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).

• Nucleotide sequence polymorphism at the apical membrane antigen-1 locus reveals population history of Plasmodium vivax in Thailand.

  PMID 19643205 · PMC2790030 · Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2009 · 8 claims · 6 setups

  Full-text index only

  The domain II loop of PvAMA-1 is almost completely conserved at the amino acid level, consistent with strong purifying selection.

  plasmodium pvama-1 vivax pcr molecular merozoite

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

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

  Full-text index only

  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

• MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data.

  PMID 29901703 · PMC6025204 · GigaScience · 2018 · 6 claims · 7 setups

  Has reproduction · 95

  A two-step 'omni' RNA-seq pipeline (MetaMap) combining STAR human alignment with CLARK-S metagenomic classification can quantify archaeal, bacterial, and viral reads from the non-human read fraction of human RNA-seq data

  clinical hela tumor rutkowski bulk dual negative

• A four-gene signature from blood to exclude bacterial etiology of lower respiratory tract infection in adults.

  PMID 41285807 · PMC12644739 · Nature communications · 2025 · 8 claims · 8 setups

  Has reproduction · 94

  A 4-gene whole-blood signature (ITGB4, ITGA7, IFI27, FAM20A) discriminates any bacterial from nonbacterial ARI with cross-validated AUC = 0.90

  hospitalized ari febrile infection bulk rna-seq microarray

• Candida albicans genome sequence: a platform for genomics in the absence of genetics.

  PMID 15239821 · PMC463275 · Genome biology · 2004 · 8 claims · 5 setups

  Full-text index only

  Publication of the complete diploid C. albicans genome sequence will accelerate research into the pathogenesis of Candida infections

  candida sc5314 whole-genome fingerprinting multi-locus

• Target cell APOBEC3C can induce limited G-to-A mutation in HIV-1.

  PMID 17967058 · PMC2042017 · PLoS pathogens · 2007 · 8 claims · 8 setups

  Full-text index only

  APOBEC3C is necessary and sufficient to induce G-to-A mutation in some HIV-1 strains despite Vif expression

  magi pbmc 293t supt1 sensitive rt-pcr western

• Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis.

  PMID 19903332 · PMC3091321 · Genome biology · 2009 · 6 claims · 5 setups

  Full-text index only

  A candidate 37-transcript diagnostic signature distinguishes septicemic melioidosis from sepsis caused by other organisms with 100% accuracy in the training set and 78%/80% accuracy in two independent validation sets

  blood whole-genome unsupervised class

• The HCV Envelope Glycoprotein Down-Modulates NF-κB Signalling and Associates With Stimulation of the Host Endoplasmic Reticulum Stress Pathway.

  PMID 35371105 · PMC8964954 · Frontiers in immunology · 2022 · 8 claims · 8 setups

  Has reproduction · 50

  HCV E1E2 glycoproteins, and more so E2, down-modulate HIV-1 LTR activation in 293T, TZM-bl and Huh7 cells

  293t tzm-bl tzm-bl-e1e2 hiv-1 pseudo-typed transcriptomic

• Dual and recombinant infections: an integral part of the HIV-1 epidemic in Brazil.

  PMID 10081673 · PMC2627691 · Emerging infectious diseases · 1999 · 8 claims · 8 setups

  Full-text index only

  Among 79 HIV-1 infected patients, 3 (3.8%) had dual infections, 6 (7.6%) had recombinant infections, and 70 (88.6%) had single-subtype infections

  pbmc uncultured pcr-amplified aligned rflp heteroduplex nested

• Malarial hemozoin activates the NLRP3 inflammasome through Lyn and Syk kinases.

  PMID 19696895 · PMC2722371 · PLoS pathogens · 2009 · 7 claims · 8 setups

  Full-text index only

  Hemozoin induces IL-1β maturation and secretion in an NLRP3-, ASC- and caspase-1-dependent, but NLRC4-independent, manner

  pma-differentiated bone-marrow-derived asc nlrp3 elisa western peritoneal

• 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

  Full-text index only

  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

• Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens.

  PMID 19874620 · PMC2774872 · BMC genomics · 2009 · 8 claims · 8 setups

  Full-text index only

  Phylogenetic profiling of protein clusters across pathogen and non-pathogen genomes can identify candidate generic virulence factors

  proteins cdc candidate yersinia all-against-all computational cross-species

• Genomic signatures of human versus avian influenza A viruses.

  PMID 17073083 · PMC3294750 · Emerging infectious diseases · 2006 · 8 claims · 6 setups

  Full-text index only

  52 validated 'species-associated' amino acid positions distinguish human from avian influenza A viruses

  throat clinical 401-genome avian rt-pcr immunofluorescent sequence

• Genetic divergence of hepatitis C virus: the role of HIV-related immunosuppression.

  PMID 18769357 · PMC3071283 · Journal of acquired immune deficiency syndromes (1999) · 2008 · 7 claims · 6 setups

  Full-text index only

  HIV coinfection is associated with ~0.5 log10 higher HCV RNA levels, suggesting increased HCV replication

  chronically paired aligned hiv-infected direct genetic sliding-window