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VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium.

Bagaev DV, Vroomans RMA, Samir J, Stervbo U, Rius C, Dolton G, Greenshields-Watson A, Attaf M, Egorov ES, Zvyagin IV, Babel N, Cole DK, Godkin AJ, Sewell AK, Kesmir C, Chudakov DM, Luciani F, Shugay M.

Nucleic Acids Res. 2019 Oct 7. pii: gkz874. doi: 10.1093/nar/gkz874. [Epub ahead of print]


Rituximab depletion of intrahepatic B cells to control refractory hepatic autoimmune overlap syndrome.

Appanna GD, Pembroke TPI, Miners KL, Price DA, Gallimore AM, Ladell K, Godkin AJ.

QJM. 2019 Oct 1;112(10):793-795. doi: 10.1093/qjmed/hcz161. No abstract available.


The Ussing chamber system for measuring intestinal permeability in health and disease.

Thomson A, Smart K, Somerville MS, Lauder SN, Appanna G, Horwood J, Sunder Raj L, Srivastava B, Durai D, Scurr MJ, Keita ÅV, Gallimore AM, Godkin A.

BMC Gastroenterol. 2019 Jun 20;19(1):98. doi: 10.1186/s12876-019-1002-4.


TCR-induced alteration of primary MHC peptide anchor residue.

Madura F, Rizkallah PJ, Legut M, Holland CJ, Fuller A, Bulek A, Schauenburg AJ, Trimby A, Hopkins JR, Wells SA, Godkin A, Miles JJ, Sami M, Li Y, Liddy N, Jakobsen BK, Loveridge EJ, Cole DK, Sewell AK.

Eur J Immunol. 2019 Jul;49(7):1052-1066. doi: 10.1002/eji.201948085. Epub 2019 May 27.


The nature of the human T cell response to the cancer antigen 5T4 is determined by the balance of regulatory and inflammatory T cells of the same antigen-specificity: implications for vaccine design.

Besneux M, Greenshields-Watson A, Scurr MJ, MacLachlan BJ, Christian A, Davies MM, Hargest R, Phillips S, Godkin A, Gallimore A.

Cancer Immunol Immunother. 2019 Feb;68(2):247-256. doi: 10.1007/s00262-018-2266-1. Epub 2018 Nov 7.


In Silico and Structural Analyses Demonstrate That Intrinsic Protein Motions Guide T Cell Receptor Complementarity Determining Region Loop Flexibility.

Holland CJ, MacLachlan BJ, Bianchi V, Hesketh SJ, Morgan R, Vickery O, Bulek AM, Fuller A, Godkin A, Sewell AK, Rizkallah PJ, Wells S, Cole DK.

Front Immunol. 2018 Apr 11;9:674. doi: 10.3389/fimmu.2018.00674. eCollection 2018.


T-cell modulation by cyclophosphamide for tumour therapy.

Hughes E, Scurr M, Campbell E, Jones E, Godkin A, Gallimore A.

Immunology. 2018 May;154(1):62-68. doi: 10.1111/imm.12913. Epub 2018 Mar 9. Review.


Treg Depletion Licenses T Cell-Driven HEV Neogenesis and Promotes Tumor Destruction.

Colbeck EJ, Jones E, Hindley JP, Smart K, Schulz R, Browne M, Cutting S, Williams A, Parry L, Godkin A, Ware CF, Ager A, Gallimore A.

Cancer Immunol Res. 2017 Nov;5(11):1005-1015. doi: 10.1158/2326-6066.CIR-17-0131. Epub 2017 Sep 25.


Effect of Modified Vaccinia Ankara-5T4 and Low-Dose Cyclophosphamide on Antitumor Immunity in Metastatic Colorectal Cancer: A Randomized Clinical Trial.

Scurr M, Pembroke T, Bloom A, Roberts D, Thomson A, Smart K, Bridgeman H, Adams R, Brewster A, Jones R, Gwynne S, Blount D, Harrop R, Wright M, Hills R, Gallimore A, Godkin A.

