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).

• Single-cell transcriptomics reveals maturation of transplanted stem cell-derived retinal pigment epithelial cells toward native state.

  PMID 37339216 · PMC10293804 · Proceedings of the National Academy of Sciences of the United States of America · 2023 · 8 claims · 8 setups

  Has reproduction · 59

  Subretinally transplanted stem cell-derived RPE (ESC- and iPSC-derived) retain RPE identity and survive in vivo for at least 30 days in immunocompetent rabbit eyes

  hpsc-derived day esc dutch qrt-pcr immunofluorescence transepithelial

• Metabolite-Centric Reporter Pathway and Tripartite Network Analysis of Arabidopsis Under Cold Stress.

  PMID 30258841 · PMC6143811 · Frontiers in bioengineering and biotechnology · 2018 · 7 claims · 4 setups

  Has reproduction · 83

  A metabolite-centric reporter pathway analysis (RPAm) can infer cold-stress-associated metabolites and pathways in Arabidopsis directly from transcriptome data without metabolome data

  arabidopsis tripartite affymetrix metabolite-centric network

• CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons.

  PMID 36262316 · PMC9574418 · iScience · 2022 · 7 claims · 8 setups

  Has reproduction · 62

  CASK LOF increases neuronal complexity (neurite overgrowth) in developing/immature human excitatory neurons

  cask ko1 day mature bulk qrt-pcr western

• Screening of core genes prognostic for sepsis and construction of a ceRNA regulatory network.

  PMID 36855106 · PMC9976425 · BMC medical genomics · 2023 · 8 claims · 7 setups

  Has reproduction · 86

  RNA-seq of peripheral blood from 23 sepsis patients and 10 healthy controls identifies 1,044 DEmRNAs, 66 DEmiRNAs and 155 DElncRNAs.

  peripheral demrnas blood thp-1 rna-seq annotation wgcna

• Niche Modification by Sulfate-Reducing Bacteria Drives Microbial Community Assembly in Anoxic Marine Sediments.

  PMID 36988509 · PMC10128000 · mBio · 2023 · 7 claims · 7 setups

  Has reproduction · 100

  SRB modify niches (e.g., pH) to affect species coexistence during organic matter degradation

  coastal marine marinilabiliales srb-inhibited 16s molecular physicochemical

• VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data.

  PMID 37180100 · PMC10172660 · Frontiers in immunology · 2023 · 7 claims · 7 setups

  Has reproduction · 64

  VIGET is a web portal that lets users select vaccines/ImmPort studies, run differential gene expression analysis, and perform Reactome-based pathway enrichment and functional interaction network construction

  blood lists differentially individual differential pathway functional

• Integrated analysis of genetic and proteomic data identifies biomarkers associated with adverse events following smallpox vaccination.

  PMID 18923431 · PMC2692715 · Genes and immunity · 2009 · 7 claims · 6 setups

  Full-text index only

  A two-stage strategy (Random Forest filtering followed by decision tree modeling) can integrate categorical genetic and continuous proteomic data to identify biomarkers of AE risk

  ebv-transformed serum combined rf-filtered snp serum random

• Exploring the prognostic and diagnostic value of lactylation-related genes in sepsis.

  PMID 39367086 · PMC11452377 · Scientific reports · 2024 · 8 claims · 7 setups

  Has reproduction · 73

  Intersecting sepsis-associated differentially expressed genes with a curated list of 332 lactylation genes yields 55 sepsis-related lactylation genes.

  peripheral overlapping geo pbmcs bulk kegg protein-protein

• Enforced MYC expression directs a distinct transcriptional state during plasma cell differentiation.

  PMID 40721291 · PMC12305944 · Life science alliance · 2025 · 8 claims · 7 setups

  Has reproduction · 74

  Acute MYC (T58I) and BCL2 overexpression drives an aberrant B-cell differentiation phenotype with altered surface marker expression while functional antibody secretion is retained

  peripheral rna-seq flow edu antibody

• Novel approaches for mechanistic understanding and predicting preeclampsia.

  PMID 19836839 · PMC2790420 · Journal of reproductive immunology · 2009 · 8 claims · 6 setups

  Full-text index only

  The classic two-stage hypothesis (Stage I poor placental perfusion causing Stage II maternal symptoms) needs reevaluation because reduced perfusion alone may be insufficient to cause PE.

  maternal il-10-deficient first-trimester third-trimester surgical seldi-tof genetic

• Merger of ayurveda and tissue culture-based functional genomics: inspirations from systems biology.

  PMID 18348714 · PMC2311278 · Journal of translational medicine · 2008 · 8 claims · 8 setups

  Full-text index only

  Crude LASH extract and its purified components (withanone, withaferin A) act through distinct but partially overlapping molecular gene-regulatory networks

  tumor-derived tumor lash gene cytotoxicity sirna ribozyme

• Assessing individual differences in genome-wide gene expression in human whole blood: reliability over four hours and stability over 10 months.

  PMID 19653838 · PMC3819565 · Twin research and human genetics : the official journal of the International Society for Twin Studies · 2009 · 8 claims · 5 setups

  Full-text index only

  A subset of probesets (3,414) shows 4-hour test-retest reliability exceeding r=0.70 for detecting individual differences in gene expression.

  blood edta reliably genome-wide twin sub-type