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A User's Guide to the Inverted Terminal Repeats (ITR) of Adeno-Associated Virus.

Wilmott P, Lisowski L, Alexander IE, Logan G.

Hum Gene Ther Methods. 2019 Nov 21. doi: 10.1089/hgtb.2019.276. [Epub ahead of print]


The implementation of newborn screening for spinal muscular atrophy: the Australian experience.

Kariyawasam DST, Russell JS, Wiley V, Alexander IE, Farrar MA.

Genet Med. 2019 Oct 14. doi: 10.1038/s41436-019-0673-0. [Epub ahead of print]


Systemic AAV8-mediated delivery of a functional copy of muscle glycogen phosphorylase (Pygm) ameliorates disease in a murine model of McArdle disease.

McNamara EL, Taylor RL, Clayton JS, Goullee H, Dilworth KL, Pinós T, Brull A, Alexander IE, Lisowski L, Ravenscroft G, Laing NG, Nowak KJ.

Hum Mol Genet. 2019 Sep 12. pii: ddz214. doi: 10.1093/hmg/ddz214. [Epub ahead of print]


Insights into Gene Therapy for Urea Cycle Defects by Mathematical Modeling.

Kok CY, Cunningham SC, Kuchel PW, Alexander IE.

Hum Gene Ther. 2019 Nov;30(11):1385-1394. doi: 10.1089/hum.2019.053. Epub 2019 Jul 17.


Prevention of Cholestatic Liver Disease and Reduced Tumorigenicity in a Murine Model of PFIC Type 3 Using Hybrid AAV-piggyBac Gene Therapy.

Siew SM, Cunningham SC, Zhu E, Tay SS, Venuti E, Bolitho C, Alexander IE.

Hepatology. 2019 Dec;70(6):2047-2061. doi: 10.1002/hep.30773. Epub 2019 Jun 26.


AAV-Mediated Gene Delivery to the Mouse Liver.

Cunningham SC, Alexander IE.

Methods Mol Biol. 2019;1937:213-219. doi: 10.1007/978-1-4939-9065-8_12.


Codon-Optimization of Wild-Type Adeno-Associated Virus Capsid Sequences Enhances DNA Family Shuffling while Conserving Functionality.

Cabanes-Creus M, Ginn SL, Amaya AK, Liao SHY, Westhaus A, Hallwirth CV, Wilmott P, Ward J, Dilworth KL, Santilli G, Rybicki A, Nakai H, Thrasher AJ, Filip AC, Alexander IE, Lisowski L.

Mol Ther Methods Clin Dev. 2018 Nov 1;12:71-84. doi: 10.1016/j.omtm.2018.10.016. eCollection 2019 Mar 15.


Thymocyte self-renewal and oncogenic risk in immunodeficient mouse models: relevance for human gene therapy clinical trials targeting haematopoietic stem cell populations?

Ginn SL, McCormack MP, Alexander IE.

Mamm Genome. 2018 Dec;29(11-12):771-776. doi: 10.1007/s00335-018-9780-5. Epub 2018 Sep 4. Review.


Direct recognition of hepatocyte-expressed MHC class I alloantigens is required for tolerance induction.

Paul-Heng M, Leong M, Cunningham E, Bunker DLJ, Bremner K, Wang Z, Wang C, Tay SS, McGuffog C, Logan GJ, Alexander IE, Hu M, Alexander SI, Sparwasser TD, Bertolino P, Bowen DG, Bishop GA, Sharland A.

JCI Insight. 2018 Aug 9;3(15). pii: 97500. doi: 10.1172/jci.insight.97500. eCollection 2018 Aug 9.


Age-Related Seroprevalence of Antibodies Against AAV-LK03 in a UK Population Cohort.

Perocheau DP, Cunningham S, Lee J, Antinao Diaz J, Waddington SN, Gilmour K, Eaglestone S, Lisowski L, Thrasher AJ, Alexander IE, Gissen P, Baruteau J.

Hum Gene Ther. 2019 Jan;30(1):79-87. doi: 10.1089/hum.2018.098. Epub 2018 Oct 19.


Blockade of HMGB1 Attenuates Diabetic Nephropathy in Mice.

