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Response to Comment on "A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands".

Faridi P, Li C, Ramarathinam SH, Illing PT, Mifsud NA, Ayala R, Song J, Gearing LJ, Croft NP, Purcell AW.

Sci Immunol. 2019 Aug 16;4(38). pii: eaaw8457. doi: 10.1126/sciimmunol.aaw8457.


Microbial Taxon-Specific Isotope Incorporation with DNA Quantitative Stable Isotope Probing.

Finley BK, Hayer M, Mau RL, Purcell AM, Koch BJ, van Gestel NC, Schwartz E, Hungate BA.

Methods Mol Biol. 2019;2046:137-149. doi: 10.1007/978-1-4939-9721-3_11.


The application of the maximal opposition therapy approach to an Arabic-speaking child.

Alsaad M, McCabe P, Purcell A.

J Commun Disord. 2019 Sep - Oct;81:105913. doi: 10.1016/j.jcomdis.2019.105913. Epub 2019 Jun 6.


Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTL responses.

Wu T, Guan J, Handel A, Tscharke DC, Sidney J, Sette A, Wakim LM, Sng XYX, Thomas PG, Croft NP, Purcell AW, La Gruta NL.

Nat Commun. 2019 Jun 28;10(1):2846. doi: 10.1038/s41467-019-10661-8.


A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction.

Mei S, Li F, Leier A, Marquez-Lago TT, Giam K, Croft NP, Akutsu T, Smith AI, Li J, Rossjohn J, Purcell AW, Song J.

Brief Bioinform. 2019 Jun 14. pii: bbz051. doi: 10.1093/bib/bbz051. [Epub ahead of print]


Downregulation of MHC Class I Expression by Influenza A and B Viruses.

Koutsakos M, McWilliam HEG, Aktepe TE, Fritzlar S, Illing PT, Mifsud NA, Purcell AW, Rockman S, Reading PC, Vivian JP, Rossjohn J, Brooks AG, Mackenzie JM, Mintern JD, Villadangos JA, Nguyen THO, Kedzierska K.

Front Immunol. 2019 May 29;10:1158. doi: 10.3389/fimmu.2019.01158. eCollection 2019.


Improved peptide-MHC class II interaction prediction through integration of eluted ligand and peptide affinity data.

Garde C, Ramarathinam SH, Jappe EC, Nielsen M, Kringelum JV, Trolle T, Purcell AW.

Immunogenetics. 2019 Jul;71(7):445-454. doi: 10.1007/s00251-019-01122-z. Epub 2019 Jun 10.


Clinical management of childhood apraxia of speech: A survey of speech-language pathologists in Australia and New Zealand.

Gomez M, McCabe P, Purcell A.

Int J Speech Lang Pathol. 2019 Jun;21(3):295-304. doi: 10.1080/17549507.2019.1608301. Epub 2019 May 23.


Mass spectrometry-based identification of MHC-bound peptides for immunopeptidomics.

Purcell AW, Ramarathinam SH, Ternette N.

Nat Protoc. 2019 Jun;14(6):1687-1707. doi: 10.1038/s41596-019-0133-y. Epub 2019 May 15.


The Evolving Landscape of Autoantigen Discovery and Characterization in Type 1 Diabetes.

Purcell AW, Sechi S, DiLorenzo TP.

Diabetes. 2019 May;68(5):879-886. doi: 10.2337/dbi18-0066.


The three-dimensional structure of an H-superfamily conotoxin reveals a granulin fold arising from a common ICK cysteine framework.

Nielsen LD, Foged MM, Albert A, Bertelsen AB, Søltoft CL, Robinson SD, Petersen SV, Purcell AW, Olivera BM, Norton RS, Vasskog T, Safavi-Hemami H, Teilum K, Ellgaard L.

J Biol Chem. 2019 May 31;294(22):8745-8759. doi: 10.1074/jbc.RA119.007491. Epub 2019 Apr 11.


Amyloid Self-Assembly of hIAPP8-20 via the Accumulation of Helical Oligomers, α-Helix to β-Sheet Transition, and Formation of β-Barrel Intermediates.

