By Dr Shafagh Waters

Journal articles

Livernois AM; Waters SA; Deakin JE; Marshall Graves JA; Waters PD, 2013, 'Independent Evolution of Transcriptional Inactivation on Sex Chromosomes in Birds and Mammals', Plos Genetics, 9, pp. e1003635, http://dx.doi.org/10.1371/journal.pgen.1003635

Royds JA; Al Nadaf S; Wiles AK; Chen YJ; Ahn A; Shaw A; Bowie S; Lam F; Baguley BC; Braithwaite AW; MacFarlane MR; Hung NA; Slatter TL, 2011, 'The cdkn2a g500 allele is more frequent in gbm patients with no defined telomere maintenance mechanism tumors and is associated with poorer survival', Plos One, 6, pp. e26737, http://dx.doi.org/10.1371/journal.pone.0026737

Renfree MB; Papenfuss AT; Deakin JE; Lindsay J; Heider T; Belov K; Rens W; Waters PD; Pharo EA; Shaw G; Wong ESW; Lefèvre CM; Nicholas KR; Kuroki Y; Wakefield MJ; Zenger KR; Wang C; Ferguson-Smith M; Nicholas FW; Hickford D; Yu H; Short KR; Siddle HV; Frankenberg SR; Chew KY; Menzies BR; Stringer JM; Suzuki S; Hore TA; Delbridge ML; Mohammadi A; Schneider NY; Hu Y; O'Hara W; Al Nadaf S; Wu C; Feng ZP; Cocks BG; Wang J; Flicek P; Searle SMJ; Fairley S; Beal K; Herrero J; Carone DM; Suzuki Y; Sugano S; Toyoda A; Sakaki Y; Kondo S; Nishida Y; Tatsumoto S; Mandiou I; Hsu A; McColl KA; Lansdell B; Weinstock G; Kuczek E; McGrath A; Wilson P; Men A; Hazar-Rethinam M; Hall A; Davis J; Wood D; Williams S; Sundaravadanam Y; Muzny DM; Jhangiani SN; Lewis LR; Morgan MB; Okwuonu GO; Ruiz SJ; Santibanez J; Nazareth L; Cree A; Fowler G; Kovar CL; Dinh HH; Joshi V; Jing C; Lara F; Thornton R; Chen L; Deng J; Liu Y; Shen JY; Song XZ; Edson J; Troon C; Thomas D; Stephens A; Yapa L; Levchenko T; Gibbs RA; Cooper DW; Speed TP; Fujiyama A; M Graves JA; O'Neill RJ, 2011, 'Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development', Genome Biology, 12, pp. 414, http://dx.doi.org/10.1186/gb-2011-12-8-r81

Al Nadaf S; Deakin JE; Gilbert C; Robinson TJ; Graves JA; Waters PD; Waters P, 2011, 'A cross-species comparison of escape from X inactivation in Eutheria: implications for evolution of X chromosome inactivation.', Chromosoma, 121, pp. 71 - 78, http://dx.doi.org/10.1007/s00412-011-0343-8

Al Nadaf S; Waters PD; Koina E; Deakin JE; Jordan KS; Graves JAM; Waters P, 2010, 'Activity map of the tammar X chromosome shows that marsupial X inactivation is incomplete and escape is stochastic', Genome Biology, 11, pp. r122, http://dx.doi.org/10.1186/gb-2010-11-12-r122

Conference Papers

Pandzic E; Allan KM; Whan RM; Waters SA, 2025, 'Image correlation spectroscopy approaches for the quantification of molecular and organellar dynamics in situ', in Image correlation spectroscopy approaches for the quantification of molecular and organellar dynamics in situ, ScienceOpen, presented at 13th Asia Pacific Microscopy Congress 2025, http://dx.doi.org/10.14293/apmc13-2025-0260

Frohlich M; Hillenbrand C; Prentice B; Fawcett L; Purcell M; Burke S; Grimm R; Andreas V; Vogel-Claussen J; Waters S; Owens L; Morgan L; Jaffe A, 2024, 'Assessment of outcomes using phase-resolved functional lung (PREFUL) MRI in a child with primary ciliary dyskinesia', in RESPIROLOGY, WILEY, pp. 228 - 229

Frohlich M; Ebrahimi N; Panzic E; Kardia E; Fernando B; Allen K; Owens L; Jaffe A; Morgan L; Waters S, 2024, 'Establishing in vitro models of PCD airways: A personalised medicine pipeline', in RESPIROLOGY, WILEY, pp. 136 - 137

