By Dr Charles Foster

Journal articles

Egilmezer E; Hamilton ST; Foster CSP; Marschall M; Rawlinson WD, 2024, 'Human cytomegalovirus (CMV) dysregulates neurodevelopmental pathways in cerebral organoids', Communications Biology, 7, http://dx.doi.org/10.1038/s42003-024-05923-1

Lau KA; Foster CSP; Theis T; Draper J; Sullivan MJ; Ballard S; Rawlinson WD, 2024, 'Continued improvement in the development of the SARS-CoV-2 whole genome sequencing proficiency testing program', Pathology, 56, pp. 717 - 725, http://dx.doi.org/10.1016/j.pathol.2024.02.010

Harvey E; Foster CSP, 2024, 'Emerging viral threats in Australia', Microbiology Australia, 45, pp. 32 - 37, http://dx.doi.org/10.1071/MA24010

Walker GJ; Foster CSP; Sevendal A; Domazetovska A; Kamalakkannan A; Williams PCM; Kim KW; Condylios A; Stelzer-Braid S; Bartlett AW; Rawlinson W, 2024, 'Clinical, Genomic, and Immunological Characterization of RSV Surge in Sydney, Australia, 2022', Pediatrics, 153, http://dx.doi.org/10.1542/peds.2023-063667

Beasley-Hall PG; Kinjo Y; Rose HA; Walker J; Foster CSP; Kovacs TGL; Bourguignon T; Ho SYW; Lo N, 2024, 'Shrinking in the dark: Parallel endosymbiont genome erosions are associated with repeated host transitions to an underground life', Insect Science, http://dx.doi.org/10.1111/1744-7917.13339

Akerman A; Milogiannakis V; Jean T; Esneau C; Silva MR; Ison T; Fichter C; Lopez JA; Chandra D; Naing Z; Caguicla J; Li D; Walker G; Amatayakul-Chantler S; Roth N; Manni S; Hauser T; Barnes T; Condylios A; Yeang M; Wong M; Foster CSP; Sato K; Lee S; Song Y; Mao L; Sigmund A; Phu A; Vande More AM; Hunt S; Douglas M; Caterson I; Britton W; Sandgren K; Bull R; Lloyd A; Triccas J; Tangye S; Bartlett NW; Darley D; Matthews G; Stark DJ; Petoumenos K; Rawlinson WD; Murrell B; Brilot F; Cunningham AL; Kelleher AD; Aggarwal A; Turville SG, 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, http://dx.doi.org/10.1016/j.ebiom.2023.104545

Foster CSP; Bull RA; Tedla N; Santiago F; Agapiou D; Adhikari A; Walker GJ; Shrestha LB; Van Hal SJ; Kim KW; Rawlinson WD, 2023, 'Persistence of a Frameshifting Deletion in SARS-CoV-2 ORF7a for the Duration of a Major Outbreak', Viruses, 15, http://dx.doi.org/10.3390/v15020522

Zufan SE; Lau KA; Donald A; Hoang T; Foster CSP; Sikazwe C; Theis T; Rawlinson WD; Ballard SA; Stinear TP; Howden BP; Jennison AV; Seemann T, 2023, 'Bioinformatic investigation of discordant sequence data for SARS-CoV-2: insights for robust genomic analysis during pandemic surveillance', Microbial Genomics, 9, http://dx.doi.org/10.1099/mgen.0.001146

Beasley-Hall PG; Bertozzi T; Bradford TM; Foster CSP; Jones K; Tierney SM; Humphreys WF; Austin AD; Cooper SJB, 2022, 'Differential transcriptomic responses to heat stress in surface and subterranean diving beetles', Scientific Reports, 12, http://dx.doi.org/10.1038/s41598-022-20229-0

Aggarwal A; Akerman A; Milogiannakis V; Silva MR; Walker G; Stella AO; Kindinger A; Angelovich T; Waring E; Amatayakul-Chantler S; Roth N; Manni S; Hauser T; Barnes T; Condylios A; Yeang M; Wong M; Jean T; Foster CSP; Christ D; Hoppe AC; Munier ML; Darley D; Churchill M; Stark DJ; Matthews G; Rawlinson WD; Kelleher AD; Turville SG, 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, http://dx.doi.org/10.1016/j.ebiom.2022.104270