JAMA Oncol. 2017 Oct 12;3(10):e172579. doi: 10.1001/jamaoncol.2017.2579. Epub 2017 Oct 12.


Low-Dose Cyclophosphamide Induces Antitumor T-Cell Responses, which Associate with Survival in Metastatic Colorectal Cancer.

Scurr M, Pembroke T, Bloom A, Roberts D, Thomson A, Smart K, Bridgeman H, Adams R, Brewster A, Jones R, Gwynne S, Blount D, Harrop R, Hills R, Gallimore A, Godkin A.

Clin Cancer Res. 2017 Nov 15;23(22):6771-6780. doi: 10.1158/1078-0432.CCR-17-0895. Epub 2017 Aug 29.


Chronic infections with viruses or parasites: breaking bad to make good.

Godkin A, Smith KA.

Immunology. 2017 Apr;150(4):389-396. doi: 10.1111/imm.12703. Epub 2017 Jan 19. Review.


Cytomegalovirus-Specific IL-10-Producing CD4+ T Cells Are Governed by Type-I IFN-Induced IL-27 and Promote Virus Persistence.

Clement M, Marsden M, Stacey MA, Abdul-Karim J, Gimeno Brias S, Costa Bento D, Scurr MJ, Ghazal P, Weaver CT, Carlesso G, Clare S, Jones SA, Godkin A, Jones GW, Humphreys IR.

PLoS Pathog. 2016 Dec 7;12(12):e1006050. doi: 10.1371/journal.ppat.1006050. eCollection 2016 Dec.


Remarkably low affinity of CD4/peptide-major histocompatibility complex class II protein interactions.

Jönsson P, Southcombe JH, Santos AM, Huo J, Fernandes RA, McColl J, Lever M, Evans EJ, Hudson A, Chang VT, Hanke T, Godkin A, Dunne PD, Horrocks MH, Palayret M, Screaton GR, Petersen J, Rossjohn J, Fugger L, Dushek O, Xu XN, Davis SJ, Klenerman D.

Proc Natl Acad Sci U S A. 2016 May 17;113(20):5682-7. doi: 10.1073/pnas.1513918113. Epub 2016 Apr 25.


Enhanced Detection of Antigen-Specific CD4+ T Cells Using Altered Peptide Flanking Residue Peptide-MHC Class II Multimers.

Holland CJ, Dolton G, Scurr M, Ladell K, Schauenburg AJ, Miners K, Madura F, Sewell AK, Price DA, Cole DK, Godkin AJ.

J Immunol. 2015 Dec 15;195(12):5827-36. doi: 10.4049/jimmunol.1402787. Epub 2015 Nov 9.


Comparing ELISA test-positive prevalence, risk factors and management recommendations for Johne's disease prevention between organic and conventional dairy farms in Ontario, Canada.

Pieper L, Sorge US, DeVries T, Godkin A, Lissemore K, Kelton D.

Prev Vet Med. 2015 Nov 1;122(1-2):83-91. doi: 10.1016/j.prevetmed.2015.09.004. Epub 2015 Sep 10.


Eliminating roles for T-bet and IL-2 but revealing superior activation and proliferation as mechanisms underpinning dominance of regulatory T cells in tumors.

Colbeck EJ, Hindley JP, Smart K, Jones E, Bloom A, Bridgeman H, McPherson RC, Turner DG, Ladell K, Price DA, O'Connor RA, Anderton SM, Godkin AJ, Gallimore AM.

Oncotarget. 2015 Sep 22;6(28):24649-59. doi: 10.18632/oncotarget.5584.


Evaluation of the Johne's disease risk assessment and management plan on dairy farms in Ontario, Canada.

Pieper L, Sorge US, DeVries TJ, Godkin A, Lissemore K, Kelton DF.

J Dairy Sci. 2015 Oct;98(10):6792-800. doi: 10.3168/jds.2014-8813. Epub 2015 Aug 5.


Electrostatic Limit of Detection of Nanowire-Based Sensors.

Henning A, Molotskii M, Swaminathan N, Vaknin Y, Godkin A, Shalev G, Rosenwaks Y.

