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).

• The genome sequence of the Acorn Weevil, Curculio glandium (T.Marsham, 1802) (Coleoptera: Curculionidae).

  PMID 42021765 · PMC13096787 · Wellcome open research · 2026 · 8 claims · 8 setups

  Full-text index only

  A chromosomally complete genome assembly was produced for Curculio glandium (Acorn Weevil) as part of the Darwin Tree of Life project

  curculio assembled alternate pacbio hi-c sequencing

• The genome sequence of the Woodland Grayling, Hipparchia fagi (Scopoli, 1763) (Lepidoptera: Nymphalidae).

  PMID 42078576 · PMC13133624 · Wellcome open research · 2026 · 8 claims · 8 setups

  Full-text index only

  A chromosome-level, haplotype-resolved genome assembly was produced for Hipparchia fagi (Woodland Grayling) as part of Project Psyche.

  organism pacbio computational assembled pacbio hi-c k-mer

• Optimized mixed Markov models for motif identification.

  PMID 16749929 · PMC1534070 · BMC bioinformatics · 2006 · 8 claims · 4 setups

  Full-text index only

  OMiMa can incorporate more than NNSplice's pairwise dependencies

  simulated regulatory splice biological motif pairwise

• LoRA-TV: read depth profile-based clustering of tumor cells in single-cell sequencing.

  PMID 38877886 · PMC11179121 · Briefings in bioinformatics · 2024 · 6 claims · 2 setups

  Has reproduction · 90

  LoRA-TV jointly processes read-depth profiles of all cells by stacking them into a matrix and applying low-rank approximation plus total-variation smoothing to capture shared genomic signatures for clustering.

  tumor simulated single-cell simulation

• Gene-expression patterns in peripheral blood classify familial breast cancer susceptibility.

  PMID 26538066 · PMC4634735 · BMC medical genomics · 2015 · 8 claims · 7 setups

  Has reproduction · 83

  A multigene expression biomarker from PBMCs accurately classifies familial breast cancer (FBC) status

  pbmcs utah blood normal microarray svm-rfe svm

• Experimental identification and in silico prediction of bacterivory in green algae.

  PMID 33649548 · PMC8245530 · The ISME journal · 2021 · 7 claims · 6 setups

  Has reproduction · 93

  Five prasinophyte strains (Pterosperma cristatum NIES626, Pyramimonas parkeae CCMP726, Pyramimonas parkeae NIES254, Nephroselmis pyriformis RCC618, Dolichomastix tenuilepis CCMP3274) ingest live fluorescently labeled bacteria, detected by microscopy and/or flow cytometry

  prasinophyte same green pelagibaca flow epifluorescence gene-based

• Pathway signatures derived from on-treatment tumor specimens predict response to anti-PD1 blockade in metastatic melanoma.

  PMID 34654806 · PMC8519947 · Nature communications · 2021 · 6 claims · 8 setups

  Has reproduction · 100

  A pathway-based super signature from on-treatment samples (PASS-ON) predicts anti-PD1 response with high accuracy (validation AUC 0.85-0.89, combined AUC 0.88) and outperforms existing signatures across all four datasets.

  metastatic pathway bulk gene elastic-net

• Single cell analysis reveals the roles and regulatory mechanisms of type-I interferons in Parkinson's disease.

  PMID 38566100 · PMC10985960 · Cell communication and signaling : CCS · 2024 · 8 claims · 8 setups

  Has reproduction · 55

  Microglia, endothelial cells, and pericytes exhibit the highest IFN-I activity among PD midbrain cell types, with microglia and endothelial cells showing significantly elevated high-IFN-I-scoring proportions in PD versus controls

  midbrain single microglia substantia single-cell scenic monocle

• Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development.

  PMID 34643182 · PMC8555986 · eLife · 2021 · 7 claims · 8 setups

  Has reproduction · 84

  Tbx5 directly maintains Aldh1a2 expression in the foregut lateral plate mesoderm via an evolutionarily conserved intronic enhancer

  e9.5 xenopus bulk rt-qpcr whole-mount

• Macrophages on the run: Exercise balances macrophage polarization for improved health.

  PMID 39476967 · PMC11585839 · Molecular metabolism · 2024 · 8 claims · 7 setups

  Has reproduction · 81

  Immediate/acute exercise triggers an M1 (pro-inflammatory) macrophage polarization surge.

  gene affymetrix pooled muscle meta-analysis stepminer gene

• DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues.

