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).

• SIRE 2.0: a novel method for estimating polygenic host effects underlying infectious disease transmission, and analytical expressions for prediction accuracies.

  PMID 40169992 · PMC11963337 · Genetics, selection, evolution : GSE · 2025 · 8 claims · 2 setups

  Has reproduction · 83

  SIRE 2.0 is a novel Bayesian methodology and software tool for estimating polygenic contributions (variance components and additive genetic effects) to host susceptibility, infectivity and recoverability from temporal epidemic data using pedigree/genomic relationship matrices.

  simulated bayesian systematic

• Distributed biotin-streptavidin transcription roadblocks for mapping cotranscriptional RNA folding.

  PMID 28398514 · PMC5499547 · Nucleic acids research · 2017 · 6 claims · 6 setups

  Has reproduction · 77

  Randomly distributed biotin–SAv roadblocks in cotranscriptional SHAPE-Seq identify the same RNA structural transitions related to a riboswitch decision-making process as EcoRI E111Q roadblocking

  coli randomly bacillus radiolabeled pellet greb

• Cell type- and species-specific regulation of hepatic lncRNAs by TCDD-activated aryl hydrocarbon receptor.

  PMID 41136526 · PMC12552753 · Scientific reports · 2025 · 8 claims · 6 setups

  Has reproduction · 71

  AHR-mediated lncRNA dysregulation may be a contributing mechanism in TCDD-elicited progression of steatosis to steatohepatitis with fibrosis

  liver mm39 bulk single-nuclei ahr

• eDNAmap: A Metabarcoding Web Tool for Comparing Marine Biodiversity, With Special Reference to Teleost Fish.

  PMID 41189540 · PMC12627913 · Molecular ecology resources · 2026 · 6 claims · 5 setups

  Has reproduction · 59

  eDNAmap is a web-based platform that stores marine eDNA metabarcoding data and lets users plot sampling locations, generate heatmaps, and run nMDS/cluster analyses on uploaded or database species/ASV composition data.

  teleost dinoflagellates 12s asv edna blast phylogenetic

• Unveiling the immunometabolic landscape of colorectal cancer through PANoptosis-related gene expression.

  PMID 41601652 · PMC12832467 · Frontiers in immunology · 2025 · 8 claims · 8 setups

  Has reproduction · 41

  PANoptosis-related genes show significant expression heterogeneity across CRC samples, with apoptosis-related genes comprising the largest proportion (87.4%)

  crc hct116 bulk bulk single-cell rt-qpcr

• RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment.

  PMID 31978147 · PMC6980424 · PloS one · 2020 · 7 claims · 6 setups

  Has reproduction · 71

  RNAmountAlign performs pairwise local, global, and semiglobal (query search) alignment and progressive multiple alignment (global and local) using incremental ensemble mountain height, running in O(n^3) time and O(n^2) space for two sequences of length n

  sequences sets target single secondary pairwise sequence

• Tracing human genetic histories and natural selection with precise local ancestry inference.

  PMID 40379651 · PMC12084304 · Nature communications · 2025 · 7 claims · 7 setups

  Has reproduction · 76

  Orchestra, a two-stage LAI method combining a recombination-distance base layer with a deep learning (convolutional + attention) smoothing module, outperforms RFmix, FLARE and Gnomix in precision and recall across simulated admixture generations.

  1kgp-16pops independent simulated 1kgp simulated population-level local

• rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data.

  PMID 34110280 · PMC8461470 · Microbial genomics · 2021 · 8 claims · 8 setups

  Has reproduction · 50

  rMAP is a pipeline capable of profiling the resistomes of ESKAPE pathogens using Illumina WGS data

  eskape same novo snp phylogenetic

• Polyploidy and the petal transcriptome of Gossypium.

  PMID 24393201 · PMC3890615 · BMC plant biology · 2014 · 8 claims · 8 setups

  Has reproduction · 51

  Most homoeologous gene pairs in polyploid cotton petals are expressed at equal levels, indicating a surprising level of expression homeostasis; only ~20% of expressed genes show significant genome bias.

  petal rna-seq commonly polyploid rna-seq read universal

• High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

  PMID 18988630 · PMC2662491 · Nucleic acids research · 2009 · 8 claims · 8 setups

  Full-text index only

  Incorporating H3K4me3 chromatin modification estimates greatly improves the accuracy of in silico prediction of in vivo TF binding for a wide range of TFs in human and mouse

  embryonic neural t-cells mm8 chip-seq chip-chip pwm

• A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

  PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups

  Full-text index only

  A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types

  maqc hepatocytes japanese illeum microarray dasl sequence

• Quality control method for RNA-seq using single nucleotide polymorphism allele frequency.

  PMID 25243705 · PMC4231238 · Genes to cells : devoted to molecular & cellular mechanisms · 2014 · 8 claims · 8 setups

  Has reproduction · 50

  SNP allele frequency distributions from RNA-seq reads can detect contaminating cells whose genomic background differs from the target cells; the mode of the distribution reflects the cellular composition while its variance reflects PCR bias.

  mathematical escs pure stap simulation rna-seq contamination

• Water mass specific genes dominate the Southern Ocean microbiome.

  PMID 41803086 · PMC12972064 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  The Southern Ocean microbial gene catalog is highly original and largely distinct from existing marine gene catalogs

  seawater ace tara polar-specific shotgun comparative agnostos

• Genomic profiling of active vitamin D colonic responses in African- and European-Americans identifies an ancestry-related regulatory variant of POLB.

  PMID 41505470 · PMC12810902 · PLoS genetics · 2026 · 8 claims · 6 setups

  Full-text index only

  1,25D treatment induces widespread transcriptional and chromatin accessibility changes in colonic organoids

  colonic bulk atac-seq gene