Sun Y, Kakinen A, Xing Y, Faridi P, Nandakumar A, Purcell AW, Davis TP, Ke PC, Ding F.

Small. 2019 May;15(18):e1805166. doi: 10.1002/smll.201805166. Epub 2019 Mar 25.


HLA-associated antiepileptic drug-induced cutaneous adverse reactions.

Mullan KA, Anderson A, Illing PT, Kwan P, Purcell AW, Mifsud NA.

HLA. 2019 Jun;93(6):417-435. doi: 10.1111/tan.13530. Epub 2019 Apr 9. Review.


Positive-unlabelled learning of glycosylation sites in the human proteome.

Li F, Zhang Y, Purcell AW, Webb GI, Chou KC, Lithgow T, Li C, Song J.

BMC Bioinformatics. 2019 Mar 6;20(1):112. doi: 10.1186/s12859-019-2700-1.


Human CD8+ T cell cross-reactivity across influenza A, B and C viruses.

Koutsakos M, Illing PT, Nguyen THO, Mifsud NA, Crawford JC, Rizzetto S, Eltahla AA, Clemens EB, Sant S, Chua BY, Wong CY, Allen EK, Teng D, Dash P, Boyd DF, Grzelak L, Zeng W, Hurt AC, Barr I, Rockman S, Jackson DC, Kotsimbos TC, Cheng AC, Richards M, Westall GP, Loudovaris T, Mannering SI, Elliott M, Tangye SG, Wakim LM, Rossjohn J, Vijaykrishna D, Luciani F, Thomas PG, Gras S, Purcell AW, Kedzierska K.

Nat Immunol. 2019 May;20(5):613-625. doi: 10.1038/s41590-019-0320-6. Epub 2019 Feb 18.


Most viral peptides displayed by class I MHC on infected cells are immunogenic.

Croft NP, Smith SA, Pickering J, Sidney J, Peters B, Faridi P, Witney MJ, Sebastian P, Flesch IEA, Heading SL, Sette A, La Gruta NL, Purcell AW, Tscharke DC.

Proc Natl Acad Sci U S A. 2019 Feb 19;116(8):3112-3117. doi: 10.1073/pnas.1815239116. Epub 2019 Feb 4.


American Academy of Physical Medicine and Rehabilitation Position Statement on Definitions for Rehabilitation Physician and Director of Rehabilitation in Inpatient Rehabilitation Settings.

Laker SR, Adair WA 3rd, Annaswamy TM, Frank LW, Hatzakis M Jr, Hubbell SL, Ifejika NL, Ivanhoe CB, Jones VA, Lupinacci MF, Purcell AD, Standaert CJ, Dolak MA.

PM R. 2019 Jan;11(1):98-102. doi: 10.1002/pmrj.12052. Epub 2019 Jan 22. No abstract available.


Physical and Toxicological Profiles of Human IAPP Amyloids and Plaques.

Kakinen A, Sun Y, Javed I, Faridi A, Pilkington EH, Faridi P, Purcell AW, Zhou R, Ding F, Lin S, Chun Ke P, Davis TP.

Sci Bull (Beijing). 2019 Jan 15;64(1):26-35. doi: 10.1016/j.scib.2018.11.012. Epub 2018 Nov 22.


The use of proteomics to understand antiviral immunity.

Woon AP, Purcell AW.

Semin Cell Dev Biol. 2018 Dec;84:22-29. doi: 10.1016/j.semcdb.2017.12.002. Epub 2018 Oct 8. Review.


HLA-B57 micropolymorphism defines the sequence and conformational breadth of the immunopeptidome.

Illing PT, Pymm P, Croft NP, Hilton HG, Jojic V, Han AS, Mendoza JL, Mifsud NA, Dudek NL, McCluskey J, Parham P, Rossjohn J, Vivian JP, Purcell AW.

Nat Commun. 2018 Nov 8;9(1):4693. doi: 10.1038/s41467-018-07109-w.


Design and delivery of an innovative speech pathology service-learning program for primary school children in Far West NSW, Australia.

Kirby S, Lyle D, Jones D, Brunero C, Purcell A, Dettwiller P.

