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).

• A new chromosome-level genome assembly for western painted turtle Chrysemys picta bellii, a model for extreme physiological adaptations.

  PMID 41792601 · PMC13077969 · BMC genomics · 2026 · 6 claims · 8 setups

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  A new haplotype-resolved, chromosome-level reference genome assembly (SLU_Cpb5.0) was generated for C. picta bellii using combined PacBio HiFi, 10x Genomics Chromium, Hi-C, and Bionano optical mapping data from a single individual.

  genomic ultra-high tissues heart 10x pacbio hi-c

• scDenorm: a denormalization tool for integrating single-cell transcriptomics data.

  PMID 41915012 · PMC13142155 · GigaScience · 2026 · 8 claims · 7 setups

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  Inconsistent delta-method normalization across datasets introduces biases (e.g., B-cell separation) that persist even after integration with Harmony, scanorama, or BBKNN.

  10x brain ucsc datasets scrna-seq integration snrna-seq

• 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

• Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet.

  PMID 41786602 · PMC13138013 · Genome research · 2026 · 7 claims · 5 setups

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  NNet uses PCA embedding followed by local KNN regression in PC space to construct cell-specific coexpression networks (CSNs), improving computational efficiency and estimate stability versus pairwise approaches.

  pbmc thp-1 lin small scrna-seq perturb-seq

• CSsingle: a unified tool for robust decomposition of bulk and spatial transcriptomic data across diverse single-cell references.

  PMID 42080261 · PMC13136905 · Nucleic acids research · 2026 · 8 claims · 8 setups

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  CSsingle explicitly corrects for cell-type-specific RNA content (cell size) differences using ERCC spike-ins or a novel computational estimator

  blood breast developing colorectal bulk scrna-seq spatial

• Exploring the prognostic and diagnostic value of lactylation-related genes in sepsis.

  PMID 39367086 · PMC11452377 · Scientific reports · 2024 · 8 claims · 7 setups

  Has reproduction · 73

  Intersecting sepsis-associated differentially expressed genes with a curated list of 332 lactylation genes yields 55 sepsis-related lactylation genes.

  peripheral overlapping geo pbmcs bulk kegg protein-protein

• Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing.

  PMID 36681937 · PMC10025442 · Briefings in bioinformatics · 2023 · 8 claims · 8 setups

  Has reproduction · 94

  HiCAT is a hierarchical, marker-based cell-type identifier that uses gene set analysis (GSA) scoring with markers structured in a three-level taxonomy tree (major-type, minor-type, subset)

  pbmc cord melanoma lung scrna-seq computational

• Assessing personalized molecular portraits underlying endothelial-to-mesenchymal transition within pulmonary arterial hypertension.

  PMID 39462326 · PMC11513636 · Molecular medicine (Cambridge, Mass.) · 2024 · 8 claims · 8 setups

  Has reproduction · 81

  scRNA-seq of PAH and control lung tissue identifies nine distinct cell populations with high heterogeneity in composition, function, distribution, and communication

  lung pah scrna-seq-derived endothelial scrna-seq bulk cell-cell

• Pan-Cancer Single-Cell RNA Sequencing Analysis Refines Multi-Origin Monocyte and Macrophage Lineages.

  PMID 41231218 · PMC12865363 · Cancer immunology research · 2026 · 6 claims · 8 setups

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  TAMs arise from two distinct origins: C1QC+ TAMs likely derive from resident tissue macrophages, while SPP1+ TAMs and ISG15+ TAMs likely originate from circulating monocytes.

  myeloid melanoma monocyte-to-macrophage coad-read scrna-seq differential developmental

• 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

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  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

• Alginate oligosaccharides improve germ cell development and testicular microenvironment to rescue busulfan disrupted spermatogenesis.

  PMID 32194870 · PMC7053202 · Theranostics · 2020 · 8 claims · 8 setups

  Has reproduction · 79

  AOS rescues busulfan-disrupted spermatogenesis in vivo by increasing the proportion of germ cells (spermatocytes and spermatids)

  icr spermatozoa testis plasma single-cell computer-assisted immunofluorescence

• A single-cell compendium of human cerebrospinal fluid identifies disease-associated immune cell populations.

  PMID 39744938 · PMC11684814 · The Journal of clinical investigation · 2025 · 8 claims · 4 setups

  Has reproduction · 78

  Integration of public and newly generated scRNA-seq datasets yields a compendium of 139 subjects (193 samples, 403,973 immune cells) spanning CSF and blood across healthy controls and multiple neurologic diseases.

  csf scrna-seq trajectory flow

• Spatial transcriptomics demonstrates the role of CD4 T cells in effector CD8 T cell differentiation during chronic viral infection.

  PMID 36450262 · PMC9792173 · Cell reports · 2022 · 8 claims · 6 setups

  Has reproduction · 50

  IL-21-producing Tfh CD4 T cells repopulate after CD4 depletion but remain at reduced frequency compared with control mice

  cd44+ splenocytes spleen tcr scrna-seq flow spatial

• Creation of a Single Cell RNASeq Meta-Atlas to Define Human Liver Immune Homeostasis.

  PMID 34335581 · PMC8322955 · Frontiers in immunology · 2021 · 7 claims · 8 setups

  Has reproduction · 63

  Three independently generated human liver CD45+ scRNA-seq datasets (LACEe, Lnb, LCD45e) can be co-clustered and integrated despite differing sequencing platforms and processing protocols.

  liver pbmc integrated gene scrna-seq differential ingenuity

• 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

• 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

• FLASH-MM: fast and scalable single-cell differential expression analysis using linear mixed-effects models.

  PMID 41644528 · PMC12982622 · Nature communications · 2026 · 8 claims · 6 setups

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  FLASH-MM produces LMM parameter estimates identical to lmer (lme4) up to the sixth decimal place while being 50- to 140-fold faster as sample size increases from 20,000 to 120,000 cells

  simulated same healthy female-biased simulated comparative single-cell