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Dr Charles Foster
Lecturer

Dr Charles Foster

Medicine & Health
School of Biomedical Sciences

Dr Charles Foster is a Bioinformatics Research Associate in the Virology Research Lab at University of New South Wales/Prince of Wales Hospital: http://www.virologyresearch.unsw.edu.au/people/scientists/charles-foster/

Dr Foster completed his Bachelor of Science (Advanced) degree at the University of Sydney, receiving 1st Class Honours and the University Medal for his research into the evolution of the Australian flora. Dr Foster’s PhD research focused heavily on developing bioinformatics skills for research into the evolution of different biological groups, with a specific focus on using phylogenomics to understand the evolution of flowering plants. Dr Foster received an award for the best PhD thesis in his year of completion.

Dr Foster’s previous postdoctoral research focused on using transcriptomics to understand the changes in gene expression that underpin pregnancy in different vertebrate groups (mammals, lizards, sharks). Currently, Dr Foster is responsible for developing pipelines for genomic analysis of viruses, especially SARS-CoV-2, within the Virology Research Laboratory. These duties include routine genomic sequencing of viral samples from positive COVID-19 cases, as well as urgent cases flagged by NSW Health.
Phone
+61-2-9382 9096
E-mail
charles.foster@unsw.edu.au
Location
POW & UNSW Virology Research Laboratory Prince of Wales Hospital Level 3, Clinical Sciences Building High Street, Randwick NSW 2031, Australia
  • Journal articles | 2023
    2023, 'Emergence and antibody evasion of BQ, BA.2.75 and SARS-CoV-2 recombinant sub-lineages in the face of maturing antibody breadth at the population level', eBioMedicine, 90, pp. 104545, http://dx.doi.org/10.1016/j.ebiom.2023.104545
    Journal articles | 2023
    2023, 'Persistence of a Frameshifting Deletion in SARS-CoV-2 ORF7a for the Duration of a Major Outbreak', Viruses, 15, pp. 522 - 522, http://dx.doi.org/10.3390/v15020522
    Journal articles | 2022
    2022, 'Assessment of Inter-Laboratory Differences in SARS-CoV-2 Consensus Genome Assemblies between Public Health Laboratories in Australia', Viruses, 14, pp. 185 - 185, http://dx.doi.org/10.3390/v14020185
    Journal articles | 2022
    2022, 'Detection of Ganciclovir-Resistant Cytomegalovirus in a Prospective Cohort of Kidney Transplant Recipients Receiving Subtherapeutic Valganciclovir Prophylaxis', Microbiology Spectrum, 10, http://dx.doi.org/10.1128/spectrum.02684-21
    Journal articles | 2022
    2022, 'Different Genes are Recruited during Convergent Evolution of Pregnancy and the Placenta', Molecular Biology and Evolution, 39, http://dx.doi.org/10.1093/molbev/msac077
    Journal articles | 2022
    2022, 'Differential transcriptomic responses to heat stress in surface and subterranean diving beetles.', Sci Rep, 12, pp. 16194, http://dx.doi.org/10.1038/s41598-022-20229-0
    Journal articles | 2022
    2022, 'Evolution of the SARS-CoV-2 omicron variants BA.1 to BA.5: Implications for immune escape and transmission', Reviews in Medical Virology, 32, http://dx.doi.org/10.1002/rmv.2381
    Journal articles | 2022
    2022, 'Persistent high-level shedding of cultivable SARS-CoV-2 Delta virus 33 days after onset of COVID-19 in a hospitalized patient with pneumonia', Journal of Medical Virology, 94, pp. 4043 - 4046, http://dx.doi.org/10.1002/jmv.27832
    Journal articles | 2022
    2022, 'Platform for isolation and characterization of SARS-CoV-2 variants enables rapid characterization of Omicron in Australia', Nature Microbiology, 7, pp. 896 - 908, http://dx.doi.org/10.1038/s41564-022-01135-7
    Journal articles | 2022
    2022, 'SARS-CoV-2 N-gene mutation leading to Xpert Xpress SARS-CoV-2 assay instability', Pathology, 54, pp. 499 - 501, http://dx.doi.org/10.1016/j.pathol.2022.02.001
    Journal articles | 2022
    2022, 'SARS-CoV-2 Omicron BA.5: Evolving tropism and evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern', eBioMedicine, 84, pp. 104270, http://dx.doi.org/10.1016/j.ebiom.2022.104270
