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).
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Has reproduction · 97
Determination of complete chromosomal haplotypes by bulk DNA sequencing.
PMID 33957932 · PMC8101039 · Genome biology · 2021 · 8 claims · 8 setups
A hierarchical computational strategy that first builds high-confidence local haplotype blocks from long-range/linked-read linkage and then concatenates them into whole-chromosome haplotypes using Hi-C contacts
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Has reproduction · 81
Assessing personalized molecular portraits underlying endothelial-to-mesenchymal transition within pulmonary arterial hypertension.
PMID 39462326 · PMC11513636 · Molecular medicine (Cambridge, Mass.) · 2024 · 8 claims · 8 setups
scRNA-seq of PAH and control lung tissue identifies nine distinct cell populations with high heterogeneity in composition, function, distribution, and communication
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Has reproduction · 91
A reference profile-free deconvolution method to infer cancer cell-intrinsic subtypes and tumor-type-specific stromal profiles.
PMID 32111252 · PMC7049190 · Genome medicine · 2020 · 8 claims · 8 setups
DeClust is a reference profile-free deconvolution method that simultaneously deconvolves bulk tumor expression into cancer, immune, and stromal compartments and clusters samples into cancer cell-intrinsic molecular subtypes, outputting subtype-specific reference profiles for the cohort rather than for individuals.
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Has reproduction · 67
Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data.
PMID 37994351 · PMC10663991 · F1000Research · 2023 · 7 claims · 7 setups
A reproducible R-based workflow combines Seurat (QC, clustering, integration), monocle3 (trajectory inference), and edgeR (pseudo-bulk time course analysis) to perform single-cell pseudotemporal time course analysis.
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Has reproduction · 94
iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type-Specific Markers of Immune-Cell Infiltration.
PMID 37023414 · PMC10236149 · Cancer immunology research · 2023 · 8 claims · 8 setups
Malignant cells cluster by patient in scRNA-seq data while immune and stromal cells cluster by cell type, making malignant cells uniquely suited to carry patient-level inflamed/cold signal
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Has reproduction · 84
Integrative Transcriptomic and Evolutionary Analysis of Drought and Heat Stress Responses in Solanum tuberosum and Solanum lycopersicum.
PMID 41470732 · PMC12736803 · Plants (Basel, Switzerland) · 2025 · 7 claims · 8 setups
Drought and heat stress induce coordinated transcriptional reprogramming in potato and tomato: induction of molecular chaperone activity, oxidative stress responses, and immune signaling, with repression of photosynthetic and primary metabolic pathways reflecting energy reallocation.
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Has reproduction · 50
auts2 Features and Expression Are Highly Conserved during Evolution Despite Different Evolutionary Fates Following Whole Genome Duplication.
PMID 36078102 · PMC9454499 · Cells · 2022 · 8 claims · 7 setups
auts2a and auts2b originate from the teleost-specific whole genome duplication (TGD)
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Has reproduction · 50
Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.
PMID 24558256 · PMC3971588 · Genome biology and evolution · 2014 · 8 claims · 8 setups
Nearly all (99.4%) ancient paralog pairs in Gossypium raimondii are differentially expressed in at least one of three tissues (petal, leaf, seed), indicating massive, near-complete expression-level divergence.
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Has reproduction · 76
Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in DSRCTs.
PMID 38781959 · PMC11228554 · Cell reports. Medicine · 2024 · 8 claims · 8 setups
DSRCT tumor cells cluster into consistent subpopulations with partially overlapping lineage- and metabolism-related transcriptional programs across patients and samples
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Has reproduction · 73
Exploring the prognostic and diagnostic value of lactylation-related genes in sepsis.
PMID 39367086 · PMC11452377 · Scientific reports · 2024 · 8 claims · 7 setups
Intersecting sepsis-associated differentially expressed genes with a curated list of 332 lactylation genes yields 55 sepsis-related lactylation genes.
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Has reproduction · 93
Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling.
PMID 25520726 · PMC4251292 · Frontiers in plant science · 2014 · 8 claims · 8 setups
24 h of waterlogging significantly alters mRNA abundance of 1968 genes in Jatropha roots (931 up, 1037 down).
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Has reproduction
Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise.
PMID 29335641 · PMC5864184 · The ISME journal · 2018 · 7 claims · 6 setups
Increasing salinity to >=43 ppt inhibits Trichodesmium growth/increases mortality while stimulating growth of associated Alteromonas, shifting community dominance to the heterotroph
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Has reproduction · 53
Gene Dosage Analysis on the Single-Cell Transcriptomes Linking Cotranslational Protein Targeting to Metastatic Triple-Negative Breast Cancer.
PMID 34577617 · PMC8472593 · Pharmaceuticals (Basel, Switzerland) · 2021 · 7 claims · 5 setups
A computational framework integrating independently measured CNV (DNA sequencing) and single-cell RNA-seq from the same patients identifies recurrent concordant copy number gain and gene upregulation (CNG-UP) events and functional modules at the single-cell level.