Chen X, Ma J, Kwan T, Stribos EGD, Messchendorp AL, Loh YW, Wang X, Paul M, Cunningham EC, Habib M, Alexander IE, Sharland AF, Chadban SJ, Wu H.

Sci Rep. 2018 May 29;8(1):8319. doi: 10.1038/s41598-018-26637-5.


Partial pancreatic transdifferentiation of primary human hepatocytes in the livers of a humanised mouse model.

Ren B, La QT, O'Brien BA, Nassif NT, Tan Y, Gerace D, Martiniello-Wilks R, Torpy F, Dane AP, Alexander IE, Simpson AM.

J Gene Med. 2018 May;20(5):e3017. doi: 10.1002/jgm.3017. Epub 2018 Apr 16.


Gene therapy clinical trials worldwide to 2017: An update.

Ginn SL, Amaya AK, Alexander IE, Edelstein M, Abedi MR.

J Gene Med. 2018 May;20(5):e3015. doi: 10.1002/jgm.3015. Epub 2018 Apr 19. Review.


Clinical Trial of MGMT(P140K) Gene Therapy in the Treatment of Pediatric Patients with Brain Tumors.

Kramer B, Singh R, Wischusen J, Dent R, Rush A, Middlemiss S, Ching YW, Alexander IE, McCowage G.

Hum Gene Ther. 2018 Aug;29(8):874-885. doi: 10.1089/hum.2017.235. Epub 2018 Mar 23.


AAV-mediated gene delivery of the calreticulin anti-angiogenic domain inhibits ocular neovascularization.

Tu L, Wang JH, Barathi VA, Prea SM, He Z, Lee JH, Bender J, King AE, Logan GJ, Alexander IE, Bee YS, Tai MH, Dusting GJ, Bui BV, Zhong J, Liu GS.

Angiogenesis. 2018 Feb;21(1):95-109. doi: 10.1007/s10456-017-9591-4. Epub 2018 Jan 9.


Bioengineered AAV Capsids with Combined High Human Liver Transduction In Vivo and Unique Humoral Seroreactivity.

Paulk NK, Pekrun K, Zhu E, Nygaard S, Li B, Xu J, Chu K, Leborgne C, Dane AP, Haft A, Zhang Y, Zhang F, Morton C, Valentine MB, Davidoff AM, Nathwani AC, Mingozzi F, Grompe M, Alexander IE, Lisowski L, Kay MA.

Mol Ther. 2018 Jan 3;26(1):289-303. doi: 10.1016/j.ymthe.2017.09.021. Epub 2017 Sep 25.


Identification of liver-specific enhancer-promoter activity in the 3' untranslated region of the wild-type AAV2 genome.

Logan GJ, Dane AP, Hallwirth CV, Smyth CM, Wilkie EE, Amaya AK, Zhu E, Khandekar N, Ginn SL, Liao SHY, Cunningham SC, Sasaki N, Cabanes-Creus M, Tam PPL, Russell DW, Lisowski L, Alexander IE.

Nat Genet. 2017 Aug;49(8):1267-1273. doi: 10.1038/ng.3893. Epub 2017 Jun 19.


Ub-ISAP: a streamlined UNIX pipeline for mining unique viral vector integration sites from next generation sequencing data.

Kamboj A, Hallwirth CV, Alexander IE, McCowage GB, Kramer B.

BMC Bioinformatics. 2017 Jun 17;18(1):305. doi: 10.1186/s12859-017-1719-4.


Gene therapy for monogenic liver diseases: clinical successes, current challenges and future prospects.

Baruteau J, Waddington SN, Alexander IE, Gissen P.

J Inherit Metab Dis. 2017 Jul;40(4):497-517. doi: 10.1007/s10545-017-0053-3. Epub 2017 May 31. Review.


Human Connexin40 Mutations Slow Conduction and Increase Propensity for Atrial Fibrillation.

Kanthan A, Fahmy P, Rao R, Pouliopoulos J, Alexander IE, Thomas SP, Kizana E.

Heart Lung Circ. 2018 Jan;27(1):114-121. doi: 10.1016/j.hlc.2017.02.010. Epub 2017 Mar 21.


