Senior Author:

• Pallawi Kumari1, Manmeet Kaur1, Kiran Dindhoria1, Bruce Ashford2, Shanika L. Amarasinghe 3,4, Amarinder S. Thind2,5,* Advances in long-read single-cell transcriptomic (Human Genetics, 2024 (https://link.springer.com/article/10.1007/s00439-024-02678-x )). 

• Dindhoria, K., Monga, I., & Thind, A. S. Computational approaches and challenges for identification and annotation of non-coding RNAs using RNA-Seq. Functional & Integrative Genomics,  (2022). 22(6), 1105-1112. 

First Author: 

• Thind, Amarinder, et al. CTCF Binding Site Mutations: Linking Topologically Associated Domains Dysregulation to Cutaneous Squamous Cell Carcinoma Progression. Preprint, Research Square, 2025, https://doi.org/10.21203/rs.3.rs-6844715/v1.  

• Thind, Amarinder S., and Somdatta Sinha. "Using Chaos-Game-Representation for Analysing the SARS-CoV-2 Lineages, Newly Emerging Strains and Recombinants." Current Genomics 24, no. 3 (2023): 187-195. 

•  Thind, A. S., Ashford, B., Strbenac, D., Mitchell, J., Lee, J., Mueller, S. A., ... & Ranson, M. Whole genome analysis reveals the genomic complexity in metastatic cutaneous squamous cell carcinoma. Frontiers in oncology, (2022). 12, 919118. 

• Thind, A. S., Kaur, K., & Monga, I. . An Overview of Databases and Tools for lncRNA Genomics Advancing Precision Medicine. Machine Learning and Systems Biology in Genomics and Health, 49-67, springer. (2022)

• Thind, A.S., Monga, I., Thakur, P.K., Kumari, P., Dindhoria, K., Krzak, M., Ranson, M. and Ashford, B., Demystifying emerging bulk RNA-Seq applications: the application and utility of bioinformatics methodology. Briefings in Bioinformatics  (2021).

• Thind AS, Vitali V, Guarracino MR, Catania F. What's Genetic Variation Got to Do with It? Starvation-Induced SelfFertilization Enhances Survival in Paramecium. Genome Biol Evol. (2020);12(5):626-638. doi:10.1093/gbe/evaa052

• Thind AS, Tripathi KP, Guarracino MR. RankerGUI: A Computational Framework to Compare Differential Gene Expression Profiles Using Rank Based Statistics. Int J Mol Sci. 2019;20(23):6098. Published 2019 Dec 3. doi:10.3390/ijms20236098 

Co-Author: 

• Hulme et. al "Induced Proprioceptor and Low-Threshold Mechanoreceptor Neurons Derived from Human Pluripotent Stem Cells Exhibit Distinct Functional Mechanosensory Properties" Advanced Science, (2025) https://doi.org/10.1002/advs.202512413 

• Tomas Bencomo,  Amarinder Thind,  Bruce Ashford,  Marie Ranson,  Carolyn S. Lee Extrachromosomal DNA in cutaneous squamous cell carcinoma is associated with increased nodal disease, Feb 2024, bioRxiv  https://doi.org/10.1101/2024.02.04.578845 

• Gupta, Ashish, Amarinder Thind, and Rituraj Purohit. "EGFRAP: A Predictive Machine Learning Model for Assessing Small Molecule Activity Against the Epidermal Growth Factor Receptor." RSC Medicinal Chemistry (2025). https://doi.org/10.1039/D5MD00361J 

• Perry JR, Genenger B, Thind AS, Ashford B, Ranson M. PIK Your Poison: The Effects of Combining PI3K and CDK Inhibitors against Metastatic Cutaneous Squamous Cell Carcinoma In Vitro. Cancers. (2024); 16(2):370. https://doi.org/10.3390/cancers16020370 

• Sylvia Ai, Amarinder Thind, Gurdeep Parmar  Differences in survival of patients with multiple myeloma in rural vs metropolitan regions: analysis of population data of an Australian local health district, AJRH,2024

• Yeo, N., Genenger, B., Aghmesheh, M., Thind, A., Napaki, S., Perry, J., ... & Brungs, D. Sex as a Predictor of Response to Immunotherapy in Advanced Cutaneous Squamous Cell Carcinoma. Cancers, (2023).15(20), 5026. 

• Gupta, R., Strbenac, D., Satgunaseelan, L., Cheung, V.K.Y., Narayanappa, H., Ashford, B., Mitchell, J., Thind, A., Palme, C.E., Ch’ng, S. and Low, T.H.H., Comparing Genomic Landscapes of Oral and Cutaneous Squamous Cell Carcinoma of the Head and Neck: Quest for Novel Diagnostic Markers. Modern Pathology, (2023). 36(8), p.100190. 

• Minaei, E., Mueller, S. A., Ashford, B., Thind, A. S., Mitchell, J., Perry, J. R., ... & Ranson, M. . Cancer Progression Gene Expression Profiling Identifies the Urokinase Plasminogen Activator Receptor as a Biomarker of Metastasis in Cutaneous Squamous Cell Carcinoma. Frontiers in Oncology (2022), 1188. 

•  Perry, J., Ashford, B., Thind, A. S., Gauthier, M. E., Minaei, E., Major, G., ... & Ranson, M. Comprehensive Mutational and Phenotypic Characterization of New Metastatic Cutaneous Squamous Cell Carcinoma Cell Lines Reveal Novel Drug Susceptibilities. International journal of molecular sciences, (2020). 21(24), 9536. 

• Sangiovanni M, Granata I, Thind AS, Guarracino MR. From trash to treasure: detecting unexpected contamination in unmapped NGS data. BMC Bioinformatics. 2019;20(Suppl 4):168. Published (2019) Apr 18. doi:10.1186/s12859- 019-2684-x 

•  Balasco N, Esposito L, Thind AS, Guarracino MR, Vitagliano L. Dissection of Factors Affecting the Variability of the Peptide Bond Geometry and Planarity. Biomed Res Int. (2017) ;2017:2617629. doi:10.1155/2017/2617629