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).

• Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning.

  PMID 36611079 · PMC9825621 · NPJ precision oncology · 2023 · 8 claims · 8 setups

  Has reproduction

  Tree-based (XGBoost, LightGBM) and deep-learning (TabNet) tabular ML classifiers achieve state-of-the-art somatic vs germline classification in tumor-only WES samples, outperforming PureCN.

  tcga same metastatic tumor-only whole-exome wes copy-number

• HArmonized single-cell RNA-seq Cell type Assisted Deconvolution (HASCAD).

  PMID 37907883 · PMC10619225 · BMC medical genomics · 2023 · 6 claims · 4 setups

  Has reproduction · 67

  Removal of batch effects in reference scRNA-seq datasets (via Harmony-Symphony) benefits the task of cell composition deconvolution

  pbmc derived tcga-lihc scrna-seq simulated bulk

• Forseti: a mechanistic and predictive model of the splicing status of scRNA-seq reads.

  PMID 38940130 · PMC11256924 · Bioinformatics (Oxford, England) · 2024 · 7 claims · 5 setups

  Has reproduction · 87

  Forseti is the first probabilistic model for resolving the splicing status of exonic scRNA-seq reads by scoring putative fragments linking read alignments to proximate priming sites

  training simulated held-out paired-end cubic mlp

• Enhanced Generalizability of RNA Secondary Structure Prediction via Convolutional Block Attention Network and Ensemble Learning.

  PMID 40871599 · PMC12388828 · Molecules (Basel, Switzerland) · 2025 · 8 claims · 8 setups

  Has reproduction · 87

  TrioFold integrates base-pairing clues from thermodynamic- and DL-based methods via ensemble learning and a convolutional block attention mechanism to enhance RSS prediction generalizability.

  testseta bprna-new ts-inter individual jaccard pca ensemble

• Machine-learning approaches for classifying haplogroup from Y chromosome STR data.

  PMID 18551166 · PMC2396484 · PLoS computational biology · 2008 · 8 claims · 5 setups

  Full-text index only

  Y-STR allelic variability is partitioned more by differences among haplogroups than by differences among populations, suggesting Y-STRs carry haplogroup information

  globally same computational publicly y-str snp supervised

• omnideconv: a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data.

  PMID 41582216 · PMC12837286 · Genome biology · 2026 · 8 claims · 6 setups

  Full-text index only

  omnideconv is an R package providing a unified interface to twelve second-generation deconvolution methods (AutoGeneS, BayesPrism, Bseq-SC, Bisque, CDseq, CIBERSORTx, CPM, DWLS, MOMF, MuSiC, SCDC, Scaden)

  blood-derived pbmc blood spleen bulk scrna-seq pseudo-bulk

• 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

• DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning.

  PMID 33662629 · PMC9801043 · Genomics, proteomics & bioinformatics · 2022 · 8 claims · 8 setups

  Has reproduction · 50

  DeeReCT-APA quantitatively predicts the usage of all competing PASs of a gene simultaneously, rather than casting the problem as pairwise comparison like prior methods.

  fibroblast genomic same 3'-region 3'-mrna deep