    Journal articles | 2022
    2022, 'Stressed out underground?: Illuminating the genomic response to heat stress in surface and subterranean predaceous diving beetles', ARPHA Conference Abstracts, 5, http://dx.doi.org/10.3897/aca.5.e90170
    Journal articles | 2021
    2021, 'Assessment of inter-laboratory differences in SARS-CoV-2 consensus genome assemblies between public health laboratories in Australia', , http://dx.doi.org/10.1101/2021.08.19.21262296
    Journal articles | 2021
    2021, 'Background, testing methods, and laboratory approaches to SARS coronavirus-2 (SARS-CoV-2) and Covid19', Pathology, 53, pp. S7 - S7, http://dx.doi.org/10.1016/j.pathol.2021.05.025
    Journal articles | 2021
    2021, 'Background, testing methods, and laboratory approaches to SARS coronavirus-2 (SARS-CoV-2) and covid19', Pathology, 53, pp. S17 - S17, http://dx.doi.org/10.1016/j.pathol.2021.05.060
    Journal articles | 2021
    2021, 'Background, testing methods, and laboratory approaches to sars coronavirus-2 (SARS-CoV-2) and covid19', Pathology, 53, pp. S2 - S3, http://dx.doi.org/10.1016/j.pathol.2021.05.006
    Journal articles | 2021
    2021, 'Phyllodes and bipinnate leaves of Acacia exhibit contemporary continental-scale environmental correlation and evolutionary transition-rate heterogeneity', Australian Systematic Botany, 34, pp. 595 - 608, http://dx.doi.org/10.1071/SB21009
    Journal articles | 2021
    2021, 'Rapid spread of a SARS-CoV-2 Delta variant with a frameshift deletion in ORF7a', , http://dx.doi.org/10.1101/2021.08.18.21262089
    Journal articles | 2021
    2021, 'Simple and reliable protocol for identifying talented junior players in team sports using small-sided games', Scandinavian Journal of Medicine and Science in Sports, 31, pp. 1647 - 1656, http://dx.doi.org/10.1111/sms.13969
    Journal articles | 2020
    2020, 'Accounting for uncertainty in the evolutionary timescale of green plants through clock-partitioning and fossil calibration strategies', Systematic Biology, 69, pp. 1 - 16, http://dx.doi.org/10.1093/sysbio/syz032
    Journal articles | 2020
    2020, 'Emergence of an evolutionary innovation: Gene expression differences associated with the transition between oviparity and viviparity', Molecular Ecology, 29, pp. 1315 - 1327, http://dx.doi.org/10.1111/mec.15409
    Journal articles | 2020
    2020, 'Increased diversification rates are coupled with higher rates of climate space exploration in Australian Acacia (Caesalpinioideae)', New Phytologist, 226, pp. 609 - 622, http://dx.doi.org/10.1111/nph.16349
    Journal articles | 2020
    2020, 'Linking branch lengths across sets of loci provides the highest statistical support for phylogenetic inference', Molecular Biology and Evolution, 37, pp. 1202 - 1210, http://dx.doi.org/10.1093/molbev/msz291
    Journal articles | 2020
    2020, 'Paternally-biased gene expression follows kin-selected predictions in female honey bee embryos', Molecular Ecology, 29, pp. 1523 - 1533, http://dx.doi.org/10.1111/mec.15419
    Journal articles | 2020
    2020, 'Phylogenomic Insights into Deep Phylogeny of Angiosperms Based on Broad Nuclear Gene Sampling', Plant Communications, 1, http://dx.doi.org/10.1016/j.xplc.2020.100027
    Journal articles | 2019
    2019, 'Assemblage accumulation curves: A framework for resolving species accumulation in biological communities using DNA sequences', Methods in Ecology and Evolution, 10, pp. 971 - 981, http://dx.doi.org/10.1111/2041-210X.13181
    Journal articles | 2019
    2019, 'Digest: The phylogenetic distance effect: Understanding parasite host switching*', Evolution, 73, pp. 1494 - 1495, http://dx.doi.org/10.1111/evo.13765
    Journal articles | 2018
    2018, 'Plastome sequences and exploration of tree-space help to resolve the phylogeny of riceflowers (Thymelaeaceae: Pimelea)', Molecular Phylogenetics and Evolution, 127, pp. 156 - 167, http://dx.doi.org/10.1016/j.ympev.2018.05.018
    Journal articles | 2017