  PMID 38600112 · PMC11006913 · Nature communications · 2024 · 8 claims · 5 setups

  Has reproduction · 93

  Many of the 92 assayed HD missense variants alter DNA binding affinity and/or specificity compared to their corresponding reference alleles

  homeodomain hoxd13 cerevisiae amino universal chip-seq electrophoretic

• Comparing the utility of in vivo transposon mutagenesis approaches in yeast species to infer gene essentiality.

  PMID 32681306 · PMC7599172 · Current genetics · 2020 · 7 claims · 7 setups

  Has reproduction · 81

  A machine-learning (Random Forest) approach trained on transposon insertion features can predict gene essentiality genome-wide in yeast species

  saccharomyces schizosaccharomyces candida computational transposon random

• Refining breast cancer biomarker discovery and drug targeting through an advanced data-driven approach.

  PMID 38253993 · PMC10810249 · BMC bioinformatics · 2024 · 8 claims · 8 setups

  Has reproduction · 59

  The BGWO_SA_Ens algorithm (hybrid BGWO + simulated annealing with an ensemble classifier objective function) selects predictive breast cancer biomarker genes with high classification performance

  merged gse45827 superior differential feature comparative

• TransOrGAN: An Artificial Intelligence Mapping of Rat Transcriptomic Profiles between Organs, Ages, and Sexes.

  PMID 37200521 · PMC10433534 · Chemical research in toxicology · 2023 · 8 claims · 5 setups

  Has reproduction · 84

  TransOrGAN can infer transcriptomic profiles between any 2 of 9 rat organs with an average cosine similarity of 0.984 versus real profiles

  fischer computational transcriptomic same bulk gan-based autoencoder

• A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference.

  PMID 32019526 · PMC7001327 · BMC plant biology · 2020 · 8 claims · 6 setups

  Has reproduction · 62

  Inter-specific differences in vertical distribution/microhabitat preference are associated with distinct dynamics of gene expression during dehydration and rehydration phases

  hymenophyllum caudiculatum annotated rna-seq chlorophyll relative

• A comparative analysis of blastoid models through single-cell transcriptomics.

  PMID 39524369 · PMC11543915 · iScience · 2024 · 8 claims · 7 setups

  Has reproduction · 60

  EPSC-derived blastoids are transcriptomically distinct from nPSC-derived blastoids, with nPSC-blastoids clustering closer to natural blastocysts.

  blastoid natural combined integrated scrnaseq lineage kolmogorov-smirnov

• Transcriptome and machine learning analysis of the impact of COVID-19 on mitochondria and multiorgan damage.

  PMID 38295140 · PMC10830027 · PloS one · 2024 · 6 claims · 7 setups

  Has reproduction · 71

  Potential cardiac, hepatic, and renal impairments in COVID-19 are associated with ACE2, inflammatory cytokine storms, and mitochondrial pathways.

  nasopharyngeal heart leukocytes blood bulk pathway machine

• Multi-omic identification of perineurial hyperplasia and lipid-associated nerve macrophages in human polyneuropathies.

  PMID 40849297 · PMC12375038 · Nature communications · 2025 · 8 claims · 8 setups

  Has reproduction · 90

  Multi-omic profiling (snRNA-seq + spatial transcriptomics) of human sural nerves identifies novel cell type markers (MLIP in mySC; GRIK3, PRIMA1 in nmSC; CXCL14 in periC) not previously described in rodent or human literature

  sural peripheral snrna-seq nerve single-nucleus subcellular situ

• Cross-species comparative hippocampal transcriptomics in Alzheimer's disease.

  PMID 38292167 · PMC10824791 · iScience · 2024 · 8 claims · 8 setups

  Has reproduction · 75

  The three mouse models (5xFAD, APP/PS1, hAβ-KI) share more DEGs and GOBP terms with LOAD than with EOAD patients

  hippocampus postmortem computational bulk publicly qrt-pcr

• Developing prognostic gene panel of survival time in lung adenocarcinoma patients using machine learning.

  PMID 35117753 · PMC8799101 · Translational cancer research · 2020 · 8 claims · 5 setups

  Has reproduction · 32

  Naïve Bayes using a 22-gene panel is the best-performing and most stable machine learning model for predicting LUAD survival time (>3 vs <3 years)

  tcga geo rna-seq methylation sequencing