publications

2026

1. Brief. Bioinform.

   Graph-based RNA structural representation reveals determinants of subcellular localization

   Y. Hao, H. Sun, Z. Ran, X. Guo, M. Liu, Y. Bi, J.M. Polo, N. Liu^‡, and F. Li^‡

   bioRxiv (accepted, Briefings in Bioinformatics), 2026

   Bib Code

   

   @article{hao2026graphrna,
     title = {Graph-based RNA structural representation reveals determinants of subcellular localization},
     author = {Hao, Y. and Sun, H. and Ran, Z. and Guo, X. and Liu, M. and Bi, Y. and Polo, J.M. and Liu, N. and Li, F.},
     journal = {bioRxiv (accepted, Briefings in Bioinformatics)},
     year = {2026},
   }

2. Nat. Methods

   cellNexus: Quality control, annotation, aggregation and analytical layers for the Human Cell Atlas data

   Mengyuan Shen^†, Yingnan Gao^†, Ning Liu^†, Dharmesh Bhuva, Michael Milton, Juan Henao, Jared Andrews, Edward Yang, Chen Zhan, Nora Liu, Susan Si, J. William Hutchison, M. Haroon Shakeel, Martin Morgan, T. Anthony Papenfuss, Julie Iskander, M. José Polo, and Stefano Mangiola

   bioRxiv (accepted, Nature Methods), 2026

   Bib

   

   @article{shu2026cellnexus,
     title = {cellNexus: Quality control, annotation, aggregation and analytical layers for the Human Cell Atlas data},
     author = {Shen, Mengyuan and Gao, Yingnan and Liu, Ning and Bhuva, Dharmesh and Milton, Michael and Henao, Juan and Andrews, Jared and Yang, Edward and Zhan, Chen and Liu, Nora and Si, Susan and Hutchison, J. William and Shakeel, M. Haroon and Morgan, Martin and Papenfuss, T. Anthony and Iskander, Julie and Polo, M. José and Mangiola, Stefano},
     journal = {bioRxiv (accepted, Nature Methods)},
     year = {2026},
   }

3. bioRxiv

   Integrative epigenomic and transcriptomic profiling reveals dysregulated T cell regulatory networks in Stage 3 Type 1 diabetes

   Y.Y. Wong, J.E. Harbison, D. Hassan, B. Gundsambuu, C.M. Hope, S.W. Wong, J.J. Couper, J.A. Gummow, J. Breen, N. Liu, and S.M. Pederson

   bioRxiv, 2026

   

2025

1. bioRxiv

   Preserving tissue structure through density-based spatial analysis with scider

   M. Li^†, N. Liu^†, Q.H. Nguyen, and Y. Chen

   bioRxiv, 2025

   Bib HTML Code

   

   @article{li2025scider,
     title = {Preserving tissue structure through density-based spatial analysis with scider},
     author = {Li, M. and Liu, N. and Nguyen, Q.H. and Chen, Y.},
     journal = {bioRxiv},
     year = {2025},
   }

2. Nat. Commun.

   DOMINO: diffusion-optimised graph learning identifies domain structures with enhanced accuracy and scalability

   P. Jia, N.W. Liu, Z. Ran, S. Maiolo, T. Zhang, M. Mohenska, X. Guo, C. Wang, E. Walter, C. Ricciardelli, N.A. Lokman, R. Morrow, M. Oehler, J.M. Polo, N. Liu^‡, and F.Y. Li^‡

   bioRxiv (under review, Nature Communications), 2025

   Bib Code

   

   @article{jia2025domino,
     title = {DOMINO: diffusion-optimised graph learning identifies domain structures with enhanced accuracy and scalability},
     author = {Jia, P. and Liu, N.W. and Ran, Z. and Maiolo, S. and Zhang, T. and Mohenska, M. and Guo, X. and Wang, C. and Walter, E. and Ricciardelli, C. and Lokman, N.A. and Morrow, R. and Oehler, M. and Polo, J.M. and Liu, N. and Li, F.Y.},
     journal = {bioRxiv (under review, Nature Communications)},
     year = {2025},
   }

3. Spatial multiomics

   Spatial multiomic profiling identifies metabolic and inflammatory signatures driving recurrence in adjuvant-treated NSCLC

