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).

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

  PMID 31533612 · PMC6751684 · BMC bioinformatics · 2019 · 8 claims · 6 setups

  Has reproduction · 69

  An ensemble feature selection strategy using consensus of feature relevance across 8 classifier types identifies a 100-miRNA signature from a 1046-feature TCGA dataset

  tcga geo mirnas mirna feature bibliographic

• Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine.

  PMID 16381612 · PMC1360673 · BMC bioinformatics · 2005 · 7 claims · 7 setups

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  A 32-dimensional triplet structure-sequence feature vector combined with SVM (triplet-SVM) can distinguish real human pre-miRNAs from pseudo pre-miRNA hairpins with ~90% accuracy.

  pre-mirnas test conserved-hairpin cross-species secondary svm cross-species

• Graph Random Forest: A Graph Embedded Algorithm for Identifying Highly Connected Important Features.

  PMID 37509188 · PMC10377046 · Biomolecules · 2023 · 8 claims · 6 setups

  Has reproduction · 89

  GRF identifies effective features that form highly connected sub-graphs on the underlying biological network

  synthetic tcga embryonic simulation sub-graph reproducibility

• Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites.

  PMID 37847658 · PMC10628388 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 6 setups

  Has reproduction · 67

  PSPred-ALE outperforms state-of-the-art SARS-CoV-2 phosphorylation site predictors (e.g. DeepIPs) and handcrafted feature-based methods in benchmarking comparisons

  a549 sequence same bulk pathway gene

• Developing prognostic gene panel of survival time in lung adenocarcinoma patients using machine learning.

  PMID 35117753 · PMC8799101 · Translational cancer research · 2020 · 8 claims · 5 setups

  Has reproduction · 32

  Naïve Bayes using a 22-gene panel is the best-performing and most stable machine learning model for predicting LUAD survival time (>3 vs <3 years)

  tcga geo rna-seq methylation sequencing

• A modified T-test feature selection method and its application on the HapMap genotype data.

  PMID 18267305 · PMC5054219 · Genomics, proteomics & bioinformatics · 2007 · 7 claims · 4 setups

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  A modified t-test ranking measure, extended to handle nominal SNP genotype data via vector transformation, can effectively rank SNPs by their discriminative capability for population classification.

  hapmap modified f-statistics informativeness

• Supervised learning-based tagSNP selection for genome-wide disease classifications.

  PMID 18366619 · PMC2386071 · BMC genomics · 2008 · 7 claims · 2 setups

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  SRFA (Supervised Recursive Feature Addition) is a novel feature selection method combining supervised learning and statistical redundancy measures for SNP selection

  micc narac snp

• In silico analysis of missense substitutions using sequence-alignment based methods.

  PMID 18951440 · PMC3431198 · Human mutation · 2008 · 8 claims · 7 setups

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  Carefully validated PMSA-based computational algorithms can achieve predictive values of ~75-95% for classifying missense substitutions as pathogenic or neutral.

  clinically sequence curated deep blosum62 sift align-gvgd

• Impact of short-read sequencing on the misassembly of a plant genome.

  PMID 33530937 · PMC7852129 · BMC genomics · 2021 · 7 claims · 6 setups

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  Short-read tomato assembly has substantial high-coverage (0.6%, 5.1 Mb) and low-coverage (9.7%, 79.6 Mb) regions relative to background coverage

  tomato whole-genome cnv machine

• CellPredX, a computational framework for cross-data type, cross-sample, and cross-protocol cell type annotation through domain adaptation and deep metric learning.

  PMID 41481570 · PMC12758788 · PLoS computational biology · 2026 · 8 claims · 7 setups

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  CellPredX is a unified semi-supervised framework integrating domain adaptation and deep metric learning to align heterogeneous embeddings for cross-modality cell type annotation.

  pbmc fetal pancreas gse149683 matched unmatched cross-protocol

• Therapeutic Targeting of Oxidative Phosphorylation in Microsatellite Instability-High Gastric Cancer.

  PMID 42038020 · PMC13104725 · Journal of Cancer · 2026 · 7 claims · 8 setups

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  MSI gastric cancer samples show significantly greater T cell infiltration and a lower proportion of epithelial cells compared to GS samples

  gastric epithelial stomach nod-scid single-cell cnv differential

• Does distance matter? Variations in alternative 3' splicing regulation.

  PMID 17704130 · PMC2018619 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  Alternative 3' splice sites can be distinguished from constitutive splice sites by a combination of sequence/conservation properties that vary depending on the distance between the splice sites.

  intronic human-mouse same comparative polypyrimidine branch

• FineST: contrastive learning integrates histology and spatial transcriptomics for nuclei-resolved ligand-receptor analysis.

  PMID 41839892 · PMC13201544 · Nature communications · 2026 · 8 claims · 6 setups

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  FineST, a bimodal contrastive learning model integrating histology (Virchow2 ViT features) and spatial gene expression, enables nuclei-resolved high-resolution RNA imputation.

  colorectal crc breast he-stained spatial type ccc