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).

• Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning.

  PMID 34575658 · PMC8472680 · Journal of personalized medicine · 2021 · 6 claims · 4 setups

  Has reproduction · 86

  A training gene set of 719 unique upregulated DEGs (subtype-specific) can be used to build ML models that classify TNBC into BLIA, BLIS, MES, and LAR subtypes.

  known tnbc unique unknown gene machine term

• Application of Machine Learning in Predicting Hepatic Metastasis or Primary Site in Gastroenteropancreatic Neuroendocrine Tumors.

  PMID 37887568 · PMC10605255 · Current oncology (Toronto, Ont.) · 2023 · 8 claims · 7 setups

  Has reproduction · 59

  Multi-gene random forest models classify primary tumor vs. liver metastasis samples with 100% accuracy in training/test cohorts and >90% accuracy in an independent validation cohort

  pancreatic rna-seq liver tumor bulk machine multi-label

• Integration of Transcriptomics With Interpretable Artificial Intelligence for Identifying Molecular Signatures of Physiological Stress in Sleep Deprivation.

  PMID 42216239 · PMC13240488 · Journal of cellular and molecular medicine · 2026 · 8 claims · 8 setups

  Has reproduction · 49

  S100A3 is a robust candidate biomarker showing consistent discriminatory performance across the acute sleep deprivation training cohort, an independent sleep deprivation cohort, and a chronic insomnia cohort.

  peripheral blood normal integrated bulk interpretable immune

• Assembly of Macromolecular Complexes in the Whole-Cell Model of a Minimal Cell.

  PMID 41427637 · PMC12794154 · The journal of physical chemistry. B · 2026 · 8 claims · 6 setups

  Has reproduction · 67

  The assembly of 21 unique macromolecular complexes (20 plus a reduced ribosome biogenesis model) was incorporated into the existing whole-cell kinetic model of Syn3A.

  jcvi-syn3a syn3a simulated hybrid chemical ordinary

• Enhancing chemotherapy response prediction via matched colorectal tumor-organoid gene expression analysis and network-based biomarker selection.

  PMID 39754813 · PMC11754497 · Translational oncology · 2025 · 6 claims · 8 setups

  Has reproduction · 78

  A consensus WGCNA approach combining matched tumor-organoid and independent organoid drug-response expression data identifies gene modules and hub genes predictive of 5-FU chemotherapy response

  colorectal matched combined expression microarray rna-seq consensus

• Prediction of Antimicrobial Resistance in Gram-Negative Bacteria From Whole-Genome Sequencing Data.

  PMID 32528441 · PMC7262952 · Frontiers in microbiology · 2020 · 8 claims · 4 setups

  Has reproduction · 100

  WGS data enables prediction of antimicrobial resistance in Gram-negative bacteria using machine learning

  baumannii gram-negative in-house cchmc whole-genome xgboost antimicrobial

• STAT1 and IL-7 as potential diagnostic biomarkers for distinguishing high-grade from low-grade serous ovarian cancer: a multi-cohort analysis.

  PMID 42058211 · PMC13120972 · Frontiers in immunology · 2026 · 7 claims · 6 setups

  Has reproduction · 50

  STAT1 and IL-7 are differentially expressed immune-related genes that can distinguish HGSOC from LGSOC and may serve as ancillary diagnostic biomarkers.

  hgsoc training independent paraffin-embedded transcriptome machine-learning diagnostic

• 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

• iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data.

  PMID 35899080 · PMC9310080 · NAR genomics and bioinformatics · 2022 · 8 claims · 4 setups

  Has reproduction · 58

  iCOMIC provides a GUI-driven, Snakemake-based pipeline integrating multiple tools for DNA-Seq and RNA-Seq analysis with minimal command-line interaction.

  giab monocyte missense somatic germline rna-seq machine

• 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