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).

• Prediction of myeloid malignant cells in Fanconi anemia using machine learning.

  PMID 41557613 · PMC12818649 · PloS one · 2026 · 6 claims · 7 setups

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  A DNN classifier trained on AML scRNA-seq data accurately predicts AML-like transcriptional profiles at single-cell resolution

  bone predicted-aml healthy scrna-seq reference-based stemnet

• PICDGI: A framework for predicting cancer driver genes through dynamic gene-gene interaction modeling of single-cell data.

  PMID 42044093 · PMC13119913 · PLoS computational biology · 2026 · 8 claims · 3 setups

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  PICDGI is a Bayesian framework that predicts driver-like regulatory genes by integrating dynamic gene-gene interaction modeling with scRNA-seq data, without using DNA mutation calls

  lung pediatric same scrna-seq moran's

• Deconvolving cell-type-specific gene expression profiles from bulk RNA-seq samples.

  PMID 41886524 · PMC13038110 · PLoS computational biology · 2026 · 8 claims · 6 setups

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  BLUE, a U-Net-based deep learning model with dual branches (U-Net for GEPs, MLP for proportions), accurately predicts cell-type proportions and cell-type-specific gene expression profiles from bulk RNA-seq.

  pbmc pancreatic aml scrna-seq-derived real scrna-seq

• Increased IL4I1 expression predicts poor survival and modulates the immune microenvironment in acute myeloid leukemia.

  PMID 41680858 · PMC12910993 · Journal of translational medicine · 2026 · 8 claims · 8 setups

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  IL4I1 mRNA expression is significantly elevated in AML compared to normal controls

  tcga-laml bone thp-1-derived thp-1 bulk kaplan-meier deg

• Single cell transcriptional evolution of myeloid leukemia of Down syndrome.

  PMID 42026063 · PMC13106683 · Nature communications · 2026 · 8 claims · 5 setups

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  Transcriptional changes induced by TAM-defining GATA1 mutations are retained in and account for most of the ML-DS transcriptome, persisting even in progressive disease that has undergone further genetic evolution.

  foetal blasts leukaemias normal single-cell bulk whole-genome

• RMzyme: regulations of RNA-modifying enzymes in humans.

  PMID 41672979 · PMC12895048 · Signal transduction and targeted therapy · 2026 · 8 claims · 7 setups

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  RMzyme is a comprehensive multiomics knowledgebase covering 179 human RNA-modifying proteins across 18 major RNA modification types and 63 human tissues

  nomo1 molm13 tissues cptac merip-seq bulk single-cell

• Identification and validation of lymphangiogenesis-related genes for predicting acute myeloid leukemia prognosis: insights from bulk RNA sequencing and single-cell RNA sequencing analyses.

  PMID 41772327 · PMC12979290 · Clinical and experimental medicine · 2026 · 7 claims · 8 setups

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  A 6-LYMRG risk model (ANGPT1, HGF, MAPK8, PCNA, TBL1XR1, TLR4) is the optimal prognostic signature for AML

  gse142698 tcga-laml tcga-laml1 gse116256 differential univariate kaplan-meier

• treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses.

  PMID 34001188 · PMC8127214 · Genome biology · 2021 · 7 claims · 6 setups

  Has reproduction · 73

  treeclimbR proposes multiple candidate resolutions on a tree and selects the optimal one in a data-driven manner using three criteria (FDR-controlling range of t, number of rejected leaves, fewest internal nodes)

  synthetic semi-simulated microbiome mirna differential microbiome microrna