Shrestha LB; Foster C; Rawlinson W; Tedla N; Bull RA, 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

Kim KW; Wang X; Adhikari A; Yeang M; Jenkins F; Naing Z; Walker GJ; Foster CSP; Stelzer-Braid S; Deveson I; Craig ME; Tedla N; Bull RA; Martinello M; Pinto AN; Chan R; Turville S; Rawlinson WD; van Hal S, 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

Beasley-Hall P; Bertozzi T; Bradford T; Foster C; Jones K; Humphreys W; Austin A; Cooper S, 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

Wong DD; van Zuylen WJ; Novos T; Stocker S; Reuter SE; Au J; Foster CSP; Day RO; Horvath AR; Endre Z; Rawlinson WD, 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

Aggarwal A; Stella AO; Walker G; Akerman A; Esneau C; Milogiannakis V; Burnett DL; McAllery S; Silva MR; Lu Y; Foster CSP; Brilot F; Pillay A; Van Hal S; Mathivanan V; Fichter C; Kindinger A; Hoppe AC; Munier ML; Amatayakul-Chantler S; Roth N; Coppola G; Symonds GP; Schofield P; Jackson J; Lenthall H; Henry JY; Mazigi O; Jäck HM; Davenport MP; Darley DR; Matthews GV; Khoury DS; Cromer D; Goodnow CC; Christ D; Robosa R; Starck DJ; Bartlett NW; Rawlinson WD; Kelleher AD; Turville SG, 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

Foster CSP; Madden M; Chan R; Agapiou D; Bull RA; Rawlinson WD; Van Hal SJ, 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

Foster CSP; Stelzer-Braid S; Deveson IW; Bull RA; Yeang M; Au JP; Ruiz Silva M; van Hal SJ; Rockett RJ; Sintchenko V; Kim KW; Rawlinson WD, 2022, 'Assessment of Inter-Laboratory Differences in SARS-CoV-2 Consensus Genome Assemblies between Public Health Laboratories in Australia', Viruses, 14, http://dx.doi.org/10.3390/v14020185

Foster CSP; Van Dyke JU; Thompson MB; Smith NMA; Simpfendorfer CA; Murphy CR; Whittington CM, 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

Renner MAM; Foster CSP; Miller JT; Murphy DJ, 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

Wilson RS; Hunter AH; Camata TV; Foster CSP; Sparkes GR; Moura FA; Santiago PRP; Smith NMA, 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

Foster CSP; Stelzer-Braid S; Deveson I; Bull R; Yeang M; Phan-Au J; Silva MR; van Hal S; Rockett R; Sintchenko V; Kim KW; Rawlinson W, 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

Rawlinson WD; van Hal S; Yeang M; Condylios A; Naing Z; Au J-P; Ruiz da Silva M; Foster C, 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

Rawlinson WD; van Hal S; Yeang M; Condylios A; Naing Z; Au J-P; Ruiz da Silva M; Foster C, 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

Rawlinson WD; van Hal S; Yeang M; Condylios A; Naing Z; Au J-P; Ruiz da Silva M; Foster C, 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

Foster CSP; Rawlinson W, 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

Foster CSP; Thompson MB; Van Dyke JU; Brandley MC; Whittington CM, 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

Renner MAM; Foster CSP; Miller JT; Murphy DJ, 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

Duchêne DA; Tong KJ; Foster CSP; Duchêne S; Lanfear R; Ho SYW, 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

Smith NMA; Yagound B; Remnant EJ; Foster CSP; Buchmann G; Allsopp MH; Kent CF; Zayed A; Rose SA; Lo K; Ashe A; Harpur BA; Beekman M; Oldroyd BP, 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

Yang L; Su D; Chang X; Foster CSP; Sun L; Huang CH; Zhou X; Zeng L; Ma H; Zhong B, 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

Nie Y; Foster CSP; Zhu T; Yao R; Duchêne DA; Ho SYW; Zhong B, 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

van der Merwe M; Yap JYS; Bragg JG; Cristofolini C; Foster CSP; Ho SYW; Rossetto M, 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

Foster CSP, 2019, 'Digest: The phylogenetic distance effect: Understanding parasite host switching*', Evolution, 73, pp. 1494 - 1495, http://dx.doi.org/10.1111/evo.13765

Foster CSP; Henwood MJ; Ho SYW, 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

