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).

• Implementation of a data repository-driven approach for targeted proteomics experiments by multiple reaction monitoring.

  PMID 19121650 · PMC2706936 · Journal of proteomics · 2009 · 7 claims · 5 setups

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  A new MRM worksheet was implemented in The Global Proteome Machine database (GPMDB) that provides all information needed to design MRM transitions based solely on archived observations from previous experiments by other researchers.

  platelet proteins reaction midas mrm

• Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination.

  PMID 19031011 · PMC2756966 · Journal of structural and functional genomics · 2009 · 8 claims · 6 setups

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  A discovery-oriented pipeline using standardized single-condition methods (one expression system, one detergent, one SEC buffer) can efficiently triage large numbers of eukaryotic IMP targets to identify well-behaved candidates for crystallization

  cerevisiae ddm-solubilized sec-included tmhmm ligase-independent small-scale

• A new form of diabetes caused by INS mutations defined by zygosity, stem cell and population data.

  PMID 41484206 · PMC12905373 · EMBO molecular medicine · 2026 · 6 claims · 7 setups

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  INS R6C is a recessive loss-of-function mutation causing diabetes only in homozygous individuals, not a dominant mutation as previously classified.

  blood serum large-scale computational targeted autoantibody population

• Multiomics and deep learning dissect regulatory syntax in human development.

  PMID 41951735 · PMC13216069 · Nature · 2026 · 8 claims · 8 setups

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  The Human Development Multiomic Atlas (HDMA) is a single-cell atlas of chromatin accessibility and gene expression from 817,740 fetal cells across 12 organs, spanning 203 cell types

  fetal annotated embryo chrombpnet share-seq chromvar activity-by-contact

• TE-SCALE: a comprehensive database for exploring transposable element expression across human cancers at single-cell resolution.

  PMID 41296555 · PMC12807651 · Nucleic acids research · 2026 · 8 claims · 8 setups

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  TE-SCALE is a comprehensive single-cell database integrating TE expression across 20 human cancer types and 12 tissue origins

  tumor quality-controlled scrna-seq metacells scrna-seq subfamily automated

• isoSeQL: comparing long-read isoforms across multiple datasets.

  PMID 41452740 · PMC12790818 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 4 setups

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  isoSeQL enables comparison of long-read isoform profiles across multiple datasets by consolidating SQANTI3-annotated samples into a unified SQLite database with consistent isoform IDs

  gencode simulated gm12878 peripheral intron simulated long-read

• pmid-41547832

  PMID 41547832 · PMC12914055 · 8 claims · 8 setups

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  Af-CUT&Tag eliminates dependence on conventional target antibodies by using CRISPR-integrated HiBiT/ALFA-tags recognized by LgBiT/NbALFA-Tn5 fusion proteins

  recombinant sw480 lysates genomic bio-layer chemiluminescent co-immunoprecipitation

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

  PMID 30258841 · PMC6143811 · Frontiers in bioengineering and biotechnology · 2018 · 8 claims · 8 setups

  Has reproduction · 83

  Metabolite-centric reporter pathway analysis (RPAm) computes reporter metabolites and reporter pathways from transcriptome P-values by aggregating Z-scores of neighboring genes in a genome-scale metabolic network

  arabidopsis gene-metabolite-pathway tripartite microarray metabolite-centric reporter

• A Meta-Analysis of the Effects of Acute Sleep Deprivation on the Cortical Transcriptome in Rodent Models.

  PMID 41031900 · PMC13131251 · Journal of sleep research · 2026 · 8 claims · 8 setups

  Has reproduction · 96

  Meta-analysis of 18 SD-vs-control contrasts across 8 rodent studies (collective n=293) identified 182 differentially expressed genes (DEGs) in cerebral cortex following SD (FDR<0.05)

  c57bl genetic pooled microarray rna-seq random-effects

• QuasiFlow: a Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data.

  PMID 36699347 · PMC9722223 · Bioinformatics advances · 2022 · 6 claims · 8 setups

  Has reproduction · 78

  QuasiFlow is a Nextflow pipeline that runs entirely locally via command-line tools and a local HIVdb database copy to analyze NGS-based HIV-1 drug resistance testing data.

  hiv-1 same paired-end reads ngs-based concordance read