Small. 2015 Oct 7;11(37):4931-7. doi: 10.1002/smll.201500566. Epub 2015 Jul 14.


Monitoring regulatory T cells in clinical samples: consensus on an essential marker set and gating strategy for regulatory T cell analysis by flow cytometry.

Santegoets SJ, Dijkgraaf EM, Battaglia A, Beckhove P, Britten CM, Gallimore A, Godkin A, Gouttefangeas C, de Gruijl TD, Koenen HJ, Scheffold A, Shevach EM, Staats J, Taskén K, Whiteside TL, Kroep JR, Welters MJ, van der Burg SH.

Cancer Immunol Immunother. 2015 Oct;64(10):1271-86. doi: 10.1007/s00262-015-1729-x. Epub 2015 Jun 28.


More tricks with tetramers: a practical guide to staining T cells with peptide-MHC multimers.

Dolton G, Tungatt K, Lloyd A, Bianchi V, Theaker SM, Trimby A, Holland CJ, Donia M, Godkin AJ, Cole DK, Straten PT, Peakman M, Svane IM, Sewell AK.

Immunology. 2015 Sep;146(1):11-22. doi: 10.1111/imm.12499. Review.


High endothelial venules are rare in colorectal cancers but accumulate in extra-tumoral areas with disease progression.

Bento DC, Jones E, Junaid S, Tull J, Williams GT, Godkin A, Ager A, Gallimore A.

Oncoimmunology. 2015 Apr 2;4(3):e974374. eCollection 2015 Mar.


Tracking the kinetics of intrahepatic immune responses by repeated fine needle aspiration of the liver.

Pembroke T, Gallimore A, Godkin A.

J Immunol Methods. 2015 Sep;424:131-5. doi: 10.1016/j.jim.2015.04.011. Epub 2015 Apr 22.


Assessing the prognostic value of preoperative carcinoembryonic antigen-specific T-cell responses in colorectal cancer.

Scurr MJ, Brown CM, Costa Bento DF, Betts GJ, Rees BI, Hills RK, Gallimore A, Godkin A.

J Natl Cancer Inst. 2015 Feb 9;107(4). pii: djv001. doi: 10.1093/jnci/djv001. Print 2015 Apr.


Variability in Risk Assessment and Management Plan (RAMP) scores completed as part of the Ontario Johne's Education and Management Assistance Program(2010-2013).

Pieper L, DeVries TJ, Sorge US, Godkin A, Hand KJ, Perkins NR, Imada J, Kelton DF.

J Dairy Sci. 2015 Apr;98(4):2419-26. doi: 10.3168/jds.2014-8812. Epub 2015 Jan 31.


A distinct chemokine axis does not account for enrichment of Foxp3(+)  CD4(+) T cells in carcinogen-induced fibrosarcomas.

Ondondo B, Colbeck E, Jones E, Smart K, Lauder SN, Hindley J, Godkin A, Moser B, Ager A, Gallimore A.

Immunology. 2015 May;145(1):94-104. doi: 10.1111/imm.12430. Erratum in: Immunology. 2015 Oct;146(2):347.


Structural basis for ineffective T-cell responses to MHC anchor residue-improved "heteroclitic" peptides.

Madura F, Rizkallah PJ, Holland CJ, Fuller A, Bulek A, Godkin AJ, Schauenburg AJ, Cole DK, Sewell AK.

Eur J Immunol. 2015 Feb;45(2):584-91. doi: 10.1002/eji.201445114. Epub 2014 Dec 28.


Antibody stabilization of peptide-MHC multimers reveals functional T cells bearing extremely low-affinity TCRs.

Tungatt K, Bianchi V, Crowther MD, Powell WE, Schauenburg AJ, Trimby A, Donia M, Miles JJ, Holland CJ, Cole DK, Godkin AJ, Peakman M, Straten PT, Svane IM, Sewell AK, Dolton G.

J Immunol. 2015 Jan 1;194(1):463-74. doi: 10.4049/jimmunol.1401785. Epub 2014 Dec 1.


Comparison of peptide-major histocompatibility complex tetramers and dextramers for the identification of antigen-specific T cells.