Limiting Thymic Precursor Supply Increases the Risk of Lymphoid Malignancy in Murine X-Linked Severe Combined Immunodeficiency.

Ginn SL, Hallwirth CV, Liao SH, Teber ET, Arthur JW, Wu J, Lee HC, Tay SS, Hu M, Reddel RR, McCormack MP, Thrasher AJ, Cavazzana M, Alexander SI, Alexander IE.

Mol Ther Nucleic Acids. 2017 Mar 17;6:1-14. doi: 10.1016/j.omtn.2016.11.011. Epub 2016 Dec 10.


Delivering efficient liver-directed AAV-mediated gene therapy.

Baruteau J, Waddington SN, Alexander IE, Gissen P.

Gene Ther. 2017 May;24(5):263-264. doi: 10.1038/gt.2016.90. Epub 2017 Jan 12. No abstract available.


Synthetic certified DNA reference material for analysis of human erythropoietin transgene and transcript in gene doping and gene therapy.

Baoutina A, Bhat S, Zheng M, Partis L, Dobeson M, Alexander IE, Emslie KR.

Gene Ther. 2016 Oct;23(10):708-717. doi: 10.1038/gt.2016.47. Epub 2016 Jun 7.


Germline viral "fossils" guide in silico reconstruction of a mid-Cenozoic era marsupial adeno-associated virus.

Smith RH, Hallwirth CV, Westerman M, Hetherington NA, Tseng YS, Cecchini S, Virag T, Ziegler ML, Rogozin IB, Koonin EV, Agbandje-McKenna M, Kotin RM, Alexander IE.

Sci Rep. 2016 Jul 5;6:28965. doi: 10.1038/srep28965.


Adeno-associated virus serotypes for gene therapeutics.

Lisowski L, Tay SS, Alexander IE.

Curr Opin Pharmacol. 2015 Oct;24:59-67. doi: 10.1016/j.coph.2015.07.006. Epub 2015 Aug 25. Review.


Transient suppression of hepatocellular replication in the mouse liver following transduction with recombinant adeno-associated virus.

Dane AP, Cunningham SC, Kok CY, Logan GJ, Alexander IE.

Gene Ther. 2015 Nov;22(11):917-22. doi: 10.1038/gt.2015.66. Epub 2015 Jul 30.


Methyl-Guanine-Methyl-Transferase Transgenic Bone Marrow Transplantation Allows N,N-bis(2-chloroethyl)-Nitrosourea Driven Donor Mixed-Chimerism Without Graft-Versus-Host Disease, and With Donor-Specific Allograft Tolerance.

Hu M, Kramer B, Zhang GY, Wang YM, Watson D, Howden B, McCowage G, Alexander IE, Gunning P, Alexander SI.

Transplantation. 2015 Dec;99(12):2476-84. doi: 10.1097/TP.0000000000000825.


Coherence analysis discriminates between retroviral integration patterns in CD34(+) cells transduced under differing clinical trial conditions.

Hallwirth CV, Garg G, Peters TJ, Kramer BA, Malani NV, Hyman J, Ruan X, Ginn SL, Hetherington NA, Veeravalli L, Shahab A, Ranganathan S, Wei CL, Liddle C, Thrasher AJ, Bushman FD, Buckley MJ, Alexander IE.

Mol Ther Methods Clin Dev. 2015 Apr 29;2:15015. doi: 10.1038/mtm.2015.15. eCollection 2015.


Modeling correction of severe urea cycle defects in the growing murine liver using a hybrid recombinant adeno-associated virus/piggyBac transposase gene delivery system.

Cunningham SC, Siew SM, Hallwirth CV, Bolitho C, Sasaki N, Garg G, Michael IP, Hetherington NA, Carpenter K, de Alencastro G, Nagy A, Alexander IE.

Hepatology. 2015 Aug;62(2):417-28. doi: 10.1002/hep.27842. Epub 2015 May 23.


ACE2 Therapy Using Adeno-associated Viral Vector Inhibits Liver Fibrosis in Mice.

