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).

• Deconvolution of the hematopoietic stem cell microenvironment reveals a high degree of specialization and conservation.

  PMID 35494238 · PMC9046238 · iScience · 2022 · 7 claims · 7 setups

  Has reproduction · 60

  Integration of three scRNA-seq datasets using a custom bootstrapping-based clustering pipeline robustly identifies 14 endothelial subclusters and 11 mesenchymal (stage-specific) subclusters in mouse bone marrow.

  bone independent scrna-seq gene singler

• CanSig Benchmarks Methods for Reproducible Cancer Cell State Discovery from Single-Cell Transcriptomic Data.

  PMID 41231245 · PMC13053056 · Cancer research · 2026 · 7 claims · 7 setups

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  CanSig is a comprehensive benchmarking tool for evaluating computational methods that identify shared transcriptional signatures in cancer from scRNA-seq data

  neftel kim scrna-seq same scrna-seq ground-truth robustness

• Deep-Learning Tool ScVital Enables Species-Agnostic Integration of Cancer Cell States.

  PMID 41223329 · PMC13053053 · Cancer research · 2026 · 7 claims · 7 setups

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  scVital is a variational autoencoder with an adversarially trained discriminator that embeds scRNA-seq data from different species into a species-agnostic latent space to overcome batch effect.

  pbmc normal pancreatic lung scrna-seq

• Early feature extraction drives model performance in high-resolution chromatin accessibility prediction.

  PMID 41526189 · PMC12951969 · Genome research · 2026 · 8 claims · 6 setups

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  Early feature extraction (via ConvNeXt V2 blocks), rather than downstream architecture type, is the primary determinant of prediction accuracy in high-resolution chromatin accessibility prediction.

  lines cancer sets gm12878 atac-seq peak input-shift

• Robust and efficient annotation of cell states through gene signature scoring.

  PMID 41708334 · PMC12951948 · Genome research · 2026 · 8 claims · 8 setups

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  Established scoring methods (Seurat, SCANPY, UCell, JASMINE) fail to provide robust and comparable score distributions across diverse signatures and experimental conditions, precluding accurate unsupervised cell-state annotation.

  pbmc colorectal esophageal crc scrna-seq cross-implementation signature

• CanCellCap: robust cancer cell capture across tissue types on single-cell RNA-seq data by multi-domain learning.

  PMID 40739511 · PMC12312500 · BMC biology · 2025 · 8 claims · 7 setups

  Has reproduction · 42

  CanCellCap identifies cancer cells in scRNA-seq data across 13 tissue types, 23 cancer types, and 7 sequencing platforms with 0.977 average accuracy

  cancer testing sequencing unseen scrna-seq spatial

• Lorentz-regularized interpretable VAE for multi-scale single-cell transcriptomic and epigenomic embeddings.

  PMID 41555918 · PMC12812404 · Frontiers in genetics · 2025 · 7 claims · 5 setups

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  LiVAE, a dual-pathway VAE with Lorentzian geometric regularization between a primary Euclidean pathway and an information-bottleneck pathway, balances local fidelity with global topology coherence in single-cell embeddings

  single-cell same dapp1 benchmarking umap component-wise

• Single-nucleus multiple-organ chromatin accessibility landscape in the adult rat.

  PMID 41632074 · PMC12954174 · GigaScience · 2026 · 8 claims · 5 setups

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  Generated a multi-organ snATAC-seq atlas of 9 adult rat organs comprising 25 libraries and over 110,000 cells

  organs publicly snatac-seq group-level snatac-seq scrna-seq gene

• scATD: a high-throughput and interpretable framework for single-cell cancer drug resistance prediction and biomarker identification.

  PMID 40501071 · PMC12159290 · Briefings in bioinformatics · 2025 · 8 claims · 6 setups

  Has reproduction · 62

  scATD enables high-throughput single-cell drug sensitivity prediction for new patients without model parameter retraining via bidirectional Bi-AdaIN style transfer

  panglaodb cancer geo gse137829 single-cell bulk

• CLAMP: predicting specific protein-mediated chromatin loops in diverse species with a chromatin accessibility language model.

  PMID 41555433 · PMC12903630 · Genome biology · 2026 · 8 claims · 8 setups

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  CLAMP, a chromatin-accessibility language model, predicts protein-mediated chromatin loops across 10 species, 18 proteins, and 24 cell types with superior performance versus existing methods.

  species gm12878 types chromatin cross-protein cross-cell-type

• spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data.

  PMID 36321549 · PMC9627675 · Molecular systems biology · 2022 · 8 claims · 8 setups

  Has reproduction · 53

  spliceJAC uses unspliced and spliced mRNA count matrices to construct cell state-specific gene-gene regulatory interaction (Jacobian) matrices from scRNA-seq data

  bistable three-gene emt circuits simulation mixed-state grn

• BLIT: an R package for seamless integration of command-line bioinformatics tool universe.

  PMID 42164079 · PMC13183670 · Bioinformatics advances · 2026 · 8 claims · 5 setups

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  BLIT provides a unified R6-based framework for seamless integration of command-line bioinformatics tools within R, replacing fragile string-based system() calls.

  core circrna clinical europe unit pipeline production

• STARCall integrates image stitching, alignment, and read calling to enable scalable analysis of in situ sequencing data.

  PMID 42044152 · PMC13160441 · PLoS computational biology · 2026 · 8 claims · 8 setups

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  STARCall combines image stitching and cross-cycle alignment into a single joint optimization step (via ConStitch) that minimizes both inter-cycle and intra-cycle alignment error.

  stem slice a549 u2os image situ simulated

• Benchmarking LLM-based agents for single-cell omics analysis.

  PMID 41742311 · PMC13064268 · Genome biology · 2026 · 8 claims · 8 setups

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  Introduces a comprehensive benchmarking evaluation system comprising an open-source agent platform, 18 evaluation metrics across four dimensions, and 50 real-world single-cell omics tasks

  agent single-cell spatial scatac-seq llm-agent scrna-seq spatial