Public Health Res Pract. 2018 Sep 27;28(3). pii: 28231806. doi: 10.17061/phrp28231806.


Mitigating Human IAPP Amyloidogenesis In Vivo with Chiral Silica Nanoribbons.

Faridi A, Sun Y, Okazaki Y, Peng G, Gao J, Kakinen A, Faridi P, Zhao M, Javed I, Purcell AW, Davis TP, Lin S, Oda R, Ding F, Ke PC.

Small. 2018 Nov;14(47):e1802825. doi: 10.1002/smll.201802825. Epub 2018 Oct 7.


Clozapine for the Management of Suicidal Behavior in Borderline Personality Disorder Complicated by a Cancer Diagnosis: A Case Report and Review of the Literature.

OʼLeary J, Purcell A, Hynes C, Huet J, Romanos M, McWilliams S.

J Clin Psychopharmacol. 2018 Dec;38(6):642-644. doi: 10.1097/JCP.0000000000000970. Review. No abstract available.


A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands.

Faridi P, Li C, Ramarathinam SH, Vivian JP, Illing PT, Mifsud NA, Ayala R, Song J, Gearing LJ, Hertzog PJ, Ternette N, Rossjohn J, Croft NP, Purcell AW.

Sci Immunol. 2018 Oct 12;3(28). pii: eaar3947. doi: 10.1126/sciimmunol.aar3947.


Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods.

Li F, Wang Y, Li C, Marquez-Lago TT, Leier A, Rawlings ND, Haffari G, Revote J, Akutsu T, Chou KC, Purcell AW, Pike RN, Webb GI, Ian Smith A, Lithgow T, Daly RJ, Whisstock JC, Song J.

Brief Bioinform. 2018 Aug 29. doi: 10.1093/bib/bby077. [Epub ahead of print]


Employing proteomics in the study of antigen presentation: an update.

Ramarathinam SH, Croft NP, Illing PT, Faridi P, Purcell AW.

Expert Rev Proteomics. 2018 Aug;15(8):637-645. doi: 10.1080/14789450.2018.1509000. Epub 2018 Aug 13. Review.


Viral regulation of host cell biology by hijacking of the nucleolar DNA-damage response.

Rawlinson SM, Zhao T, Rozario AM, Rootes CL, McMillan PJ, Purcell AW, Woon A, Marsh GA, Lieu KG, Wang LF, Netter HJ, Bell TDM, Stewart CR, Moseley GW.

Nat Commun. 2018 Aug 3;9(1):3057. doi: 10.1038/s41467-018-05354-7.


Eutectic mixture of local anaesthetics (EMLA®) as a primary dressing on painful chronic leg ulcers: a pilot randomised controlled trial.

Purcell A, Buckley T, King J, Moyle W, Marshall AP.

Pilot Feasibility Stud. 2018 Jul 7;4:123. doi: 10.1186/s40814-018-0312-6. eCollection 2018.


Isolation of T cell receptors targeting recurrent neoantigens in hematological malignancies.

Tubb VM, Schrikkema DS, Croft NP, Purcell AW, Linnemann C, Freriks MR, Chen F, Long HM, Lee SP, Bendle GM.

J Immunother Cancer. 2018 Jul 13;6(1):70. doi: 10.1186/s40425-018-0386-y.


Immunopeptidomics Special Issue.

Ternette N, Purcell AW.

Proteomics. 2018 Jun;18(12):e1800145. doi: 10.1002/pmic.201800145. No abstract available.


Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.

Li F, Li C, Marquez-Lago TT, Leier A, Akutsu T, Purcell AW, Ian Smith A, Lithgow T, Daly RJ, Song J, Chou KC.

Bioinformatics. 2018 Dec 15;34(24):4223-4231. doi: 10.1093/bioinformatics/bty522.


Minimal Information About an Immuno-Peptidomics Experiment (MIAIPE).

Lill JR, van Veelen PA, Tenzer S, Admon A, Caron E, Elias JE, Heck AJR, Marcilla M, Marino F, Müller M, Peters B, Purcell A, Sette A, Sturm T, Ternette N, Vizcaíno JA, Bassani-Sternberg M.