Mak KY, Chin R, Cunningham SC, Habib MR, Torresi J, Sharland AF, Alexander IE, Angus PW, Herath CB.

Mol Ther. 2015 Sep;23(9):1434-43. doi: 10.1038/mt.2015.92. Epub 2015 May 25.


Lymphoid regeneration from gene-corrected SCID-X1 subject-derived iPSCs.

Menon T, Firth AL, Scripture-Adams DD, Galic Z, Qualls SJ, Gilmore WB, Ke E, Singer O, Anderson LS, Bornzin AR, Alexander IE, Zack JA, Verma IM.

Cell Stem Cell. 2015 Apr 2;16(4):367-72. doi: 10.1016/j.stem.2015.02.005. Epub 2015 Mar 12.


Exploiting the unique regenerative capacity of the liver to underpin cell and gene therapy strategies for genetic and acquired liver disease.

Logan GJ, de Alencastro G, Alexander IE, Yeoh GC.

Int J Biochem Cell Biol. 2014 Nov;56:141-52. doi: 10.1016/j.biocel.2014.10.023. Epub 2014 Oct 27. Review.


A novel intronic splice site deletion of the IL-2 receptor common gamma chain results in expression of a dysfunctional protein and T-cell-positive X-linked Severe combined immunodeficiency.

Gray PE, Logan GJ, Alexander IE, Poulton S, Roscioli T, Ziegler J.

Int J Immunogenet. 2015 Feb;42(1):11-4. doi: 10.1111/iji.12166. Epub 2014 Nov 28.


A genome-wide map of adeno-associated virus-mediated human gene targeting.

Deyle DR, Hansen RS, Cornea AM, Li LB, Burt AA, Alexander IE, Sandstrom RS, Stamatoyannopoulos JA, Wei CL, Russell DW.

Nat Struct Mol Biol. 2014 Nov;21(11):969-75. doi: 10.1038/nsmb.2895. Epub 2014 Oct 5.


Intrahepatic activation of naive CD4+ T cells by liver-resident phagocytic cells.

Tay SS, Wong YC, Roediger B, Sierro F, Lu B, McDonald DM, McGuffog CM, Meyer NJ, Alexander IE, Parish IA, Heath WR, Weninger W, Bishop GA, Gamble JR, McCaughan GW, Bertolino P, Bowen DG.

J Immunol. 2014 Sep 1;193(5):2087-95. doi: 10.4049/jimmunol.1400037. Epub 2014 Jul 28.


Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence.

Deakin CT, Deakin JJ, Ginn SL, Young P, Humphreys D, Suter CM, Alexander IE, Hallwirth CV.

Nucleic Acids Res. 2014;42(16):e129. doi: 10.1093/nar/gku607. Epub 2014 Jul 10.


Antigen expression level threshold tunes the fate of CD8 T cells during primary hepatic immune responses.

Tay SS, Wong YC, McDonald DM, Wood NA, Roediger B, Sierro F, Mcguffog C, Alexander IE, Bishop GA, Gamble JR, Weninger W, McCaughan GW, Bertolino P, Bowen DG.

Proc Natl Acad Sci U S A. 2014 Jun 24;111(25):E2540-9. doi: 10.1073/pnas.1406674111. Epub 2014 Jun 10.


Selection and evaluation of clinically relevant AAV variants in a xenograft liver model.

Lisowski L, Dane AP, Chu K, Zhang Y, Cunningham SC, Wilson EM, Nygaard S, Grompe M, Alexander IE, Kay MA.

Nature. 2014 Feb 20;506(7488):382-6. doi: 10.1038/nature12875. Epub 2013 Dec 25.


The transcriptional and functional properties of mouse epiblast stem cells resemble the anterior primitive streak.

Kojima Y, Kaufman-Francis K, Studdert JB, Steiner KA, Power MD, Loebel DA, Jones V, Hor A, de Alencastro G, Logan GJ, Teber ET, Tam OH, Stutz MD, Alexander IE, Pickett HA, Tam PP.

Cell Stem Cell. 2014 Jan 2;14(1):107-20. doi: 10.1016/j.stem.2013.09.014. Epub 2013 Oct 17.


