Ning Liu

Research Interests

Cancer Biology and Clinical Oncology Bioinformatics and computational biology Bioinformatics Software Epigenetics (incl. genome methylation and epigenomics) Genomics and transcriptomics Spatial statistics Machine learning Bioinformatics

Dr Ning Liu

Grant-Funded Researcher (B)

School of Pharmacy and Biomedical Sciences

College of Health

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

 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 packageThe 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 packageThe 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.

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 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

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)

Year Citation
2024 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), 64.
DOI Scopus10 WoS9 Europe PMC15
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, 105016-1-105016-4.
DOI Scopus5 WoS5 Europe PMC5
2024 Huang, W., O'Hara, S. E., Xie, C., Liu, N., Rayner, C. K., Nicholas, L. M., & Wu, T. (2024). Effects of a bitter substance, denatonium benzoate, on pancreatic hormone secretion. American Journal of Physiology: Endocrinology and Metabolism, 326(4), E537-E544.
DOI Scopus4 WoS4 Europe PMC3
2024 Bhuva, D. D., Tan, C. W., Salim, A., Marceaux, C., Pickering, M. A., Chen, J., . . . Davis, M. J. (2024). Library size confounds biology in spatial transcriptomics data. Genome Biology, 25(1), 99-1-99-10.
DOI Scopus17 WoS19 Europe PMC40
2024 Sadeghirad, H., Monkman, J., Tan, C. W., Liu, N., Yunis, J., Donovan, M. L., . . . Kulasinghe, A. (2024). Spatial dynamics of tertiary lymphoid aggregates in head and neck cancer: insights into immunotherapy response. Journal of Translational Medicine, 22(1), 13 pages.
DOI Scopus18 WoS20 Europe PMC21
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.
DOI Scopus1 WoS1 Europe PMC1
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), 5506-1-5506-15.
DOI Scopus8 WoS8 Europe PMC11
2023 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.
DOI Scopus27 WoS24 Europe PMC25
2023 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 Res, 51(W1), W593-W600.
DOI Scopus3 WoS3 Europe PMC3
2023 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.
DOI Scopus52 WoS47 Europe PMC60
2023 Liu, N., Bhuva, D. D., Mohamed, A., Bokelund, M., Kulasinghe, A., Tan, C. W., & Davis, M. J. (2023). standR: spatial transcriptomic analysis for GeoMx DSP data. Nucleic Acids Research, 52(1), e2-1-e2-11.
DOI Scopus32 WoS34 Europe PMC38
2023 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.
DOI Scopus22 WoS21 Europe PMC24
2022 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.
DOI
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.
DOI Scopus4 WoS3 Europe PMC4
2021 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.
DOI Scopus8 WoS9 Europe PMC11
2021 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.
DOI
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.
DOI Scopus15 WoS16 Europe PMC14
2020 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.
DOI Europe PMC1
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.
DOI Scopus2 WoS2 Europe PMC3

Year Citation
2025 Li, M., Liu, N., Nguyen, Q. H., & Chen, Y. (2025). Preserving tissue structure through density-based spatial analysis with scider.
DOI
2024 Liu, N., Martin, J., Bhuva, D., Chen, J., Li, M., Lee, S., . . . Davis, M. (2024). hoodscanR: profiling single-cell neighborhoods in spatial transcriptomics data.
DOI Europe PMC2
2023 Bhuva, D., Tan, C. W., Marceaux, C., Chen, J., Kharbanda, M., Jin, X., . . . Davis, M. (2023). Library size confounds biology in spatial transcriptomics data.
DOI Europe PMC3

Grant

Funding Organization

Chief Investigators

Status

Amount

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

Australian Bioinformatics and Computational Biology Society (ABACBS) – Best poster talk

ABACBS

Ning Liu

2019

$ 500

ABACBS travel grant

Illumina, Inc.

Ning Liu

2019

$ 500

ABACBS travel grant

ABACBS

Ning Liu

2018

$ 500

EMBL Australia PhD Course

EMBL Australia

Ning Liu

2018

$ 5000

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.

Date Role Research Topic Program Degree Type Student Load Student Name
2024 Co-Supervisor Somatic cell reprogramming of fibroblasts from different mammals to model early development. Doctor of Philosophy Doctorate Full Time Miss Elly Deidre Walters
2024 Co-Supervisor Somatic cell reprogramming of fibroblasts from different mammals to model early development. Doctor of Philosophy Doctorate Full Time Miss Elly Deidre Walters

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

Date Role Membership Country
2017 - ongoing Member Australian Bioinformatics & Computational Biology Society (ABACBS) Australia

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