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 17

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

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

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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

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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
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

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

hiv-1 hla-genotyped predicted bioinformatic longitudinal ancestral
NovelFam3000--uncharacterized human protein domains conserved across model organisms.

PMID 16533400 · PMC1440326 · BMC genomics · 2006 · 8 claims · 7 setups

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NovelFam3000 is an online data centre unifying bioinformatics resource links, news, comments, and user-submitted experimental data (including a Gene Characterization Index) for ~3000 uncharacterized Pfam-B/DUF domain families conserved across worm, fly, and human

lines mammalian hek drosophila rt-pcr immunofluorescence counterstaining
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

PMID 22955991 · PMC3431496 · Genome research · 2012 · 8 claims · 8 setups

Has reproduction · 74

ENCODE/modENCODE define a set of working standards and guidelines for ChIP-seq covering antibody validation, experimental replication, sequencing depth, data/metadata reporting, and data quality assessment.

small-genome nuclear whole-cell encode chip-seq chip-chip immunoblot
Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures.

PMID 18632963 · PMC2577380 · The Journal of general virology · 2008 · 7 claims · 6 setups

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NS3 shows less evidence of purifying selection acting on its CTL epitopes than the other 9 HCV proteins, while outside the CTL epitopes NS3 is more conserved than the other proteins.

complete hcv-1b sequence nonsynonymous comparative neighbor-joining maximum
Phosphoproteomics: new insights into cellular signaling.

PMID 16168091 · PMC1242200 · Genome biology · 2005 · 8 claims · 8 setups

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Protein kinases are one of the largest gene families in humans and mice, accounting for 1.7% of the human genome

yeast hela beta2-adrenergic erk phosphopeptide targeted silac
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

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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
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

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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
Mutant, wild type, or overall p53 expression: freedom from clinical progression in tumours of astrocytic lineage.

PMID 15494720 · PMC2409947 · British journal of cancer · 2004 · 8 claims · 7 setups

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Significant overexpression of p53 protein was found in 48% of 74 astrocytic tumours

archival subset recombinant same immunohistochemistry antibody cytokeratin
Determinants of human immunodeficiency virus type 1 escape from the primary CD8+ cytotoxic T lymphocyte response.

PMID 15545352 · PMC2211924 · The Journal of experimental medicine · 2004 · 7 claims · 4 setups

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CD8+ CTL responses contribute to containment of viral replication in acute/early HIV-1 infection, and HIV-1 rapidly selects escape variants within epitope-containing regions beginning within weeks of infection.

pbmcs autologous vaccinia plasma ifn-γ 51cr recombinant
Proteomic-based identification of haptoglobin-1 precursor as a novel circulating biomarker of ovarian cancer.

PMID 15199385 · PMC2364749 · British journal of cancer · 2004 · 7 claims · 7 setups

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Six serum protein spots (~40 kDa, pI 5.9–6.6) significantly overexpressed in grade 1, 2 and 3 ovarian cancer patients were identified by MALDI-TOFMS and n-ESIQ(q)TOFMS as isoforms of haptoglobin-1 precursor (HAP1)

serum tryptic 2de-separated paraffin-embedded two-dimensional affi-gel maldi-tofms
Genetic diversity of vaccine candidate antigens in Plasmodium falciparum isolates from the Amazon basin of Peru.

PMID 18505558 · PMC2432069 · Malaria journal · 2008 · 8 claims · 7 setups

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CSP (Th2R/Th3R region) is polymorphic in Peruvian isolates, with four distinct alleles identified, none identical to the 3D7 vaccine strain

pfcsp pfmsp-1 pfama-1 pflsa-1 pcr polymorphism multilocus
The integrated world of functional genomics.

PMID 12537543 · PMC151279 · Genome biology · 2003 · 8 claims · 8 setups

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Integrating chromatin immunoprecipitation (promoter-binding) data with expression data reveals the yeast cell-cycle transcriptional regulatory network, including network motifs such as autoregulation, multi-component loops, and feedforward loops.

cerevisiae sequenced elegans drosophila chromatin integration comparative
Effects of HIV type-1 immune selection on susceptability to integrase inhibitor resistance.

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

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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
The N-terminus and alpha-5, alpha-6 helices of the pro-apoptotic protein Bax, modulate functional interactions with the anti-apoptotic protein Bcl-xL.

PMID 17519046 · PMC1890283 · BMC cell biology · 2007 · 8 claims · 8 setups

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Deletion of the first 29 N-terminal amino acids (Bax 30-192) causes constitutive mitochondrial accumulation and high cytotoxicity that is poorly inhibited by Bcl-xL or Bcl-2.

jurkat drosophila hek apoptotic uas-gal4 western
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

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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

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.

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

NovelFam3000--uncharacterized human protein domains conserved across model organisms.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures.

Phosphoproteomics: new insights into cellular signaling.

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

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

Mutant, wild type, or overall p53 expression: freedom from clinical progression in tumours of astrocytic lineage.

Determinants of human immunodeficiency virus type 1 escape from the primary CD8+ cytotoxic T lymphocyte response.

Proteomic-based identification of haptoglobin-1 precursor as a novel circulating biomarker of ovarian cancer.

Genetic diversity of vaccine candidate antigens in Plasmodium falciparum isolates from the Amazon basin of Peru.

The integrated world of functional genomics.

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

The N-terminus and alpha-5, alpha-6 helices of the pro-apoptotic protein Bax, modulate functional interactions with the anti-apoptotic protein Bcl-xL.

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