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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Integrative analysis of RUNX1 downstream pathways and target genes.
PMID 18671852 · PMC2529319 · BMC genomics · 2008 · 7 claims · 8 setups
Integrating gene expression profiles from three independent RUNX1 perturbation platforms (FPD-AML patient cell lines, RUNX1/CBFβ overexpression in HeLa cells, Runx1 knockout mouse embryos) identifies RUNX1-regulated genes and downstream pathways
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Up regulation in gene expression of chromatin remodelling factors in cervical intraepithelial neoplasia.
PMID 18248679 · PMC2277413 · BMC genomics · 2008 · 8 claims · 4 setups
Chromatin remodelling-associated genes SMARCC1, NCOR1, MRFAP1 and MORF4L2 are upregulated during progression of cervical intraepithelial neoplasia
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Has reproduction · 90
Stemness genes and miR-1247-3p expression associate with clinicopathological parameters and prognosis in lung adenocarcinoma.
PMID 37948380 · PMC10637681 · PloS one · 2023 · 6 claims · 7 setups
Three stem cell-related genes (ORC1L, KIF20A, DLGAP5) are differentially expressed in LUAD and correlate with altered immune infiltration and reduced patient survival.
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Has reproduction · 55
Identification of TYR, TYRP1, DCT and LARP7 as related biomarkers and immune infiltration characteristics of vitiligo via comprehensive strategies.
PMID 34107850 · PMC8806433 · Bioengineered · 2021 · 6 claims · 6 setups
TYR, TYRP1, DCT and LARP7 are biomarkers associated with vitiligo
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Has reproduction · 80
Specific signature biomarkers highlight the potential mechanisms of circulating neutrophils in aneurysmal subarachnoid hemorrhage.
PMID 36438795 · PMC9685413 · Frontiers in pharmacology · 2022 · 7 claims · 8 setups
Six genes (CST7, HSP90AB1, PADI4, PLBD1, RAB32, SLAMF6) are signature diagnostic biomarkers for aSAH identified by LASSO and SVM-RFE.
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Has reproduction
Methylation patterns of the nasal epigenome of hospitalized SARS-CoV-2 positive patients reveal insights into molecular mechanisms of COVID-19.
PMID 40170038 · PMC11963311 · BMC medical genomics · 2025 · 8 claims · 5 setups
The nasal methylome shows differential DNA methylation in intergenic regions and low methylated regions (LMRs), highlighting distal regulatory/enhancer-like elements in COVID-19 gene regulation
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Interpretation of genomic data: questions and answers.
PMID 18582627 · PMC2528831 · Seminars in hematology · 2008 · 8 claims · 6 setups
The main challenge in using genomic technology in cancer research is not managing the volume of data but the proper design, analysis, and reporting of studies.
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Application of OMICS technologies in occupational and environmental health research; current status and projections.
PMID 19933307 · PMC2910417 · Occupational and environmental medicine · 2010 · 8 claims · 6 setups
Five OMICS technologies are well established: genotyping, transcriptomics, epigenomics, proteomics, and metabolomics
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Has reproduction · 53
PulmonDB: a curated lung disease gene expression database.
PMID 31949184 · PMC6965635 · Scientific reports · 2020 · 6 claims · 6 setups
PulmonDB is a curated, web-based gene expression database and R package integrating microarray and RNA-seq data for COPD and IPF with manually curated controlled-vocabulary annotation.
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Has reproduction · 67
Reverse Engineering of the Pediatric Sepsis Regulatory Network and Identification of Master Regulators.
PMID 34680414 · PMC8533457 · Biomedicines · 2021 · 7 claims · 8 setups
A set of 15 TFs was identified as sepsis-specific master regulators of pediatric sepsis, dividing into two non-overlapping clusters.
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Has reproduction · 30
Genomic and transcriptomic plasticity in treatment-naive ovarian cancer.
PMID 24221193 · PMC3912411 · Genome research · 2014 · 8 claims · 8 setups
Treatment-naïve epithelial ovarian cancers show extensive intra-tumor heterogeneity of genomic rearrangements, with the most substantial differences occurring between omentum/peritoneum metastases and ovarian tumor sites.
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Has reproduction · 88
Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States.
PMID 35269470 · PMC8909161 · Cells · 2022 · 7 claims · 7 setups
COVID-19 and HLH share immunological pathways, yielding 237 common up-regulated DEGs dominated by cytokine/chemokine signaling and neutrophil-mediated immune responses.
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Has reproduction · 62
Predicting Bone Metastasis Using Gene Expression-Based Machine Learning Models.
PMID 34858485 · PMC8631472 · Frontiers in genetics · 2021 · 7 claims · 5 setups
A DNN model using the top 34 betweenness-centrality-ranked hub genes predicts bone metastasis with AUC of 92.11% on the GEO validation data.
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Has reproduction · 53
Molecular Biomarker of Drug Resistance Developed From Patient-Derived Organoids Predicts Survival of Colorectal Cancer Patients.
PMID 35425715 · PMC9004628 · Frontiers in oncology · 2022 · 8 claims · 7 setups
Patient-derived colorectal cancer organoids (CRCOs) can be established from surgical CRC tissue with an 82% success rate (41/50)
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Has reproduction · 78
A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP).
PMID 22719821 · PMC3374610 · PloS one · 2012 · 8 claims · 7 setups
METAREP version 1.3.1 is an open-source, scalable tool for querying, browsing and comparing extremely large volumes of metagenomic annotations, with an extended data model, dynamic weighting, distributed searches and advanced clustering.