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 9

System / cell line: over ✕ Assay: ifn-γ ✕ Clear

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
Predicting position along a looping immune response trajectory.

PMID 30296270 · PMC6175499 · PloS one · 2018 · 8 claims · 6 setups

Has reproduction · 98

Looper is a computational method that automatically identifies phase-shifted gene pairs (using SAX symbolic representation) that trace loops in longitudinal expression data.

monocytes blood pbmcs montreal microarray qrt-pcr topological
Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment.

PMID 37471455 · PMC10393163 · PLoS computational biology · 2023 · 8 claims · 7 setups

Has reproduction · 100

A network-based meta-analysis of 27 discovery cohorts identified a common 45-gene signature specific to active TB disease across studies.

blood aggregated 45-gene independent bulk network-based gene
A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling.

PMID 35729113 · PMC9213456 · Nature communications · 2022 · 7 claims · 5 setups

Has reproduction · 84

Developed a python-based, scalable model creation and simulation pipeline that converts structured text files into an SBML-standard model and is high-performance/cloud-computing ready.

sparced mcf10a deterministic hybrid comparison
HIV-1 evolution following transmission to an HLA-B*5801-positive patient.

PMID 19909081 · PMC2779566 · The Journal of infectious diseases · 2009 · 8 claims · 8 setups

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Multiple escape mutations developed rapidly in HLA-B*5801-restricted epitopes in Gag, Nef, and Pol following transmission

plasma transmitter subject genomic full-length population ifn-γ
Somatically acquired JAK1 mutations in adult acute lymphoblastic leukemia.

PMID 18362173 · PMC2292215 · The Journal of experimental medicine · 2008 · 8 claims · 8 setups

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Somatic JAK1 mutations occur in ALL and are more prevalent among adult T-cell precursor ALL (T-ALL) than B-ALL

genomic jak1-deficient u4c bw5147 dhplc stat1 cytokine-independent
RAS mutations affect tumor necrosis factor-induced apoptosis in colon carcinoma cells via ERK-modulatory negative and positive feedback circuits along with non-ERK pathway effects.

PMID 19789336 · PMC2927135 · Cancer research · 2009 · 8 claims · 8 setups

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K-RAS and N-RAS mutation status differentially determine the level of TNFα-induced apoptosis in an isogenic colon carcinoma cell panel

isogenic same conditioned dld-1 flow luminex immunoblot
Metabolic profiling during malaria reveals the role of the aryl hydrocarbon receptor in regulating kidney injury.

PMID 33021470 · PMC7538157 · eLife · 2020 · 8 claims · 8 setups

Has reproduction · 62

Plasma AHR ligands derived from heme metabolism (biliverdin, bilirubin) and tryptophan/kynurenine pathway metabolites increase during acute Pc malaria in mice and acute cerebral malaria in humans

c57bl pediatric littermate untargeted targeted bilirubin
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

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

Predicting position along a looping immune response trajectory.

Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment.

A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling.

HIV-1 evolution following transmission to an HLA-B*5801-positive patient.

Somatically acquired JAK1 mutations in adult acute lymphoblastic leukemia.

RAS mutations affect tumor necrosis factor-induced apoptosis in colon carcinoma cells via ERK-modulatory negative and positive feedback circuits along with non-ERK pathway effects.

Metabolic profiling during malaria reveals the role of the aryl hydrocarbon receptor in regulating kidney injury.

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