Dr Hardip Patel

PhD
Research Fellow - NCIG BioLead

Research interests

  • Bioinformatics
  • Genomics
  • Gene Expression (Incl. Microarray And Other Genome Wide Approaches)
  • Genome Structure And Regulation
  • Molecular Evolution
  • Phylogeny And Comparative Analysis
  • Quantitative Genetics (Including Disease And Trait Mapping Genetics)
  • Wagner, S, Whiteley, S, Castelli, M et al. 2023, 'Gene expression of male pathway genes sox9 and amh during early sex differentiation in a reptile departs from the classical amniote model', BMC Genomics, vol. 24.
  • Zhang, X, Wagner, S, Holleley, C et al. 2022, 'Sex-specific splicing of Z- and W-borne nr5a1 alleles suggests sex determination is controlled by chromosome conformation', PNAS - Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 4, pp. 1-9.
  • McCartney, A, Anderson, J, Liggins, L et al. 2022, 'Balancing openness with Indigenous data sovereignty: An opportunity to leave no one behind in the journey to sequence all of life', PNAS - Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 4, pp. 1-9.
  • Jadhao, S, Hoy, W, Lee, S et al. 2022, 'The genomic landscape of blood groups in Indigenous Australians in remote communities', Transfusion, vol. 62, no. 5, pp. 1110ââ¬â1120.
  • Hu, L, Long, J, Lin, Y et al. 2022, 'Arctic introgression and chromatin regulation facilitated rapid Qinghai-Tibet Plateau colonization by an avian predator', Nature Communications, vol. 13, no. 1, pp. 1-18.
  • Shankar, A, Jadhao, S, Hoy, W et al. 2021, 'Pharmacogenomic analysis of a genetically distinct Indigenous population', Pharmacogenomics Journal, vol. 22, pp. 100ââ¬â108.
  • Prabhakaran, D, Patel, H, Chandrika, S et al. 2021, 'Genomic attributes differ between Vibrio parahaemolyticus environmental and clinical isolates including pathotypes', Environmental Microbiology Reports, vol. 14, no. 3, pp. 365-375.
  • Li, Y, Patel, H & Lin, Y 2021, 'Kmer2SNP: Reference-free SNP calling from raw reads based on matching', 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
    , IEEE, United States, pp. 208-212.
  • Waters, P, Patel, H, Ruiz-Herrera, A et al. 2021, 'Microchromosomes are building blocks of bird, reptile, and mammal chromosomes', PNAS - Proceedings of the National Academy of Sciences of the United States of America, vol. 118, no. 45, pp. 1-11.
  • Chu-Tan, J, Cioanca, V, Feng, Z et al. 2021, 'Functional microRNA targetome undergoes degeneration-induced shift in the retina', Molecular Neurodegeneration, vol. 16, no. 1.
  • Acera Mateos, P, Balboa, R, Easteal, S et al. 2021, 'PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses', Scientific Reports, vol. 11, no. 1.
  • McInerney, T, Fulton-Howard, B, Patterson, C et al. 2021, 'A globally diverse reference alignment and panel for imputation of mitochondrial DNA variants', BMC Bioinformatics, vol. 22, no. 417.
  • Easteal, S, Arkell, R, Balboa, R et al. 2020, 'Equitable Expanded Carrier Screening Needs Indigenous Clinical and Population Genomic Data', American Journal of Human Genetics, vol. 107, no. 2, pp. 175-182.
  • Easteal, S, Arkell, R, Balboa, R et al. 2020, 'Equitable Expanded Carrier Screening Needs Indigenous Clinical and Population Genomic Data', American Journal of Human Genetics, vol. 107, no. 2, pp. 175-182.
  • Capraro, A, O'Meally, D, Waters, S et al. 2020, 'MicroRNA dynamics during hibernation of the Australian central bearded dragon (Pogona vitticeps)', Scientific Reports, vol. 10, no. 1.
  • Hart, N, Lamb, T, Patel, H et al. 2020, 'Visual opsin diversity in sharks and rays', Molecular Biology and Evolution, vol. 37, no. 3, pp. 811-827.
  • Capraro, A, O'Meally, D, Waters, S et al. 2019, 'Waking the sleeping dragon: Gene expression profiling reveals adaptive strategies of the hibernating reptile Pogona vitticeps', BMC Genomics, vol. 20, no. 1.
  • Arcos-Burgos PhD, M, Velez Valbuena, J, Martinez, A et al. 2019, 'ADGRL3 (LPHN3) variants predict substance use disorder', Translational Psychiatry, vol. 9, no. 42, pp. 15pp.
  • Arcos-Burgos, M, Velez, J, Martinez, A, Lidbury BA, et al 2019, 'ADGRL3 (LPHN3) variants predict substance use disorder', Translational Psychiatry, vol. 9, no. 42, pp. 15pp.
