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).

• Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.

  PMID 35456910 · PMC9025732 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

  Has reproduction · 78

  73 IQD gene family members were identified in the wheat genome and classified into six phylogenetic groups

  triticum taiqd wheat rice genome-wide phylogenetic gene

• 5-methylcytosine RNA modification regulators-based patterns and features of immune microenvironment in acute myeloid leukemia.

  PMID 38277218 · PMC10911375 · Aging · 2024 · 8 claims · 8 setups

  Has reproduction · 93

  m5C regulators are differentially expressed between AML and normal samples and correlate with AML prognosis

  tcga aml gse12417 bulk mutation methylation

• A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases.

  PMID 31290545 · PMC6616200 · Database : the journal of biological databases and curation · 2019 · 7 claims · 8 setups

  Has reproduction · 62

  A curated collection of 33 GEO transcriptome datasets (1860 profiles) relevant to IgE-mediated atopic disease was assembled and made available on the Gene Expression Browser (GXB) platform

  pbmc bronchial nasal skin gene rna-seq

• Identification of a PRDM1-regulated T cell network to regulate atherosclerotic plaque inflammation.

  PMID 41039608 · PMC12490039 · Genome medicine · 2025 · 7 claims · 7 setups

  Has reproduction · 100

  A distinct gene co-expression module with a prominent T cell signature is associated with unstable plaques.

  carotid calcified atherosclerotic cell-specific microarray single-cell immunohistochemistry

• CanCellCap: robust cancer cell capture across tissue types on single-cell RNA-seq data by multi-domain learning.

  PMID 40739511 · PMC12312500 · BMC biology · 2025 · 8 claims · 7 setups

  Has reproduction · 42

  CanCellCap identifies cancer cells in scRNA-seq data across 13 tissue types, 23 cancer types, and 7 sequencing platforms with 0.977 average accuracy

  cancer testing sequencing unseen scrna-seq spatial

• A Reference DNA Barcode Library for UK Fungi associated with Bark and Ambrosia Beetles.

  PMID 41022899 · PMC12480477 · Scientific data · 2025 · 6 claims · 6 setups

  Has reproduction · 44

  A reference DNA barcode library of fungi associated with over 1000 UK bark and ambrosia beetles across 25 native weevil species was generated, resulting in 5274 identified fungal OTUs.

  individual extracted pooled fungal its2 pcr sequence

• An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity.

  PMID 42147490 · PMC13179517 · Cell press blue · 2026 · 8 claims · 8 setups

  Has reproduction · 85

  Fibroblasts act as central regulators of structural immunity in the human oral cavity, forming peri-epithelial hubs enriched in effector cytokines

  oral ffpe scrna-seq integrated scrna-seq spatial ligand-receptor

• Heterogeneity of cancer-associated fibroblasts in head and neck squamous cell carcinoma.

  PMID 37320872 · PMC10277597 · Translational oncology · 2023 · 8 claims · 9 setups

  Has reproduction · 50

  Seven distinct CAF subsets exist in HNSCC, identified via integration of scRNA-seq, bulk transcriptomic, and spatial transcriptomic data.

  hnscc tcga-hnscc caf fibroblast single-cell bulk spatial

• An attenuated phenotype of Costello syndrome in three unrelated individuals with a HRAS c.179G>A (p.Gly60Asp) mutation correlates with uncommon functional consequences.

  PMID 25914166 · PMC4830354 · American journal of medical genetics. Part A · 2015 · 7 claims · 8 setups

  Has reproduction

  HRAS c.179G>A (p.Gly60Asp) causes an attenuated Costello syndrome phenotype without severe failure-to-thrive, intellectual disability, or cancer predisposition

  cos-7 transiently patients parental ras co-immunoprecipitation immunoblotting

• Detection of Virus-Related Sequences Associated With Potential Etiologies of Hepatitis in Liver Tissue Samples From Rats, Mice, Shrews, and Bats.

  PMID 34177835 · PMC8221242 · Frontiers in microbiology · 2021 · 8 claims · 6 setups

  Has reproduction · 79

  Viral metagenomics of liver tissue from rats, mice, shrews, and bats revealed a diverse set of sequences related to herpesviruses, orthomyxoviruses, anelloviruses, hepeviruses, hepadnaviruses, flaviviruses, parvoviruses, and picornaviruses

  pooled individual liver serum viral pcr strand-specific

• Organelle Genomes and Transcriptomes of Nymphaea Reveal the Interplay between Intron Splicing and RNA Editing.