Fawcett L; Jaffe A; Waters S, 2023, 'Paediatric in vitro airway cell models to predict CFTR modulator patient outcomes', in RESPIROLOGY, WILEY, pp. 44 - 44

Fawcett LK; Jaffe A; Waters SA, 2023, 'WS14.02 Cystic fibrosis personalised medicine; paediatric in vitro airway cell models to predict CFTR modulator patient outcomes', in Journal of Cystic Fibrosis, Elsevier BV, pp. S28 - S28, http://dx.doi.org/10.1016/s1569-1993(23)00266-7

Hewson C; Wong S; Awatade N; Bridge W; Jaffe A; Waters S, 2020, 'A NOVEL COMPOUND FOR CYSTIC FIBROSIS THERAPY, TARGETING THE PROTEOSTASIS NETWORK', in Respirology, Wiley, Melbourne, Australia_Cancelled due to COVID-19, presented at TSANZ20_The Thoracic Society of Australia and New Zealand (ANZSRS/TSANZ) Annual Scientific Meeting for Leaders in Lung Health, Melbourne, Australia_Cancelled due to COVID-19, http://dx.doi.org/10.1111/resp.13777

Fawcett L; Wakefield C; Widger J; Jaffe A; Waters S, 2020, 'ACCEPTABILITY OF USING PERSONALISED MINI‐ORGAN‐AVATARS TO ACCELERATE DRUG DISCOVERY AND PREDICT DRUG RESPONSE IN CYSTIC FIBROSIS PATIENTS', in TSANZSRS 2020 The Australia & New Zealand Society of Respiratory Science and The Thoracic Society of Australia and New Zealand (ANZSRS/TSANZ) Annual Scientific Meeting for Leaders in Lung Health & Respiratory Science, Melbourne - cancelled due to COVID, presented at TSANZSRS 2020, Melbourne - cancelled due to COVID, http://dx.doi.org/10.1111/resp.13778

Allan K; Awatade N; Wong S; Jaffe A; Waters S, 2020, 'COMBINATION THERAPY ORKAMBI® (VX‐770/VX‐809) IMPROVES FUNCTION FOR A RARE CFTR MUTATION R117H IN PATIENT‐DERIVED AIRWAY CELL MODELS', in Respirology, Wiley, Melbourne - cancelled due to COVID., presented at TSANZ20_The Thoracic Society of Australia and New Zealand (ANZSRS/TSANZ) Annual Scientific Meeting for Leaders in Lung Health, Melbourne - cancelled due to COVID., http://dx.doi.org/10.1111/resp.13777

Wong S; Awatade N; Jaffe A; Waters S, 2020, 'ESTABLISHING PATIENT‐DERIVED NASAL SPHEROIDS AS A NON‐INVASIVE PERSONALISED MODEL FOR ASSESSING CFTR MODULATORS EFFECTIVENESS IN PATIENTS WITH CF', in Respirology, Wiley, Melbourne, Australia_Cancelled due to COVID-19, presented at TSANZ20_The Thoracic Society of Australia and New Zealand (ANZSRS/TSANZ) Annual Scientific Meeting for Leaders in Lung Health, Melbourne, Australia_Cancelled due to COVID-19, http://dx.doi.org/10.1111/resp.13778

Wong S; Awatade N; Fawcett L; Ooi KC; Jaffe A; Waters S, 2020, 'FUNCTIONAL AND PHARMACOLOGICAL CHARACTERIZATION OF RARE R352Q CFTR MUTATION IN PATIENT‐DERIVED DIFFERENTIATED NASAL EPITHELIAL CELLS AND INTESTINAL ORGANOIDS', in Respirology, Wiley, Melbourne, Australia_Cancelled due to COVID-19, presented at TSANZ20_The Thoracic Society of Australia and New Zealand (ANZSRS/TSANZ) Annual Scientific Meeting for Leaders in Lung Health, Melbourne, Australia_Cancelled due to COVID-19, http://dx.doi.org/10.1111/resp.13777

Awatade NIO; Wong S; Jaffe A; Ooi KC; Waters S, 2020, 'INTESTINAL CURRENT MEASUREMENT AS DIAGNOSTIC AND SURROGATE MARKER OF CFTR FUNCTION IN CF', in Respirology, Wiley, Melbourne, Australia_Cancelled due to COVID-19, presented at INTESTINAL CURRENT MEASUREMENT AS DIAGNOSTIC AND SURROGATE MARKER OF CFTR FUNCTION IN CF, Melbourne, Australia_Cancelled due to COVID-19, http://dx.doi.org/10.1111/resp.13777

