(Q48372980)

11 February 2018

title

Modeling the adaptive immune system: predictions and simulations (English)

1 reference

11 February 2018

main subject

adaptive immune system

1 reference

4

1 reference

11 February 2018

Morten Nielsen

5

1 reference

11 February 2018

Ole Lund

object named as

Ole Lund

2

0 references

Claus Lundegaard

1

object named as

Claus Lundegaard

1 reference

11 February 2018

Can Kesmir

3

object named as

Can Kesmir

1 reference

11 February 2018

language of work or name

English

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publication date

28 November 2007

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11 February 2018

published in

Bioinformatics

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11 February 2018

volume

23

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11 February 2018

issue

24

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11 February 2018

page(s)

3265-3275

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11 February 2018

The ABCs of immunology: structure and function of TAP, the transporter associated with antigen processing

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Identification of immunodominant regions among promiscuous HLA-DR-restricted CD4+ T-cell epitopes on the tumor antigen MAGE-3

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Support-vector networks

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Epitope mapping and topographic analysis of VAR2CSA DBL3X involved in P. falciparum placental sequestration

21 January 2018

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Understanding the mechanisms and limitations of immune control of HIV.

21 January 2018

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Harnessing bioinformatics to discover new vaccines

21 January 2018

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Genetic divergence of the rhesus macaque major histocompatibility complex

21 January 2018

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Immunomics: discovering new targets for vaccines and therapeutics

21 January 2018

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Predictions of the secondary structure and antigenicity of human and bovine tropoelastins

21 January 2018

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Integrated modeling of the major events in the MHC class I antigen processing pathway

21 January 2018

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EpiJen: a server for multistep T cell epitope prediction

21 January 2018

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Decline in excision circles requires homeostatic renewal or homeostatic death of naive T cells

21 January 2018

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The mapping and reconstitution of a conformational discontinuous B-cell epitope of HIV-1.

21 January 2018

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Cellular peptide composition governed by major histocompatibility complex class I molecules.

21 January 2018

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Efficient MHC class I-independent amino-terminal trimming of epitope precursor peptides in the endoplasmic reticulum

21 January 2018

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A cellular calculus for signal integration by T cells

21 January 2018

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Naturally processed HLA class II peptides reveal highly conserved immunogenic flanking region sequence preferences that reflect antigen processing rather than peptide-MHC interactions.

21 January 2018

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Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools

21 January 2018

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Two complementary methods for predicting peptides binding major histocompatibility complex molecules.

21 January 2018

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21 January 2018

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Prediction of residues in discontinuous B-cell epitopes using protein 3D structures

21 January 2018

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Increased cell division but not thymic dysfunction rapidly affects the T-cell receptor excision circle content of the naive T cell population in HIV-1 infection

21 January 2018

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Thymic output: a bad TREC record

21 January 2018

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Measurement of T-cell kinetics: recent methodologic advances

21 January 2018

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Identifying HLA supertypes by learning distance functions

21 January 2018

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21 January 2018

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21 January 2018

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21 January 2018

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21 January 2018

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21 January 2018

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21 January 2018

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A combined transmembrane topology and signal peptide prediction method

21 January 2018

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Prediction of MHC class II binders using the ant colony search strategy

21 January 2018

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AAindex: amino acid index database

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTM471

Prediction of proteasome cleavage motifs by neural networks

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTM471

A systematic approach to vaccine complexity using an automaton model of the cellular and humoral immune system. I. Viral characteristics and polarized responses

21 January 2018

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Two distinct HLA-A*0101-specific submotifs illustrate alternative peptide binding modes

21 January 2018

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Immunoinformatics comes of age

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTM471

CEP: a conformational epitope prediction server.

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTM471

An algorithm for the prediction of proteasomal cleavages

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTM471

Improved method for predicting linear B-cell epitopes

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTM471

An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions.

21 January 2018

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Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment

21 January 2018

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IMGT, the international ImMunoGeneTics information system: a standardized approach for immunogenetics and immunoinformatics

21 January 2018

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A simplified representation of protein conformations for rapid simulation of protein folding

21 January 2018

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The generation of antibody diversity through somatic hypermutation and class switch recombination

21 January 2018

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Discovery of cancer vaccination protocols with a genetic algorithm driving an agent based simulator

21 January 2018

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Antigen presentation and the ubiquitin-proteasome system in host-pathogen interactions

21 January 2018

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T-cell epitope repertoire as predicted from human and viral genomes.

