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).

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

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

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  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

• 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

• An AI-Enabled Single-Cell Transcriptomic Analysis Pipeline for Gene Signature Discovery in Natural Killer Cells Linked to Remission Outcomes in Chronic Myeloid Leukemia.

  PMID 41972591 · PMC13072394 · Biology · 2026 · 8 claims · 7 setups

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  GAFA integrates latent-space representation, pseudotime trajectory modeling, GRN inference, and machine learning-based gene panel discovery into a single coherent pipeline, unlike existing workflows that treat these steps independently.

  peripheral subset immune assigned scrna-seq latent-space automated

• Bayesian prediction of microbial oxygen requirement.

  PMID 26913185 · PMC4743139 · F1000Research · 2013 · 7 claims · 8 setups

  Has reproduction · 76

  A naive Bayesian classifier based on presence/absence of class-associated Pfam-A domains can distinguish three oxygen requirement classes (aerobe, anaerobe, facultative anaerobe) from genome sequence, unlike prior studies that only made pairwise distinctions.

  bacterial selected predicted pfam-a genome gene domain

• DoBSeqWF: a framework for sensitive detection of individual genetic variation in pooled sequencing data.

  PMID 41704565 · PMC12907731 · NAR genomics and bioinformatics · 2026 · 7 claims · 5 setups

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  DoBSeqWF, a Nextflow-based pipeline, processes pooled DoBSeq sequencing data through alignment, variant calling, machine-learning-based filtering, and variant pinpointing/assignment to individuals.

  individual pooled individuals gatk-called whole-genome overlapped simulated