Proteomics. 2018 Jun;18(12):e1800110. doi: 10.1002/pmic.201800110.


Inability To Detect Cross-Reactive Memory T Cells Challenges the Frequency of Heterologous Immunity among Common Viruses.

Rowntree LC, Nguyen THO, Halim H, Purcell AW, Rossjohn J, Gras S, Kotsimbos TC, Mifsud NA.

J Immunol. 2018 Jun 15;200(12):3993-4003. doi: 10.4049/jimmunol.1800010. Epub 2018 May 7.


Reply to Roudier et al.: HLA-DRB1 polymorphism, anti-citrullinated protein antibodies, and rheumatoid arthritis.

Ting YT, Purcell AW, Reid HH, Rossjohn J.

J Biol Chem. 2018 May 4;293(18):7039. doi: 10.1074/jbc.RL118.003013. No abstract available.


Venous thromboembolism prophylaxis in mental health in-patient services: a qualitative study.

Purcell A, Clarke M, Maidment I.

Int J Clin Pharm. 2018 Jun;40(3):543-549. doi: 10.1007/s11096-018-0599-7. Epub 2018 Apr 27.


Tadpole-like Conformations of Huntingtin Exon 1 Are Characterized by Conformational Heterogeneity that Persists regardless of Polyglutamine Length.

Newcombe EA, Ruff KM, Sethi A, Ormsby AR, Ramdzan YM, Fox A, Purcell AW, Gooley PR, Pappu RV, Hatters DM.

J Mol Biol. 2018 May 11;430(10):1442-1458. doi: 10.1016/j.jmb.2018.03.031. Epub 2018 Apr 5.


Treating Childhood Apraxia of Speech With the Kaufman Speech to Language Protocol: A Phase I Pilot Study.

Gomez M, McCabe P, Jakielski K, Purcell A.

Lang Speech Hear Serv Sch. 2018 Jul 5;49(3):524-536. doi: 10.1044/2018_LSHSS-17-0100.


The Use of CRISPR/Cas9 Gene Editing to Confirm Congenic Contaminations in Host-Pathogen Interaction Studies.

Ferrand J, Croft NP, Pépin G, Diener KR, Wu D, Mangan NE, Pedersen J, Behlke MA, Hayball JD, Purcell AW, Ferrero RL, Gantier MP.

Front Cell Infect Microbiol. 2018 Mar 19;8:87. doi: 10.3389/fcimb.2018.00087. eCollection 2018.


T cell autoreactivity directed toward CD1c itself rather than toward carried self lipids.

Wun KS, Reijneveld JF, Cheng TY, Ladell K, Uldrich AP, Le Nours J, Miners KL, McLaren JE, Grant EJ, Haigh OL, Watkins TS, Suliman S, Iwany S, Jimenez J, Calderon R, Tamara KL, Leon SR, Murray MB, Mayfield JA, Altman JD, Purcell AW, Miles JJ, Godfrey DI, Gras S, Price DA, Van Rhijn I, Moody DB, Rossjohn J.

Nat Immunol. 2018 Apr;19(4):397-406. doi: 10.1038/s41590-018-0065-7. Epub 2018 Mar 12.


Identification of Native and Posttranslationally Modified HLA-B*57:01-Restricted HIV Envelope Derived Epitopes Using Immunoproteomics.

Ramarathinam SH, Gras S, Alcantara S, Yeung AWS, Mifsud NA, Sonza S, Illing PT, Glaros EN, Center RJ, Thomas SR, Kent SJ, Ternette N, Purcell DFJ, Rossjohn J, Purcell AW.

Proteomics. 2018 Jun;18(12):e1700253. doi: 10.1002/pmic.201700253. Epub 2018 Apr 10.


In Immunopeptidomics We Need a Sniper Instead of a Shotgun.

Faridi P, Purcell AW, Croft NP.

Proteomics. 2018 Jun;18(12):e1700464. doi: 10.1002/pmic.201700464. Epub 2018 Mar 7.


