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 · 50
Integrative analysis of transcriptomic data reveals a predictive gene signature for chemoradiotherapy response in rectal cancer.
PMID 41550766 · PMC12803930 · iScience · 2026 · 8 claims · 5 setups
A 186-gene signature derived from six GEO transcriptomic datasets predicts nCRT response in LARC with AUC 0.80 in cross-validation
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Has reproduction · 92
Synergism between IL7R and CXCR4 drives BCR-ABL induced transformation in Philadelphia chromosome-positive acute lymphoblastic leukemia.
PMID 32581241 · PMC7314847 · Nature communications · 2020 · 8 claims · 8 setups
IL7R interacts/colocalizes with CXCR4 on the cell surface, recruiting BCR-ABL1 and JAK kinases into close proximity to form a platform for transformation
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Has reproduction · 72
Neoadjuvant sintilimab plus chemotherapy in EGFR-mutant NSCLC: Phase 2 trial interim results (NEOTIDE/CTONG2104).
PMID 38897205 · PMC11293361 · Cell reports. Medicine · 2024 · 8 claims · 8 setups
Neoadjuvant sintilimab plus carboplatin/nab-paclitaxel is clinically feasible and tolerable in resectable EGFR-mutant NSCLC, with all 18 patients completing treatment and undergoing radical surgery.
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Has reproduction · 81
An Erg-driven transcriptional program controls B cell lymphopoiesis.
PMID 32541654 · PMC7296042 · Nature communications · 2020 · 8 claims · 8 setups
Erg is essential for early B-cell development, with its loss causing developmental arrest at the pre–proB (Hardy fraction A-to-B) stage
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Has reproduction · 69
Clinical and molecular correlation defines activity of physiological pathways in life-sustaining kidney xenotransplantation.
PMID 37311769 · PMC10264453 · Nature communications · 2023 · 7 claims · 8 setups
Porcine kidney xenografts transplanted into NHPs show only modest growth over time.
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Has reproduction · 68
Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.
PMID 35012625 · PMC8743438 · Genome biology · 2022 · 7 claims · 8 setups
GENEVA is a semi-automated, study-design-agnostic framework that mines large-scale public RNA-seq data to identify conditions modulating a gene of interest's expression
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Has reproduction · 63
Community assessment of methods to deconvolve cellular composition from bulk gene expression.
PMID 39191725 · PMC11350143 · Nature communications · 2024 · 8 claims · 4 setups
Most deconvolution methods accurately predict coarse-grained immune/stromal cell populations from bulk expression.
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Has reproduction · 37
RNA Editing Alterations Define Disease Manifestations in the Progression of Experimental Autoimmune Encephalomyelitis (EAE).
PMID 36429012 · PMC9688714 · Cells · 2022 · 6 claims · 7 setups
RNA-editing events mediated by APOBEC and ADAR deaminases are significantly reduced throughout the course of EAE disease progression.
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Has reproduction · 50
Transcriptome profiling of osteoclast subsets associated with arthritis: A pathogenic role of CCR2(hi) osteoclast progenitors.
PMID 36591261 · PMC9797520 · Frontiers in immunology · 2022 · 8 claims · 6 setups
CCR2hi and CCR2lo periarticular bone marrow OCP subsets show a disparate transcriptome (863 differentially expressed genes)
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Has reproduction · 69
Manual curation for improved genome annotation of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni).
PMID 41490125 · PMC12768360 · PloS one · 2026 · 7 claims · 7 setups
Manual curation of RNA-seq-derived de novo transcripts increased the number of functional genes in the NWR annotation by 81% (from 8,701 to 15,738).
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Has reproduction · 81
Enabling Single-Cell Drug Response Annotations from Bulk RNA-Seq Using SCAD.
PMID 36762572 · PMC10104628 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023 · 7 claims · 7 setups
SCAD, a transfer learning framework integrating adversarial discriminative domain adaptation (ADDA), can infer single-cell drug sensitivities by transferring knowledge from bulk RNA-seq pharmacogenomic data (GDSC) to scRNA-seq target domains
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Has reproduction · 50
Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.
PMID 25122667 · PMC4232532 · G3 (Bethesda, Md.) · 2014 · 8 claims · 8 setups
330,995 SNPs were identified in transcribed regions between B. rapa genotypes R500 and IMB211, at an average frequency of one SNP per 200 bases.
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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 · 71
Blood and tissue correlates of steroid non-response in checkpoint inhibition-induced immune-related adverse events.
PMID 41254329 · PMC12627558 · Communications medicine · 2025 · 7 claims · 6 setups
An enhanced type 1/type 17 (Th1/Th17, TC1/TC17) immune response in blood and tissue is associated with steroid non-response in irAEs
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Has reproduction · 61
Multi-omics analyses identify mannose phosphate isomerase-centered hypoxia-induced angiogenesis signature in colorectal cancer.
PMID 41204349 · PMC12595641 · Journal of translational medicine · 2025 · 8 claims · 8 setups
Twelve HIA-related genes were identified that are transcriptionally activated by HIFs and functionally implicated in angiogenesis in CRC.
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Has reproduction · 68
Regulatory and evolutionary adaptation of yeast to acute lethal ethanol stress.
PMID 33170850 · PMC7654773 · PloS one · 2020 · 8 claims · 4 setups
Yeast cells activate a rapid transcriptional reprogramming process following acute lethal ethanol stress that is likely adaptive for post-stress survival.
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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 · 85
COVID-19 lung disease shares driver AT2 cytopathic features with Idiopathic pulmonary fibrosis.
PMID 35870428 · PMC9297827 · EBioMedicine · 2022 · 8 claims · 8 setups
COVID-19 lung disease resembles IPF at a fundamental level, recapitulating ViP/IPF gene expression patterns, an IL15-centric cytokine storm, and AT2 cytopathic changes (injury, DNA damage, transient progenitor-state arrest, senescence/SASP).
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Has reproduction · 73
Expression of neurofibromin 1 in colorectal cancer and cetuximab resistance.
PMID 34779495 · PMC8611403 · Oncology reports · 2022 · 8 claims · 8 setups
NF1 is highly expressed in cetuximab-sensitive CRC cell lines and minimally expressed in cetuximab-resistant ones