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).

• 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

• Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection.

  PMID 19890401 · PMC2768328 · PloS one · 2009 · 7 claims · 7 setups

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  Reverse mutations to the wild type (HIV-1C consensus) in Gag appear significantly earlier than escape mutations from the wild type during primary infection

  hiv-1 same sequenced gag single-genome mhc hypermutation

• HIV-1 sequence evolution in vivo after superinfection with three viral strains.

  PMID 17716368 · PMC2020475 · Retrovirology · 2007 · 8 claims · 8 setups

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  gag and env-V3 nucleotide evolution follows a similar pattern in all three strains: low substitution rate in the first 2-3 years of infection, then an increase driven mainly by synonymous substitutions

  blood seminal pbmcs biological strain-specific bulk in-house

• Clinical and genotypic findings in HIV-infected patients with the K65R mutation failing first-line antiretroviral therapy in Nigeria.

  PMID 19644383 · PMC2815152 · Journal of acquired immune deficiency syndromes (1999) · 2009 · 8 claims · 3 setups

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  K65R mutation is present in a substantial proportion (10.9%) of Nigerian patients failing first-line ART, including many with no prior tenofovir exposure

  plasma k65r-positive hiv-1 comparative clinical

• scTWAS: a powerful statistical framework for single-cell transcriptome-wide association studies.

  PMID 41820391 · PMC13121454 · Nature communications · 2026 · 8 claims · 5 setups

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  scTWAS uses a latent-variable expression-measurement model combined with a moment-based regression to more accurately estimate genetic regulation of gene expression from single-cell data, improving GReX prediction across cell types and datasets

  onek1k-derived onek1k-based immune brain simulated two-sample stage

• First report of an HIV-1 triple recombinant of subtypes B, C and F in Buenos Aires, Argentina.

  PMID 16959032 · PMC1570496 · Retrovirology · 2006 · 8 claims · 6 setups

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  Nearly full-length sequencing of 10 HIV-1 seroincident MSM samples revealed 6 subtype B, 3 unique BF recombinants, and 1 novel B/C/F triple recombinant

  pbmcs assembled hiv-1 triple nearly phylogenetic bootscan

• Distinct lncRNA transcriptional fingerprints characterize progressive stages of multiple myeloma.

  PMID 26895470 · PMC4924754 · Oncotarget · 2016 · 8 claims · 8 setups

  Has reproduction · 36

  160 lncRNAs are differentially expressed between normal plasma cells and MGUS, SMM, MM, or PCL patients, with 31 lncRNAs shared across at least three comparisons

  bone gene plasma normal microarray custom unsupervised

• Evidence for limited genetic compartmentalization of HIV-1 between lung and blood.

  PMID 19759830 · PMC2736399 · PloS one · 2009 · 8 claims · 7 setups

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  Statistical evidence of genetic compartmentalization between lung and blood HIV-1 env sequences was found in 10 of 18 subjects.

  paired lung tissue-pair pooled hiv-1 maximum statistical

• Ovarian cancer biomarkers: current options and future promise.

  PMID 18926090 · PMC3381792 · Journal of the National Comprehensive Cancer Network : JNCCN · 2008 · 8 claims · 8 setups

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  CA125 lacks the sensitivity and specificity needed for reliable early-stage ovarian cancer detection, since only ~50% of stage I/II cases show elevated levels

  serum plasma preoperative advanced serum plasma elisa

• Net positive charge of HIV-1 CRF01_AE V3 sequence regulates viral sensitivity to humoral immunity.

  PMID 18787705 · PMC2527523 · PloS one · 2008 · 8 claims · 5 setups

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  Reduction in V3's net positive charge makes V3 less variable due to limited positive selection

  hiv-1 recombinant plasma gp120 sequence single-round v3-peptide-based

• Proteomics as a method for early detection of cancer: a review of proteomics, exhaled breath condensate, and lung cancer screening.

  PMID 18095050 · PMC2150625 · Journal of general internal medicine · 2008 · 8 claims · 7 setups

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  Protein expression is closely aligned with cellular activity, unlike genomic changes which may have no functional significance

  serum resected plasma lower microarray two-dimensional proteomic

• Lineage-Specific Disruption of Hematopoiesis by Oxaliplatin: Mechanisms of Erythropoietin Resistance and Immune Suppression.

  PMID 41868970 · PMC13005433 · Journal of hematology and oncology research · 2026 · 8 claims · 5 setups

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  Oxaliplatin induces coordinated, lineage-dependent suppression of hematopoiesis, strongest in erythroid and lymphoid lineages while neutrophils are relatively spared

  bone peripheral plasma bulk complete multiplex

• Ectopic NMDAR expression in cancer unmasks germline-encoded autoimmunity.

  PMID 41882353 · PMC13216075 · Nature · 2026 · 8 claims · 8 setups

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  GluN1 and GluN2B NMDAR subunits are ectopically expressed in cancer cells of human TNBC tumours

  breast tnbc 4t1-nmdar orthotopic bulk spatial immunofluorescence

• DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations.

  PMID 17576693 · PMC1934997 · Nucleic acids research · 2007 · 6 claims · 7 setups

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  DNA bar coding combined with pyrosequencing allows parallel, deep characterization of drug resistance mutations across many HIV populations in a single experiment

  hiv pooled plasma pyrosequencing conventional rt-pcr

• The Presence of CD11c+ B Cells with Potent Effector Memory Phenotype in Lung Adenocarcinoma Correlates with Overall Patient Survival.

  PMID 41686183 · PMC12988592 · Cancer immunology research · 2026 · 7 claims · 7 setups

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  CD79A is a reliable transcriptomic/protein quantifier of B lymphocytes across differentiation stages, unlike CD19/CD20 whose expression changes upon activation

  healthy tcga luad til-b flow bulk single-cell