(Q33564308)

28 July 2017

title

Computational immunology meets bioinformatics: the use of prediction tools for molecular binding in the simulation of the immune system (English)

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28 July 2017

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Nicolas Rapin

1

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Ole Lund

object named as

Ole Lund

series ordinal

2

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author name string

Massimo Bernaschi

series ordinal

3

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28 July 2017

Filippo Castiglione

series ordinal

4

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28 July 2017

language of work or name

English

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publication date

16 April 2010

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28 July 2017

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28 July 2017

volume

5

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28 July 2017

issue

4

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28 July 2017

page(s)

e9862

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Creative Commons Attribution 4.0 International

28 July 2017

copyright license

start time

16 April 2010

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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A discrete computer model of the immune system reveals competitive interactions between the humoral and cellular branch and between cross-reacting memory and naïve responses.

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Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research

21 June 2018

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MHC-I-restricted epitopes conserved among variola and other related orthopoxviruses are recognized by T cells 30 years after vaccination

21 June 2018

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21 June 2018

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Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan

21 June 2018

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Evaluation of MHC class I peptide binding prediction servers: applications for vaccine research

21 June 2018

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The Basic Immune Simulator: an agent-based model to study the interactions between innate and adaptive immunity

21 June 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 June 2018

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

21 June 2018

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

21 June 2018

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Improved method for predicting linear B-cell epitopes

21 June 2018

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Modelling vaccination schedules for a cancer immunoprevention vaccine

21 June 2018

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Characterization of the peptide-binding specificity of Mamu-A*11 results in the identification of SIV-derived epitopes and interspecies cross-reactivity

21 June 2018

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Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach.

21 June 2018

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THE LIMITED IN VITRO LIFETIME OF HUMAN DIPLOID CELL STRAINS

21 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=2855701

The serial cultivation of human diploid cell strains

21 June 2018

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

21 June 2018

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21 June 2018

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

21 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=2855701

HLA and HIV-1: heterozygote advantage and B*35-Cw*04 disadvantage

21 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=2855701

Viral dynamics of primary viremia and antiretroviral therapy in simian immunodeficiency virus infection

21 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=2855701

Replicative senescence of T cells: does the Hayflick Limit lead to immune exhaustion?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

21 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=2855701

Virus dynamics and drug therapy

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Decay characteristics of HIV-1-infected compartments during combination therapy

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Anti-viral drug treatment: dynamics of resistance in free virus and infected cell populations

21 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=2855701

Cytotoxic T lymphocytes and viral turnover in HIV type 1 infection

21 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=2855701

Clinical data sets of human immunodeficiency virus type 1 reverse transcriptase-resistant mutants explained by a mathematical model.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Viral dynamics in vivo: limitations on estimates of intracellular delay and virus decay

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

The maturation of the immune response

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Tolerance, danger, and the extended family

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Modeling HIV infection of CD4+ T-cell subpopulations

21 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=2855701

MHCPEP: a database of MHC-binding peptides

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Viral dynamics in human immunodeficiency virus type 1 infection

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Clonal anergy: persistence in tolerant mice of antigen-binding B lymphocytes incapable of responding to antigen or mitogen

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

The major histocompatibility complex-restricted antigen receptor on T cells. I. Isolation with a monoclonal antibody

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Somatic generation of antibody diversity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Antigen-Presenting Function of the Macrophage

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Towards a network theory of the immune system.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

The cellular basis of immunologic memory

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

The nature and role of antigen processing in T-cell activation.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

T cell selection in the thymus

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Immunological help at last.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Constraints in T-B cooperation related to epitope topology on E. coli beta-galactosidase. I. The fine specificity of T cells dictates the fine specificity of antibodies directed to conformation-dependent determinants

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

21 June 2018

Immune network theory

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Sequence logos: a new way to display consensus sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Oral tolerance in experimental autoimmune encephalomyelitis. III. Evidence for clonal anergy.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

A computer model of cellular interactions in the immune system

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Competition between zidovudine-sensitive and zidovudine-resistant strains of HIV.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

The arrangement and rearrangement of antibody genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Theoretical studies of clonal selection: Minimal antibody repertoire size and reliability of self-non-self discrimination

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Implementation of a regulatory gene network to simulate the TH1/2 differentiation in an agent-based model of hypersensitivity reactions.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Modeling the adaptive immune system: predictions and simulations.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Simulating Epstein-Barr virus infection with C-ImmSim.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Discovery of promiscuous HLA-II-restricted T cell epitopes with TEPITOPE.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Design and implementation of an immune system simulator.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Hayflick, his limit, and cellular ageing.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Identifying sequence-structure pairs undetected by sequence alignments.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Overshoot of HIV-1 viraemia after early discontinuation of antiretroviral treatment.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Dynamic multidrug therapies for HIV: a control theoretic approach.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Equilibrium binding of multivalent ligands to cells: effects of cell and receptor density.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

T-cell homeostasis, competition, and drift: AIDS as HIV-accelerated senescence of the immune repertoire.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

Dynamics of HIV infection of CD4+ T cells.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

T cell repertoires and competitive exclusion.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2855701

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

31 October 2018

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12 December 2020

Affinity maturation and hypermutation in a simulation of the humoral immune response

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12 December 2020

Isolation of cDNA clones encoding T cell-specific membrane-associated proteins

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12 December 2020

EPIMHC: a curated database of MHC-binding peptides for customized computational vaccinology

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12 December 2020

An empirical energy potential with a reference state for protein fold and sequence recognition

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12 December 2020

Antigen-specific interaction between T and B cells

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12 December 2020

Modelling thymic functions in a cellular automaton

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12 December 2020

Computational modelling and simulation of the immune system

1 reference

12 December 2020

Mutation, fitness, viral diversity, and predictive markers of disease progression in a computational model of HIV type 1 infection

1 reference

12 December 2020

10.1371/JOURNAL.PONE.0009862

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DOI

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28 July 2017

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28 July 2017

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