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 · 30
Single-Cell Sequencing of iPSC-Dopamine Neurons Reconstructs Disease Progression and Identifies HDAC4 as a Regulator of Parkinson Cell Phenotypes.
PMID 30503143 · PMC6327112 · Cell stem cell · 2019 · 8 claims · 8 setups
Single-cell transcriptomic analysis of GBA-N370S iPSC-derived dopamine neurons identifies a progressive axis of gene expression variation leading to endoplasmic reticulum stress.
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Has reproduction · 64
Comparative profiling of skeletal muscle models reveals heterogeneity of transcriptome and metabolism.
PMID 31825657 · PMC7099524 · American journal of physiology. Cell physiology · 2020 · 8 claims · 8 setups
C2C12 myotubes show enriched mRNA expression of genes coding for actin and myosin compared with L6 and HSMC.
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Has reproduction · 61
Omics Playground: a comprehensive self-service platform for visualization, analytics and exploration of Big Omics Data.
PMID 33575569 · PMC7671354 · NAR genomics and bioinformatics · 2020 · 8 claims · 5 setups
Omics Playground is a user-friendly, interactive self-service platform for in-depth analysis, visualization, and interpretation of transcriptomics and proteomics data, including single-cell RNA-seq.
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Has reproduction · 80
Curation of over 10 000 transcriptomic studies to enable data reuse.
PMID 33599246 · PMC7904053 · Database : the journal of biological databases and curation · 2021 · 8 claims · 6 setups
Gemma is a curated database and bioinformatics system that addresses metadata, probe annotation, and expression data inconsistencies in GEO to enable transcriptomic data reuse
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Has reproduction · 80
Colorectal Cancer Prediction Based on Weighted Gene Co-Expression Network Analysis and Variational Auto-Encoder.
PMID 32825264 · PMC7563725 · Biomolecules · 2020 · 6 claims · 7 setups
Combining WGCNA hub genes and VAE 10-dimensional representation as features for an SVM classifier achieves high accuracy in predicting CRC
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Has reproduction · 95
A cell atlas of the adult female Aedes aegypti midgut revealed by single-cell RNA sequencing.
PMID 38839790 · PMC11153528 · Scientific data · 2024 · 8 claims · 4 setups
Established a protocol for isolating single cells from Ae. aegypti midgut and performing scRNA-seq (dissociation, density-gradient purification, viability QC, 10x Genomics library prep and sequencing).
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Has reproduction · 83
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
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
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Has reproduction · 100
A comprehensive framework for analysis of microRNA sequencing data in metastatic colorectal cancer.
PMID 35047825 · PMC8759566 · NAR cancer · 2022 · 8 claims · 7 setups
Five miRNAs (Mir-210_3p, Mir-191_5p, Mir-8-P1b_3p, Mir-1307_5p, Mir-155_5p) are up-regulated at multiple metastatic CRC sites compared to primary CRC.
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Has reproduction
Artificial Intelligence Meets Whole Slide Images: Deep Learning Model Shapes an Immune-Hot Tumor and Guides Precision Therapy in Bladder Cancer.
PMID 36245985 · PMC9553530 · Journal of oncology · 2022 · 8 claims · 8 setups
A three-class WSI cluster (C0/C1/C2) derived via mini batch K-means clustering on Inception V3-extracted image features is significantly associated with overall survival and is an independent prognostic predictor in BLCA.
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Has reproduction · 78
A network-based model of Aspergillus fumigatus elucidates regulators of development and defensive natural products of an opportunistic pathogen.
PMID 41505094 · PMC12781895 · Nucleic acids research · 2026 · 7 claims · 6 setups
MERLIN-P-TFA network inference on 18 curated public RNA-seq datasets produced a genome-wide GRN resource for A. fumigatus called GRAsp.
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Has reproduction · 93
A comparative study on recombination activity in cattle.
PMID 41942849 · PMC13067647 · Genetics, selection, evolution : GSE · 2026 · 8 claims · 8 setups
Genotype data with high systematic missingness across breeds and arrays can be streamlined and analysed with three complementary recombination-estimation approaches (HMM-based LINKPHASE3, deterministic hsphase, likelihood-based hsrecombi)
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Has reproduction · 95
A systems-level analysis of the mutually antagonistic roles of RKIP and BACH1 in dynamics of cancer cell plasticity.
PMID 37963558 · PMC10645512 · Journal of the Royal Society, Interface · 2023 · 8 claims · 7 setups
RKIP and BACH1 are negatively correlated with each other across most cancer types in TCGA
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Has reproduction · 66
Responses of peritubular macrophages and the testis transcriptome profiles of peripubertal and adult rodents exposed to an acute dose of MEHP.
PMID 38113427 · PMC10901151 · Toxicological sciences : an official journal of the Society of Toxicology · 2024 · 8 claims · 7 setups
MEHP exposure previously increased PTMφ numbers 6-fold in peripubertal Fischer rats
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Has reproduction · 47
Comprehensive analysis of metastatic gastric cancer tumour cells using single-cell RNA-seq.
PMID 33441952 · PMC7806779 · Scientific reports · 2021 · 8 claims · 6 setups
Carcinoma cell profiles are distinct for each patient, while diverse microenvironmental (nonmalignant) subsets are shared across different patients.
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Has reproduction · 50
Loss of mutual protection between human osteoclasts and chondrocytes in damaged joints initiates osteoclast-mediated cartilage degradation by MMPs.
PMID 34811438 · PMC8608887 · Scientific reports · 2021 · 8 claims · 8 setups
Human osteoclasts differentiate on cartilage, expressing osteoclast markers, and visibly damage the cartilage surface without forming resorption pits or F-actin rings as seen on dentine.
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Has reproduction · 44
Population differentiation and epidemic tracking of Bursaphelenchus xylophilus in China based on chromosome-level assembly and whole-genome sequencing data.
PMID 34839581 · PMC9300093 · Pest management science · 2022 · 6 claims · 8 setups
Generated the first chromosome-level genome assembly (AH1) of B. xylophilus using PacBio, Illumina, BioNano, and Hi-C data
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Has reproduction · 88
Antibiotic Drug screening and Image Characterization Toolbox (A.D.I.C.T.): a robust imaging workflow to monitor antibiotic stress response in bacterial cells in vivo.
PMID 35707454 · PMC9178280 · F1000Research · 2021 · 8 claims · 6 setups
A.D.I.C.T. provides a robust, reproducible semi-automated imaging workflow for monitoring antibiotic stress response in bacteria in vivo
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Has reproduction · 75
Identification of Novel Therapeutic Candidates Against SARS-CoV-2 Infections: An Application of RNA Sequencing Toward mRNA Based Nanotherapeutics.
PMID 35983322 · PMC9378778 · Frontiers in microbiology · 2022 · 6 claims · 7 setups
RPL29 (60S ribosomal protein L29) is highly/consistently expressed across all COVID-19 infected groups regardless of severity, suggesting it as a novel host therapeutic target for mRNA-based nanomedicines.
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Has reproduction · 89
Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes.
PMID 37032329 · PMC10084625 · Microbiome · 2023 · 8 claims · 7 setups
MAPQ ≥30 filtering improves precision but substantially reduces recall, especially for unrepresented/divergent eukaryotic taxa
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Has reproduction · 76
Tracing human genetic histories and natural selection with precise local ancestry inference.
PMID 40379651 · PMC12084304 · Nature communications · 2025 · 7 claims · 7 setups
Orchestra, a two-stage LAI method combining a recombination-distance base layer with a deep learning (convolutional + attention) smoothing module, outperforms RFmix, FLARE and Gnomix in precision and recall across simulated admixture generations.