 Europe PMC102023 Kulasinghe, A., Liu, N., Tan, C. W., Monkman, J., Sinclair, J. E., Bhuva, D. D., . . . Fraser, J. F. (2023). Transcriptomic profiling of cardiac tissues from SARS-CoV-2 patients identifies DNA damage. Immunology, 168(3), 403-419.
Scopus11 WoS6 Europe PMC92022 Kulasinghe, A., Liu, N., Tan, C. W., Monkman, J., Sinclair, J., Bhuva, D., . . . Fraser, J. (2022). Transcriptomic profiling of cardiac tissues from SARS-CoV-2 patients identifies DNA damage.
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 PMC32021 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.
Scopus1 Europe PMC12021 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.
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 PMC112020 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.
2019 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 PMC2 -
Preprint
Year Citation 2024 Liu, N., Martin, J., Bhuva, D. D., Chen, J., Li, M., Lee, S. C., . . . Davis, M. J. (2024). hoodscanR: profiling single-cell neighborhoods in spatial transcriptomics data.
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Grant |
Funding Organization |
Chief Investigators |
Status |
Amount |
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MRF2031100 METASPATIAL Study: Metabolic Spatial Analysis of Lung Cancer study |
Medical Research Future Fund (MRFF) |
Dr. Arutha Kulasinghe Dr. Dharmesh D Bhuva Dr. Amelia Parker Prof. Gabrielle Belz Prof. Melissa Davis Dr. Sophie Curio Dr. Chin Wee Tan Dr. Mark Adams Dr. Ning Liu Dr. Qiutong Huang Prof. Ken O’Byrne Prof. Brett Hughes Dr. Jenny Gunter Dr. Charles Bidgood A/Prof. Haitham Tuffaha |
2024-2028 |
$ 1,999,650 |
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Australian Bioinformatics and Computational Biology Society (ABACBS) – Best poster talk |
ABACBS |
Ning Liu |
2019 |
$ 500 |
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ABACBS travel grant |
Illumina, Inc. |
Ning Liu |
2019 |
$ 500 |
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ABACBS travel grant |
ABACBS |
Ning Liu |
2018 |
$ 500 |
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EMBL Australia PhD Course |
EMBL Australia |
Ning Liu |
2018 |
$ 5000 |
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Adelaide Graduate Research Scholarship |
The University of Adelaide |
Ning Liu |
2017-2021 |
$ 150,000 fee waiver + 24,000 stipend p.a. |
- Course designer and lecturer of undergraduate course Science Process and Practice in 2024, Haide College, Ocean University of China and the University of Adelaide.
- Course workshop designer and instructor of postgraduate course Genomics Applications (BIOINF 7150) in 2020, University of Adelaide.
- Workshop tutor of postgraduate course Bioinformatics and Systems Modelling (BIOTECH 7005) in 2018, University of Adelaide.
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Committee Memberships
Date Role Committee Institution Country 2018 - 2019 Member COMBINE Executive Committee Australian Bioinformatics & Computational Biology Society (ABACBS) Australia 2018 - 2018 Member COMBINE Conference Committee Australian Bioinformatics & Computational Biology Society (ABACBS) Australia 2017 - 2017 Member COMBINE Conference Committee Australian Bioinformatics & Computational Biology Society (ABACBS) Australia -
Memberships
Date Role Membership Country 2017 - ongoing Member Australian Bioinformatics & Computational Biology Society (ABACBS) Australia
Connect With Me
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