Allan K; Awatade N; Wong S; Turgutoglu N; Jaffe A; Waters S, 2020, 'COMBINATION THERAPY ORKAMBI (R) (VX-770/VX-809) IMPROVES FUNCTION FOR A RARE CFTR MUTATION R117H IN PATIENT-DERIVED AIRWAY CELL MODELS', in RESPIROLOGY, WILEY, pp. 36 - 36, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000538684200067&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Waters S; Villamizar O; Jaffe A; Morris K, 2019, 'Targeted Activation of Cystic Fibrosis Transmembrane Conductance Regulator', in Targeted Activation of Cystic Fibrosis Transmembrane Conductance Regulator, WILEY, pp. S183 - S184, presented at 33rd Annual North American Cystic Fibrosis Conference, http://dx.doi.org/10.26190/unsworks/27426

McKay IR; Coffey MJ; Doumit M; Bramley L; Sharp M; Kasparian N; Chuang S; Stelzer-Braid S; Waters S; Thomas T; Jaffe A; Katz TE; Ooi CY, 2019, 'A GUT FEELING: CORRELATING DIETARY INTAKE WITH THE GASTROINTESTINAL AND RESPIRATORY MICROBIOTA IN CYSTIC FIBROSIS', in PEDIATRIC PULMONOLOGY, WILEY, pp. S261 - S262, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000484544000375&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Coffey MJ; Zhong L; Jaffe A; Ooi CY; Waters S, 2019, 'THE INTESTINAL PROTEOME IN CHILDREN WITH CYSTIC FIBROSIS DIFFERS FROM HEALTHY CONTROLS', in PEDIATRIC PULMONOLOGY, WILEY, pp. S265 - S265, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000484544000385&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Coffey MJ; Zhong L; Jaffe A; Ooi CY; Waters S, 2019, 'THE HUMAN INTESTINAL PROTEOME IN CHILDREN WITH CYSTIC FIBROSIS', in GASTROENTEROLOGY, W B SAUNDERS CO-ELSEVIER INC, CA, San Diego, pp. S1153 - S1153, presented at Digestive Disease Week (DDW), CA, San Diego, 18 May 2019 - 21 May 2019, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000467106004413&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Fawcett L; Turgutoglu N; Awatade N; Wong S; Widger J; Jaffe A; Waters S, 2019, 'COMPARISON OF TWO DIFFERENT CYTOLOGY BRUSHES FOR COLLECTION OF NASAL MUCOSAL CELLS', in RESPIROLOGY, WILEY, pp. 115 - 115, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000461458900217&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Hng Y; Waters S; Chen Y; Thomas P; Herbert C, 2019, 'EXOSOME-RELATED MEDIATORS IN SERUM AND EXHALED BREATH CONDENSATE IN SARCOIDOSIS', in RESPIROLOGY, WILEY, pp. 116 - 116, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000461458900219&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Waters S; Awatade N; Wong S; Hewson C; Fawcett L; Ooi K; Widger J; Jaffe A, 2019, 'TRANSFORMATIVE THERAPIES FOR ULTRA-RARE CFTR MUTATIONS IN PRIMARY PRE-CLINICAL MODELS', in RESPIROLOGY, WILEY, pp. 141 - 141, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000461458900268&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Coffey MJ; Zhong L; Jaffe A; Ooi CY; Waters S, 2019, 'Tu1872 – The Human Intestinal Proteome in Children with Cystic Fibrosis', in Gastroenterology, Elsevier BV, pp. S - 1153, http://dx.doi.org/10.1016/s0016-5085(19)39855-5

Coffey MJ; Zhong L; Jaffe A; Ooi CY; Waters S, 2018, 'The human intestinal proteome in children with cystic fibrosis', in JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, WILEY, pp. 144 - 144, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000530647800252&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Prentice B; Hameed S; Verge C; Ooi C; Strachan R; Waters S; Widger J, 2018, 'HYPERGLYCAEMIA IN YOUNG CHILDREN WITH CYSTIC FIBROSIS CORRELATES WITH INFECTION AND NEUTROPHIL BURDEN ON BRONCHOALVEOLAR LAVAGE', in RESPIROLOGY, WILEY, pp. 34 - 34, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000427591800055&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Working Papers

