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Immuno-proteomic interrogation of dengue infection reveals novel HLA haplotype-specific MHC-I antigens

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Measurement of MHC/Peptide Interactions by Gel Filtration

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Reversed‐phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells

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T‐Cell Immunopeptidomes Reveal Cell Subtype Surface Markers Derived From Intracellular Proteins

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Exploiting heterogeneous sequence properties improves prediction of protein disorder

inferredcites →https://doi.org/10.1006/jmbi.1997.0937openalex-snapshot

Two complementary methods for predicting peptides binding major histocompatibility complex molecules

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Relative Protein Quantification Using Tandem Mass Tag Mass Spectrometry

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Relationship between the inhibition constant (KI) and the concentration of inhibitor which causes 50 per cent inhibition (I50) of an enzymatic reaction

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An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

inferredcites →https://doi.org/10.1016/j.antiviral.2015.10.013openalex-snapshot

Targeting host lipid synthesis and metabolism to inhibit dengue and hepatitis C viruses

inferredcites →https://doi.org/10.1016/j.chom.2010.10.006openalex-snapshot

Dengue Virus-Induced Autophagy Regulates Lipid Metabolism

inferredcites →https://doi.org/10.1016/j.immuni.2017.02.007openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.it.2016.08.010openalex-snapshot

Present Yourself! By MHC Class I and MHC Class II Molecules

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Evaluation of the interferon-γ ELISPOT-assay for quantification of peptide specific T lymphocytes from peripheral blood

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Basic Local Alignment Search Tool

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The Selective Downregulation of Class I Major Histocompatibility Complex Proteins by HIV-1 Protects HIV-Infected Cells from NK Cells

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Quantitating Protein Synthesis, Degradation, and Endogenous Antigen Processing

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Tandem Mass Tags: A Novel Quantification Strategy for Comparative Analysis of Complex Protein Mixtures by MS/MS

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MultiNotch MS3 Enables Accurate, Sensitive, and Multiplexed Detection of Differential Expression across Cancer Cell Line Proteomes

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The diversity of zinc-finger genes on human chromosome 19 provides an evolutionary mechanism for defense against inherited endogenous retroviruses

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Complete but curtailed T-cell response to very low-affinity antigen

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Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens

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Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens

inferredcites →https://doi.org/10.1038/nmeth.1344openalex-snapshot

Simultaneous detection of many T-cell specificities using combinatorial tetramer staining

inferredcites →https://doi.org/10.1038/nmeth1019openalex-snapshot

Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry

inferredcites →https://doi.org/10.1038/nmeth1113openalex-snapshot

Semi-supervised learning for peptide identification from shotgun proteomics datasets

inferredcites →https://doi.org/10.1038/nprot.2006.121openalex-snapshot

Generation of peptide–MHC class I complexes through UV-mediated ligand exchange

inferredcites →https://doi.org/10.1038/nprot.2007.261openalex-snapshot

Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips

inferredcites →https://doi.org/10.1038/srep37829openalex-snapshot

Sphingomyelin generated by sphingomyelin synthase 1 is involved in attachment and infection with Japanese encephalitis virus

inferredcites →https://doi.org/10.1073/pnas.0910997107openalex-snapshot

Compartmentalized MHC class I antigen processing enhances immunosurveillance by circumventing the law of mass action

inferredcites →https://doi.org/10.1073/pnas.1305227110openalex-snapshot

Comprehensive analysis of dengue virus-specific responses supports an HLA-linked protective role for CD8 + T cells

inferredcites →https://doi.org/10.1073/pnas.86.9.3296openalex-snapshot

Prediction of major histocompatibility complex binding regions of protein antigens by sequence pattern analysis.