Dolton G, Lissina A, Skowera A, Ladell K, Tungatt K, Jones E, Kronenberg-Versteeg D, Akpovwa H, Pentier JM, Holland CJ, Godkin AJ, Cole DK, Neller MA, Miles JJ, Price DA, Peakman M, Sewell AK.

Clin Exp Immunol. 2014 Jul;177(1):47-63. doi: 10.1111/cei.12339.


Escalating regulation of 5T4-specific IFN-γ+ CD4+ T cells distinguishes colorectal cancer patients from healthy controls and provides a target for in vivo therapy.

Scurr M, Bloom A, Pembroke T, Srinivasan R, Brown C, Smart K, Bridgeman H, Davies M, Hargest R, Phillips S, Christian A, Hockey T, Gallimore A, Godkin A.

Cancer Immunol Res. 2013 Dec;1(6). doi: 10.1158/2326-6066.CIR-13-0035.


T-cell receptor (TCR)-peptide specificity overrides affinity-enhancing TCR-major histocompatibility complex interactions.

Cole DK, Miles KM, Madura F, Holland CJ, Schauenburg AJ, Godkin AJ, Bulek AM, Fuller A, Akpovwa HJ, Pymm PG, Liddy N, Sami M, Li Y, Rizkallah PJ, Jakobsen BK, Sewell AK.

J Biol Chem. 2014 Jan 10;289(2):628-38. doi: 10.1074/jbc.M113.522110. Epub 2013 Nov 6.


Progression of carcinogen-induced fibrosarcomas is associated with the accumulation of naïve CD4+ T cells via blood vessels and lymphatics.

Ondondo B, Jones E, Hindley J, Cutting S, Smart K, Bridgeman H, Matthews KK, Ladell K, Price DA, Jackson DG, Godkin A, Ager A, Gallimore A.

Int J Cancer. 2014 May 1;134(9):2156-67. doi: 10.1002/ijc.28556. Epub 2013 Nov 8.


Highly prevalent colorectal cancer-infiltrating LAP⁺ Foxp3⁻ T cells exhibit more potent immunosuppressive activity than Foxp3⁺ regulatory T cells.

Scurr M, Ladell K, Besneux M, Christian A, Hockey T, Smart K, Bridgeman H, Hargest R, Phillips S, Davies M, Price D, Gallimore A, Godkin A.

Mucosal Immunol. 2014 Mar;7(2):428-39. doi: 10.1038/mi.2013.62. Epub 2013 Sep 25.


Home sweet home: the tumor microenvironment as a haven for regulatory T cells.

Ondondo B, Jones E, Godkin A, Gallimore A.

Front Immunol. 2013 Jul 16;4:197. doi: 10.3389/fimmu.2013.00197. eCollection 2013.


Interleukin-6 limits influenza-induced inflammation and protects against fatal lung pathology.

Lauder SN, Jones E, Smart K, Bloom A, Williams AS, Hindley JP, Ondondo B, Taylor PR, Clement M, Fielding C, Godkin AJ, Jones SA, Gallimore AM.

Eur J Immunol. 2013 Oct;43(10):2613-25. doi: 10.1002/eji.201243018. Epub 2013 Aug 12.


Re-Directing CD4(+) T Cell Responses with the Flanking Residues of MHC Class II-Bound Peptides: The Core is Not Enough.

Holland CJ, Cole DK, Godkin A.

Front Immunol. 2013 Jul 1;4:172. doi: 10.3389/fimmu.2013.00172. eCollection 2013.


Flow cytometry makes all the difference.

Pembroke T, Gallimore A, Godkin A.

J Hepatol. 2013 Oct;59(4):909-10. doi: 10.1016/j.jhep.2013.05.047. Epub 2013 Jun 20. No abstract available.


High endothelial venules: Help or hindrance in the quest for antitumor immunity?

Gallimore A, Godkin A, Ager A.

Oncoimmunology. 2013 May 1;2(5):e24272.


The paradox of NKp46+ natural killer cells: drivers of severe hepatitis C virus-induced pathology but in-vivo resistance to interferon α treatment.

