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 · 86
Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning.
PMID 34575658 · PMC8472680 · Journal of personalized medicine · 2021 · 7 claims · 4 setups
TNBC can be divided into four gene-expression-defined subtypes: BLIA, BLIS, MES, and LAR
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Has reproduction · 75
Identification of Key Differentially Expressed Genes in Arabidopsis thaliana Under Short- and Long-Term High Light Stress.
PMID 40869111 · PMC12386182 · International journal of molecular sciences · 2025 · 8 claims · 6 setups
Meta-analysis of 21 experiments covering 58 HL conditions yielded ~218,000 DEG instances corresponding to ~19,000 unique A. thaliana genes
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Placental gene signatures associated with high neonatal adiposity: role for immune cell activation.
PMID 41958865 · PMC13061145 · Journal of the Endocrine Society · 2026 · 8 claims · 8 setups
A placental transcriptomic signature is associated with high neonatal adiposity
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Has reproduction · 88
From bud formation to flowering: transcriptomic state defines the cherry developmental phases of sweet cherry bud dormancy.
PMID 31830909 · PMC6909552 · BMC genomics · 2019 · 7 claims · 7 setups
Flower bud developmental stages (organogenesis, paradormancy, endodormancy, dormancy release, ecodormancy) are defined by distinct, stage-specific gene expression programs
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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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scArchon: a scalable benchmarking framework for assessing single-cell perturbation models.
PMID 42121287 · PMC13162514 · Genome biology · 2026 · 8 claims · 8 setups
scArchon is a reproducible, modular, Snakemake-based benchmarking platform that evaluates perturbation response prediction tools in a standardized, containerized, extensible manner.
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Has reproduction · 62
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
Immature (day 7) CASK KO induced neurons show increased dendritic complexity/neurite overgrowth and upregulated gene networks for cell adhesion, neurite outgrowth, and cytoskeletal organization.
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Has reproduction · 27
Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.
PMID 23840502 · PMC3688795 · PloS one · 2013 · 8 claims · 5 setups
A de novo radish root transcriptome of 68,940 assembled transcripts including 33,337 unigenes was generated, providing the first comprehensive molecular characterization of the radish root response to Pb stress.
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Eduomics: a Nextflow pipeline to simulate -omics data for education.
PMID 41816779 · PMC12972896 · NAR genomics and bioinformatics · 2026 · 8 claims · 4 setups
Eduomics is a Nextflow DSL2 pipeline that automates generation of validated variant-calling and RNA-seq datasets for education while abstracting away technical requirements
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Epigenetic profiling of hematopoietic stem cells from male mice identifies KDR and PU.1 as regulators of aging transcriptome and caloric restriction response.
PMID 41720793 · PMC13035812 · Nature communications · 2026 · 8 claims · 8 setups
Lifelong CR reduces white blood cell production and shifts hematopoiesis toward myeloid and thrombo-erythroid lineages while suppressing lymphoid output
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A tissue-resolved, network-based transcriptomic framework for abiotic stress responses in sorghum.
PMID 41904985 · PMC13033392 · The Plant journal : for cell and molecular biology · 2026 · 8 claims · 8 setups
Tissue specificity is the dominant determinant of abiotic stress-induced gene reprogramming across drought, heat, and salinity stress in sorghum
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Transcriptomics Reveal Molecular Signatures of a Resolved Sexual Conflict and Potential Association With Colour Polymorphism in Tawny Owls.
PMID 41964128 · PMC13069001 · Molecular ecology · 2026 · 8 claims · 8 setups
Substantial sex-specific variation exists in differentially expressed genes, SNPs and alternative exon usage in genes involved in life history traits (ZGRF1, VLDLR), behaviour (GSK3B, SLC12A) and growth (GHR, EGF, EPS8L2)
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Has reproduction · 62
Comprehensive Transcriptome Analysis Reveals Genome-Wide Changes Associated with Endoplasmic Reticulum (ER) Stress in Potato (Solanum tuberosum L.).
PMID 36430273 · PMC9696714 · International journal of molecular sciences · 2022 · 8 claims · 3 setups
TM treatment of potato leaves produces widespread, time-dependent differential gene expression associated with ER stress and the UPR
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Has reproduction · 46
De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia.
PMID 35773379 · PMC9247108 · Scientific reports · 2022 · 6 claims · 7 setups
De novo transcriptome assembly of S. latifolia produced 48,549 unigenes, 71.53% (34,728) of which were annotated against KEGG, GO, and/or KOG databases