inferredcites →https://doi.org/10.1074/jbc.m110.126722openalex-snapshot

A Conserved E7-derived Cytotoxic T Lymphocyte Epitope Expressed on Human Papillomavirus 16-transformed HLA-A2+ Epithelial Cancers

inferredcites →https://doi.org/10.1074/mcp.m111.010587openalex-snapshot

PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification

inferredcites →https://doi.org/10.1074/mcp.m114.042812openalex-snapshot

Mass Spectrometry of Human Leukocyte Antigen Class I Peptidomes Reveals Strong Effects of Protein Abundance and Turnover on Antigen Presentation

inferredcites →https://doi.org/10.1074/mcp.m114.045401openalex-snapshot

The Viral Transcription Group Determines the HLA Class I Cellular Immune Response Against Human Respiratory Syncytial Virus*

inferredcites →https://doi.org/10.1074/mcp.r110.000935openalex-snapshot

Overcoming Key Technological Challenges in Using Mass Spectrometry for Mapping Cell Surfaces in Tissues

inferredcites →https://doi.org/10.1084/jem.146.1.201openalex-snapshot

Dengue viruses and mononuclear phagocytes. I. Infection enhancement by non-neutralizing antibody

inferredcites →https://doi.org/10.1084/jem.20021840openalex-snapshot

DC-SIGN (CD209) Mediates Dengue Virus Infection of Human Dendritic Cells

inferredcites →https://doi.org/10.1086/382280openalex-snapshot

Relationship of Preexisting Dengue Virus (DV) Neutralizing Antibody Levels to Viremia and Severity of Disease in a Prospective Cohort Study of DV Infection in Thailand

inferredcites →https://doi.org/10.1093/bioinformatics/16.4.404openalex-snapshot

The PSIPRED protein structure prediction server

inferredcites →https://doi.org/10.1093/bioinformatics/btp033openalex-snapshot

Jalview Version 2—a multiple sequence alignment editor and analysis workbench

inferredcites →https://doi.org/10.1093/clinids/19.3.500openalex-snapshot

Antibody-Dependent Enhancement of Infection and the Pathogenesis of Viral Disease

inferredcites →https://doi.org/10.1093/emboj/18.4.1081openalex-snapshot

A cytomegalovirus glycoprotein re‐routes MHC class I complexes to lysosomes for degradation

inferredcites →https://doi.org/10.1093/infdis/jiv289openalex-snapshot

Human CD8+T-Cell Responses Against the 4 Dengue Virus Serotypes Are Associated With Distinct Patterns of Protein Targets

inferredcites →https://doi.org/10.1093/nar/gkn202openalex-snapshot

NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8–11

inferredcites →https://doi.org/10.1093/nar/gkv1145openalex-snapshot

2016 update of the PRIDE database and its related tools

inferredcites →https://doi.org/10.1099/vir.0.2008/002535-0openalex-snapshot

Functional importance of dengue virus maturation: infectious properties of immature virions

inferredcites →https://doi.org/10.1111/imm.12905openalex-snapshot

Predicted MHC peptide binding promiscuity explains MHC class I ‘hotspots’ of antigen presentation defined by mass spectrometry eluted ligand data

inferredcites →https://doi.org/10.1111/tra.12469openalex-snapshot

Beyond attachment: Roles of DC‐SIGN in dengue virus infection

inferredcites →https://doi.org/10.1126/science.274.5284.94openalex-snapshot

Phenotypic Analysis of Antigen-Specific T Lymphocytes

inferredcites →https://doi.org/10.1126/science.358.6370.1514openalex-snapshot

Safety concerns derail dengue vaccination program

inferredcites →https://doi.org/10.1126/science.aaf4384openalex-snapshot

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

inferredcites →https://doi.org/10.1128/.74.11.5300-5309.2000openalex-snapshot

Downregulation of Major Histocompatibility Complex Class I Molecules by Kaposi's Sarcoma-Associated Herpesvirus K3 and K5 Proteins

inferredcites →https://doi.org/10.1128/jvi.00300-07openalex-snapshot

Characterization of the Early Events in Dengue Virus Cell Entry by Biochemical Assays and Single-Virus Tracking

inferredcites →https://doi.org/10.1128/jvi.00320-10openalex-snapshot

Additive Contribution of HLA Class I Alleles in the Immune Control of HIV-1 Infection

inferredcites →https://doi.org/10.1128/jvi.01914-14openalex-snapshot

Direct Interrogation of Viral Peptides Presented by the Class I HLA of HIV-Infected T Cells

inferredcites →https://doi.org/10.1128/jvi.02188-08openalex-snapshot

NS5 of Dengue Virus Mediates STAT2 Binding and Degradation

inferredcites →https://doi.org/10.1128/jvi.03627-14openalex-snapshot

Early Kinetics of the HLA Class I-Associated Peptidome of MVA.HIVconsv-Infected Cells

inferredcites →https://doi.org/10.1172/jci118964openalex-snapshot

Dominant recognition by human CD8+ cytotoxic T lymphocytes of dengue virus nonstructural proteins NS3 and NS1.2a.

