(Q38947679)

19 June 2018

title

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

1 reference

19 June 2018

12

Nir Hacohen

0 references

John Sidney

6

object named as

John Sidney

1 reference

19 June 2018

Siranush Sarkizova

3

object named as

Siranush Sarkizova

1 reference

19 June 2018

author name string

Jennifer G Abelin

1

1 reference

19 June 2018

Derin B Keskin

2

1 reference

19 June 2018

Christina R Hartigan

4

1 reference

19 June 2018

Wandi Zhang

5

1 reference

19 June 2018

Jonathan Stevens

7

1 reference

19 June 2018

William Lane

8

1 reference

19 June 2018

Guang Lan Zhang

9

1 reference

19 June 2018

Thomas M Eisenhaure

10

1 reference

19 June 2018

Karl R Clauser

11

1 reference

19 June 2018

Michael S Rooney

13

1 reference

19 June 2018

Steven A Carr

14

1 reference

19 June 2018

Catherine J Wu

15

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19 June 2018

language of work or name

English

0 references

publication date

1 February 2017

1 reference

19 June 2018

published in

Immunity

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19 June 2018

volume

46

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19 June 2018

issue

2

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19 June 2018

page(s)

315-326

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19 June 2018

Unsupervised HLA Peptidome Deconvolution Improves Ligand Prediction Accuracy and Predicts Cooperative Effects in Peptide-HLA Interactions

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The Length Distribution of Class I-Restricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC Allele-Specific Binding Preference

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Sampling From the Proteome to the Human Leukocyte Antigen-DR (HLA-DR) Ligandome Proceeds Via High Specificity

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

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22 June 2018

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Using Data Independent Acquisition (DIA) to Model High-responding Peptides for Targeted Proteomics Experiments

22 June 2018

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Automated benchmarking of peptide-MHC class I binding predictions

22 June 2018

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

22 June 2018

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High-throughput epitope discovery reveals frequent recognition of neo-antigens by CD4+ T cells in human melanoma

22 June 2018

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22 June 2018

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22 June 2018

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22 June 2018

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Identification and characterisation of peptide binding motifs of six autoimmune disease-associated human leukocyte antigen-class I molecules including HLA-B*39:06.

22 June 2018

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The nature and extent of contributions by defective ribosome products to the HLA peptidome.

22 June 2018

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Re-examining class-I presentation and the DRiP hypothesis

22 June 2018

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Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells

22 June 2018

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Positional bias of MHC class I restricted T-cell epitopes in viral antigens is likely due to a bias in conservation

22 June 2018

1 reference

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Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.

22 June 2018

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22 June 2018

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Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.

22 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

Fast gapped-read alignment with Bowtie 2

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

Defining human ERAD networks through an integrative mapping strategy

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

DRiPs solidify: progress in understanding endogenous MHC class I antigen processing

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

CONSeQuence: prediction of reference peptides for absolute quantitative proteomics using consensus machine learning approaches

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

An integrated approach to epitope analysis I: Dimensional reduction, visualization and prediction of MHC binding using amino acid principal components and regression approaches

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

Network organization of the human autophagy system

22 June 2018

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Derivation of an amino acid similarity matrix for peptide: MHC binding and its application as a Bayesian prior

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

Systematic characterisation of cellular localisation and expression profiles of proteins containing MHC ligands

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

Defining the human deubiquitinating enzyme interaction landscape

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

Prediction of high-responding peptides for targeted protein assays by mass spectrometry

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

NetMHCpan, a method for MHC class I binding prediction beyond humans

22 June 2018

1 reference

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A detailed analysis of the murine TAP transporter substrate specificity

22 June 2018

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

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

Measurement of MHC/peptide interactions by gel filtration

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

Identification of breast cancer peptide epitopes presented by HLA-A*0201.

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

Detection of artifacts and peptide modifications in liquid chromatography/mass spectrometry data using two-dimensional signal intensity map data visualization.

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

Toward a definition of self: proteomic evaluation of the class I peptide repertoire

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

Predicting proteasomal cleavage sites: a comparison of available methods

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

The ER aminopeptidase ERAP1 enhances or limits antigen presentation by trimming epitopes to 8-9 residues

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

Discrete cleavage motifs of constitutive and immunoproteasomes revealed by quantitative analysis of cleavage products

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

MHC ligands and peptide motifs: first listing

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

Characterization of peptides bound to the class I MHC molecule HLA-A2.1 by mass spectrometry

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

Gapped sequence alignment using artificial neural networks: application to the MHC class I system.

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

ERAP1-ERAP2 dimerization increases peptide-trimming efficiency.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

NetMHCstab - predicting stability of peptide-MHC-I complexes; impacts for cytotoxic T lymphocyte epitope discovery.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

Elicitation from virus-naive individuals of cytotoxic T lymphocytes directed against conserved HIV-1 epitopes.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

The turnover kinetics of major histocompatibility complex peptides of human cancer cells.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

Concerted peptide trimming by human ERAP1 and ERAP2 aminopeptidase complexes in the endoplasmic reticulum.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

Prediction of proteasome cleavage motifs by neural networks

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5405381

10.1016/J.IMMUNI.2017.02.007

2 December 2018

Identifiers

DOI

1 reference

19 June 2018

PMC publication ID

5405381

1 reference

19 June 2018

PubMed publication ID

28228285

1 reference

19 June 2018