AAV-encoded OTC activity persisting to adulthood following delivery to newborn spf(ash) mice is insufficient to prevent shRNA-induced hyperammonaemia.

Cunningham SC, Kok CY, Spinoulas A, Carpenter KH, Alexander IE.

Gene Ther. 2013 Dec;20(12):1184-7. doi: 10.1038/gt.2013.51. Epub 2013 Oct 10.


Adeno-associated virus-mediated rescue of neonatal lethality in argininosuccinate synthetase-deficient mice.

Kok CY, Cunningham SC, Carpenter KH, Dane AP, Siew SM, Logan GJ, Kuchel PW, Alexander IE.

Mol Ther. 2013 Oct;21(10):1823-31. doi: 10.1038/mt.2013.139. Epub 2013 Jul 2.


Pancreatic transdifferentiation in porcine liver following lentiviral delivery of human furin-cleavable insulin.

Gerace D, Ren B, Hawthorne WJ, Byrne MR, Phillips PM, O'Brien BA, Nassif N, Alexander IE, Simpson AM.

Transplant Proc. 2013 Jun;45(5):1869-74. doi: 10.1016/j.transproceed.2013.01.051.


Mitochondrial respiratory chain hepatopathies: role of liver transplantation. A case series of five patients.

De Greef E, Christodoulou J, Alexander IE, Shun A, O'Loughlin EV, Thorburn DR, Jermyn V, Stormon MO.

JIMD Rep. 2012;4:5-11. doi: 10.1007/8904_2011_29. Epub 2011 Nov 4.


Gene therapy clinical trials worldwide to 2012 - an update.

Ginn SL, Alexander IE, Edelstein ML, Abedi MR, Wixon J.

J Gene Med. 2013 Feb;15(2):65-77. doi: 10.1002/jgm.2698. Review.


Gene therapy researchers' assessments of risks and perceptions of risk acceptability in clinical trials.

Deakin CT, Alexander IE, Hooker CA, Kerridge IH.

Mol Ther. 2013 Apr;21(4):806-15. doi: 10.1038/mt.2012.230. Epub 2013 Jan 22.


Gene therapy for tolerance: high-level expression of donor major histocompatibility complex in the liver overcomes naive and memory alloresponses to skin grafts.

Cunningham EC, Tay SS, Wang C, Rtshiladze M, Wang ZZ, McGuffog C, Cubitt J, McCaughan GW, Alexander IE, Bertolino P, Sharland AF, Bowen DG, Bishop GA.

Transplantation. 2013 Jan 15;95(1):70-7. doi: 10.1097/TP.0b013e318278d39a.


Comparison of gene transfer to the murine liver following intraperitoneal and intraportal delivery of hepatotropic AAV pseudo-serotypes.

Dane AP, Wowro SJ, Cunningham SC, Alexander IE.

Gene Ther. 2013 Apr;20(4):460-4. doi: 10.1038/gt.2012.67. Epub 2012 Aug 16.


Adeno-associated virus vectors: immunobiology and potential use for immune modulation.

Logan GJ, Alexander IE.

Curr Gene Ther. 2012 Aug;12(4):333-43. Review.


Study of LPIN1, LPIN2 and LPIN3 in rhabdomyolysis and exercise-induced myalgia.

Michot C, Hubert L, Romero NB, Gouda A, Mamoune A, Mathew S, Kirk E, Viollet L, Rahman S, Bekri S, Peters H, McGill J, Glamuzina E, Farrar M, von der Hagen M, Alexander IE, Kirmse B, Barth M, Laforet P, Benlian P, Munnich A, JeanPierre M, Elpeleg O, Pines O, Delahodde A, de Keyzer Y, de Lonlay P.

J Inherit Metab Dis. 2012 Nov;35(6):1119-28. doi: 10.1007/s10545-012-9461-6. Epub 2012 Apr 6.


Gene therapy for metabolic disorders: an overview with a focus on urea cycle disorders.

Alexander IE, Kok C, Dane AP, Cunningham SC.

J Inherit Metab Dis. 2012 Jul;35(4):641-5. doi: 10.1007/s10545-012-9467-0. Epub 2012 Mar 9.


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