Capraro A; Wong S; Adhikari A; Allan K; Patel H; Zhong L; Raftery M; Jaffe A; Yeang M; Aggarwal A; Wu L; Pandzic E; Whan R; Turville S; Vittorio O; Bull R; Kaakoush N; Rawlinson W; Tedla N; Vafaee F; Waters S, 2021, Ageing impairs the airway epithelium defence response to SARS-CoV-2, http://dx.doi.org10.1101/2021.04.05.437453

Media

Waters S; Jaffe A, 2019, Patients’ avatars being used to test cystic fibrosis drugs, https://newsroom.unsw.edu.au/news/health/patients%E2%80%99-avatars-being-used-test-cystic-fibrosis-drugs

Waters S; Jaffe A, 2019, AVATARS: A revolution in cystic fibrosis treatment. INSPIRE Research Australia, https://issuu.com/researchaustralia/docs/inspire_issue_13_final

Waters S; Jaffe A, 2019, Avatars-a-game-changer-for-children-with-cystic-fibrosis, https://www.schn.health.nsw.gov.au/news/articles/2019/07/avatars-a-game-changer-for-children-with-cystic-fibrosis

Waters S; Jaffe A, 2019, New treatment giving hope to kids with cystic fibrosis, https://www.youtube.com/watch?time_continue=1&v=66eXL0fy1JA&feature=emb_logo

Waters S; Prentice B; Jaffe A, 2018, Avatars take lead role in future CF therapy., https://www.ausdoc.com.au/therapy-update/avatars-take-lead-role-future-cf-therapy

Preprints

Gödde N; O’Brien C; Vincan E; Vashi A; Olliff S; Tran B; Waters S; Goldie S; van Vuren PJ; Riddell S; Bruce M; Agarwal V; Athan E; Blasdell K; Chahal S; Creek D; Faheem ; Jain H; Kirkpatrick C; Kumar A; MacRaild C; Muzaffar-Ur-Rehman M; Sankaranarayanan M; Shah R; Styles I; Tachedjian M; Trevaskis N; Singanallur N; McAuley A; Vasan S, 2024, 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

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 theXistandRSXprotein interactomes: X chromosome inactivation in marsupials, http://dx.doi.org/10.1101/2023.10.08.560959

Lister N; Milton A; Patel H; Waters S; Hanrahan B; McIntyre K; Livernois A; Wee LK; Ringel A; Mundlos S; Robson M; Shearwin-Whyatt L; Grützner F; Marshall Graves J; Ruiz-Herrera A; Waters P, 2023, Incomplete transcriptional dosage compensation of vertebrate sex chromosomes is balanced by post-transcriptional compensation, http://dx.doi.org/10.1101/2023.02.23.529605

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, 2022, 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, 2022, Copper chelation inhibits TGF-βpathways and suppresses epithelial-mesenchymal transition in cancer, http://dx.doi.org/10.1101/2022.10.03.510707

Azad AKM; Fatima S; Capraro A; Waters SA; Vafaee F, 2021, An Integrative Resource for Network-Based Investigation of COVID-19 Combinatorial Drug Repositioning and Mechanism of Action, http://dx.doi.org/10.33774/chemrxiv-2021-tk6rt-v2

Azad AKM; Fatima S; Capraro A; Waters SA; Vafaee F, 2021, An Integrative Resource for Network-Based Investigation of COVID-19 Combinatorial Drug Repositioning and Mechanism of Action, http://dx.doi.org/10.26434/chemrxiv-2021-tk6rt-v2

Wong S; Awatade N; Astore M; Allan K; Carnell M; Slapetova I; Chen P-C; Capraro A; Fawcett L; Whan R; Griffith R; Ooi C; Kuyucak S; Jaffe A; Waters S, 2021, In silicoand functional characterisation of an ultra-rareCFTRmutation identifies novel lasso motif interactions regulating channel gating, http://dx.doi.org/10.1101/2021.12.12.472297

Wong S; Awatade N; Astore M; Allan K; Carnell M; Slapetova I; Chen P-C; Setiadi J; Pandzic E; Fawcett L; Widger J; Whan R; Griffith R; Ooi C; Kuyucak S; Jaffe A; Waters S, 2021, 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, 2019, 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

Other

Frohlich M; Prentice B; Owens L; Waters S; Morgan L, 2025, Beyond the present: current and future perspectives on the role of infections in pediatric PCD, http://dx.doi.org/10.3389/fped.2025.1564156

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