The interplay between citrullination and HLA-DRB1 polymorphism in shaping peptide binding hierarchies in rheumatoid arthritis.

Ting YT, Petersen J, Ramarathinam SH, Scally SW, Loh KL, Thomas R, Suri A, Baker DG, Purcell AW, Reid HH, Rossjohn J.

J Biol Chem. 2018 Mar 2;293(9):3236-3251. doi: 10.1074/jbc.RA117.001013. Epub 2018 Jan 9.


Australian children with cleft palate achieve age-appropriate speech by 5 years of age.

Chacon A, Parkin M, Broome K, Purcell A.

Int J Pediatr Otorhinolaryngol. 2017 Dec;103:93-102. doi: 10.1016/j.ijporl.2017.09.030. Epub 2017 Sep 28.


The SysteMHC Atlas project.

Shao W, Pedrioli PGA, Wolski W, Scurtescu C, Schmid E, Vizcaíno JA, Courcelles M, Schuster H, Kowalewski D, Marino F, Arlehamn CSL, Vaughan K, Peters B, Sette A, Ottenhoff THM, Meijgaarden KE, Nieuwenhuizen N, Kaufmann SHE, Schlapbach R, Castle JC, Nesvizhskii AI, Nielsen M, Deutsch EW, Campbell DS, Moritz RL, Zubarev RA, Ytterberg AJ, Purcell AW, Marcilla M, Paradela A, Wang Q, Costello CE, Ternette N, van Veelen PA, van Els CACM, Heck AJR, de Souza GA, Sollid LM, Admon A, Stevanovic S, Rammensee HG, Thibault P, Perreault C, Bassani-Sternberg M, Aebersold R, Caron E.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1237-D1247. doi: 10.1093/nar/gkx664.


Comparative Transcriptomics Highlights the Role of the Activator Protein 1 Transcription Factor in the Host Response to Ebolavirus.

Wynne JW, Todd S, Boyd V, Tachedjian M, Klein R, Shiell B, Dearnley M, McAuley AJ, Woon AP, Purcell AW, Marsh GA, Baker ML.

J Virol. 2017 Nov 14;91(23). pii: e01174-17. doi: 10.1128/JVI.01174-17. Print 2017 Dec 1.


The molecular basis for peptide repertoire selection in the human leucocyte antigen (HLA) C*06:02 molecule.

Mobbs JI, Illing PT, Dudek NL, Brooks AG, Baker DG, Purcell AW, Rossjohn J, Vivian JP.

J Biol Chem. 2017 Oct 20;292(42):17203-17215. doi: 10.1074/jbc.M117.806976. Epub 2017 Aug 30.


The Effectiveness of EMLA as a Primary Dressing on Painful Chronic Leg Ulcers: Effects on Wound Healing and Health-Related Quality of Life.

Purcell A, Buckley T, Fethney J, King J, Moyle W, Marshall AP.

Int J Low Extrem Wounds. 2017 Sep;16(3):163-172. doi: 10.1177/1534734617726678. Epub 2017 Aug 24.


The Effectiveness of EMLA as a Primary Dressing on Painful Chronic Leg Ulcers: A Pilot Randomized Controlled Trial.

Purcell A, Buckley T, Fethney J, King J, Moyle W, Marshall AP.

Adv Skin Wound Care. 2017 Aug;30(8):354-363. doi: 10.1097/01.ASW.0000516197.13492.1a.


The role of HLA genes in pharmacogenomics: unravelling HLA associated adverse drug reactions.

Illing PT, Purcell AW, McCluskey J.

Immunogenetics. 2017 Aug;69(8-9):617-630. doi: 10.1007/s00251-017-1007-5. Epub 2017 Jul 10. Review.


Structural and regulatory diversity shape HLA-C protein expression levels.

Kaur G, Gras S, Mobbs JI, Vivian JP, Cortes A, Barber T, Kuttikkatte SB, Jensen LT, Attfield KE, Dendrou CA, Carrington M, McVean G, Purcell AW, Rossjohn J, Fugger L.

Nat Commun. 2017 Jun 26;8:15924. doi: 10.1038/ncomms15924.

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