   A. Kulasinghe, N. Berrell, C.W. Tan, A. Kilgallon, J. Monkman, C. Bidgood, C. Janke, M. Donovan, N. Liu, K. Embaye, and J. Yunis

   Preprint, 2025

   

2024

1. Nucleic Acids Res.

   standR: spatial transcriptomic analysis for GeoMx DSP data

   N. Liu, D.D. Bhuva, A. Mohamed, M. Bokelund, A. Kulasinghe, C.W. Tan, and M.J. Davis

   Nucleic Acids Research, 2024

   DOI Bib HTML Code

   

   @article{liu2024standr,
     title = {standR: spatial transcriptomic analysis for GeoMx DSP data},
     author = {Liu, N. and Bhuva, D.D. and Mohamed, A. and Bokelund, M. and Kulasinghe, A. and Tan, C.W. and Davis, M.J.},
     journal = {Nucleic Acids Research},
     volume = {52},
     number = {1},
     pages = {e2--e2},
     year = {2024},
     doi = {10.1093/nar/gkad1026},
   }

2. Bioinformatics

   hoodscanR: profiling single-cell neighborhoods in spatial transcriptomics data

   N. Liu, J. Martin, D.D. Bhuva, J. Chen, M. Li, S.C. Lee, M. Kharbanda, J. Cheng, A. Mohamed, A. Kulasinghe, and Y. Chen

   bioRxiv (under review, Bioinformatics), 2024

   Bib HTML Code

   

   @article{liu2024hoodscanr,
     title = {hoodscanR: profiling single-cell neighborhoods in spatial transcriptomics data},
     author = {Liu, N. and Martin, J. and Bhuva, D.D. and Chen, J. and Li, M. and Lee, S.C. and Kharbanda, M. and Cheng, J. and Mohamed, A. and Kulasinghe, A. and Chen, Y.},
     journal = {bioRxiv (under review, Bioinformatics)},
     year = {2024},
   }

3. J. Transl. Med.

   Spatial dynamics of tertiary lymphoid aggregates in head and neck cancer: insights into immunotherapy response

   H. Sadeghirad, J. Monkman, C.W. Tan, N. Liu, J. Yunis, M.L. Donovan, A. Moradi, N. Jhaveri, C. Perry, M.N. Adams, and K. O’Byrne

   Journal of Translational Medicine, 2024

   
4. Genome Biol.

   Library size confounds biology in spatial transcriptomics data

   D.D. Bhuva, C.W. Tan, A. Salim, C. Marceaux, M.A. Pickering, J. Chen, M. Kharbanda, X. Jin, N. Liu, K. Feher, and G. Putri

   Genome Biology, 2024

   
5. BMC Bioinformatics

   vissE: a versatile tool to identify and visualise higher-order molecular phenotypes from functional enrichment analysis

   D.D. Bhuva, C.W. Tan, N. Liu, H.J. Whitfield, N. Papachristos, S.C. Lee, M. Kharbanda, A. Mohamed, and M.J. Davis

   BMC Bioinformatics, 2024

   
6. eBioMedicine

   In situ single-cell profiling sheds light on IFI27 localisation during SARS-CoV-2 infection

   C.W. Tan, J. Chen, N. Liu, D.D. Bhuva, T. Blick, J. Monkman, C. Cooper, M. Kharbanda, K. Feher, B. Phipson, and E.E. Killingbeck

   eBioMedicine, 2024

   
7. Am. J. Physiol.

   Effects of a bitter substance, denatonium benzoate, on pancreatic hormone secretion

   W. Huang, S.E. O’Hara, C. Xie, N. Liu, C.K. Rayner, L.M. Nicholas, and T. Wu

   American Journal of Physiology-Endocrinology and Metabolism, 2024

   

2023

1. Nature

   Transient naive reprogramming corrects hiPS cells functionally and epigenetically

   S. Buckberry, X. Liu, D. Poppe, J.P. Tan, G. Sun, J. Chen, T.V. Nguyen, N. Liu, J.F. Ouyang, F.J. Rossello, R. Lister, and J.M. Polo

   Nature, 2023

   Bib

   