  • Johnson, R, O' Meally, D, Chen, Z et al 2018, 'Adaptation and conservation insights from the koala genome', Nature Genetics, vol. 50, no. 8, pp. 1102-1111pp.
  • Hsieh JF, Chuah A, Patel HR, Sandhu KS, Foley WJ, Külheim C. 2018, 'Transcriptome Profiling of Melaleuca quinquenervia Challenged by Myrtle Rust Reveals Differences in Defense Responses Among Resistant Individuals', Phytopathology, vol. 108, no. 4, pp. 495-509.
  • Lamb, T, Patel, H, Chuah, A et al 2018, 'Evolution of the shut-off steps of vertebrate phototransduction', Open Biology, vol. 8, 170232.
  • Natoli R, Mason E, Jiao H, Chuah A, Patel HR, Fernando N, Valter K, Wells CA, Provis J, Rutar M 2018, 'Dynamic Interplay of Innate and Adaptive Immunity During Sterile Retinal Inflammation: Insights From the Transcriptome', Frontiers in Immunology, vol. 9, no. 1666, pp. 1-17pp.
  • Urbarova, I, Patel, H, Foret, S, Karlsen B, Jørgensen, T, Hall-Spencer, J, Johansen, S, 2018, 'Elucidating the Small Regulatory RNA Repertoire of the Sea Anemone Anemonia viridis Based on Whole Genome and Small RNA Sequencing', Genome Biology and Evolution, vol. 10, no. 2, pp. 410-426.
  • Waters SA, Livernois AM, Patel H, O'Meally D, Craig JM, Graves JA, Suter CM, Waters PD, 2018, 'Landscape of DNA Methylation on the Marsupial X', Molecular Biology and Evolution, vol. 35, no. 2, pp. 431-439.
  • O'Brien, C, Patel, H, Freeman, T et al. 2017, 'Gene expression differences between Crohn's disease aphthous ulcers and healthy Peyer's patches highlight novel therapeutic targets', Gastroenterological Society of Australia Australian Gastroenterology Week Precision Medicine in Gastroenterology, 2017, John Wiley & Sons Ltd., Australia, pp. 119-119.
  • O'Brien, C, Patel, H, Freeman, T et al. 2017, 'Gene expression differences between Crohn's disease aphthous ulcers and healthy Peyer's patches highlights potential treatment strategies [meeting abstract]', 12th Congress of European Crohn's and Colitis Organisation, ECCO 2017, ed. Laurence J Egan, Oxford University Press, United Kingdom, pp. S470-S470.
  • Soetanto, R, Hynes, C, Patel, H et al. 2016, 'Role of miRNAs and alternative mRNA 3 '-end cleavage and polyadenylation of their mRNA targets in cardiomyocyte hypertrophy', Biochimica et Biophysica Acta - Gene Regulatory Mechanisms, vol. 1859, no. 5, pp. 744-756.
  • Velez Valbuena, J, Rivera, D, Mastronardi, C et al. 2016, 'A Mutation in DAOA Modifies the Age of Onset in PSEN1 E280A Alzheimer's Disease', Neural Plasticity, vol. 2016, pp. 9760314-9760314.
  • Johar, A, Sarmiento-Monroy, J, Rojas-Villarraga, A et al. 2016, 'Definition of mutations in polyautoimmunity', Journal of Autoimmunity, vol. 72, pp. 65-72.
  • Deakin, J, Edwards, M, Patel, H et al 2016, 'Anchoring genome sequence to chromosomes of the central bearded dragon (Pogona vitticeps) enables reconstruction of ancestral squamate macrochromosomes and identifies sequence content of the Z chromosome', BMC Genomics, vol. 17, no. 1, pp. -.
  • Lamb, T, Patel, H, Chuah, A et al 2016, 'Evolution of Vertebrate Phototransduction: Cascade Activation', Molecular Biology and Evolution, vol. 33, no. 8, pp. 2064-2087.
  • Velez Valbuena, J, Lopera, F, Patel, H et al. 2016, 'Mutations modifying sporadic Alzheimer's disease age of onset', American Journal of Medical Genetics, Part B: Neuropsychiatric, vol. 171, no. 8, pp. 1116-1130.
  • Mastronardi, C, Pillai, E, Pineda, D et al. 2016, 'Linkage and association analysis of ADHD endophenotypes in extended and multigenerational pedigrees from a genetic isolate', Molecular Psychiatry, vol. 21, no. 10, pp. 1434-1440.
  • Galgamuwa Arachchige, R, Hardy, K, Dahlstrom, J et al 2016, 'Dichloroacetate Prevents Cisplatin-Induced Nephrotoxicity without Compromising Cisplatin Anticancer Properties', Journal of the American Society of Nephrology, vol. 27, no. 11, pp. 3331-3344.
  • Galgamuwa Arachchige, R, Hardy, K, Dahlstrom, J et al 2016, 'Dichloroacetate Prevents Cisplatin-Induced Nephrotoxicity without Compromising Cisplatin Anticancer Properties', Journal of the American Society of Nephrology, vol. 27, no. 11, pp. 3331-3344.
