John Sidney

John Sidney

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John Sidney

Publications by authors named "John Sidney"

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A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2.

Cell Host Microbe 2020 Mar 12. Epub 2020 Mar 12.

Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California, San Diego, San Diego, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chom.2020.03.002DOI Listing
March 2020

Restricted myeloperoxidase epitopes drive the adaptive immune response in MPO-ANCA vasculitis.

J Autoimmun 2020 Jan 2;106:102306. Epub 2019 Aug 2.

UNC Kidney Center, Department of Medicine, 7024 Burnett-Womack, CB #7155, Chapel Hill, NC, 27599, USA; UNC Department of Pathology and Laboratory Medicine, CB #7525, Brinkhous-Bullitt Building, Chapel Hill, NC, 27599, USA.

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http://dx.doi.org/10.1016/j.jaut.2019.102306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6930338PMC
January 2020

A survey of known immune epitopes in the enteroviruses strains associated with acute flaccid myelitis.

Hum Immunol 2019 Nov 23;80(11):923-929. Epub 2019 Aug 23.

Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California, San Diego, CA 92093, USA.

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http://dx.doi.org/10.1016/j.humimm.2019.08.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6876747PMC
November 2019

Recognition of Class II MHC Peptide Ligands That Contain β-Amino Acids.

J Immunol 2019 Sep 7;203(6):1619-1628. Epub 2019 Aug 7.

Boston Children's Hospital and Harvard Medical School, Boston, MA 02115;

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http://dx.doi.org/10.4049/jimmunol.1900536DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736755PMC
September 2019

Naturally processed HLA-DR3-restricted HHV-6B peptides are recognized broadly with polyfunctional and cytotoxic CD4 T-cell responses.

Eur J Immunol 2019 Aug 2;49(8):1167-1185. Epub 2019 May 2.

Department of Pathology, University of Massachusetts Medical School, Worcester, MA.

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http://dx.doi.org/10.1002/eji.201948126DOI Listing
August 2019

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

Nat Commun 2019 06 28;10(1):2846. Epub 2019 Jun 28.

Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia.

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http://dx.doi.org/10.1038/s41467-019-10661-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6599079PMC
June 2019

Hepatitis D Virus-Specific CD8 T Cells Have a Memory-Like Phenotype Associated With Viral Immune Escape in Patients With Chronic Hepatitis D Virus Infection.

Gastroenterology 2019 05 18;156(6):1805-1819.e9. Epub 2019 Jan 18.

Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland. Electronic address:

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http://dx.doi.org/10.1053/j.gastro.2019.01.035DOI Listing
May 2019

Counter-regulation of regulatory T cells by autoreactive CD8 T cells in rheumatoid arthritis.

J Autoimmun 2019 May 16;99:81-97. Epub 2019 Feb 16.

Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, 00161, Rome, Italy; Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, 00161, Rome, Italy; Istituto Pasteur - Fondazione Cenci Bolognetti, 00185, Rome, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.jaut.2019.02.001DOI Listing
May 2019

New epitopes in ovalbumin provide insights for cancer neoepitopes.

JCI Insight 2019 Mar 14;5. Epub 2019 Mar 14.

Department of Immunology, University of Connecticut School of Medicine, Farmington, Connecticut, USA.

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http://dx.doi.org/10.1172/jci.insight.127882DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6538383PMC
March 2019

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

Proc Natl Acad Sci U S A 2019 02 4;116(8):3112-3117. Epub 2019 Feb 4.

John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia;

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http://dx.doi.org/10.1073/pnas.1815239116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6386720PMC
February 2019

Mapping the MHC Class I-Spliced Immunopeptidome of Cancer Cells.

Cancer Immunol Res 2019 01 13;7(1):62-76. Epub 2018 Nov 13.

Centre for Inflammation Biology and Cancer Immunology (CIBCI) and Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom.