21 January 2018

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Definition of supertypes for HLA molecules using clustering of specificity matrices.

21 January 2018

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Predicting peptides that bind to MHC molecules using supervised learning of hidden Markov models.

21 January 2018

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Two novel T cell epitope prediction algorithms based on MHC-binding motifs; comparison of predicted and published epitopes from Mycobacterium tuberculosis and HIV protein sequences.

21 January 2018

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Mimotopes: realization of an unlikely concept

21 January 2018

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Dominant epitopes and allergic cross-reactivity: complex formation between a Fab fragment of a monoclonal murine IgG antibody and the major allergen from birch pollen Bet v 1

21 January 2018

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Rapid turnover of T lymphocytes in SIV-infected rhesus macaques.

21 January 2018

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Increased turnover of T lymphocytes in HIV-1 infection and its reduction by antiretroviral therapy

21 January 2018

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Discontinuous epitope prediction based on mimotope analysis.

21 January 2018

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Modelling vaccination schedules for a cancer immunoprevention vaccine

21 January 2018

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A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virus

21 January 2018

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A new method for mapping discontinuous antibody epitopes to reveal structural features of proteins.

21 January 2018

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Prediction of MHC class II binding peptides based on an iterative learning model

21 January 2018

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Reliable prediction of T-cell epitopes using neural networks with novel sequence representations

21 January 2018

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Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach

21 January 2018

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

21 January 2018

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NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence

21 January 2018

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Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method

21 January 2018

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Antigenic determinants in proteins coincide with surface regions accessible to large probes (antibody domains).

21 January 2018

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21 January 2018

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21 January 2018

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8 Predicting location of continuous epitopes in proteins from their primary structures

21 January 2018

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Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method

21 January 2018

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Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors.

21 January 2018

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The immune epitope database and analysis resource: from vision to blueprint

21 January 2018

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A community resource benchmarking predictions of peptide binding to MHC-I molecules

21 January 2018

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Bioinformatics for study of autoimmunity

21 January 2018

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SYFPEITHI: database for MHC ligands and peptide motifs

21 January 2018

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Modelling the human immune system by combining bioinformatics and systems biology approaches

21 January 2018

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Prediction of MHC class I binding peptides using profile motifs.

21 January 2018

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Functional antigen-independent synapses formed between T cells and dendritic cells

21 January 2018

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Modeling deuterated glucose labeling of T-lymphocytes

21 January 2018

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Predicting proteasomal cleavage sites: a comparison of available methods

21 January 2018

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Prediction of well-conserved HIV-1 ligands using a matrix-based algorithm, EpiMatrix.

21 January 2018

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Combining computer algorithms with experimental approaches permits the rapid and accurate identification of T cell epitopes from defined antigens

21 January 2018

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3D-Epitope-Explorer (3DEX): localization of conformational epitopes within three-dimensional structures of proteins

21 January 2018

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A model for simulating cognate recognition and response in the immune system

21 January 2018

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Nine major HLA class I supertypes account for the vast preponderance of HLA-A and -B polymorphism

21 January 2018

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

21 January 2018

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21 January 2018

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Selection and combination of machine learning classifiers for prediction of linear B-cell epitopes on proteins.

21 January 2018

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Machine learning approaches for prediction of linear B-cell epitopes on proteins

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTM471

Two new proteases in the MHC class I processing pathway

21 January 2018

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Peptide binding specificity of major histocompatibility complex class I resolved into an array of apparently independent subspecificities: quantitation by peptide libraries and improved prediction of binding.

