By Dr Shafagh Waters

Book Chapters

McIntyre K; Waters S; Waters P, 2018, 'Sex Chromosomes', in Skinner MK (ed.), Encyclopedia of Reproduction, edn. 2, Academic Press, pp. 238 - 244, http://dx.doi.org/10.1016/B978-0-12-801238-3.64459-8

Al Nadaf S; Waters PD; Deakin JE; Graves JAM, 2010, 'Marsupial genetics reveals insights into evolution of mammalian X chromosome inactivation', in Marsupial Genetics and Genomics, pp. 259 - 280, http://dx.doi.org/10.1007/978-90-481-9023-2_13

Journal articles

Fawcett LK; Turgutoglu N; Allan KM; Belessis Y; Widger J; Jaffe A; Waters SA, 2023, 'Comparing Cytology Brushes for Optimal Human Nasal Epithelial Cell Collection: Implications for Airway Disease Diagnosis and Research.', J Pers Med, 13, pp. 864 - 864, http://dx.doi.org/10.3390/jpm13050864

Molley TG; Jiang S; Ong L; Kopecky C; Ranaweera CD; Jalandhra GK; Milton L; Kardia E; Zhou Z; Rnjak-Kovacina J; Waters SA; Toh YC; Kilian KA, 2023, 'Gas-modulating microcapsules for spatiotemporal control of hypoxia', Proceedings of the National Academy of Sciences of the United States of America, 120, pp. e2217557120, http://dx.doi.org/10.1073/pnas.2217557120

Westhaus A; Cabanes-Creus M; Dilworth KL; Zhu E; Salas Gómez D; Navarro RG; Amaya AK; Scott S; Kwiatek M; McCorkindale AL; Hayman TE; Frahm S; Perocheau DP; Tran BM; Vincan E; Wong SL; Waters SA; Riddiough GE; Perini MV; Wilson LOW; Baruteau J; Diecke S; González-Aseguinolaza G; Santilli G; Thrasher AJ; Alexander IE; Lisowski L, 2023, 'Assessment of Pre-Clinical Liver Models Based on Their Ability to Predict the Liver-Tropism of Adeno-Associated Virus Vectors', Human gene therapy, 34, pp. 273 - 288, http://dx.doi.org/10.1089/hum.2022.188

Wong SL; Kardia E; Vijayan A; Umashankar B; Pandzic E; Zhong L; Jaffe A; Waters SA, 2023, 'Molecular and Functional Characteristics of Airway Epithelium under Chronic Hypoxia', International Journal of Molecular Sciences, 24, pp. 6475 - 6475, http://dx.doi.org/10.3390/ijms24076475

Allan KM; Astore MA; Fawcett LK; Wong SL; Chen PC; Griffith R; Jaffe A; Kuyucak S; Waters SA, 2022, 'S945L-CFTR molecular dynamics, functional characterization and tezacaftor/ivacaftor efficacy in vivo and in vitro in matched pediatric patient-derived cell models', Frontiers in Pediatrics, 10, pp. 1062766, http://dx.doi.org/10.3389/fped.2022.1062766

Wong SL; Pandzic E; Kardia E; Allan KM; Whan RM; Waters SA, 2022, 'Quantifying Intracellular Viral Pathogen: Specimen Preparation, Visualization and Quantification of Multiple Immunofluorescent Signals in Fixed Human Airway Epithelium Cultured at Air-Liquid Interface', Journal of Personalized Medicine, 12, pp. 1668 - 1668, http://dx.doi.org/10.3390/jpm12101668

Wong SL; Awatade NT; Astore MA; Allan KM; Carnell MJ; Slapetova I; Chen PC; Setiadi J; Pandzic E; Fawcett LK; Widger JR; Whan RM; Griffith R; Ooi CY; Kuyucak S; Jaffe A; Waters SA, 2022, 'Molecular Dynamics and Theratyping in Airway and Gut Organoids Reveal R352Q-CFTR Conductance Defect', American Journal of Respiratory Cell and Molecular Biology, 67, pp. 99 - 111, http://dx.doi.org/10.1165/rcmb.2021-0337OC

