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
Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.
PMID 33304461 · PMC7710658 · Computational and structural biotechnology journal · 2020 · 7 claims · 6 setups
Expression stability in CHO cell lines is controlled at three levels: choice of integration site, integrity/concatemerization pattern of the transgene, and stress-related cellular processes.
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Has reproduction · 58
iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data.
PMID 35899080 · PMC9310080 · NAR genomics and bioinformatics · 2022 · 8 claims · 4 setups
iCOMIC provides a GUI-driven, Snakemake-based pipeline integrating multiple tools for DNA-Seq and RNA-Seq analysis with minimal command-line interaction.
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Has reproduction · 80
Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity.
PMID 36928603 · PMC10101853 · Nature genetics · 2023 · 8 claims · 6 setups
The WHO histopathological classification of MPM accounts for only up to ~10% of interpatient molecular differences
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Has reproduction · 73
Proteogenomic analysis prioritises functional single nucleotide variants in cancer samples.
PMID 29221171 · PMC5707065 · Oncotarget · 2017 · 8 claims · 6 setups
A customised SAAV peptide database built from RNA-seq/WGS variant calls can be used to search proteomics data and detect single amino acid variant (SAAV)-containing peptides at the protein level
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Has reproduction · 98
Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis.
PMID 33253310 · PMC7738170 · PLoS pathogens · 2020 · 7 claims · 8 setups
Non-synonymous mutations in dnaA are statistically associated with drug resistance (INH, RIF, SM) in clinical M. tuberculosis strains across two independent GWAS cohorts (China and Vietnam)
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Full-text index only
DDBJ in collaboration with mass-sequencing teams on annotation.
PMID 15608189 · PMC539974 · Nucleic acids research · 2005 · 7 claims · 5 setups
DDBJ collected and released 1,066,084 entries (718,072,425 bases) in the past year, including the complete chimpanzee chromosome 22 sequence and silkworm whole-genome shotgun data
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Has reproduction
Accelerating rare disease diagnostics by linking DNA and RNA through an explainable and interactive RNA-guided workflow.
PMID 41685349 · PMC12891912 · NAR genomics and bioinformatics · 2026 · 7 claims · 7 setups
An integrated RNA-guided variant interpretation workflow combining OUTRIDER, FRASER, MOLGENIS VIP, and Borzoi enhances clinical variant interpretation and reclassification of VUS in rare disease cases.
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Full-text index only
DDBJ dealing with mass data produced by the second generation sequencer.
PMID 18927114 · PMC2686496 · Nucleic acids research · 2009 · 8 claims · 7 setups
DDBJ collected and released 2,368,110 entries (1,415,106,598 bases) of original DNA sequence data from July 2007 to June 2008.
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Has reproduction · 79
Contribution of retrotransposition to developmental disorders.
PMID 31604926 · PMC6789007 · Nature communications · 2019 · 8 claims · 6 setups
De novo retrotransposition events cause a small but detectable fraction of severe developmental disorders, with 4 of 9 de novo MEIs deemed likely causative (~0.04%).