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 · 91
De Novo Assembly and Annotation of the Larval Transcriptome of Two Spadefoot Toads Widely Divergent in Developmental Rate.
PMID 31217263 · PMC6686947 · G3 (Bethesda, Md.) · 2019 · 8 claims · 8 setups
De novo transcriptome assemblies were generated for larval P. cultripes and S. couchii, providing new genomic resources for spadefoot toads
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Has reproduction · 83
Multimodal data integration for biologically-relevant artificial intelligence to guide adjuvant chemotherapy in stage II colorectal cancer.
PMID 40472802 · PMC12171563 · EBioMedicine · 2025 · 6 claims · 7 setups
AI-derived radiological clustering identifies stage II CRC patients with significantly different survival benefit from adjuvant chemotherapy
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Has reproduction · 51
Unveiling prognostics biomarkers of tyrosine metabolism reprogramming in liver cancer by cross-platform gene expression analyses.
PMID 32542016 · PMC7295234 · PloS one · 2020 · 6 claims · 8 setups
Five tyrosine catabolic enzymes (TAT, HPD, HGD, GSTZ1, FAH) are downregulated in HCC versus normal liver at mRNA and protein levels
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Has reproduction · 46
De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia.
PMID 35773379 · PMC9247108 · Scientific reports · 2022 · 6 claims · 7 setups
De novo transcriptome assembly of S. latifolia produced 48,549 unigenes, 71.53% (34,728) of which were annotated against KEGG, GO, and/or KOG databases
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A comprehensive modular map of molecular interactions in RB/E2F pathway.
PMID 18319725 · PMC2290939 · Molecular systems biology · 2008 · 8 claims · 4 setups
A comprehensive, curated map of RB/E2F pathway molecular interactions was built using SBGN notation in CellDesigner and converted to BioPAX 2.0 format
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Has reproduction · 93
Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling.
PMID 25520726 · PMC4251292 · Frontiers in plant science · 2014 · 8 claims · 8 setups
24 h of waterlogging significantly alters mRNA abundance of 1968 genes in Jatropha roots (931 up, 1037 down).
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Has reproduction · 57
Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod.
PMID 33782539 · PMC8007741 · Communications biology · 2021 · 8 claims · 7 setups
t-SNE clustering of all-gene expression data groups field-collected (diapause program) samples into one cluster while early and late culture (reproductive program) samples separate into two distinct phenotypes
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Has reproduction · 66
RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.
PMID 23145190 · PMC3493385 · PLoS neglected tropical diseases · 2012 · 8 claims · 8 setups
S. stercoralis possesses homologs of nearly all C. elegans dauer genes, but with significant differences in protein structure, developmental regulation, and gene family expansion.
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Has reproduction · 67
A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.
PMID 25009556 · PMC4070175 · Frontiers in genetics · 2014 · 8 claims · 8 setups
Multiple k-mer (MK) assemblies are more complete than single k-mer (SK) assemblies, showing higher reads-mapped-back-to-transcripts (RMBT) and higher CEGMA complete-gene percentages for all three tools.
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Has reproduction · 51
Cell type-specific eQTL analysis of COVID-19 based on single-cell transcriptomic data.
PMID 41064594 · PMC12501775 · NAR genomics and bioinformatics · 2025 · 8 claims · 8 setups
Single-cell eQTL analysis across eight immune cell types identified 2593 genes whose expression is significantly associated with common genetic polymorphisms, with most genes showing cell type-specific effects
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Has reproduction · 79
A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis.
PMID 34545398 · PMC8527503 · G3 (Bethesda, Md.) · 2021 · 8 claims · 8 setups
A chromosome-scale genome assembly of H. californensis spans 110 Mb in 44 scaffolds, with 99.47% of bases in 13 scaffolds
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Has reproduction · 78
annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing.
PMID 36472574 · PMC9724561 · GigaScience · 2022 · 7 claims · 8 setups
annotate_my_genomes is an easy-to-use genome-guided pipeline that uses hybrid (PacBio+Illumina) assembled transcripts to distinguish coding genes from long non-coding RNAs and reconcile them with prior annotations.
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Has reproduction
Single-cell RNA-sequencing of circulating tumour cells: A practical guide to workflow and translational applications.
PMID 41053409 · PMC12500777 · Cancer metastasis reviews · 2025 · 7 claims · 8 setups
A 12-step CTC-specific scRNA-seq workflow spanning enrichment, single-cell sorting, sequencing, data pre-processing and downstream analysis is proposed to overcome methodological inconsistencies.
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Has reproduction · 88
Age Deceleration and Reversal Gene Patterns in Dauer Diapause.
PMID 41104926 · PMC12686545 · Aging cell · 2025 · 8 claims · 8 setups
Dauer arrest, regardless of duration, does not cause lasting functional decline in lifespan, brood size, or developmental resumption
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Has reproduction · 89
Evolution of Highly Repetitive Silk Genes in the Luna Moth, Actias luna.
PMID 41738778 · PMC12962854 · Genome biology and evolution · 2026 · 8 claims · 8 setups
Eight sericin genes were identified in the Actias luna genome, including two clusters of closely related paralogs.
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Has reproduction · 74
Toward a Consensus in the Repertoire of Hemocytes Identified in Drosophila.
PMID 33748138 · PMC7969988 · Frontiers in cell and developmental biology · 2021 · 8 claims · 8 setups
Comparative analysis of three scRNAseq studies identifies eight common, robust hemocyte subgroups associated with distinct functions (proliferation, immune response, phagocytosis, secretion)
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Has reproduction
Unlocking the microbial studies through computational approaches: how far have we reached?
PMID 36920617 · PMC10016191 · Environmental science and pollution research international · 2023 · 8 claims · 8 setups
Metagenomics enables culture-independent study of microbial communities directly from their natural environments, bypassing the need for clonal isolation.
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Has reproduction
Association between Arsenic Level, Gene Expression in Asian Population, and In Vitro Carcinogenic Bladder Tumor.
PMID 35039759 · PMC8760535 · Oxidative medicine and cellular longevity · 2022 · 8 claims · 5 setups
A unique set of 147 genes is associated with arsenic exposure and linked to molecular mechanisms of cancer.
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Toxoplasma: the next 100years.
PMID 18672085 · PMC2596634 · Microbes and infection · 2008 · 8 claims · 8 setups
Micronemes, rhoptries, and dense granules are specialized secretory organelles that mediate T. gondii host cell invasion and remodeling
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Has reproduction · 63
Genetic analysis of Leishmania donovani tropism using a naturally attenuated cutaneous strain.
PMID 24992200 · PMC4081786 · PLoS pathogens · 2014 · 8 claims · 8 setups
The CL-SL L. donovani isolate is severely attenuated for survival in visceral organs (liver, spleen) of BALB/c mice compared with the VL-SL isolate, while inducing transient footpad swelling that VL-SL does not.