   @article{buckberry2023reprogramming,
     title = {Transient naive reprogramming corrects hiPS cells functionally and epigenetically},
     author = {Buckberry, S. and Liu, X. and Poppe, D. and Tan, J.P. and Sun, G. and Chen, J. and Nguyen, T.V. and Liu, N. and Ouyang, J.F. and Rossello, F.J. and Lister, R. and Polo, J.M.},
     journal = {Nature},
     volume = {620},
     number = {7975},
     pages = {863--872},
     year = {2023},
   }

2. Immunology

   Transcriptomic profiling of cardiac tissues from SARS-CoV-2 patients identifies DNA damage

   A. Kulasinghe^†, N. Liu^†, C.W. Tan, J. Monkman, J.E. Sinclair, D.D. Bhuva, D. Godbolt, L. Pan, A. Nam, H. Sadeghirad, and K. Sato

   Immunology, 2023

   
3. Front. Immunol.

   Compartmentalised spatial profiling of the tumour microenvironment in head and neck squamous cell carcinoma identifies immune checkpoint molecules and TNF receptor superfamily members as biomarkers of response to immunotherapy

   H. Sadeghirad^†, N. Liu^†, J. Monkman, N. Ma, B.B. Cheikh, N. Jhaveri, C.W. Tan, M.E. Warkiani, M.N. Adams, Q. Nguyen, and R. Ladwa

   Frontiers in Immunology, 2023

   
4. Nucleic Acids Res.

   vissE.cloud: a webserver to visualise higher order molecular phenotypes from enrichment analysis

   A. Mohamed, D.D. Bhuva, S. Lee, N. Liu, C.W. Tan, and M.J. Davis

   Nucleic Acids Research, 2023

   
5. Sci. Rep.

   Parallel recovery of chromatin accessibility and gene expression dynamics from frozen human regulatory T cells

   Y.Y. Wong, J.E. Harbison, C.M. Hope, B. Gundsambuu, K.A. Brown, S.W. Wong, C.Y. Brown, J.J. Couper, J. Breen, N. Liu, and S.M. Pederson

   Scientific Reports, 2023

   
6. Anim. Genet.

   Topologically associating domains in the POLLED region are the same for Angus- and Brahman-specific Hi-C reads from F1 hybrid fetal tissue

   J.E. Aldersey, N. Liu, R. Tearle, W.Y. Low, J. Breen, J.L. Williams, and C.D.K. Bottema

   Animal Genetics, 2023

   

2022

1. Epigenetics Chromatin

   3DFAACTS-SNP: using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of type 1 diabetes (T1D) risk

   N. Liu, T. Sadlon, Y.Y. Wong, S. Pederson, J. Breen, and S.C. Barry

   Epigenetics & Chromatin, 2022

   Bib

   

   @article{liu20223dfaacts,
     title = {3DFAACTS-SNP: using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of type 1 diabetes (T1D) risk},
     author = {Liu, N. and Sadlon, T. and Wong, Y.Y. and Pederson, S. and Breen, J. and Barry, S.C.},
     journal = {Epigenetics & Chromatin},
     volume = {15},
     number = {1},
     pages = {24},
     year = {2022},
   }

2021

1. Epigenetics Chromatin

   Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C

   N. Liu, W.Y. Low, H. Alinejad-Rokny, S. Pederson, T. Sadlon, S. Barry, and J. Breen

   Epigenetics & Chromatin, 2021

   Bib

   

   @article{liu2021hic,
     title = {Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C},
     author = {Liu, N. and Low, W.Y. and Alinejad-Rokny, H. and Pederson, S. and Sadlon, T. and Barry, S. and Breen, J.},
     journal = {Epigenetics & Chromatin},
     volume = {14},
     number = {1},
     pages = {41},
     year = {2021},
   }

2020

1. Front. Immunol.

   Molecular insights into regulatory T-cell adaptation to self, environment, and host tissues: plasticity or loss of function in autoimmune disease

   C.Y. Brown, T. Sadlon, C.M. Hope, Y.Y. Wong, S. Wong, N. Liu, H. Withers, K. Brown, V. Bandara, B. Gundsambuu, and S. Pederson

   Frontiers in Immunology, 2020

   

2019

1. Placenta

   Quality control measures for placental sample purity in DNA methylation array analyses

   Q. Wan, S.Y.L. Leemaqz, S.M. Pederson, D. McCullough, D.C. McAninch, T. Jankovic-Karasoulos, M.D. Smith, K.J. Bogias, N. Liu, J. Breen, and C.T. Roberts

   Placenta, 2019