Wong SL; Awatade NT; Astore MA; Allan KM; Carnell MJ; Slapetova I; Chen PC; Capraro A; Fawcett LK; Whan RM; Griffith R; Ooi CY; Kuyucak S; Jaffe A; Waters SA, 2022, 'Molecular dynamics and functional characterization of I37R-CFTR lasso mutation provide insights into channel gating activity', iScience, 25, pp. 103710 - 103710, http://dx.doi.org/10.1016/j.isci.2021.103710

Tran BM; Grimley SL; McAuley JL; Hachani A; Earnest L; Wong SL; Caly L; Druce J; Purcell DFJ; Jackson DC; Catton M; Nowell CJ; Leonie L; Deliyannis G; Waters SA; Torresi J; Vincan E, 2022, 'Air-Liquid-Interface Differentiated Human Nose Epithelium: A Robust Primary Tissue Culture Model of SARS-CoV-2 Infection', International Journal of Molecular Sciences, 23, pp. 835 - 835, http://dx.doi.org/10.3390/ijms23020835

Astore MA; Chen P-C; Waters S; Kuyucak S, 2022, 'Computer modelling the root cause of cystic fibrosis', Biophysical Journal, 121, pp. 506a - 506a, http://dx.doi.org/10.1016/j.bpj.2021.11.268

Dunnet MJ; Ortega-Recalde OJ; Waters SA; Weeks RJ; Morison IM; Hore TA, 2022, 'Leukocyte-specific DNA methylation biomarkers and their implication for pathological epigenetic analysis', Epigenetics Communications, 2, http://dx.doi.org/10.1186/s43682-022-00011-z

Deshpande NP; Riordan SM; Gorman CJ; Nielsen S; Russell TL; Correa-Ospina C; Fernando BSM; Waters SA; Castaño-Rodríguez N; Man SM; Tedla N; Wilkins MR; Kaakoush NO, 2021, 'Multi-omics of the esophageal microenvironment identifies signatures associated with progression of Barrett’s esophagus', Genome Medicine, 13, pp. 133, http://dx.doi.org/10.1186/s13073-021-00951-6

Allan KM; Wong SL; Fawcett LK; Capraro A; Jaffe A; Herbert C; Pandzic E; Waters SA, 2021, 'Collection, Expansion, and Differentiation of Primary Human Nasal Epithelial Cell Models for Quantification of Cilia Beat Frequency', Journal of Visualized Experiments, http://dx.doi.org/10.3791/63090-v

Allan KM; Wong SL; Fawcett LK; Capraro A; Jaffe A; Herbert C; Pandzic E; Waters SA, 2021, 'Collection, expansion, and differentiation of primary human nasal epithelial cell models for quantification of cilia beat frequency', Journal of Visualized Experiments, http://dx.doi.org/10.3791/63090

Prentice BJ; Jaffe A; Hameed S; Verge CF; Waters S; Widger J, 2021, 'Cystic fibrosis-related diabetes and lung disease: An update', European Respiratory Review, 30, pp. 200293 - 200293, http://dx.doi.org/10.1183/16000617.0293-2020

Allen K; Jaffe A; Waters S, 2021, 'Treatment of Cystic Fibrosis: From Gene- to Cell-Based Therapies', Frontiers in Pharmacology, http://dx.doi.org/10.3389/fphar.2021.639475

Awatade N; Wong S; Capraro A; Pandzic E; Slapetova I; Zhong L; Fawcett L; Whan R; Jaffe A; Waters S, 2021, 'Significant functional differences in differentiated Conditionally Reprogrammed (CRC)- and Feeder-free Dual SMAD inhibited-expanded human nasal epithelial cells', Journal of Cystic Fibrosis, http://dx.doi.org/10.1016/j.jcf.2020.12.019