  • Padovan, A, Patel, H, Chuah, A et al 2015, 'Transcriptome Sequencing of Two Phenotypic Mosaic Eucalyptus Trees Reveals Large Scale Transcriptome Re-Modelling', PLOS ONE (Public Library of Science), vol. 10, no. 5, pp. e0123226-e0123226.
  • Johar, A, Anaya, J, Andrews, D et al. 2015, 'Candidate gene discovery in autoimmunity by using extreme phenotypes, next generation sequencing and whole exome capture', Autoimmunity Reviews, vol. 14, no. 3, pp. 204-209.
  • Johar, A, Mastronardi, C, Rojas-Villarraga, A et al. 2015, 'Novel and rare functional genomic variants in multiple autoimmune syndrome and Sjögren's syndrome', Journal of Translational Medicine, vol. 13, no. 173, pp. 173-173.
  • Georges, A, Li, Q, Lian, J et al 2015, 'High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps', GigaScience, vol. 4, no. 45, pp. 1-10.
  • Velez Valbuena, J, Lopera, F, Falla, D et al. 2015, 'APOE*E2 allele delays age of onset in PSEN1 E280A Alzheimer's disease', Molecular Psychiatry, vol. 21, no. 7, pp. 916-924.
  • Perez-Bercoff, A, Papanicolaou, A, Ramsperger, M et al 2015, 'DRAFT GENOME OF AUSTRALIAN ENVIRONMENTAL STRAIN WM 09 24 OF THE OPPORTUNISTIC HUMAN PATHOGEN SCEDOSPORIUM AURANTIACUM', Genome Announcements, vol. 3, no. 1, pp. e01526-14.
  • Srivastava, M, Duan, G, Kershaw, NJ et al 2015, 'Roquin binds microRNA-146a and Argonaute2 to regulate microRNA homeostasis.', Nature Communications, vol. 6, no. 6253.
  • Clancy, JL, Patel, HR, Hussein, SMI et al 2014, 'Small RNA changes en route to distinct cellular states of induced pluripotency', Nature Communications, vol. 5, p. 5522.
  • Hussein, SMI, Puri, MC, Tonge, PD et al 2014, 'Genome-wide characterization of the routes to pluripotency', Nature, vol. 516, no. 7530, pp. 198-206.
  • Da Paz Filho, G, Boguszewski, M, Mastronardi, C et al. 2014, 'Whole Exome Sequencing of Extreme Morbid Obesity Patients: Translational Implications for Obesity and Related Disorders', GENES, vol. 5, no. 3, pp. 709-725.
  • Li, R, Patel, H, Perriman, D et al 2014, 'MICRORNA PROFILING IN WEAR PARTICLE ASSOCIATED OSTEOLYSIS', Bone and Joint Journal, vol. 96-B, no. SUPP 11 43.
  • Sibbritt, T, Patel, H & Preiss, T 2013, 'Mapping and significance of the mRNA methylome', Wiley Interdisciplinary Reviews: WIREs RNA, vol. 4, no. 4, pp. 397-422.
  • Squires, J, Patel, H, Nousch, M et al 2012, 'Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA', Nucleic Acids Research, vol. 40, no. 11, pp. 5023-33.
  • Humphreys, D, Clancy, J, Patel, H et al. 2012, 'Complexity of Murine Cardiomyocyte miRNA Biogenesis, Sequence Variant Expression and Function', PLoS ONE, vol. 7, no. 2, pp. 1-18.
  • Renfree, M, Papenfuss, A, Deakin, J et al 2011, 'Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development', Genome Biology, vol. 12, no. 8, pp. R81-R81.
  • Wang, C, Webley, L, Wei, K et al 2011, 'A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii)', BMC Genetics, vol. 12, no. 72, pp. 1-16.
  • O'Meally, D, Patel, H, Stiglec, R et al 2010, 'Non-homologous sex chromosomes of birds and snakes share repetitive sequences', Chromosome Research, vol. 18, no. 7, pp. 787-800.
  • Patel, H, Delbridge, M & Graves, J 2010, 'Organization and Evolution of the Marsupial X Chromosome', in Janine E Deakin, Paul D Waters & Jennifer A Marshall Graves (ed.), Marsupial Genetics and Genomics, Springer, Dordrecht; London, pp. 151-171.
  • O'Meally, D, Miller, H, Patel, H et al 2009, 'The First Cytogenetic Map of the Tuatara, Sphenodon punctatus', Cytogenetic and Genome Research, vol. 127, no. 2, pp. 213-223.
  • Delbridge, M, Patel, H, Waters, P et al 2009, 'Does the human X contain a third evolutionary block: Origin of genes on human Xp11 and Xq28', Genome Research, vol. 19, no. 8, pp. 1350-1360.