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 · 90
Optimal Dual RNA-Seq Mapping for Accurate Pathogen Detection in Complex Eukaryotic Hosts.
PMID 39959292 · PMC11825298 · Bio-protocol · 2025 · 7 claims · 6 setups
Mapping adapter-trimmed reads first to the pathogen genome recovers more pathogen reads than the traditional host-first mapping approach.
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Has reproduction · 76
Correcting scale distortion in RNA sequencing data.
PMID 39875825 · PMC11776150 · BMC bioinformatics · 2025 · 8 claims · 8 setups
Local averaging reveals expression-level-dependent biases that differ from sample to sample across all RNA-seq datasets studied, and are not corrected by conventional normalization (TPM/FPKM)
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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 · 7 claims · 5 setups
Short- and long-term HL responses in Arabidopsis leaves are driven by distinct transcriptional programs, with duration of HL treatment as the primary factor separating transcriptomic clusters.
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Has reproduction · 64
Blood Transcriptome Analysis of Septic Patients Reveals a Long Non-Coding Alu-RNA in the Complement C5a Receptor 1 Gene.
PMID 35447887 · PMC9027897 · Non-coding RNA · 2022 · 6 claims · 7 setups
A computational pipeline intersecting immune gene coordinates with Alu element coordinates can identify candidate Alu-lncRNAs
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Has reproduction · 71
IL-6 trans-Signaling Regulates Neutrophilic Inflammation in Alcohol-Associated Hepatitis.
PMID 40562277 · PMC13168973 · The American journal of pathology · 2026 · 8 claims · 8 setups
Hepatic IL-6R expression progressively declines with increasing severity of alcohol-related liver disease, from normal to early ASH to nonsevere and severe AH
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Has reproduction · 61
lncEvo: automated identification and conservation study of long noncoding RNAs.
PMID 33563213 · PMC7871587 · BMC bioinformatics · 2021 · 8 claims · 5 setups
lncEvo is an integrated Nextflow/Docker pipeline combining transcriptome assembly, lncRNA identification, and cross-species conservation analysis into a single workflow.
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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 · 87
Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design.
PMID 34553212 · PMC8458035 · GigaScience · 2021 · 8 claims · 7 setups
Genetic variation–based demultiplexing tools can be effectively deployed on cancer scRNA-seq tissue using a pooled experimental design, achieving high recall at acceptable precision-recall tradeoffs in both high-CNV (HGSOC) and high-SNV (lung adenocarcinoma) cancers, even with extremely high doublet proportions.