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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.


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.


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.


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.


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.


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.


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.


Dominant protection from HLA-linked autoimmunity by antigen-specific regulatory T cells.

Ooi JD, Petersen J, Tan YH, Huynh M, Willett ZJ, Ramarathinam SH, Eggenhuizen PJ, Loh KL, Watson KA, Gan PY, Alikhan MA, Dudek NL, Handel A, Hudson BG, Fugger L, Power DA, Holt SG, Coates PT, Gregersen JW, Purcell AW, Holdsworth SR, La Gruta NL, Reid HH, Rossjohn J, Kitching AR.

Nature. 2017 May 11;545(7653):243-247. doi: 10.1038/nature22329. Epub 2017 May 3.


HIVed, a knowledgebase for differentially expressed human genes and proteins during HIV infection, replication and latency.

Li C, Ramarathinam SH, Revote J, Khoury G, Song J, Purcell AW.

Sci Rep. 2017 Mar 30;7:45509. doi: 10.1038/srep45509.


MHC-I peptides get out of the groove and enable a novel mechanism of HIV-1 escape.

Pymm P, Illing PT, Ramarathinam SH, O'Connor GM, Hughes VA, Hitchen C, Price DA, Ho BK, McVicar DW, Brooks AG, Purcell AW, Rossjohn J, Vivian JP.

Nat Struct Mol Biol. 2017 Apr;24(4):387-394. doi: 10.1038/nsmb.3381. Epub 2017 Feb 20.


A Systems Approach to Understand Antigen Presentation and the Immune Response.

Dudek NL, Croft NP, Schittenhelm RB, Ramarathinam SH, Purcell AW.

Methods Mol Biol. 2016;1394:189-209. doi: 10.1007/978-1-4939-3341-9_14.


An open-source computational and data resource to analyze digital maps of immunopeptidomes.

Caron E, Espona L, Kowalewski DJ, Schuster H, Ternette N, AlpĂ­zar A, Schittenhelm RB, Ramarathinam SH, Lindestam Arlehamn CS, Chiek Koh C, Gillet LC, Rabsteyn A, Navarro P, Kim S, Lam H, Sturm T, Marcilla M, Sette A, Campbell DS, Deutsch EW, Moritz RL, Purcell AW, Rammensee HG, Stevanovic S, Aebersold R.

Elife. 2015 Jul 8;4. doi: 10.7554/eLife.07661.


A comprehensive analysis of constitutive naturally processed and presented HLA-C*04:01 (Cw4)-specific peptides.

Schittenhelm RB, Dudek NL, Croft NP, Ramarathinam SH, Purcell AW.

Tissue Antigens. 2014 Mar;83(3):174-9. doi: 10.1111/tan.12282. Epub 2014 Jan 7.


Discovery of an archetypal protein transport system in bacterial outer membranes.

Selkrig J, Mosbahi K, Webb CT, Belousoff MJ, Perry AJ, Wells TJ, Morris F, Leyton DL, Totsika M, Phan MD, Celik N, Kelly M, Oates C, Hartland EL, Robins-Browne RM, Ramarathinam SH, Purcell AW, Schembri MA, Strugnell RA, Henderson IR, Walker D, Lithgow T.

Nat Struct Mol Biol. 2012 Apr 1;19(5):506-10, S1. doi: 10.1038/nsmb.2261.


Secreted HLA recapitulates the immunopeptidome and allows in-depth coverage of HLA A*02:01 ligands.

Scull KE, Dudek NL, Corbett AJ, Ramarathinam SH, Gorasia DG, Williamson NA, Purcell AW.

Mol Immunol. 2012 Jun;51(2):136-42. doi: 10.1016/j.molimm.2012.02.117. Epub 2012 Mar 17.


Stable isotope shifted matrices enable the use of low mass ion precursor scanning for targeted metabolite identification.

Reilly CB, Ramarathinam SH, Williamson NA, Purcell AW.

Proteome Sci. 2011 Jan 17;9(1):2. doi: 10.1186/1477-5956-9-2.


A novel strategy for the targeted analysis of protein and peptide metabolites.

Williamson NA, Reilly C, Tan CT, Ramarathinam SH, Jones A, Hunter CL, Rooney FR, Purcell AW.

Proteomics. 2011 Jan;11(2):183-92. doi: 10.1002/pmic.201000474. Epub 2010 Dec 15.


Rapid microscale in-gel processing and digestion of proteins using surface acoustic waves.

Kulkarni KP, Ramarathinam SH, Friend J, Yeo L, Purcell AW, Perlmutter P.

Lab Chip. 2010 Jun 21;10(12):1518-20. doi: 10.1039/c001501f. Epub 2010 Mar 26.


A modular BAM complex in the outer membrane of the alpha-proteobacterium Caulobacter crescentus.

Anwari K, Poggio S, Perry A, Gatsos X, Ramarathinam SH, Williamson NA, Noinaj N, Buchanan S, Gabriel K, Purcell AW, Jacobs-Wagner C, Lithgow T.

PLoS One. 2010 Jan 8;5(1):e8619. doi: 10.1371/journal.pone.0008619.


Phosphorylated self-peptides alter human leukocyte antigen class I-restricted antigen presentation and generate tumor-specific epitopes.

Petersen J, Wurzbacher SJ, Williamson NA, Ramarathinam SH, Reid HH, Nair AK, Zhao AY, Nastovska R, Rudge G, Rossjohn J, Purcell AW.

Proc Natl Acad Sci U S A. 2009 Feb 24;106(8):2776-81. doi: 10.1073/pnas.0812901106. Epub 2009 Feb 5.


Can alpha- and beta-alanine containing peptides be distinguished based on the CID spectra of their protonated ions?

Lam AK, Ramarathinam SH, Purcell AW, O'Hair RA.

J Am Soc Mass Spectrom. 2008 Dec;19(12):1743-54. doi: 10.1016/j.jasms.2008.09.007. Epub 2008 Sep 12.


Prevention of cytotoxic T cell escape using a heteroclitic subdominant viral T cell determinant.

Butler NS, Theodossis A, Webb AI, Nastovska R, Ramarathinam SH, Dunstone MA, Rossjohn J, Purcell AW, Perlman S.

PLoS Pathog. 2008 Oct;4(10):e1000186. doi: 10.1371/journal.ppat.1000186. Epub 2008 Oct 24.


Structural and biological basis of CTL escape in coronavirus-infected mice.

Butler NS, Theodossis A, Webb AI, Dunstone MA, Nastovska R, Ramarathinam SH, Rossjohn J, Purcell AW, Perlman S.

J Immunol. 2008 Mar 15;180(6):3926-37.

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