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).

• ConNIS and labeling instability: New statistical methods for improving the detection of essential genes in TraDIS libraries.

  PMID 41790830 · PMC12991369 · PLoS computational biology · 2026 · 7 claims · 4 setups

  Has reproduction · 83

  ConNIS provides an analytic probability distribution for the length of the longest insertion-free sequence within a gene, given gene length and expected insertion count.

  synthetic four real tradis simulation semi-synthetic real-world

• Trajectory-guided dimensionality reduction for multi-sample single-cell RNA-seq data reveals biologically relevant sample-level heterogeneity.

  PMID 42024616 · PMC13188987 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

  Full-text index only

  MUSTARD is a trajectory-guided dimensionality reduction method for multi-sample, multi-condition scRNA-seq data that simultaneously captures gene expression variation along pseudotime and across samples

  simulated covid-su covid-stephenson tuberculosis data-driven scrna-seq pseudobulk-pca

• SGCP: a spectral self-learning method for clustering genes in co-expression networks.

  PMID 38956463 · PMC11221046 · BMC bioinformatics · 2024 · 7 claims · 4 setups

  Has reproduction · 51

  SGCP, a spectral self-learning method, yields gene co-expression modules with higher GO enrichment than WGCNA, CoExpNets, and CEMiTool across 12 real gene expression datasets.

  real microarray rna-seq same gene dna-microarray rna-sequencing

• scDEBGCL: a deep embedding approach based on bipartite graph contrastive learning for single-cell RNA-seq data.

  PMID 41981652 · PMC13188691 · BMC biology · 2026 · 7 claims · 3 setups

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  scDEBGCL is a deep embedding method for scRNA-seq data based on bipartite graph contrastive learning, integrating contrastive learning, graph reconstruction, and ZINB-based data reconstruction losses.

  nine yan dpt scrna-seq trajectory

• Compact and informative representation learning for scRNA-seq data clustering with masked information bottleneck.

  PMID 41917934 · PMC13162528 · BMC biology · 2026 · 6 claims · 4 setups

  Full-text index only

  scMIB achieves state-of-the-art and more stable clustering performance across diverse scRNA-seq datasets compared with ten baseline methods

  real same splatter-simulated scrna-seq clustering denoising

• GDSim: accurate simulation for single-cell transcriptomes based on the guided diffusion model.

  PMID 41978379 · PMC13076945 · Briefings in bioinformatics · 2026 · 8 claims · 4 setups

  Full-text index only

  GDSim, a label-guided diffusion-based deep generative network, can simulate scRNA-seq data that closely reflects the true distribution of original data

  real simulated annotated scrna-seq subtype differential

• Integrating and mapping single-cell transcriptomics across the entire gene expression space.

  PMID 42059480 · PMC13130072 · Briefings in bioinformatics · 2026 · 8 claims · 1 setups

  Full-text index only

  scGES is a deep learning framework that corrects batch effects across the entire gene expression space by leveraging information from both HVGs and LVGs

  real scrna-seq

• Detecting tipping points of complex diseases by network information entropy.

  PMID 38960408 · PMC11221888 · Briefings in bioinformatics · 2024 · 8 claims · 4 setups

  Has reproduction · 78

  NIEE can detect critical states or tipping points in diverse data types, including bulk and single-sample expression data

  real stringdb individual genes network background sample-specific

• SpaJoint: a transfer learning method for spatial transcriptomics deconvolution.

  PMID 41955028 · PMC13069903 · Briefings in bioinformatics · 2026 · 8 claims · 1 setups

  Full-text index only

  SpaJoint is a transfer-learning-based deconvolution method that integrates scRNA-seq and ST gene expression while accounting for spatial correlation across spots.

  simulated spatial

• Estimating sparse regression models in multi-task learning and transfer learning through adaptive penalisation.