Pembroke T, Christian A, Jones E, Hills RK, Wang EC, Gallimore AM, Godkin A.

Gut. 2014 Mar;63(3):515-24. doi: 10.1136/gutjnl-2013-304472. Epub 2013 May 11.


Epithelial barriers, microbiota, and colorectal cancer.

Gallimore AM, Godkin A.

N Engl J Med. 2013 Jan 17;368(3):282-4. doi: 10.1056/NEJMcibr1212341. No abstract available.


Rapid innate control of antigen abrogates adaptive immunity.

Pembroke TP, Gallimore AM, Godkin A.

Immunology. 2013 Apr;138(4):293-7. doi: 10.1111/imm.12048. Review.


Hunting for clues: Regulatory T cells and colorectal cancer.

Gallimore A, Godkin A.

Oncoimmunology. 2012 Oct 1;1(7):1163-1164.


T cell subsets and colorectal cancer: discerning the good from the bad.

Scurr M, Gallimore A, Godkin A.

Cell Immunol. 2012 Sep;279(1):21-4. doi: 10.1016/j.cellimm.2012.08.004. Epub 2012 Sep 14. Review.


Avidity of influenza-specific memory CD8+ T-cell populations decays over time compromising antiviral immunity.

Humphreys IR, Clement M, Marsden M, Ladell K, McLaren JE, Smart K, Hindley JP, Bridgeman HM, van den Berg HA, Price DA, Ager A, Wooldridge L, Godkin A, Gallimore AM.

Eur J Immunol. 2012 Dec;42(12):3235-42. doi: 10.1002/eji.201242575. Epub 2012 Oct 16.


T-cell trafficking facilitated by high endothelial venules is required for tumor control after regulatory T-cell depletion.

Hindley JP, Jones E, Smart K, Bridgeman H, Lauder SN, Ondondo B, Cutting S, Ladell K, Wynn KK, Withers D, Price DA, Ager A, Godkin AJ, Gallimore AM.

Cancer Res. 2012 Nov 1;72(21):5473-82. doi: 10.1158/0008-5472.CAN-12-1912. Epub 2012 Sep 7.


Minimal conformational plasticity enables TCR cross-reactivity to different MHC class II heterodimers.

Holland CJ, Rizkallah PJ, Vollers S, Calvo-Calle JM, Madura F, Fuller A, Sewell AK, Stern LJ, Godkin A, Cole DK.

Sci Rep. 2012;2:629. doi: 10.1038/srep00629. Epub 2012 Sep 4.


Herd characteristics and cow-level factors associated with Prototheca mastitis on dairy farms in Ontario, Canada.

Pieper L, Godkin A, Roesler U, Polleichtner A, Slavic D, Leslie KE, Kelton DF.

J Dairy Sci. 2012 Oct;95(10):5635-44. doi: 10.3168/jds.2011-5106. Epub 2012 Aug 9.


Rapid early innate control of hepatitis C virus during IFN-α treatment compromises adaptive CD4+ T-cell immunity.

Pembroke T, Rees I, Gallagher K, Jones E, Mizen P, Navruzov T, Freedman A, Fielding C, Humphreys IR, Wang EC, Gallimore AM, Godkin A.

Eur J Immunol. 2012 Sep;42(9):2383-94. doi: 10.1002/eji.201142072. Epub 2012 Aug 6.


Milk production and somatic cell counts: a cow-level analysis.

Hand KJ, Godkin A, Kelton DF.

J Dairy Sci. 2012 Mar;95(3):1358-62. doi: 10.3168/jds.2011-4927.


Modification of the carboxy-terminal flanking region of a universal influenza epitope alters CD4⁺ T-cell repertoire selection.

Cole DK, Gallagher K, Lemercier B, Holland CJ, Junaid S, Hindley JP, Wynn KK, Gostick E, Sewell AK, Gallimore AM, Ladell K, Price DA, Gougeon ML, Godkin A.

Nat Commun. 2012 Feb 7;3:665. doi: 10.1038/ncomms1665.

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