    2017, 'Evaluating the impact of genomic data and priors on Bayesian estimates of the angiosperm evolutionary timescale', Systematic Biology, 66, pp. 338 - 351, http://dx.doi.org/10.1093/sysbio/syw086
    Journal articles | 2017
    2017, 'Strategies for Partitioning Clock Models in Phylogenomic Dating: Application to the Angiosperm Evolutionary Timescale', , http://dx.doi.org/10.1101/144287
    Journal articles | 2017
    2017, 'Strategies for partitioning clockmodels in phylogenomic dating: Application to the angiosperm evolutionary timescale', Genome Biology and Evolution, 9, pp. 2752 - 2763, http://dx.doi.org/10.1093/gbe/evx198
    Journal articles | 2017
    2017, 'The ancestral flower of angiosperms and its early diversification', Nature Communications, 8, http://dx.doi.org/10.1038/ncomms16047
    Journal articles | 2016
    2016, 'Estimating the number and assignment of clock models in analyses of multigene datasets', Bioinformatics, 32, pp. 1281 - 1285, http://dx.doi.org/10.1093/bioinformatics/btw005
    Journal articles | 2016
    2016, 'Molecular phylogenetics provides new insights into the systematics of Pimelea and Thecanthes (Thymelaeaceae)', Australian Systematic Botany, 29, pp. 185 - 196, http://dx.doi.org/10.1071/SB16013
    Journal articles | 2016
    2016, 'The evolutionary history of flowering plants', Journal and Proceedings of the Royal Society of New South Wales, 149, pp. 65 - 82
    Journal articles | 2015
    2015, 'Biogeographic calibrations for the molecular clock', Biology Letters, 11, http://dx.doi.org/10.1098/rsbl.2015.0194
    Journal articles | 2014
    2014, 'Molecular data support Orianthera: a new genus of Australian Loganiaceae', TELOPEA, 16, pp. 149 - 158, http://dx.doi.org/10.7751/telopea20147853
    Journal articles | 2014
    2014, 'Molecular systematics and biogeography of Logania R.Br. (Loganiaceae)', Molecular Phylogenetics and Evolution, 78, pp. 324 - 333, http://dx.doi.org/10.1016/j.ympev.2014.06.001
    Journal articles | 2013
    2013, 'Status of Logania imbricata (Guillaumin) Steenis & Leenh. (Loganiaceae)', Telopea, 15, pp. 1 - 4, http://dx.doi.org/10.7751/telopea2013001
  • Preprints | 2023
    2023, Bioinformatic investigation of discordant sequence data for SARS-CoV-2: insights for robust genomic analysis during pandemic surveillance, , http://dx.doi.org/10.1101/2023.02.01.526694
    Preprints | 2022
    2022, Emergence and antibody evasion of BQ, BA.2.75 and SARS-CoV-2 recombinant sublineages in the face of maturing antibody breadth at the population level, , http://dx.doi.org/10.1101/2022.12.06.22283000
    Preprints | 2022
    2022, Persistence of a SARS-CoV-2 variant with a frameshifting deletion for the duration of a major outbreak, , http://dx.doi.org/10.1101/2022.09.06.22279658
    Preprints | 2022
    2022, SARS-CoV-2 Omicron BA.5: Evolving tropism and evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern, , http://dx.doi.org/10.1101/2022.07.07.22277128
    Preprints | 2022
    2022, Spatial and Temporal Origin of The Third SARS-Cov-2 Outbreak in Taiwan, , http://dx.doi.org/10.1101/2022.07.04.498645
    Preprints | 2021
    2021, Differential transcriptomic responses to heat stress in surface and subterranean diving beetles, , http://dx.doi.org/10.1101/2021.12.12.470823
    Preprints | 2018
    2018, Linking Branch Lengths Across Loci Provides the Best Fit for Phylogenetic Inference, , http://dx.doi.org/10.1101/467449
    Preprints |
    SARS-CoV-2 Omicron BA.5: Evolving Tropism and Evasion of Potent Humoral Responses and Resistance to Clinical Immunotherapeutics Relative to Viral Variants of Concern, , http://dx.doi.org/10.2139/ssrn.4157473
    Preprints |
    Spatial and Temporal Origin of the Third SARS-CoV-2 Outbreak in Taiwan, , http://dx.doi.org/10.2139/ssrn.4201397

  • Establishment of analytical pipelines to accurately capture the genomic variation in viral/bacterial samples
  • Development of best practices for ensuring analytical consistency of genomics analyses between different sites/jurisdictions
  • Researching the spread of SARS-CoV-2 in real-time to understand how emerging pathogens evolve