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http://cancerimmunolres.aacrjournals.org/lookup/doi/10.1158/
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http://dx.doi.org/10.1158/2326-6066.CIR-18-0424DOI Listing
January 2019

Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 496 adults from San Diego, California, USA.

Hum Immunol 2018 Dec 29;79(12):821-822. Epub 2018 Sep 29.

Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S01988859183077
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http://dx.doi.org/10.1016/j.humimm.2018.09.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6537871PMC
December 2018

Development of a novel clustering tool for linear peptide sequences.

Immunology 2018 11 6;155(3):331-345. Epub 2018 Aug 6.

Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.

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http://dx.doi.org/10.1111/imm.12984DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6187223PMC
November 2018

Predicting HLA CD4 Immunogenicity in Human Populations.

Front Immunol 2018 14;9:1369. Epub 2018 Jun 14.

Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.

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http://dx.doi.org/10.3389/fimmu.2018.01369DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6010533PMC
June 2018

Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 159 individuals from the Worcester region of the Western Cape province of South Africa.

Hum Immunol 2018 Mar;79(3):143-144

Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA. Electronic address:

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http://dx.doi.org/10.1016/j.humimm.2018.01.004DOI Listing
March 2018

Development of a strategy and computational application to select candidate protein analogues with reduced HLA binding and immunogenicity.

Immunology 2018 01 28;153(1):118-132. Epub 2017 Sep 28.

Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.

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http://dx.doi.org/10.1111/imm.12816DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5721253PMC
January 2018

Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 339 adults from Managua, Nicaragua.

Hum Immunol 2018 Jan 7;79(1):1-2. Epub 2017 Nov 7.

Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1016/j.humimm.2017.11.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5788571PMC
January 2018

Novel Plasmodium antigens identified via genome-based antibody screen induce protection associated with polyfunctional T cell responses.

Sci Rep 2017 11 8;7(1):15053. Epub 2017 Nov 8.

QIMR Berghofer Medical Research Institute, Infectious Diseases Programme, Herston, QLD 4006, Australia.

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http://dx.doi.org/10.1038/s41598-017-15354-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5678182PMC
November 2017

Experimental validation of the RATE tool for inferring HLA restrictions of T cell epitopes.

BMC Immunol 2017 06 21;18(Suppl 1):20. Epub 2017 Jun 21.

Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, San Diego, CA, 92037, USA.

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http://dx.doi.org/10.1186/s12865-017-0204-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499093PMC
June 2017

Atheroprotective vaccination with MHC-II-restricted ApoB peptides induces peritoneal IL-10-producing CD4 T cells.

Am J Physiol Heart Circ Physiol 2017 Apr 13;312(4):H781-H790. Epub 2017 Jan 13.

Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, California; and

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http://dx.doi.org/10.1152/ajpheart.00798.2016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5407161PMC
April 2017

Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction.

Immunity 2017 02;46(2):315-326

Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA; Harvard Medical School, Boston, MA, 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2017.02.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5405381PMC
February 2017

Protective Role of Cross-Reactive CD8 T Cells Against Dengue Virus Infection.

EBioMedicine 2016 Nov 7;13:284-293. Epub 2016 Oct 7.

Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States. Electronic address:

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http://dx.doi.org/10.1016/j.ebiom.2016.10.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5264312PMC
November 2016

An ontology for major histocompatibility restriction.

J Biomed Semantics 2016 11;7. Epub 2016 Jan 11.

La Jolla Institute for Allergy and Immunology, 9420 Athena Circle La Jolla, San Diego, California 92037 USA.

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http://dx.doi.org/10.1186/s13326-016-0045-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4709943PMC
October 2016

A large fraction of HLA class I ligands are proteasome-generated spliced peptides.

Science 2016 10 20;354(6310):354-358. Epub 2016 Oct 20.

Institut für Biochemie, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany.

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http://dx.doi.org/10.1126/science.aaf4384DOI Listing
October 2016

Automatic Generation of Validated Specific Epitope Sets.