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTM471

Measuring the accuracy of diagnostic systems

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTM471

SARS CTL vaccine candidates; HLA supertype-, genome-wide scanning and biochemical validation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTM471

Mapping a neutralizing epitope on the SARS coronavirus spike protein: computational prediction based on affinity-selected peptides.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTM471

Modeling the MHC class I pathway by combining predictions of proteasomal cleavage, TAP transport and MHC class I binding

21 January 2018

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Quantitative analysis of prion-protein degradation by constitutive and immuno-20S proteasomes indicates differences correlated with disease susceptibility

21 January 2018

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New insights into V(D)J recombination and its role in the evolution of the immune system

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTM471

Methods and protocols for prediction of immunogenic epitopes

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTM471

Mapping Epitope Structure and Activity: From One-Dimensional Prediction to Four-Dimensional Description of Antigenic Specificity

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTM471

CTL epitopes for influenza A including the H5N1 bird flu; genome-, pathogen-, and HLA-wide screening.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTM471

Immunodominance in major histocompatibility complex class I-restricted T lymphocyte responses

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTM471

PRED(TAP): a system for prediction of peptide binding to the human transporter associated with antigen processing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTM471

Assembly of MHC class I molecules within the endoplasmic reticulum

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTM471

Signal peptide prediction based on analysis of experimentally verified cleavage sites

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTM471

Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules

21 January 2018

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Transporter Associated with Antigen Processing Preselection of Peptides Binding to the MHC: A Bioinformatic Evaluation

21 January 2018

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Physicochemical explanation of peptide binding to HLA-A*0201 major histocompatibility complex: A three-dimensional quantitative structure-activity relationship study

21 January 2018

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Changes in thymic function with age and during the treatment of HIV infection

21 January 2018

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Expression and deletion analysis of the Trypanosoma brucei rhodesiense cysteine protease in Escherichia coli

21 January 2018

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12 December 2020

ADEPT: a computer program for prediction of protein antigenic determinants.

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12 December 2020

Definition of specific peptide motifs for four major HLA-A alleles

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12 December 2020

MAPPP: MHC class I antigenic peptide processing prediction.

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12 December 2020

Location of 'continuous' antigenic determinants in the protruding regions of proteins

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12 December 2020

Stochastic Model of T Cell Proliferation: A Calculus Revealing IL-2 Regulation of Precursor Frequencies, Cell Cycle Time, and Survival

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12 December 2020

Estimating average cellular turnover from 5–bromo–2'–deoxyuridine (BrdU) measurements

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12 December 2020

Analysis of vaccine's schedules using models

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12 December 2020

Predicting antigenic determinants in proteins: looking for unidimensional solutions to a three-dimensional problem?

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12 December 2020

Hidden Markov model-based prediction of antigenic peptides that interact with MHC class II molecules.

1 reference

12 December 2020

T cell renewal rates, telomerase, and telomere length shortening.

1 reference

12 December 2020

Structural evidence for recognition of a single epitope by two distinct antibodies

1 reference

12 December 2020

Exact prediction of a natural T cell epitope

1 reference

12 December 2020

Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains.

1 reference

12 December 2020

Customized versus universal scoring functions: application to class I MHC-peptide binding free energy predictions

1 reference

12 December 2020

A computer program for predicting protein antigenic determinants

1 reference

12 December 2020

Relationship between peptide selectivities of human transporters associated with antigen processing and HLA class I molecules

1 reference

12 December 2020

The antigenic index: a novel algorithm for predicting antigenic determinants.

1 reference

12 December 2020

BEPITOPE: predicting the location of continuous epitopes and patterns in proteins

1 reference

12 December 2020

Correlation between the location of antigenic sites and the prediction of turns in proteins

1 reference

12 December 2020

Hidden Markov models for sequence analysis: extension and analysis of the basic method

1 reference

12 December 2020

Methods for prediction of peptide binding to MHC molecules: a comparative study.

1 reference

12 December 2020

Different views of protein antigenicity

1 reference

12 December 2020

HLA supertypes and supermotifs: a functional perspective on HLA polymorphism

1 reference

12 December 2020

A sequence pattern common to T cell epitopes

1 reference

12 December 2020

Toward the quantitative prediction of T-cell epitopes: QSAR studies on peptides having affinity with the class I MHC molecular HLA-A*0201

1 reference

12 December 2020

Prediction of immunogenicity for therapeutic proteins: state of the art.

1 reference

12 December 2020

10.1093/BIOINFORMATICS/BTM471

Identifiers

DOI

1 reference

11 February 2018

journals/bioinformatics/LundegaardLKBN07

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

release_zbp7q6imrfgklixo2thivrup5i

28 January 2021

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/zbp7q6imrfgklixo2thivrup5i

24 November 2022

mapped directly with Wikidata item

PMC publication ID

7110254

0 references

1 reference

11 February 2018