Fawcett LK; Wakefield CE; Sivam S; Middleton PG; Wark P; Widger J; Jaffe A; Waters SA, 2021, 'Avatar acceptability: Views from the australian cystic fibrosis community on the use of personalised organoid technology to guide treatment decisions', ERJ Open Research, 7, pp. 1 - 10, http://dx.doi.org/10.1183/23120541.00448-2020

Azad AKM; Fatima S; Capraro A; Waters SA; Vafaee F, 2021, 'Integrative resource for network-based investigation of COVID-19 combinatorial drug repositioning and mechanism of action', Patterns, pp. 100325, http://dx.doi.org/10.1016/j.patter.2021.100325

Villamizar O; Waters SA; Scott T; Grepo N; Jaffe A; Morris KV, 2021, 'Mesenchymal Stem Cell exosome delivered Zinc Finger Protein activation of cystic fibrosis transmembrane conductance regulator', Journal of Extracellular Vesicles, 10, http://dx.doi.org/10.1002/jev2.12053

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.org/10.1101/2021.04.05.437453

Capraro A; O‘Meally D; Waters SA; Patel HR; Georges A; Waters PD, 2020, 'MicroRNA dynamics during hibernation of the Australian central bearded dragon (Pogona vitticeps)', Scientific Reports, 10, http://dx.doi.org/10.1038/s41598-020-73706-9

Capraro A; Whan R; Thomas S; Jaffe A; Bridge W; Waters S, 2020, 'Novel Antioxidant Therapy with the Immediate Precursor to Glutathione, -Glutamylcysteine (GGC), Ameliorates LPS-Induced Cellular Stress in In Vitro 3D-Differentiated Airway Model from Primary Cystic Fibrosis Human Bronchial Cells', Antioxidants, http://dx.doi.org/10.3390/antiox9121204

Coffey MJ; Mckay IR; Doumit M; Chuang S; Adams S; Stelzer-Braid S; Waters SA; Kasparian NA; Thomas T; Jaffe A; Katz T; Ooi CY, 2020, 'Evaluating the Alimentary and Respiratory Tracts in Health and disease (EARTH) research programme: a protocol for prospective, longitudinal, controlled, observational studies in children with chronic disease at an Australian tertiary paediatric hospital', BMJ Open, 10, pp. e033916, http://dx.doi.org/10.1136/bmjopen-2019-033916

Hewson C; Capraro A; Wong S; Pandzic E; Fernando BSM; Awatade N; Zhong L; Hart-Smith G; Whan R; Thomas S; Jaffe A; Bridge W; Waters S, 2020, '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

Awatade N; Wong S; Pandzic E; Slapetova I; Capraro A; Zhong L; Turgutoglu N; Fawcett L; Whan R; Jaffe A; Waters S, 2020, '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

Prentice BJ; Ooi CY; Strachan RE; Hameed S; Ebrahimkhani S; Waters SA; Verge CF; Widger J, 2019, 'Early glucose abnormalities are associated with pulmonary inflammation in young children with cystic fibrosis', Journal of Cystic Fibrosis, 18, pp. 869 - 873, http://dx.doi.org/10.1016/j.jcf.2019.03.010

Villamizar O; Waters SA; Scott T; Saayman S; Grepo N; Urak R; Davis A; Jaffe A; Morris KV, 2019, 'Targeted Activation of Cystic Fibrosis Transmembrane Conductance Regulator', Molecular Therapy, 27, pp. 1737 - 1748, http://dx.doi.org/10.1016/j.ymthe.2019.07.002

Waters S; Waters P; Capraro A, 2019, 'Waking the sleeping dragon: gene expression profiling reveals adaptive strategies of the hibernating reptile Pogona vitticeps', BMC Genomics, http://dx.doi.org/10.1186/s12864-019-5750-x

Sprague D; Waters SA; Kirk JM; Wang JR; Samollow PB; Waters PD; Calabrese JM, 2019, 'Nonlinear sequence similarity between the Xist and Rsx long noncoding RNAs suggests shared functions of tandem repeat domains', RNA, 25, pp. 1004 - 1019, http://dx.doi.org/10.1261/rna.069815.118

