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 · 88
AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression.
PMID 27082953 · PMC4833304 · PLoS computational biology · 2016 · 7 claims · 4 setups
Sample-sample correlation of transcript abundances is trivially high regardless of condition and gives misleading estimates of the replicability of conditional (differential) variation in expression.
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Has reproduction · 58
Comprehensive analysis of peroxisome proliferator-activated receptors to predict the drug resistance, immune microenvironment, and prognosis in stomach adenocarcinomas.
PMID 38529307 · PMC10962337 · PeerJ · 2024 · 8 claims · 8 setups
PPARA, PPARD and PPARG are more abnormally expressed in STAD samples and cell lines compared to most of 32 cancer types in TCGA
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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 · 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 · 70
GAUGE-Annotated Microbial Transcriptomic Data Facilitate Parallel Mining and High-Throughput Reanalysis To Form Data-Driven Hypotheses.
PMID 33758032 · PMC8547006 · mSystems · 2021 · 7 claims · 6 setups
GAUGE automatically annotates GEO microbial microarray and RNA-seq data sets, increasing the percentage amenable to analysis from 4% to 33%.
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Has reproduction · 67
HArmonized single-cell RNA-seq Cell type Assisted Deconvolution (HASCAD).
PMID 37907883 · PMC10619225 · BMC medical genomics · 2023 · 6 claims · 5 setups
HASCAD, a DNN-based cell composition deconvolution model, predicts the fractions of up to 15 immune cell types from bulk RNA-seq.
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Has reproduction · 67
Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.
PMID 23951250 · PMC3741199 · PloS one · 2013 · 8 claims · 8 setups
Cryosectioning single blastoderm-stage D. melanogaster embryos along the A–P axis and sequencing mRNA from each slice yields reliable genome-wide spatial expression patterns.
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Has reproduction · 86
RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.
PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups
RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.
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Has reproduction · 50
ZAP targets aberrant mRNA transcripts encoding proteins with defective signal peptides for degradation.
PMID 41820617 · PMC13084044 · The EMBO journal · 2026 · 8 claims · 7 setups
ZAP (ZC3HAV1/PARP13) is a key component of the RAPP quality control pathway