  PMID 34576004 · PMC8466565 · International journal of molecular sciences · 2021 · 8 claims · 8 setups

  Has reproduction · 76

  Both cis- and trans-splicing group II introns in Nymphaea organelle genomes are spliced in random order, generating diverse co-existing intermediates rather than following a fixed splicing sequence.

  nymphaea joey liriodendron pacbio illumina strand-specific

• Pathway-targeting gene matrix for Drosophila gene set enrichment analysis.

  PMID 34710184 · PMC8553153 · PloS one · 2021 · 8 claims · 4 setups

  Has reproduction · 95

  Gene matrix files for GSEA are largely unavailable for Drosophila, limiting pathway-level enrichment analysis in this model organism

  drosophila reactome kegg gene fluorescence manual

• Utility of Triti-Map for bulk-segregated mapping of causal genes and regulatory elements in Triticeae.

  PMID 35605195 · PMC9284283 · Plant communications · 2022 · 8 claims · 4 setups

  Has reproduction · 95

  Triti-Map is a computational package suite plus web interface specifically optimized for bulk-segregated gene mapping in Triticeae, accepting DNA-seq, RNA-seq/ChIP-seq, and traditional QTL data as input

  wheat hordeum bulk-segregated interval novo

• binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets.

  PMID 36239393 · PMC9677464 · Briefings in bioinformatics · 2022 · 8 claims · 8 setups

  Has reproduction · 67

  binny outperforms or is highly competitive with commonly used and state-of-the-art binning methods (MetaBAT2, MaxBin2, CONCOCT, VAMB, SemiBin, MetaDecoder)

  cami real-world metagenomic binned genome binning mag

• A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata.

  PMID 36333777 · PMC9636832 · Microbiome · 2022 · 7 claims · 6 setups

  Has reproduction · 64

  Genome-resolved metagenomics of separated foregut and midgut reconstructed 20 MAGs including novel lineages of Hepatoplasmataceae (foregut) and Deferribacteres (midgut).

  rimicaris foregut deferribacteres shotgun fluorescence yoyo-1

• Genetic architecture of natural variation of cardiac performance from flies to humans.

  PMID 36383075 · PMC9668334 · eLife · 2022 · 8 claims · 7 setups

  Has reproduction · 74

  Natural genetic variation significantly influences cardiac performance traits (rhythmicity and contractility) across 167 DGRP lines

  drosophila dgrp gene induced high-speed genome-wide epistasis

• Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes.

  PMID 37190091 · PMC10137100 · Cells · 2023 · 8 claims · 8 setups

  Has reproduction · 54

  Single-cell transcriptomic analysis of EPCAM+Lin- epithelial cells identified unique gene signatures/markers that distinguish ER+, HER2+, ER+HER2+, and TNBC molecular subtypes

  breast epcam+cd45-cd8a-cd4-cd19-cd3e cancer identified single-cell differential crispr-cas9

• Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.

  PMID 37216666 · PMC10411599 · G3 (Bethesda, Md.) · 2023 · 7 claims · 8 setups

  Has reproduction · 86

  CAGE sequencing of 24 tissues from 3 cattle populations (dairy, beef-dairy cross, Kinsella composite) defines TSS and coexpressed short-range enhancers in the ARS-UCD1.2 reference genome

  tissues predicted tss-enhancer cattle cage extraction coexpression

• Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma.

  PMID 33674593 · PMC7935900 · Nature communications · 2021 · 8 claims · 8 setups

  Has reproduction · 78

  A transcriptome-derived T-cell exhaustion score (ES) is prognostic for HCC patient survival independent of known clinical/molecular factors

  hcc-associated hcc malignant cd8+ single-cell bulk metabolomics

• Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics.

  PMID 28097058 · PMC5228507 · PeerJ · 2017 · 8 claims · 8 setups

  Has reproduction · 95

  Similar virus-host interactions and glycerol metabolism gene associations (notably dihydroxyacetone kinase with Haloquadratum/Halorubrum) exist across geographically diverse solar salterns

  solar saltern combined individual metagenomic taxonomic functional