By Associate Professor Shafagh Waters

Preprints

Aggarwal A; Ognenovska S; Ison T; Fichter C; Milogiannakis V; Afzal M; Stella AO; Waters S; Esneau C; Bartlett N; Pöhlmann S; Hoffmann M; Burrell L; Patel S; Ellis S; Wehrhahn M; Martinez E; Ginn A; Churchill M; Angelovich T; Rawlinson W; Yeang M; Kok J; Sintchenkov V; Parry R; Sng J; Neely G; Moreno C; Loo L; Kelleher A; Brilot F; Khromykh A; Turville S, 2025, Replication of SARS-CoV-2 Omicron lineages is defined by TMPRSS2 use in environments where ACE2 is complexed with solute carriers SLC6A19 and SLC6A20, http://dx.doi.org/10.1101/2025.07.07.663433

Chang JJ-Y; Grimley S; Tran BM; Deliyannis G; Tumpach C; Steinig E; Wong SL; Waters SA; Stinear TP; Pitt ME; Purcell D; Vincan E; Coin LJM, 2023, Uncovering strain- and age-dependent differences in innate immune response to SARS-CoV-2 infection in nasal epithelia using 10X single-cell sequencing, http://dx.doi.org/10.1101/2023.03.04.531075

McIntyre K; Waters S; Zhong L; Hart-Smith G; Raftery M; Graves JM; Waters P, 2023, Functional coherence of the Xist and RSX protein interactomes: X chromosome inactivation in marsupials, http://dx.doi.org/10.1101/2023.10.08.560959

Azad A; Fatima S; Vafaee F, An Integrative Resource for Network-Based Investigation of COVID-19 Combinatorial Drug Repositioning and Mechanism of Action, http://dx.doi.org/10.26434/chemrxiv.13271096

Westhaus A; Cabanes-Creus M; Dilworth KL; Zhu E; Gómez DS; Navarro RG; Amaya AK; Scott S; Kwiatek M; McCorkindale AL; Hayman TE; Frahm S; Perocheau DP; Tran BM; Vincan E; Wong SL; Waters SA; Wilson LOW; Baruteau J; Diecke S; González-Aseguinolaza G; Santilli G; Thrasher AJ; Alexander IE; Lisowski L, Assessment of pre-clinical liver models based on their ability to predict the liver-tropism of AAV vectors, http://dx.doi.org/10.1101/2022.09.28.510021

Poursani EM; Mercatelli D; Raninga P; Bell JL; Saletta F; Kohane FV; Zheng Y; Rouaen J; Jue TR; Michniewicz FT; Kasiou E; Tsoli M; Cirillo G; Waters S; Shai-Hee T; Valli E; Brettle M; Whan R; Vahadat L; Ziegler D; Lock JG; Giorgi FM; Khanna KK; Vittorio O, Copper chelation inhibits TGF-β pathways and suppresses epithelial-mesenchymal transition in cancer, http://dx.doi.org/10.1101/2022.10.03.510707

Allan KM; Zhang S; Wong SL; Capraro A; McCarron A; Skinner D; Kardia E; Zheng Y; Zhong L; Ng C-A; Bell JL; Farrow N; Umashankar B; Banks C; Herbert C; Kilian KA; Pandzic E; Vittorio O; Vandenberg JI; Lock JG; Jaffe A; Donnelley M; Parsons D; Woodworth BA; Cho D-Y; Waters SA, Gene-Corrected Basal Cells Restore CFTR In Vitro; Transplants Regenerate Epithelium in a Preclinical Sinus Model, http://dx.doi.org/10.1101/2025.07.21.666023

Wong SL; Awatade NT; Astore MA; Allan KM; Carnell MJ; Slapetova I; Chen P-C; Capraro A; Fawcett LK; Whan RM; Griffith R; Ooi CY; Kuyucak S; Jaffe A; Waters SA, In silico and functional characterisation of an ultra-rare CFTR mutation identifies novel lasso motif interactions regulating channel gating, http://dx.doi.org/10.1101/2021.12.12.472297

Lister NC; Milton AM; Patel HR; Waters SA; Hanrahan BJ; McIntyre KL; Livernois AM; Wee LK; Ringel AR; Mundlos S; Robson MI; Shearwin-Whyatt L; Grützner F; Graves JAM; Ruiz-Herrera A; Waters PD, Incomplete transcriptional dosage compensation of vertebrate sex chromosomes is balanced by post-transcriptional compensation, http://dx.doi.org/10.1101/2023.02.23.529605

