By Dr Charles Foster

Preprints

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

Tai J-H; Low YK; Lin H-F; Wang T-Y; Lin Y-Y; Foster C; van Hal S; Lai Y-Y; Yeh S-H; Chang S-Y; Chen P-J; Chaw S-M; Wang H-Y, 2022, Spatial and Temporal Origin of the Third SARS-CoV-2 Outbreak in Taiwan, http://dx.doi.org/10.2139/ssrn.4201397

Egilmezer E; Rawlinson W; Foster CSP, Antiviral efficacy versus host recovery: contrasting transcriptional footprints of four antivirals in human cytomegalovirus-infected brain organoids, http://dx.doi.org/10.64898/2026.05.01.722178

Foster CSP; Stelzer-Braid S; Deveson IW; Bull RA; Yeang M; Phan-Au J; Silva MR; van Hal SJ; Rockett RJ; Sintchenko V; Kim KW; Rawlinson WD, 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

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, 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

Beasley-Hall PG; Bertozzi T; Bradford TM; Foster CSP; Jones K; Tierney SM; Humphreys WF; Austin AD; Cooper SJB, Differential transcriptomic responses to heat stress in surface and subterranean diving beetles, http://dx.doi.org/10.1101/2021.12.12.470823

Akerman A; Milogiannakis V; Jean T; Esneau C; Silva MR; Ison T; Fitcher 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; More AMV; Hunt S; Douglas M; Caterson I; Sandgren K; Bull R; Lloyd A; Triccas J; Tangye S; Bartlett NW; Darley D; Matthews G; Stark DJ; Rawlinson WD; Murrell B; Brilot F; Cunningham AL; Kelleher AD; Aggarwal A; Turville SG, 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

Duchêne DA; Tong KJ; Foster CSP; Duchêne S; Lanfear R; Ho SYW, Linking Branch Lengths Across Loci Provides the Best Fit for Phylogenetic Inference, http://dx.doi.org/10.1101/467449

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

Foster CSP; Bull RA; Tedla N; Santiago F; Agapiou D; Adhikari A; Walker GJ; Shrestha LB; van Hal SJ; Kim KW; Rawlinson WD, 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

Coffey MJ; van Dorst J; Pushpakumara BLDU; Halim J; Hudson J; Plush L; Christi K; Foster C; Carzino R; Zajakovski N; Appleton L; Cheney J; Wood J; Monaghan SJ; Rawlinson W; Day AS; Oliver M; Ranganathan S; Selvadurai H; Wainwright C; Thomas T; Jaffe A; Ooi CY, Probiotics and the EARly Life effects on intestinal bacteria and inflammation in children with Cystic Fibrosis (The “PEARL-CF” Study), http://dx.doi.org/10.64898/2025.12.04.25341620

Foster CSP; Rawlinson WD, 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

Aggarwal A; Akerman A; Milogiannakis V; Silva MR; Walker G; Kidinger A; Angelovich T; Waring E; Amatayakul-Chantler S; Roth N; Coppola G; Yeang M; Jean T; Foster C; Hoppe AC; Munier CML; Darley D; Churchill M; Starck D; Christ D; Matthews G; Rawlinson W; Kelleher AD; Turville S, 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

Jin W; Mitchell A; Stadler E; Foster CSP; Schlub TE; Davenport MP; Cromer DP, Separating the effects of immune waning and viral evolution on COVID-19 vaccine effectiveness reveals improved effectiveness of updated vaccines, http://dx.doi.org/10.64898/2026.09.14.26363077

Tai J-H; Low YK; Wang SC-L; Lin H-F; Wang T-Y; Wang J-T; Liu Y-S; Lin Y-Y; Foster CSP; van Hal SJ; Lai Y-Y; Yeh S-H; Chang S-Y; Chen P-J; Chaw S-M, Spatial and Temporal Origin of The Third SARS-Cov-2 Outbreak in Taiwan, http://dx.doi.org/10.1101/2022.07.04.498645

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

Foster CSP; Rawlinson WD, vartracker: an end-to-end tool for pathogen longitudinal variant analysis and visualisation, http://dx.doi.org/10.64898/2026.05.06.723370

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