inferredcites →https://doi.org/10.1172/jci26936openalex-snapshot

Relating TCR-peptide-MHC affinity to immunogenicity for the design of tumor vaccines

inferredcites →https://doi.org/10.1186/1471-2105-7-208openalex-snapshot

Length-dependent prediction of protein intrinsic disorder

inferredcites →https://doi.org/10.1194/jlr.m064212openalex-snapshot

Host sphingomyelin increases West Nile virus infection in vivo

inferredcites →https://doi.org/10.1371/journal.pbio.0030091openalex-snapshot

The Immune Epitope Database and Analysis Resource: From Vision to Blueprint

inferredcites →https://doi.org/10.1371/journal.pcbi.1002884openalex-snapshot

Positional Bias of MHC Class I Restricted T-Cell Epitopes in Viral Antigens Is Likely due to a Bias in Conservation

inferredcites →https://doi.org/10.1371/journal.pntd.0000272openalex-snapshot

Conservation and Variability of Dengue Virus Proteins: Implications for Vaccine Design

inferredcites →https://doi.org/10.1371/journal.pone.0029286openalex-snapshot

Identification of Naturally Processed Hepatitis C Virus-Derived Major Histocompatibility Complex Class I Ligands

inferredcites →https://doi.org/10.1371/journal.ppat.1003129openalex-snapshot

Kinetics of Antigen Expression and Epitope Presentation during Virus Infection

inferredcites →https://doi.org/10.2144/00286ir01openalex-snapshot

The Sequence Manipulation Suite: JavaScript Programs for Analyzing and Formatting Protein and DNA Sequences

inferredcites →https://doi.org/10.3389/fimmu.2017.01367openalex-snapshot

‘Hotspots’ of Antigen Presentation Revealed by Human Leukocyte Antigen Ligandomics for Neoantigen Prioritization

inferredcites →https://doi.org/10.4049/jimmunol.0801974openalex-snapshot

A Protective Role for Dengue Virus-Specific CD8+ T Cells

inferredcites →https://doi.org/10.4049/jimmunol.0901907openalex-snapshot

Defective Ribosomal Products Are the Major Source of Antigenic Peptides Endogenously Generated from Influenza A Virus Neuraminidase

inferredcites →https://doi.org/10.4049/jimmunol.1401597openalex-snapshot

CD8+ T Cells Prevent Antigen-Induced Antibody-Dependent Enhancement of Dengue Disease in Mice

inferredcites →https://doi.org/10.4049/jimmunol.152.8.3904openalex-snapshot

Role of HLA-A motifs in identification of potential CTL epitopes in human papillomavirus type 16 E6 and E7 proteins.

inferredcites →https://doi.org/10.4049/jimmunol.153.12.5586openalex-snapshot

The relationship between class I binding affinity and immunogenicity of potential cytotoxic T cell epitopes.

inferredcites →https://doi.org/10.4049/jimmunol.156.9.3308openalex-snapshot

Immunogenicity of peptides bound to MHC class I molecules depends on the MHC-peptide complex stability

inferredcites →https://doi.org/10.4049/jimmunol.157.5.1823openalex-snapshot

Defective ribosomal products (DRiPs): a major source of antigenic peptides for MHC class I molecules?

inferredcites →https://doi.org/10.4049/jimmunol.167.9.4801openalex-snapshot

Cutting Edge: Neosynthesis Is Required for the Presentation of a T Cell Epitope from a Long-Lived Viral Protein

inferredcites →https://doi.org/10.4049/jimmunol.1700893openalex-snapshot

NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data

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inferred← citeshttps://doi.org/10.1016/j.exer.2024.109887openalex-snapshot

Aqueous humour protein dysregulation in Asian eyes with primary open angle glaucoma

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