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).

• Characterizing Neutrophil Subtypes in Cancer Using scRNA Sequencing Demonstrates the Importance of IL1β/CXCR2 Axis in Generation of Metastasis-specific Neutrophils.

  PMID 38358352 · PMC10903300 · Cancer research communications · 2024 · 8 claims · 7 setups

  Has reproduction · 64

  Two main neutrophil subtypes exist in primary tumors: an activated subtype sharing transcriptomic signatures with healthy neutrophils, and a tumor-specific subtype.

  colorectal sorted integrated neutrophil scrna-seq bulk immunohistochemistry

• BiCLUM: Bilateral contrastive learning for unpaired single-cell multi-omics integration.

  PMID 41632825 · PMC12904586 · PLoS computational biology · 2026 · 8 claims · 5 setups

  Full-text index only

  BiCLUM consistently outperforms or matches existing integration methods across multiple RNA+ATAC and RNA+protein datasets in visualization and quantitative benchmarks

  pbmc kidney bmmc bmcite scrna-seq cite-seq

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

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

  Full-text index only

  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

• singIST: An integrative method for comparative single-cell transcriptomics between disease models and humans.

  PMID 41838773 · PMC13008255 · PLoS computational biology · 2026 · 8 claims · 7 setups

  Full-text index only

  singIST provides explainable quantitative measures of disease model similarity to a human reference at the pathway, cell type, and gene levels

  skin ear simulated scrna-seq simulation

• FUNCellA: A Tool for Single-Sample Enrichment Analysis and Relative Pathway Activity Estimation in Single-Cell RNA Sequencing Data.

  PMID 42021835 · PMC13096679 · Computational and structural biotechnology journal · 2026 · 7 claims · 8 setups

  Full-text index only

  FUNCellA integrates 7 single-sample enrichment algorithms with novel relative activation thresholding methods to identify active, inactive, and intermediate cellular states in scRNA-Seq data

  pbmcs bone liver blood scrna-seq simulated microarray

• Interactive analysis of single-cell trajectories in 3D space with Cell Journey.

  PMID 41773942 · PMC13042281 · GigaScience · 2026 · 7 claims · 3 setups

  Full-text index only

  Cell Journey is an interactive platform for computing and visualizing RNA velocity-based single-cell trajectories in 3D space.

  pancreatic bone hematopoietic scrna-seq cite-seq clonal

• Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data.

  PMID 41825449 · PMC13030991 · Cell reports methods · 2026 · 7 claims · 3 setups

  Full-text index only

  NCLUSION matches the performance of state-of-the-art single-cell clustering techniques with significantly reduced runtime

  brain-large scdesign3-simulated facs-purified scrna-seq simulated

• AutoGERN: single-cell RNA-seq gene regulatory network inference via explicit link modeling and adaptive architectures.

  PMID 41871930 · PMC13064981 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 3 setups

  Full-text index only

  AutoGERN explicitly models regulatory information in the message-passing space via learned link (edge) embeddings, which are scored by a lightweight MLP to infer TF–target interactions.

  seven same scrna-seq-based chip-seq cold-start

• Harvesting more reads from single-cell combinatorial barcoding data with scarecrow.

  PMID 41967853 · PMC13125751 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 3 setups

  Full-text index only

  scarecrow screens a subsample of reads to generate position-specific barcode profiles, then flexibly identifies barcode sequences in reads while accounting for positional jitter

  pbmc scrna-seq single-cell

• 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

  Full-text index only

  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

• Agent-based modeling of cellular dynamics in adoptive cell therapy.

  PMID 41673469 · PMC13004971 · Communications biology · 2026 · 7 claims · 7 setups

  Full-text index only

  ABMACT, an agent-based model of adoptive cell therapy, recapitulated cellular dynamics in two cancer preclinical models (lymphoma and glioblastoma mouse models).

  xenograft il-15-armored cord shanley scrna-seq autonomous rechallenge

• Bayesian inference of RNA velocity incorporating timepoints, lineage bifurcations, and count data.

  PMID 41860983 · PMC13021174 · PLoS computational biology · 2026 · 8 claims · 8 setups

  Full-text index only

  VeloVAE significantly outperforms previous RNA velocity methods in data fit, accuracy of inferred differentiation directions, and transcription rate estimation.

  pancreas developing induced embryo scrna-seq

• Unveiling gene perturbation effects through gene regulatory networks inference from single-cell transcriptomic data.

  PMID 41984780 · PMC13082667 · PLoS computational biology · 2026 · 7 claims · 4 setups

  Full-text index only

  IGNITE is an unsupervised framework that infers directed, weighted, and signed GRNs directly from unperturbed scRNA-seq data using the inverse problem for a kinetic Ising model.

  pluripotent scrna-seq gene perturbation

• 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

• 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

• Single-cell omics data-driven decoding of tumor clonal evolution through reinforcement learning.

  PMID 41998716 · PMC13224513 · Genome medicine · 2026 · 8 claims · 3 setups

  Full-text index only

  scRevol is an RL-based model that infers tumor clonal evolution from scRNA-seq-derived CNV profiles via a label assignment learning strategy.

  simulated lineage ovarian scrna-seq-derived

• scSurv: a deep generative model for single-cell survival analysis.

  PMID 41429574 · PMC12797213 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

  Full-text index only

  scSurv combines a Cox proportional hazards model with a deep generative model (VAE) of single-cell transcriptomes to estimate individual cellular contributions to clinical outcomes

  simulated tcga melanoma renal scrna-seq bulk single-cell

• TiRank prioritizes phenotypic niches in tumor microenvironment for clinical biomarker discovery.

  PMID 41689080 · PMC12910759 · Genome medicine · 2026 · 7 claims · 4 setups

  Full-text index only

  TiRank is a framework that integrates scRNA-seq, ST, and bulk transcriptomes using an REO-transformation module and multitask transfer learning to align data into a unified embedding space for prioritizing clinically relevant spatial niches

  benchmark pan-cancer gastric independent scrna-seq bulk spatial

• Hypergraph representations of single-cell RNA sequencing data for improved cell clustering.

  PMID 41896196 · PMC13070707 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

  Full-text index only

  Unipartite network projections (e.g. cell/gene co-expression networks) of scRNA-seq data lose higher-order information and are an inefficient, inflated representation of sparse transcriptomic data

  pancreas brain lung simulated scrna-seq simulated

• WASP: a versatile, web-accessible single cell RNA-Seq processing platform.

  PMID 33736596 · PMC7977290 · BMC genomics · 2021 · 7 claims · 7 setups

  Has reproduction · 59

  WASP is a software platform for processing Drop-Seq-based scRNA-seq data generated with ddSEQ or 10x protocols, combining a Snakemake pre-processing pipeline with an R Shiny post-processing application.

  specified generic scrna-seq read reference