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).

• Towards the identification of essential genes using targeted genome sequencing and comparative analysis.

  PMID 17052348 · PMC1624830 · BMC genomics · 2006 · 8 claims · 8 setups

  Full-text index only

  Phyletic retention (ortholog presence across organisms) is the single most predictive feature of gene essentiality in both E. coli and S. cerevisiae.

  coli cerevisiae comparative machine single-gene

• A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data.

  PMID 19772600 · PMC2765429 · Journal of translational medicine · 2009 · 7 claims · 3 setups

  Full-text index only

  The naive Bayes model with the wrapper-based feature selection approach performed best among all predictive models tested for distinguishing CFS from controls.

  subjects naive svm c4.5

• A scale space approach for unsupervised feature selection in mass spectra classification for ovarian cancer detection.

  PMID 19828085 · PMC2762074 · BMC bioinformatics · 2009 · 7 claims · 1 setups

  Full-text index only

  A scale-space based unsupervised feature extraction method combined with SVM classification achieves high accuracy in ovarian cancer detection from serum mass spectra.

  serum high-resolution

• Prediction of prognostic signatures in triple-negative breast cancer based on the differential expression analysis via NanoString nCounter immune panel.

  PMID 33138797 · PMC7607642 · BMC cancer · 2020 · 8 claims · 8 setups

  Has reproduction · 72

  edgeR-based DEG selection is more appropriate for feature selection than Elastic Net when sample sizes are small.

  ffpe same nanostring tnbc nanostring immunohistochemistry differential

• Towards alignment independent quantitative assessment of homology detection.

  PMID 17205117 · PMC1762415 · PloS one · 2006 · 8 claims · 6 setups

  Full-text index only

  The Fhom Estimator uses the prevalence of a conserved protein feature (X) in two protein sets to estimate the fraction of true homologs among paired proteins, independent of alignment quality.

  curated homologene swiss-prot fruit signalp homologene-based fhom

• 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

• stDyer-image improves clustering analysis of spatially resolved transcriptomics and proteomics with morphological images.

  PMID 41692960 · PMC12960910 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

  Has reproduction · 75

  stDyer-image directly associates the image modality with predicted cluster labels rather than using images to enhance/impute gene expression data

  non-small morphology brain breast spatial image

• MACSIMS: multiple alignment of complete sequences information management system.

  PMID 16792820 · PMC1539025 · BMC bioinformatics · 2006 · 8 claims · 5 setups

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  MACSIMS is a multiple alignment-based information management system combining knowledge-based database mining with ab initio sequence predictions

  balibase-derived sequences same query automatic database initio

• A workflow reproducibility scale for automatic validation of biological interpretation results.

  PMID 37150537 · PMC10164546 · GigaScience · 2022 · 8 claims · 4 setups

  Has reproduction · 100

  Comparing output files by checksum alone is insufficient to verify reproducibility, since checksums can differ even when the underlying biological interpretation is unchanged

  nf-core sam vcf workflow checksum biological workflow

• A comprehensive literature review of haplotyping software and methods for use with unrelated individuals.

  PMID 15814067 · PMC3525117 · Human genomics · 2005 · 7 claims · 2 setups

  Full-text index only

  Forty-six haplotyping programs were identified and reviewed, split into 43 designed for individual genotype data and three designed for pooled DNA samples.

  pubmed identified literature software

• SNP-RFLPing: restriction enzyme mining for SNPs in genomes.

  PMID 16503968 · PMC1386656 · BMC genomics · 2006 · 8 claims · 2 setups

  Full-text index only

  SNP-RFLPing accepts three flexible input types (dbSNP rs#/ss# IDs, HUGO gene name/Entrez gene ID, or free-form SNP-in-sequence including IUPAC or [dNTP1/dNTP2] formats) for human, rat, and mouse genomes

  software existing string-matching feature

• 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

• Smart spatial omics (S2-omics) optimizes region of interest selection to capture molecular heterogeneity in diverse tissues.

  PMID 41298871 · PMC12662399 · Nature cell biology · 2025 · 7 claims · 6 setups

  Has reproduction · 100

  S2-omics is an end-to-end workflow that automatically selects ROIs from H&E histology images to maximize molecular information content for spatial omics profiling.

  gastric colorectal additional breast xenium visium histology

• An OMICs-based meta-analysis to support infection state stratification.

  PMID 33560295 · PMC8388022 · Bioinformatics (Oxford, England) · 2021 · 7 claims · 6 setups

  Has reproduction · 44

  Multi-class Random Forest models built from meta-analyzed blood gene expression data can predict infection state (bacterial/viral/none) with high accuracy, correctly classifying 93% of bacterial and 89% of viral samples in the best model.

  blood merged affymetrix-trained microarray random gene

• Constructing support vector machine ensembles for cancer classification based on proteomic profiling.

  PMID 16689692 · PMC5173238 · Genomics, proteomics & bioinformatics · 2005 · 7 claims · 4 setups

  Full-text index only

  CSVME, built by selecting a subset of base SVMs via SVM-RFE ranking and fusing them with a trained upper-layer SVM, achieves better classification performance than an ensemble of all base SVMs.

  serum computational seldi-tof svm-rfe-based 10-fold

• miRBase: tools for microRNA genomics.

  PMID 17991681 · PMC2238936 · Nucleic acids research · 2008 · 8 claims · 6 setups

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  miRBase release 10.0 contains 5071 miRNA hairpin loci from 58 species, expressing 5922 distinct mature miRNA sequences, a growth of over 2000 sequences in 2 years

  species utrs genomic chromosome genome-wide target transcription

• Fast-evolving noncoding sequences in the human genome.

  PMID 17578567 · PMC2394770 · Genome biology · 2007 · 8 claims · 6 setups

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  1,356 conserved noncoding sequences show human-specific accelerated substitution rates (ANC sequences) relative to chimpanzee

  chimpanzee genome hapmap comparative genomic segmental

• Next-generation high-density self-assembling functional protein arrays.

  PMID 18469824 · PMC3070491 · Nature methods · 2008 · 8 claims · 7 setups

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  A next-generation NAPPA method produces high-density protein microarrays displaying over 1500 unique proteins with >90% expression success

  test high-density amine-coated array picogreen anti-gst fluorescently

• VarDetect: a nucleotide sequence variation exploratory tool.

  PMID 19091032 · PMC2638149 · BMC bioinformatics · 2008 · 8 claims · 2 setups

  Full-text index only

  VarDetect is a stand-alone software tool that automatically detects nucleotide variation (SNPs) from fluorescence-based chromatogram traces using pre-calculated peak content ratios and artifact-handling rules.

  genomic vardetect automatic software

• Identification of TYR, TYRP1, DCT and LARP7 as related biomarkers and immune infiltration characteristics of vitiligo via comprehensive strategies.

  PMID 34107850 · PMC8806433 · Bioengineered · 2021 · 7 claims · 8 setups

  Has reproduction · 55

  131 robust DEGs (89 upregulated, 42 downregulated) were identified by RRA integration of three vitiligo datasets and are closely associated with melanogenesis and vitiligo development

  lesional merged robust verification gene robust weighted