Foster CSP; Ho SYW, 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

Sauquet H; Von Balthazar M; Magallón S; Doyle JA; Endress PK; Bailes EJ; Barroso De Morais E; Bull-Hereñu K; Carrive L; Chartier M; Chomicki G; Coiro M; Cornette R; El Ottra JHL; Epicoco C; Foster CSP; Jabbour F; Haevermans A; Haevermans T; Hernández R; Little SA; Löfstrand S; Luna JA; Massoni J; Nadot S; Pamperl S; Prieu C; Reyes E; Dos Santos P; Schoonderwoerd KM; Sontag S; Soulebeau A; Staedler Y; Tschan GF; Wing-Sze Leung A; Schönenberger J, 2017, 'The ancestral flower of angiosperms and its early diversification', Nature Communications, 8, http://dx.doi.org/10.1038/ncomms16047

Foster CSP; Sauquet H; Van Der Merwe M; McPherson H; Rossetto M; Ho SYW, 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

Foster C; Ho S, 2017, 'Strategies for Partitioning Clock Models in Phylogenomic Dating: Application to the Angiosperm Evolutionary Timescale', , http://dx.doi.org/10.1101/144287

Foster CSP; Cantrill DJ; James EA; Syme AE; Jordan R; Douglas R; Ho SYW; Henwood MJ, 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

Duchêne S; Foster CSP; Ho SYW, 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

Foster CSP, 2016, 'The evolutionary history of flowering plants', Journal and Proceedings of the Royal Society of New South Wales, 149, pp. 65 - 82

Ho SYW; Tong KJ; Foster CSP; Ritchie AM; Lo N; Crisp MD, 2015, 'Biogeographic calibrations for the molecular clock', Biology Letters, 11, http://dx.doi.org/10.1098/rsbl.2015.0194

Foster CSP; Conn BJ; Henwood MJ; Ho SYW, 2014, 'Molecular data support Orianthera: a new genus of Australian Loganiaceae', Telopea, 16, pp. 149 - 158, http://dx.doi.org/10.7751/telopea20147853

Foster CSP; Ho SYW; Conn BJ; Henwood MJ, 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

Foster CSP; Conn BJ, 2013, 'Status of Logania imbricata (Guillaumin) Steenis & Leenh. (Loganiaceae)', Telopea, 15, pp. 1 - 4, http://dx.doi.org/10.7751/telopea2013001

Conference Papers

Foster CS; Dana MR; MerayoLloves J; Schaumberg DA, 1996, 'Visual outcomes prognosticators in juvenile rheumatoid arthritis-associated uveitis.', in ARTHRITIS AND RHEUMATISM, LIPPINCOTT-RAVEN PUBL, pp. 186 - 186, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1996VH88300186&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Preprints

Zufan S; Lau K; Donald A; Hoang T; Foster CSP; Sikazwe C; Theis T; Rawlinson W; Ballard S; Stinear T; Howden B; Jennison A; Seemann T, 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

Foster CSP; Walker G; Jean T; Wong M; Brassil L; Isaacs S; Lyu Y; Turville S; Kelleher A; Rawlinson W, 2023, Long-term serial passaging of SARS-CoV-2 reveals signatures of convergent evolution, http://dx.doi.org/10.1101/2023.11.02.565396

Beasley-Hall P; Kinjo Y; Rose H; Walker J; Foster C; Kovacs T; Bourguignon T; Ho S; Lo N, 2023, Shrinking in the dark: Parallel endosymbiont genome erosions are associated with repeated host transitions to an underground life, http://dx.doi.org/10.1101/2023.09.11.557272

Akerman A; Milogiannakis V; Jean T; Esneau C; Silva MR; Ison T; Fitcher C; Lopez J; Chandra D; Naing Z; Caguicla J; Li D; Walker G; Amatayakul-Chantler S; Roth N; Manni S; Hauser T; Barnes T; Condylios A; Yeang M; Wong M; Foster CSP; Sato K; Lee S; Song Y; Mao L; Sigmund A; Phu A; Vande More AM; Hunt S; Douglas M; Caterson I; Sandgren K; Bull R; Lloyd A; Triccas J; Tangye S; Bartlett N; Darley D; Matthews G; Stark D; Rawlinson W; Murrell B; Brilot F; Cunningham A; Kelleher A; Aggarwal A; Turville S, 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

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