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).

• Integrated multi-omic atlas reveals the hierarchy of spatiotemporal regulatory networks of mouse gastrulation.

  PMID 41526381 · PMC12902073 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  BioCRE, a novel bi-orientation regression algorithm, more accurately links genes to candidate cis-regulatory elements (CREs) than existing tools Signac and ArchR

  gastrulating gastrula gold-standard embryo single-cell computational promoter

• 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

• Genome-scale modeling identifies dynamic metabolic vulnerabilities during the epithelial to mesenchymal transition.

  PMID 39730911 · PMC11681178 · Communications biology · 2024 · 8 claims · 8 setups

  Full-text index only

  EMT involves temporal, stage-specific metabolic reprogramming with distinct dependencies in glycolysis and glutamine metabolism.

  a549 recon1 cancer lung bulk single-cell genome-scale

• scTWAS: a powerful statistical framework for single-cell transcriptome-wide association studies.

  PMID 41820391 · PMC13121454 · Nature communications · 2026 · 8 claims · 5 setups

  Full-text index only

  scTWAS uses a latent-variable expression-measurement model combined with a moment-based regression to more accurately estimate genetic regulation of gene expression from single-cell data, improving GReX prediction across cell types and datasets

  onek1k-derived onek1k-based immune brain simulated two-sample stage

• Resolving clonal evolution and selection of extrachromosomal DNA at single-cell resolution.

  PMID 41606654 · PMC12853921 · Genome biology · 2026 · 7 claims · 8 setups

  Full-text index only

  ecSingle, a computational method integrating allelic imbalance (BAF deviation) and outlier expression from scRNA-seq, can identify oncogene-carrying ecDNA at single-cell resolution.

  colo320dm glioblastoma medulloblastoma ce26 scrna-seq whole-genome long-read

• Identification and validation of key PANoptosis-related genes via integrative machine learning and single-cell sequencing in AILI.

  PMID 41858622 · PMC12995703 · iScience · 2026 · 8 claims · 8 setups

  Full-text index only

  Cdkn1a and Pdk1 are key PANoptosis-related genes with high diagnostic potential for AILI

  liver training bulk wgcna machine

• FLYNC: a machine-learning-driven framework for discovering long noncoding RNAs in Drosophila melanogaster.

  PMID 41551930 · PMC12805895 · NAR genomics and bioinformatics · 2026 · 7 claims · 8 setups

  Full-text index only

  FLYNC, an explainable boosting machine (EBM) model, accurately predicts the probability that a newly identified RNA transcript in D. melanogaster is a lncRNA

  melanogaster drosophila automated ebm hyperparameter

• Neural network-assisted RNA velocity imputation for empowering transcript dynamics-based analyses.

  PMID 41736867 · PMC12927306 · iScience · 2026 · 8 claims · 8 setups

  Full-text index only

  NARVI, a deep neural network trained on expression-velocity relationships of passed genes, can impute RNA velocity for dropped genes that conventional tools (e.g., scVelo, UniTVelo) fail to calculate

  hematopoietic lung erythroid bone scrna-seq cross-validation

• Integrative transcriptomic and machine learning framework reveals candidate genes and potential mechanisms of aflatoxin B1 exposure in breast cancer.

  PMID 41688730 · PMC12982753 · Scientific reports · 2026 · 7 claims · 8 setups

  Has reproduction · 83

  170 unique human AFB1 targets were identified by merging ChEMBL, SwissTargetPrediction, and PharmMapper predictions

  afb1 breast training candidate computational bulk weighted