Dr Shila Ghazanfar
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Dr Shila Ghazanfar

Address
F07 - Carslaw Building
The University of Sydney
Details
Dr Shila Ghazanfar

Dr Shila Ghazanfar is an Australian Research Council DECRA Fellow at the University of Sydney, and is an expert in statistical and computational analysis of spatial transcriptomics and single cell RNA-seq data. Dr Ghazanfar completed her undergraduate and PhD studies in statistics and statistical bioinformatics at The University of Sydney, before completing a Royal Society Newton International Fellowship at The University of Cambridge under the mentorship of Dr John Marioni in computational biology.

Dr Ghazanfar's interests are in developing statistical bioinformatic and biomedical data science approaches for the meaningful integration of complex and high dimensional biological datasets, particularly across various technological or omics modalities, and using these statistical and computational techniques to extract novel biological insights. Her multidisciplinary knowledge and skills in statistics, statistical bioinformatics, and computational biology enable her to devise strategies to jointly model the processes generating diverse data sources.

Dr Ghazanfar's interests are in developing statistical bioinformatic and biomedical data science approaches for the meaningful integration of complex and high dimensional biological datasets, particularly across various technological or omics modalities, and using these statistical and computational techniques to extract novel biological insights. Her multidisciplinary knowledge and skills in statistics, statistical bioinformatics, and computational biology enable her to devise strategies to jointly model the processes generating diverse data sources.

Her interests are in developing statistical bioinformatic and biomedical data science approaches for the meaningful integration of complex and high dimensional biological datasets, particularly across various technological or omics modalities, and using these statistical and computational techniques to extract novel biological insights. Her multidisciplinary knowledge and skills in statistics, statistical bioinformatics, and computational biology enable her to devise strategies to jointly model the processes generating diverse data sources.
Project titleResearch student
Dissecting cancer and immune vulnerabilities in advanced melanoma patients treated with immunotherapyAngel GUAN

Publications

Journals

  • Fu, X., Lin, Y., Lin, D., Mechtersheimer, D., Wang, C., Ameen, F., Ghazanfar, S., Patrick, E., Kim, J., Yang, J. (2024). BIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data. Nature Communications, 15(Article 509), 1-17. [More Information]
  • Patrick, R., Janbandhu, V., Tallapragada, V., Tan, S., McKinna, E., Contreras, O., Ghazanfar, S., Humphreys, D., Murray, N., Tran, Y., Hume, R., Chong, J., et al (2024). Integration mapping of cardiac fibroblast single-cell transcriptomes elucidates cellular principles of fibrosis in diverse pathologies. Science Advances, 10(25), eadk8501-1-eadk8501-27. [More Information]
  • Janbandhu, V., Tallapragada, V., Li, J., Bharti, S., Ghazanfar, S., Patrick, R., Cox, C., Harvey, R. (2024). Novel Mouse Model for Selective Tagging, Purification, and Manipulation of Cardiac Myofibroblasts. Circulation, 149(24), 1931-1934. [More Information]

2024

  • Fu, X., Lin, Y., Lin, D., Mechtersheimer, D., Wang, C., Ameen, F., Ghazanfar, S., Patrick, E., Kim, J., Yang, J. (2024). BIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data. Nature Communications, 15(Article 509), 1-17. [More Information]
  • Patrick, R., Janbandhu, V., Tallapragada, V., Tan, S., McKinna, E., Contreras, O., Ghazanfar, S., Humphreys, D., Murray, N., Tran, Y., Hume, R., Chong, J., et al (2024). Integration mapping of cardiac fibroblast single-cell transcriptomes elucidates cellular principles of fibrosis in diverse pathologies. Science Advances, 10(25), eadk8501-1-eadk8501-27. [More Information]
  • Janbandhu, V., Tallapragada, V., Li, J., Bharti, S., Ghazanfar, S., Patrick, R., Cox, C., Harvey, R. (2024). Novel Mouse Model for Selective Tagging, Purification, and Manipulation of Cardiac Myofibroblasts. Circulation, 149(24), 1931-1934. [More Information]

2023

  • Cao, Y., Ghazanfar, S., Yang, P., Yang, J. (2023). Benchmarking of analytical combinations for COVID-19 outcome prediction using single-cell RNA sequencing data. Briefings in Bioinformatics, 24(3). [More Information]
  • Peters Couto, B., Robertson, N., Patrick, E., Ghazanfar, S. (2023). MoleculeExperiment enables consistent infrastructure for molecule-resolved spatial omics data in bioconductor. Bioinformatics, 39(9), 1-5. [More Information]
  • Cao, Y., Tran, A., Kim, H., Robertson, N., Lin, Y., Torkel, M., Yang, P., Patrick, E., Ghazanfar, S., Yang, J. (2023). Thinking process templates for constructing data stories with SCDNEY. F1000Research, 12, 261-1-261-18. [More Information]

2022

  • Havula, E., Ghazanfar, S., Lamichane, N., Francis, D., Hasygar, K., Liu, Y., Alton, L., Johnstone, J., Needham, E., Pulpitel, T., Clark, T., Niranjan, H., Shang, V., Tong, V., Jiwnani, N., Audia, G., Neely, G., Yang, J., Simpson, S., Senior, A., et al (2022). Genetic variation of macronutrient tolerance in Drosophila melanogaster. Nature Communications, 13(1637), 1-16. [More Information]
  • Lin, X., Swedlund, B., Ton, M., Ghazanfar, S., Guibentif, C., Paulissen, C., Baudelet, E., Plaindoux, E., Achouri, Y., Calonne, E., et al (2022). Mesp1 controls the chromatin and enhancer landscapes essential for spatiotemporal patterning of early cardiovascular progenitors. Nature Cell Biology, 24(7), 1114-1128. [More Information]
  • Righelli, D., Weber, L., Crowell, H., Pardo, B., Collado-Torres, L., Ghazanfar, S., Lun, A., Hicks, S., Risso, D. (2022). SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor. Bioinformatics, 38(11), 3128-3131. [More Information]