  PMID 40674582 · PMC12502914 · Bioinformatics (Oxford, England) · 2025 · 8 claims · 3 setups

  Full-text index only

  A two-stage procedure using feature-specific and sign-specific adaptive weights shares information on feature selection, effect direction, and effect size between related regression problems.

  simulated multi-task penalised adaptive hyperparameter

• scZiva: imputation method for single-cell RNA-seq data with zero-inflated variational autoencoder.

  PMID 41857511 · PMC13122936 · BMC bioinformatics · 2026 · 8 claims · 1 setups

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  scZiva is a novel VAE-based imputation method for scRNA-seq data using a Zero-Inflated Negative Binomial (ZINB) likelihood.

  simulated scrna-seq

• scCNMF: an integrated analysis model for paired single-cell RNA sequencing and assay for transposase-accessible chromatin sequencing data leveraging cell similarity and cis-regulatory potential.

  PMID 41800139 · PMC12962131 · PeerJ · 2026 · 7 claims · 2 setups

  Full-text index only

  scCNMF is an NMF-based model for vertical integration of paired scRNA-seq and scATAC-seq data that jointly incorporates a cell similarity matrix and a cis-regulatory potential (CRP) matrix

  publicly 10x paired

• scGACL: a generative adversarial network with multi-scale contrastive learning for accurate single-cell RNA sequencing imputation.

  PMID 41632596 · PMC12866930 · Briefings in bioinformatics · 2026 · 8 claims · 6 setups

  Full-text index only

  scGACL, a GAN integrated with multi-scale contrastive learning, is proposed to overcome the over-smoothing problem in scRNA-seq imputation

  simulated real-world scrna-seq scrna-seq clustering gene

• FEDRANN: effective long-read overlap detection based on dimensionality reduction and approximate nearest neighbors.

  PMID 42102720 · PMC13201080 · GigaScience · 2026 · 8 claims · 6 setups

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  A pipeline combining IDF transformation, sparse random projection (SRP), and NNDescent (the FEDRANN strategy) enables accurate overlap detection across diverse long-read datasets

  real same chromosome genome overlap exact simulated

• scComm: a contrastive learning framework for deciphering cell-cell communications at single-cell resolution.

  PMID 41877186 · PMC13134144 · Genome biology · 2026 · 8 claims · 7 setups

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  scComm infers cell-cell communications at single-cell resolution using a data-adaptive L-R weighting module and supervised contrastive learning (SupCon loss) to distinguish significant CCC events from background noise

  simulated spatial liver single-cell simulated spatial scrna-seq

• Analyses and comparison of accuracy of different genotype imputation methods.

  PMID 18958166 · PMC2569208 · PloS one · 2008 · 8 claims · 3 setups

  Full-text index only

  Stronger LD produces higher imputation accuracy rates for all five methods

  simulated real linux genotype computational

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

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

  Full-text index only

  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

• Enhancing cell subpopulation discovery in cancer by integrating single-cell transcriptome and expressed variants.

  PMID 41647537 · PMC12869734 · Fundamental research · 2026 · 6 claims · 3 setups

  Has reproduction · 68

  scCluster, an end-to-end deep clustering model integrating gene expression and expressed variant (eSNP) features, stratifies cell subpopulations in cancer scRNA-seq data.

  raw real-world expressed gene deep

• miR-4478 Accelerates Nucleus Pulposus Cells Apoptosis Induced by Oxidative Stress by Targeting MTH1.

  PMID 36130054 · PMC9897280 · Spine · 2023 · 7 claims · 8 setups

  Has reproduction · 100

  miR-4478 is upregulated in NP tissues from IVDD patients compared to controls

  annulus npcs mirna quantitative fluorescence

• binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets.

  PMID 36239393 · PMC9677464 · Briefings in bioinformatics · 2022 · 8 claims · 8 setups

  Has reproduction · 67

  binny outperforms or is highly competitive with commonly used and state-of-the-art binning methods (MetaBAT2, MaxBin2, CONCOCT, VAMB, SemiBin, MetaDecoder)

  cami real-world metagenomic binned genome binning mag