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).

• Early cAMP signaling orchestrates single-cell synchronicity throughout Dictyostelium development.

  PMID 41792273 · PMC13096493 · Communications biology · 2026 · 7 claims · 6 setups

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  cAMP-pulse signaling during early development induces transcriptome synchronicity at the single-cell level and morphological synchronicity at the multicellular level; its absence compromises synchronicity despite continued development.

  discoideum single-cell scrna-seq dissecting

• Cosmopolitan Gene Families With Known Functions Are Hotspots for the Evolution of Novel Genes in Stony Corals.

  PMID 41873503 · PMC13044578 · Genome biology and evolution · 2026 · 8 claims · 8 setups

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  Dark gene families in corals form cosmopolitan (broadly shared) families that originated via bursts of lineage-specific duplication, often from genes with known function

  genome same montipora stylophora orthogroup busco bulk

• Degeneration and adaptive evolution of digits in ratite birds.

  PMID 41982182 · PMC13135079 · Molecular biology and evolution · 2026 · 8 claims · 6 setups

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  Hindlimb digit 5 (HD5) degeneration shares 70-77% of candidate genes between ostrich and crocodile, indicating it originated once in the Archosauria stem lineage rather than independently.

  developing digit emu ostrich bulk alcian mount

• FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.

  PMID 23768108 · PMC3691734 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 65

  FusionQ is a novel tool that detects gene fusions, constructs chimerical transcript structures, and estimates their abundances from paired-end RNA-Seq data.

  simulated four rna-seq randomly simulated paired-end read-mappability

• Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis.

  PMID 34079055 · PMC8172904 · Communications biology · 2021 · 8 claims · 8 setups

  Has reproduction · 96

  Integration of five mouse scRNAseq datasets reveals a trifurcating lineage trajectory originating from embryonic mammary stem cells (MaSCs) that differentiates into three epithelial lineages (Basal, L-Alv, L-Hor) via unipotent progenitor clusters

  mammary surgically normal single-cell whole-mount integration

• 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

  Has reproduction · 83

  AI-derived radiological clustering identifies stage II CRC patients with significantly different survival benefit from adjuvant chemotherapy

  stage patients tumour whole-tumour radiomics bulk cellular

• Benchmarking methods for genome annotation using nanopore direct RNA in a non-model crop plant.

  PMID 41800382 · PMC12967217 · Bioinformatics advances · 2026 · 6 claims · 8 setups

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  Annotation tools show substantial variation in isoform detection, structural completeness, splicing classification, and handling of 5' read truncation when applied to plant dRNA-seq data.

  barley extracted tool novel nanopore illumina transcriptome

• CRAGE-RB-PI-seq reveals transcriptional dynamics of plant-associated bacteria during root colonization.

  PMID 41723172 · PMC13036076 · Nature communications · 2026 · 8 claims · 7 setups

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  CRAGE-RB-PI-seq, combining CRAGE genome engineering with randomly-barcoded promoter-library insertion sequencing, enables targeted amplification of barcoded bacterial transcripts that bypasses plant RNA interference.

  pseudomonas arabidopsis targeted pi-seq conventional