2021

  • Su, X., Zhao, L., Shi, Y., Zhang, R., Long, Q., Bai, S., Luo, Q., Lin, Y., Zou, X., Ghazanfar, S., Yang, P., Yang, J., et al (2021). Clonal evolution in liver cancer at single-cell and single-variant resolution. Journal of Hematology and Oncology, 14(1), 22-26. [More Information]
  • Barile, M., Imaz-Rosshandler, I., Inzani, I., Ghazanfar, S., Nichols, J., Marioni, J., Guibentif, C., Göttgens, B. (2021). Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation. Genome Biology, 22(1). [More Information]
  • Guibentif, C., Griffiths, J., Imaz-Rosshandler, I., Ghazanfar, S., Nichols, J., Wilson, V., Göttgens, B., Marioni, J. (2021). Diverse Routes toward Early Somites in the Mouse Embryo. Developmental Cell, 56(1), 141-153.e6. [More Information]

2020

  • Ghazanfar, S., Lin, Y., Su, X., Lin, D., Patrick, E., Han, Z., Marioni, J., Yang, J. (2020). Investigating higher-order interactions in single-cell data with scHOT. Nature Methods, 17(8), 799-806. [More Information]
  • Su, X., Long, Q., Bo, J., Shi, Y., Zhao, L., Lin, Y., Luo, Q., Ghazanfar, S., Zhang, C., Liu, Q., Yang, J., et al (2020). Mutational and transcriptomic landscapes of a rare human prostate basal cell carcinoma. The Prostate, 80(6), 508-517. [More Information]
  • Lau, M., Ghazanfar, S., Parkin, A., Cho, A., Rouaen, J., Littleboy, J., Nessem, D., Khuong, T., Nevoltris, D., Schofield, P., Yang, J., Neely, G., et al (2020). Systematic functional identification of cancer multi-drug resistance genes. Genome Biology, 21(1), 27. [More Information]

2019

  • Lim, S., Lee, J., Gide, T., Menzies, A., Guminski, A., Carlino, M., Breen, E., Yang, J., Ghazanfar, S., Kefford, R., Scolyer, R., Long, G., Rizos, H. (2019). Circulating Cytokines Predict Immune-Related Toxicity in Melanoma Patients Receiving Anti-PD-1–Based Immunotherapy. Clinical Cancer Research, 25(5), 1557-1563. [More Information]
  • Ghazanfar, S., Strbenac, D., Ormerod, J., Yang, J., Patrick, E. (2019). DCARS: differential correlation across ranked samples. Bioinformatics, 35(5), 823-829. [More Information]
  • Lin, Y., Ghazanfar, S., Strbenac, D., Wang, A., Patrick, E., Lin, D., Speed, T., Yang, J., Yang, P. (2019). Evaluating stably expressed genes in single cells. GigaScience, 8(9), 1-10. [More Information]

2018

  • Sykes, E., McDonald, C., Ghazanfar, S., Mactier, S., Thompson, J., Scolyer, R., Yang, J., Mann, G., Christopherson, R. (2018). A 14-Protein Signature for Rapid Identification of Poor Prognosis Stage III Metastatic Melanoma. Proteomics - Clinical Applications, 12(3), 1-12. [More Information]
  • Bisogni, A., Ghazanfar, S., Williams, E., Marsh, H., Yang, J., Lin, D. (2018). Tuning of delta-protocadherin adhesion through combinatorial diversity. eLife, 7, 1-27. [More Information]

2017

  • Ghazanfar, S., Vuocolo, T., Morrison, J., Nicholas, L., McMillen, I., Yang, J., Buckley, M., Tellam, R. (2017). Gene expression allelic imbalance in ovine brown adipose tissue impacts energy homeostasis. PloS One, 12(6), 1-22. [More Information]

2016

  • Ghazanfar, S., Yang, J. (2016). Characterizing mutation-expression network relationships in multiple cancers. Computational Biology and Chemistry, 63, 73-82. [More Information]
  • Ghazanfar, S., Bisogni, A., Ormerod, J., Lin, D., Yang, J. (2016). Integrated single cell data analysis reveals cell specific networks and novel coactivation markers. BMC Systems Biology, 10(Suppl 5), 11-24. [More Information]
  • Yang, P., Patrick, E., Humphrey, S., Ghazanfar, S., James, D., Jothi, R., Yang, J. (2016). KinasePA: Phosphoproteomics data annotation using hypothesis driven kinase perturbation analysis. Proteomics, 16(13), 1868-1871. [More Information]

Selected Grants

2023

  • Statistical Bioinformatics for Single Cell, Spatial and Multiomic Biotechnologies, Ghazanfar S, Faculty of Science/Research Travel Support

2022

  • Defining spatiotemporal mechanisms that promote peripheral nerve regeneration, Ghazanfar S, Lin D, Yang J, Office of Global Engagement/Partnership Collaboration Awards
  • Multiscale data integration for single cell spatial genomics, Ghazanfar S, Chan Zuckerberg Initiative (USA)/Single-Cell Biology Data Insights
  • Statistical approaches for spatial genomics at single cell resolution, Ghazanfar S, Australian Research Council (ARC)/Discovery Early Career Researcher Award (DECRA)