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).

• Optimal Dual RNA-Seq Mapping for Accurate Pathogen Detection in Complex Eukaryotic Hosts.

  PMID 39959292 · PMC11825298 · Bio-protocol · 2025 · 7 claims · 6 setups

  Has reproduction · 90

  Mapping adapter-trimmed reads first to the pathogen genome recovers more pathogen reads than the traditional host-first mapping approach.

  monocyte-derived raw same trimmed dual fastqc adapter

• Defactinib inhibits PYK2 phosphorylation of IRF5 and reduces intestinal inflammation.

  PMID 34795257 · PMC8602323 · Nature communications · 2021 · 8 claims · 12 setups

  Has reproduction · 67

  PYK2 was identified as a putative IRF5 kinase via a kinase inhibitor library screen in macrophages

  raw264.7 hektlr4 hoxb8-derived colon kinase co-immunoprecipitation co-ip

• Vespucci: a system for building annotated databases of nascent transcripts.

  PMID 24304890 · PMC3936758 · Nucleic acids research · 2014 · 8 claims · 7 setups

  Has reproduction · 73

  Existing ChIP-seq and RNA-seq analysis platforms (e.g. Cufflinks, peak callers) are unsuited to GRO-seq because they assume spliced/exonic reads, uniform density and paired-end data, and cannot identify transcriptional units de novo across the whole genome.

  thioglycollate-elicited mcf-7 macrophages mm9 gro-seq chip-seq short-read

• A homozygous CARD9 mutation in a family with susceptibility to fungal infections.

  PMID 19864672 · PMC2793117 · The New England journal of medicine · 2009 · 7 claims · 7 setups

  Full-text index only

  A homozygous CARD9 point mutation (Q295X, premature termination codon) is associated with autosomal recessive susceptibility to chronic mucocutaneous candidiasis.

  family patients peripheral-blood peripheral snp microsatellite sanger

• Inflammatory bowel disease and mutations affecting the interleukin-10 receptor.

  PMID 19890111 · PMC2787406 · The New England journal of medicine · 2009 · 8 claims · 8 setups

  Full-text index only

  Homozygous loss-of-function mutations in IL10RA or IL10RB cause severe early-onset enterocolitis

  consanguineous patients ebv-transformed pbmcs genetic-linkage single-nucleotide-polymorphism candidate-gene

• An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data.

  PMID 17984082 · PMC2239001 · Nucleic acids research · 2008 · 8 claims · 7 setups

  Full-text index only

  The Biodefense Proteomics Resource Center (RC) is a public cyberinfrastructure that stores, integrates, and disseminates experimental data from seven Proteomics Research Centers (PRCs) on biodefense pathogens and host interactions

  brucella toxoplasma bacillus homo label-free mass genomic

• Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

  PMID 38254989 · PMC10815467 · Genes · 2024 · 8 claims · 8 setups

  Has reproduction · 85

  Combining scRNA-seq and spatial transcriptomics enables inference of malignant cells at the invasive front of the ER+ breast cancer TME and dissection of events at the tumor infiltration forefront

  normal er+ epithelial malignant single-cell spatial copy

• Asthma investigators begin to reap the fruits of genomics.

  PMID 14611649 · PMC329104 · Genome biology · 2003 · 7 claims · 8 setups

  Full-text index only

  Microarray profiling of animal models of allergic asthma can identify novel differentially expressed candidate genes involved in inflammation and airway remodeling.

  monkey models lung inbred cdna oligonucleotide northern

• Tipping the balance in autoimmune disease.

  PMID 18001485 · PMC2246277 · Genome biology · 2007 · 8 claims · 8 setups

  Full-text index only

  Human autoimmune diseases are fundamentally diseases of immune dysfunction, evidenced by predisposing genes being immune-function genes, some shared and some unique across MS, T1D, SLE, CD and RA

  patients congenic nzm2410 mrl-lpr snp induced genetic