SARS-CoV-2 human T cell epitopes: Adaptive immune response against COVID-19

A Grifoni, J Sidney, R Vita, B Peters, S Crotty… - Cell host & …, 2021 - cell.com
Over the past year, numerous studies in the peer reviewed and preprint literature have
reported on the virological, epidemiological and clinical characteristics of the coronavirus …

T cell epitope predictions

B Peters, M Nielsen, A Sette - Annual Review of Immunology, 2020 - annualreviews.org
Throughout the body, T cells monitor MHC-bound ligands expressed on the surface of
essentially all cell types. MHC ligands that trigger a T cell immune response are referred to …

Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases

A Tarke, J Sidney, CK Kidd, JM Dan, SI Ramirez… - Cell Reports …, 2021 - cell.com
T cells are involved in control of SARS-CoV-2 infection. To establish the patterns of
immunodominance of different SARS-CoV-2 antigens and precisely measure virus-specific …

NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand …

B Reynisson, B Alvarez, S Paul, B Peters… - Nucleic acids …, 2020 - academic.oup.com
Major histocompatibility complex (MHC) molecules are expressed on the cell surface, where
they present peptides to T cells, which gives them a key role in the development of T-cell …

Improved prediction of MHC II antigen presentation through integration and motif deconvolution of mass spectrometry MHC eluted ligand data

B Reynisson, C Barra, S Kaabinejadian… - Journal of proteome …, 2020 - ACS Publications
Major histocompatibility complex II (MHC II) molecules play a vital role in the onset and
control of cellular immunity. In a highly selective process, MHC II presents peptides derived …

Predicting HLA class II antigen presentation through integrated deep learning

B Chen, MS Khodadoust, N Olsson, LE Wagar… - Nature …, 2019 - nature.com
Accurate prediction of antigen presentation by human leukocyte antigen (HLA) class II
molecules would be valuable for vaccine development and cancer immunotherapies …

IEDB-AR: immune epitope database—analysis resource in 2019

SK Dhanda, S Mahajan, S Paul, Z Yan… - Nucleic acids …, 2019 - academic.oup.com
Abstract The Immune Epitope Database Analysis Resource (IEDB-AR, http://tools. iedb. org/)
is a companion website to the IEDB that provides computational tools focused on the …

[HTML][HTML] Defining HLA-II ligand processing and binding rules with mass spectrometry enhances cancer epitope prediction

JG Abelin, D Harjanto, M Malloy, P Suri, T Colson… - Immunity, 2019 - cell.com
Increasing evidence indicates CD4+ T cells can recognize cancer-specific antigens and
control tumor growth. However, it remains difficult to predict the antigens that will be …

Best practices for bioinformatic characterization of neoantigens for clinical utility

MM Richters, H **a, KM Campbell, WE Gillanders… - Genome medicine, 2019 - Springer
Neoantigens are newly formed peptides created from somatic mutations that are capable of
inducing tumor-specific T cell recognition. Recently, researchers and clinicians have …

[HTML][HTML] Machine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes

J Racle, P Guillaume, J Schmidt, J Michaux, A Larabi… - Immunity, 2023 - cell.com
CD4+ T cells orchestrate the adaptive immune response against pathogens and cancer by
recognizing epitopes presented on class II major histocompatibility complex (MHC-II) …