Coffey MJ; Zhong L; Jaffe A; Ooi CY; Waters S, 2019, 'Tu1872 – The Human Intestinal Proteome in Children with Cystic Fibrosis', Gastroenterology, 156, pp. S - 1153, http://dx.doi.org/10.1016/s0016-5085(19)39855-5

Awatade N; Wong S; Jaffe A; Waters S, 2018, 'Human Primary Epithelial Cell Models: Promising Tools in the Era of Cystic Fibrosis Personalized Medicine', Frontiers in Pharmacology, 9, pp. 1429, http://dx.doi.org/10.3389/fphar.2018.01429

Johnson RN; O’Meally D; Chen Z; Etherington GJ; Ho SYW; Nash WJ; Grueber CE; Cheng Y; Whittington CM; Dennison S; Peel E; Haerty W; O’Neill RJ; Colgan D; Russell TL; Alquezar-Planas DE; Attenbrow V; Bragg JG; Brandies PA; Chong AYY; Deakin JE; Di Palma F; Duda Z; Eldridge MDB; Ewart KM; Hogg CJ; Frankham GJ; Georges A; Gillett AK; Govendir M; Greenwood AD; Hayakawa T; Helgen KM; Hobbs M; Holleley CE; Heider TN; Jones EA; King A; Madden D; Graves JAM; Morris KM; Neaves LE; Patel HR; Polkinghorne A; Renfree MB; Robin C; Salinas R; Tsangaras K; Waters PD; Waters SA; Wright B; Wilkins MR; Timms P; Belov K, 2018, 'Adaptation and conservation insights from the koala genome', Nature Genetics, 50, pp. 1102 - 1111, http://dx.doi.org/10.1038/s41588-018-0153-5

Waters SA; Capraro A; McIntyre KL; Graves JAM; Waters PD, 2018, 'The methylome of vertebrate sex chromosomes', Genes, 9, http://dx.doi.org/10.3390/genes9050230

Waters SA; Livernois AM; Patel H; O’Meally D; Craig JM; Marshall Graves JA; Suter CM; Waters PD, 2018, 'Landscape of DNA methylation on the marsupial x', Molecular Biology and Evolution, 35, pp. 431 - 439, http://dx.doi.org/10.1093/molbev/msx297

Waters SA; McAteer SP; Kudla G; Pang I; Deshpande NP; Amos TG; Leong KW; Wilkins MR; Strugnell R; Gally DL; Tollervey D; Tree JJ, 2017, 'Small RNA interactome of pathogenic E. coli revealed through crosslinking of RNase E', EMBO Journal, 36, pp. 374 - 387, http://dx.doi.org/10.15252/embj.201694639

Alinejad-Rokny H; Anwar F; Waters SA; Davenport MP; Ebrahimi D, 2016, 'Source of CpG depletion in the HIV-1 genome', Molecular Biology and Evolution, 33, pp. 3205 - 3212, http://dx.doi.org/10.1093/molbev/msw205

Waters SA; Waters PD, 2015, 'Imprinted X chromosome inactivation: evolution of mechanisms in distantly related mammals', AIMS GENETICS, 2, pp. 110 - 126, http://dx.doi.org/10.3934/genet.2015.2.110

Rodríguez-Delgado CL; Waters SA; Waters DP, 2014, 'Paternal X inactivation does not correlate with X chromosome evolutionary strata in marsupials', BMC Evolutionary Biology, 14, http://dx.doi.org/10.1186/s12862-014-0267-z

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, 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, 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, http://dx.doi.org/10.1186/gb-2011-12-8-r81

Al Nadaf S; Deakin JE; Gilbert C; Robinson TJ; Graves JA; Waters PD, 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, 2010, 'Activity map of the tammar X chromosome shows that marsupial X inactivation is incomplete and escape is stochastic', Genome Biology, 11, http://dx.doi.org/10.1186/gb-2010-11-12-r122

Conference Papers

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

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, presented at 33rd Annual North American Cystic Fibrosis Conference, http://mc.manuscriptcentral.com/ppul

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, 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

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