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).

• MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features.

  PMID 17553836 · PMC1933124 · Nucleic acids research · 2007 · 8 claims · 8 setups

  Full-text index only

  A hybrid feature combining local contiguous triplet structure-sequence composition, MFE of the secondary structure, and P-value of a randomization test improves classification of real vs pseudo pre-miRNAs

  real combined pre-mirna training random independent repeated

• Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies.

  PMID 17610740 · PMC1925094 · BMC genomics · 2007 · 8 claims · 5 setups

  Full-text index only

  SNP-MaP can be effectively applied to the Affymetrix 500K GeneChip, providing a cost-effective, reliable and valid initial genomewide screen

  independent ceph same unrelated snp individual simulated

• CLEAN: CLustering Enrichment ANalysis.

  PMID 19640299 · PMC2734555 · BMC bioinformatics · 2009 · 8 claims · 4 setups

  Full-text index only

  The gene-specific CLEAN score improves reproducibility of cluster analysis conclusions across independent datasets compared to the traditional cluster-wide score (cwCLEAN).

  four breast combined hierarchical cluster csimm-based

• Conservation, variability and the modeling of active protein kinases.

  PMID 17912359 · PMC1989141 · PloS one · 2007 · 7 claims · 5 setups

  Full-text index only

  A novel sequence-order independent (fold-independent) structural alignment algorithm was developed that maximizes side-chain similarity to produce a consensus kinase structure.

  active-conformation same chak rio2 sequence-order pairwise structural

• Genome screen to detect linkage to common susceptibility genes for intracranial and aortic aneurysms.

  PMID 18948608 · PMC2629798 · Stroke · 2009 · 8 claims · 4 setups

  Full-text index only

  Genomewide linkage analysis in 26 multiplex IA families with AA-affected members identified LOD peaks on chromosome 11 (LOD=3.0) and chromosome 6 (LOD=2.3) using a broad IA/AA-combined phenotype

  multiplex individuals fia subjects genomewide snp medical

• PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size.

  PMID 16620382 · PMC1459209 · BMC bioinformatics · 2006 · 7 claims · 3 setups

  Full-text index only

  PedGenie is a valid, flexible statistical tool for genetic association analysis in pedigrees of arbitrary size and structure using Monte Carlo significance testing

  simulated gaw12 breast monte pedigree-based genetic

• Recent segmental and gene duplications in the mouse genome.

  PMID 12914656 · PMC193640 · Genome biology · 2003 · 8 claims · 8 setups

  Full-text index only

  33.6 Mb (1.2%) of the February 2003 mouse genome assembly (2,695 Mb) is involved in recent segmental duplications

  genome gene ensembl-annotated chromosome pairwise gene blat

• Rise of the machines.

  PMID 18670625 · PMC2467494 · PLoS genetics · 2008 · 8 claims · 4 setups

  Full-text index only

  New short-read sequencing platforms (Illumina Genome Analyzer, 454 FLX, ABI SOLiD) enable rapid, scalable whole-genome resequencing that was previously restricted to dedicated sequencing centers using Sanger methods.

  bacillus independent subtilis whole-genome read

• 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

• The tumour suppressor L(3)mbt inhibits neuroepithelial proliferation and acts on insulator elements.

  PMID 21857667 · PMC3173870 · Nature cell biology · 2011 · 8 claims · 8 setups

  Has reproduction · 90

  Brain tumors in l(3)mbt mutants originate from overproliferation of neuroepithelial cells of the optic lobes, not from defects in asymmetric cell division.

  drosophila chip-seq chip immunostaining

• An SVM-based system for predicting protein subnuclear localizations.

  PMID 16336650 · PMC1325059 · BMC bioinformatics · 2005 · 7 claims · 3 setups

  Full-text index only

  New kernels defined on k-peptide vectors mapped by BLOSUM62-based high-scored pair matrices (D1, D2, D3) improve SVM discrimination of protein subnuclear localization compared to conventional k-peptide encodings.

  single-localization multi-localization same svm sequence

• Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment.

  PMID 37471455 · PMC10393163 · PLoS computational biology · 2023 · 8 claims · 8 setups

  Has reproduction · 100

  A network-based meta-analysis across studies identifies a common 45-gene signature specific to active TB disease that accounts for cohort/population heterogeneity

  n×m common independent viral blood gene random

• Artificial intelligence-guided discovery of gastric cancer continuum.

  PMID 36692601 · PMC9871434 · Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association · 2023 · 8 claims · 8 setups

  Has reproduction · 71

  A Boolean implication network built from GSE66229 yields a GC-BoNE gene signature (Boolean paths C#11-2-4-14 and C#7-13-14) that classifies tumor vs normal/adjacent-normal gastric samples

  gastric independent models prospective microarray transcriptomics

• Increased DNA microarray hybridization specificity using sscDNA targets.

  PMID 15847692 · PMC1090574 · BMC genomics · 2005 · 7 claims · 5 setups

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  A single round of ribo-SPIA amplification produces sufficient sscDNA for microarray hybridization from as little as 5 ng of starting total RNA

  cuhr k562 input sscdna microarray quantitative capillary

• Predicting the phenotypic effects of non-synonymous single nucleotide polymorphisms based on support vector machines.

  PMID 18005451 · PMC2216041 · BMC bioinformatics · 2007 · 8 claims · 5 setups

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  Parepro, an SVM-based method integrating three attribute sets (RD, MI, IE) derived from evolutionary and residue-property information, predicts whether an nsSNP is deleterious or neutral.

  sequences target svm benchmark homology

• Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays.

  PMID 18482458 · PMC2408589 · BMC microbiology · 2008 · 8 claims · 6 setups

  Full-text index only

  CGS combined with targeted DDT sequencing and whole genome fingerprinting (WGF) can accurately determine a treponemal genome sequence using only three arrays, at accuracy comparable to or better than finished DDT sequencing

  treponema pcr-amplified ss14 pcr comparative dideoxy-terminator genome

• Cross species genomic analysis identifies a mouse model as undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma.

  PMID 19956606 · PMC2779485 · PloS one · 2009 · 8 claims · 7 setups

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  A 100-gene signature from LSL-KrasG12D;Trp53Flox/Flox mouse sarcomas (vs normal muscle) is specifically and significantly enriched in human MFH but not other soft tissue sarcoma subtypes across three independent human datasets.

  lsl-krasg12d soft combined mfh microarray gene oncogenic

• 2D-DIGE proteomic characterization of head and neck squamous cell carcinoma.

  PMID 19861202 · PMC2847880 · Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery · 2009 · 8 claims · 4 setups

  Full-text index only

  Cornulin is downregulated in HNSCC relative to normal adjacent tissue and represents a novel biomarker in HNSCC.

  hnscc excised independent identified 2d-dige lc-ms immunohistochemistry

• Bayesian coestimation of phylogeny and sequence alignment.

  PMID 15804354 · PMC1087833 · BMC bioinformatics · 2005 · 7 claims · 3 setups

  Full-text index only

  Alignment and phylogenetic inference are mutually dependent, and treating them as separate sequential steps (align then infer tree) is fundamentally flawed and produces biased, overconfident estimates.

  globin same four-sequence bayesian mcmc comparison

• Bayesian prediction of RNA translation from ribosome profiling.

  PMID 28126919 · PMC5389577 · Nucleic acids research · 2017 · 8 claims · 4 setups

  Has reproduction · 62

  Rp-Bp is an unsupervised Bayesian approach that uses a two-component 'high-low-low' mixture model to predict translated ORFs from ribosome profiles

  hek293 ribo-seq ribosome proteomics quantitative