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).

• Dynamic Gene Attention Focus (DyGAF): Enhancing Biomarker Identification Through Dual-Model Attention Networks.

  PMID 40160891 · PMC11951896 · Bioinformatics and biology insights · 2025 · 6 claims · 5 setups

  Has reproduction · 44

  DyGAF, a dual-model attention neural network (independent Model A + dependent Model B), identifies and ranks genes by significance for COVID-19 biomarker discovery more effectively than differential expression analysis (DEA) and random forest (RF) feature selection

  nasopharyngeal same dygaf-ranked bulk differential random

• Transcription-coupled and epigenome-encoded mechanisms direct H3K4 methylation.

  PMID 35953471 · PMC9372134 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 83

  ATX1, ATX2, and ATXR7 redundantly mediate H3K4 monomethylation genome-wide

  arabidopsis chip-seq western random

• 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

• Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy.

  PMID 16984653 · PMC1618409 · BMC bioinformatics · 2006 · 8 claims · 6 setups

  Full-text index only

  The proposed feature set outperforms existing published feature sets for predicting effects of amino acid substitutions

  coli bacteriophage lac proteins svm simulated pearson

• Predicting the pathogenicity of missense variants using features derived from AlphaFold2.

  PMID 37084271 · PMC10203375 · Bioinformatics (Oxford, England) · 2023 · 6 claims · 8 setups

  Has reproduction · 85

  AlphaFold2-derived structural features (solvent accessibility, amino acid network features, physicochemical environment, pLDDT) can be used to train a random forest classifier (AlphScore) that distinguishes proxy-benign from proxy-pathogenic missense variants.

  gnomad alphafold2-predicted alphscore proteins machine secondary physicochemical

• A Decentralized Kidney Transplant Biopsy Classifier for Transplant Rejection Developed Using Genes of the Banff-Human Organ Transplant Panel.

  PMID 35619722 · PMC9128066 · Frontiers in immunology · 2022 · 6 claims · 6 setups

  Has reproduction · 90

  A random forest model trained solely on B-HOT panel genes (B-HOT Model) accurately classifies kidney transplant biopsies as NR, ABMR, or TCMR.

  kidney gene combined microarray machine sequential

• Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection.

  PMID 31533612 · PMC6751684 · BMC bioinformatics · 2019 · 7 claims · 8 setups

  Has reproduction · 69

  An ensemble feature selection method based on classifier consensus identifies a robust 100-miRNA signature from TCGA data.

  tcga geo 100-mirna mirna feature bibliographic

• Speeding disease gene discovery by sequence based candidate prioritization.

  PMID 15766383 · PMC1274252 · BMC bioinformatics · 2005 · 7 claims · 8 setups

  Full-text index only

  Disease genes (OMIM) differ significantly from non-disease genes in sequence-based features including gene/cDNA/protein size, exon number, homolog conservation, secretion signal, 3' UTR length, CpG islands, and distance to nearest gene.

  ensembl training same hgmd comparative machine tenfold

• A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability.

  PMID 19941644 · PMC2789744 · BMC bioinformatics · 2009 · 7 claims · 4 setups

  Full-text index only

  Feature variability strongly influences breast cancer signature composition even when array platform and patient stratification are identical.

  breast preprocessed microarray two-color perturbation

• 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

• 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 machine learning models built from cross-platform microarray meta-analysis can distinguish bacterial, viral and no-infection states with high accuracy (best model: 93% bacterial, 89% viral correct).

  blood merged affymetrix-optimized gene feature out-of-sample

• 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 · 7 setups

  Has reproduction · 72

  edgeR identifies 9 DEGs associated with pCR and 13 DEGs associated with relapse from 579 immune genes in a small TNBC sample set (n=55)

  ffpe same nanostring training nanostring immunohistochemistry differential

• Comparative Genomics of Borderline Oxacillin-Resistant Staphylococcus aureus Detected during a Pseudo-outbreak of Methicillin-Resistant S. aureus in a Neonatal Intensive Care Unit.

  PMID 35038924 · PMC8764539 · mBio · 2022 · 7 claims · 8 setups

  Has reproduction · 63

  Of 42 isolates flagged as MRSA by screening agar, only 9 were PBP2a- and mecA-positive true MRSA, while the remaining 33 were mecA-negative and largely met criteria for BORSA

  clinical nicu genomic maldi-tof pbp2a cefoxitin

• Boosting accuracy of automated classification of fluorescence microscope images for location proteomics.

  PMID 15207009 · PMC449699 · BMC bioinformatics · 2004 · 8 claims · 8 setups

  Full-text index only

  New classifiers (SVMs, ensembles) and new wavelet-derived (Gabor, Daubechies) features improve recognition of protein subcellular location patterns over the previous neural network approach

  hela automated stepwise training-set-size

• Prioritization of candidate cancer genes--an aid to oncogenomic studies.

  PMID 18710882 · PMC2566894 · Nucleic acids research · 2008 · 8 claims · 8 setups

  Full-text index only

  Computational classifiers using combinations of protein conservation, gene structure, protein domains, protein interactions, and regulatory data can distinguish known cancer genes (CD/CR) from unlabelled human genes

  genes cancer interpro interactome averaged cross-validation domain

• Identification of common genetic characteristics of rheumatoid arthritis and major depressive disorder by bioinformatics analysis and machine learning.

  PMID 37415981 · PMC10320004 · Frontiers in immunology · 2023 · 7 claims · 8 setups

  Has reproduction · 58

  EAF1, SDCBP and RNF19B are common genetic characteristics (hub genes) shared by RA and MDD

  pbmc intersected candidate wgcna differential kegg

• Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms.

  PMID 15784611 · PMC1069129 · Nucleic acids research · 2005 · 7 claims · 8 setups

  Full-text index only

  Position-specific phylogenetic features describing evolutionary conservation at a site (e.g. SIFT score, normalized site entropy, residue frequency change) are the best individual discriminators of disease-causing versus neutral GPCR mutations.

  dbsnp gpcr transmembrane sequence six-frame sift logistic

• The molecular landscape of sepsis severity in infants: enhanced coagulation, innate immunity, and T cell repression.

  PMID 38817614 · PMC11137207 · Frontiers in immunology · 2024 · 7 claims · 7 setups

  Has reproduction · 50

  Most published adult/other-cohort sepsis gene signatures have limited utility for infant sepsis; only 2 of 7 achieved >80% accuracy in infants

  infant merged individual pairwise whole-blood coconut gene-signature

• Dcode.org anthology of comparative genomic tools.

  PMID 15980535 · PMC1160116 · Nucleic acids research · 2005 · 8 claims · 7 setups

  Full-text index only

  The dcode.org suite (zPicture, Mulan, eShadow, rVista 2.0, multiTF, Creme 2.0, ECR Browser) provides integrated tools for comparative genomic analysis and non-coding regulatory element discovery.

  dlx1 hoxa prothrombin gene comparative multi-species phylogenetic