J Immunol Res 2015 19;2015:763461. Epub 2015 Oct 19.

Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1155/2015/763461DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4629045PMC
September 2016

TepiTool: A Pipeline for Computational Prediction of T Cell Epitope Candidates.

Curr Protoc Immunol 2016 08 1;114:18.19.1-18.19.24. Epub 2016 Aug 1.

La Jolla Institute for Allergy and Immunology, Division of Vaccine Discovery, La Jolla, California.

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http://doi.wiley.com/10.1002/cpim.12
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http://dx.doi.org/10.1002/cpim.12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4981331PMC
August 2016

Dengue virus infection elicits highly polarized CX3CR1+ cytotoxic CD4+ T cells associated with protective immunity.

Proc Natl Acad Sci U S A 2015 Aug 20;112(31):E4256-63. Epub 2015 Jul 20.

Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037;

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http://dx.doi.org/10.1073/pnas.1505956112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4534238PMC
August 2015

Automated benchmarking of peptide-MHC class I binding predictions.

Bioinformatics 2015 Jul 25;31(13):2174-81. Epub 2015 Feb 25.

Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark, Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA and Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark, Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA and Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina.

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http://dx.doi.org/10.1093/bioinformatics/btv123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4481849PMC
July 2015

Fine specificities of natural regulatory T cells after IVIG therapy in patients with Kawasaki disease.

Autoimmunity 2015 May 30;48(3):181-8. Epub 2015 Mar 30.

Department of Pediatrics, Rady Children's Hospital, School of Medicine, University of California San Diego , La Jolla, CA , USA and.

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http://dx.doi.org/10.3109/08916934.2015.1027817DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4784966PMC
May 2015

Consequences of periodic α-to-β(3) residue replacement for immunological recognition of peptide epitopes.

ACS Chem Biol 2015 Mar 5;10(3):844-54. Epub 2015 Jan 5.

⊥La Jolla Institute for Allergy and Immunology, La Jolla, California United States.

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http://dx.doi.org/10.1021/cb500888qDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4372116PMC
March 2015

Immunological consequences of intragenus conservation of Mycobacterium tuberculosis T-cell epitopes.

Proc Natl Acad Sci U S A 2015 Jan 29;112(2):E147-55. Epub 2014 Dec 29.

Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; and.

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http://dx.doi.org/10.1073/pnas.1416537112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299226PMC
January 2015

Association between specific timothy grass antigens and changes in TH1- and TH2-cell responses following specific immunotherapy.

J Allergy Clin Immunol 2014 Nov 16;134(5):1076-83. Epub 2014 Jul 16.

Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, Calif. Electronic address:

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http://dx.doi.org/10.1016/j.jaci.2014.05.033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4253970PMC
November 2014

Immunodominance changes as a function of the infecting dengue virus serotype and primary versus secondary infection.

J Virol 2014 Oct 23;88(19):11383-94. Epub 2014 Jul 23.

Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA.

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http://jvi.asm.org/cgi/doi/10.1128/JVI.01108-14
Publisher Site
http://dx.doi.org/10.1128/JVI.01108-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4178794PMC
October 2014

Allergy-associated T cell epitope repertoires are surprisingly diverse and include non-IgE reactive antigens.

World Allergy Organ J 2014 22;7(1):26. Epub 2014 Oct 22.

La Jolla Institute for Allergy & Immunology, 9420 Athena Circle, La Jolla, CA 92037 USA.

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http://dx.doi.org/10.1186/1939-4551-7-26DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4210551PMC
October 2014

Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia.

Blood 2014 Jul 2;124(3):453-62. Epub 2014 Jun 2.

Cancer Vaccine Center and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA;

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http://dx.doi.org/10.1182/blood-2014-04-567933DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4102716PMC
July 2014

Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions.

BMC Bioinformatics 2014 Jul 14;15:241. Epub 2014 Jul 14.

La Jolla Institute for Allergy & Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1186/1471-2105-15-241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4111843PMC
July 2014