Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 14

System / cell line: hla ✕ Assay: epitope ✕ Clear

NeoPrecis: enhancing immunotherapy response prediction through integration of qualified immunogenicity and clonality-aware neoantigen landscapes.

PMID 41577704 · PMC12932759 · Nature communications · 2026 · 8 claims · 8 setups

Full-text index only

NeoPrecis-Immuno, a T-cell recognition model incorporating MHC-binding motif enrichment into a cross-reactivity-distance framework, improves neoantigen immunogenicity prediction.

tcr-pmhc cedar cedar-derived nci cross-reactive t-cell immunogenicity
Highlights of international conference of immunogenomics and immunomics, October 8-12, 2006 Budapest, Hungary.

PMID 17470366 · PMC7130317 · Cellular immunology · 2006 · 8 claims · 8 setups

Full-text index only

An 'immunological constant of rejection' involving interferon-stimulated genes (ISGs) and innate immune effector functions (IEF) underlies diverse immune-mediated tissue destruction processes (allograft rejection, cancer rejection, autoimmunity, infection)

hla-b44 plasma macrophages complement proteomics shotgun cap
The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

PMID 18949050 · PMC2569417 · PloS one · 2008 · 6 claims · 5 setups

Full-text index only

Within individual hosts, proteasome and TAP escape mutations in HIV-1 occur frequently

hiv-1 hla-genotyped predicted bioinformatic longitudinal ancestral
EpiToolKit--a web server for computational immunomics.

PMID 18440979 · PMC2447732 · Nucleic acids research · 2008 · 7 claims · 3 setups

Full-text index only

EpiToolKit is a web server integrating five MHC class I and two MHC class II epitope prediction methods in a unified, user-friendly interface.

randomly novel minor mhc polymorphic
T cell receptor usage and fine specificity of human immunodeficiency virus 1-specific cytotoxic T lymphocyte clones: analysis of quasispecies recognition reveals a dominant response directed against a minor in vivo variant.

PMID 8666925 · PMC2192525 · The Journal of experimental medicine · 1996 · 8 claims · 6 setups

Full-text index only

Despite heterogeneous TCR usage among clones from different HLA-B14 subjects, the fine specificity for the gp41/584-592 epitope and its variants is strikingly similar.

gp41 hiv-1 pbmc freshly 51cr-release tcr-α limiting
Integrated reiterative pipeline for rapid epitope-based pan-alphavirus vaccines.

PMID 41811958 · PMC12978219 · Science advances · 2026 · 6 claims · 7 setups

Full-text index only

An integrated pipeline combining ML-based epitope prediction (netMHCpan, EpiDope, BepiPred), TCRpMHC structural modeling/docking, and JessEV vaccine design can prioritize viral peptides by immunogenicity, allele coverage, solubility, and stability.

preexposed alphaviral peptide-hla modeled peptide epitope structural
Candidate vaccine sequences to represent intra- and inter-clade HIV-1 variation.

PMID 19812689 · PMC2753653 · PloS one · 2009 · 7 claims · 5 setups

Full-text index only

Natural CTL immunodominance toward variable proteome regions increases epitope mismatch with challenge strains and recapitulates the escape-driven CTL failure seen in natural infection, contributing to HIV vaccine failure

hiv-1 polyclonally shannon cross-clade ctl
De novo identification of CD4(+) T cell epitopes.

PMID 38658646 · PMC11093748 · Nature methods · 2024 · 7 claims · 8 setups

Has reproduction · 83

SABR-IIs (chimeric receptors linking a covalently attached peptide-MHC-II to CD28-CD3ζ signaling domains) present epitopes to CD4+ T cells and induce a readable NFAT-GFP/CD69 signal upon cognate TCR recognition

nfat-gfp hla-dq8 5kc daudi nfat-gfp co-incubation species
Effects of HIV type-1 immune selection on susceptability to integrase inhibitor resistance.

PMID 19918099 · PMC4155129 · Antiviral therapy · 2009 · 8 claims · 6 setups

Full-text index only

Primary integrase inhibitor resistance mutations (T66I, E92Q, G140S, Y143C/H/R, Q148H/R/K, N155S/H) were absent in 342 drug-naive individuals, indicating these sites are highly constrained.

plasma genomic viral aligned bulk sequence-based quantitative
BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence.

PMID 17965094 · PMC2238987 · Nucleic acids research · 2008 · 7 claims · 5 setups

Full-text index only

BioHealthBase BRC is a public integrated bioinformatics database and analysis resource for influenza virus, Francisella tularensis, Mycobacterium tuberculosis, Microsporidia species and ricin toxin.

avian pb2 dkxi35 ns1 sequence genome t-cell
Conflicting selection pressures target the NS3 protein in hepatitis C virus genotypes 1a and 1b.

PMID 19896990 · PMC3529174 · Virus research · 2010 · 7 claims · 5 setups

Full-text index only

Both HCV-1a and HCV-1b show abundant slightly deleterious nonsynonymous variants subject to ongoing purifying selection across the polyprotein.

hcv-1a phylogenetic sequence nucleotide
Genetic characterization of 2006-2008 isolates of Chikungunya virus from Kerala, South India, by whole genome sequence analysis.

PMID 19851853 · PMC7088544 · Virus genes · 2010 · 8 claims · 7 setups

Full-text index only

37 novel mutations were identified across the six sequenced CHIKV genomes, predominantly in 2007 and 2008 isolates

serum vero chikv additional rt-pcr virus whole-genome
Human endogenous retrovirus profiling reveals heterogenous expression in cutaneous melanoma.

PMID 41971443 · PMC13061668 · Frontiers in oncology · 2026 · 7 claims · 8 setups

Full-text index only

HERV expression differs between primary and metastatic cutaneous melanoma

tcga-skcm metastatic normal selected bulk consensus orf
Modified H5 promoter improves stability of insert genes while maintaining immunogenicity during extended passage of genetically engineered MVA vaccines.

PMID 19969118 · PMC2821965 · Vaccine · 2010 · 7 claims · 8 setups

Full-text index only

rMVA expressing multiple antigens under the mH5 promoter exhibit remarkable genetic stability and maintain potent immunogenicity after serial passage

rmva-infected individually bhk-21 pbmc qpcr western southern

Experiments

NeoPrecis: enhancing immunotherapy response prediction through integration of qualified immunogenicity and clonality-aware neoantigen landscapes.

Highlights of international conference of immunogenomics and immunomics, October 8-12, 2006 Budapest, Hungary.

The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

EpiToolKit--a web server for computational immunomics.

T cell receptor usage and fine specificity of human immunodeficiency virus 1-specific cytotoxic T lymphocyte clones: analysis of quasispecies recognition reveals a dominant response directed against a minor in vivo variant.

Integrated reiterative pipeline for rapid epitope-based pan-alphavirus vaccines.

Candidate vaccine sequences to represent intra- and inter-clade HIV-1 variation.

De novo identification of CD4(+) T cell epitopes.

Effects of HIV type-1 immune selection on susceptability to integrase inhibitor resistance.

BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence.

Conflicting selection pressures target the NS3 protein in hepatitis C virus genotypes 1a and 1b.

Genetic characterization of 2006-2008 isolates of Chikungunya virus from Kerala, South India, by whole genome sequence analysis.

Human endogenous retrovirus profiling reveals heterogenous expression in cutaneous melanoma.

Modified H5 promoter improves stability of insert genes while maintaining immunogenicity during extended passage of genetically engineered MVA vaccines.