Fawcett LK; Chew ZA; Schneider-Futschik EK; Allan KM; Patel HR; Jaffe A; Waters SA, INTEGRATING GENOMIC AND FUNCTIONAL TESTING TO IMPROVE CFTR MODULATOR RESPONSE PREDICTION IN CHILDREN WITH CYSTIC FIBROSIS, http://dx.doi.org/10.1101/2025.07.09.25331152

Wong SL; Awatade NT; Astore MA; Allan KM; Carnell MJ; Slapetova I; Chen P-C; Setiadi J; Pandzic E; Fawcett LK; Widger JR; Whan RM; Griffith R; Ooi CY; Kuyucak S; Jaffe A; Waters SA, Molecular dynamics and theratyping in airway and gut organoids reveal R352Q-CFTR conductance defect, http://dx.doi.org/10.1101/2021.08.11.456003

Sprague D; Waters SA; Kirk JM; Wang JR; Samollow PB; Waters PD; Calabrese JM, Non-linear sequence similarity between the Xist and Rsx long noncoding RNAs suggests shared functions of tandem repeat domains, http://dx.doi.org/10.1101/630475

Hewson CK; Capraro A; Wong SL; Pandzic E; Fernando BSM; Awatade NT; Zhong L; Hart-Smith G; Whan RM; Thomas SR; Jaffe A; Bridge WJ; Waters SA, Novel antioxidant therapy with the immediate precursor to glutathione, γ-glutamylcysteine (GGC), ameliorates LPS-induced cellular stress in an in vitro cystic fibrosis model, http://dx.doi.org/10.1101/2020.05.27.119990

Sabino LR; Kaiko GE; Dorahy D; Goodsall TT; Jaffe A; Schultz A; Waters S; Cook D; Kok H; Tong K; Totterdell J; McGree J; Snelling T; Wark PA, Organoid Guided N-of-1 (ORIGIN-1) Clinical Trial: A phase 4 study to investigate if people with cystic fibrosis with rare non-F508del CFTR mutations with an in-vitro response to Elexacaftor/ Tezacaftor/ Ivacaftor have a clinically meaningful response to Elexacaftor/ Tezacaftor/ Ivacaftor versus placebo., http://dx.doi.org/10.21203/rs.3.rs-7787221/v1

Poudyal P; Sy B; Mediati DG; Payne M; Nandel V; Norris D; McAteer S; Ullah A; Li S; Menz L; Waters SA; Dallman TJ; Baker M; Lan R; Gally D; Tree J, Phage-encoded sRNA counteracts xenogenic silencing in pathogenic E. coli, http://dx.doi.org/10.1101/2025.11.27.690950

Umashankar B; Capraro A; Vijayan A; Wong SL; Nielsen BU; Zhong L; Raftery M; Allan K; Ooi CY; Sivam S; Visser S; Prentice BJ; Fawcett L; Kovacevic Z; Eliasson L; Faurholt-Jepsen D; Jaffe A; Shaw JA; Vafaee F; Waters SA, Serum Exosomal Multi-Omic Signatures Stratify Glucose Tolerance in Cystic Fibrosis and Reveal Partial Therapeutic Reprogramming by CFTR Modulators, http://dx.doi.org/10.1101/2025.07.07.25331056

Awatade NT; Wong SL; Pandzic E; Slapetova I; Capraro A; Zhong L; Turgutoglu N; Fawcett LK; Whan RM; Jaffe A; Waters SA, Significant functional differences despite morphological and molecular similarity in fully differentiated matched Conditionally Reprogrammed (CRC) and Feeder free dual SMAD inhibited expanded human nasal epithelial cells, http://dx.doi.org/10.1101/2020.05.29.120006

Gödde NJ; O’Brien CM; Vincan E; Vashi A; Olliff S; Tran BM; Waters SA; Goldie S; van Vuren PJ; Riddell S; Bruce MP; Agarwal V; Athan E; Blasdell KR; Chahal S; Creek DJ; Faheem ; Jain HA; Kirkpatrick CM; Kumar A; MacRaild CA; Muzaffar-Ur-Rehman M; Sankaranarayanan M; Shah RM; Styles IK; Tachedjian M; Trevaskis NL; Singanallur NB; McAuley AJ; Vasan SS, Use of Stem Cell-Derived Cardiomyocyte and Nasal Epithelium Models to Establish a Multi-Tissue Model Platform to Validate Repurposed Drugs Against SARS-CoV-2 Infection, http://dx.doi.org/10.1101/2024.05.22.595397

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