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).

• Blood feeding triggers the terminal differentiation of precursor cells in tick salivary glands.

  PMID 41880507 · PMC13015885 · Science advances · 2026 · 8 claims · 8 setups

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  Unfed I. scapularis salivary glands contain a conserved population of undifferentiated precursor cells.

  scapularis scrna-seq bulk immunofluorescence single-cell

• 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

• Evaluating Distribution and Prognostic Value of New Tumor-Infiltrating Lymphocytes in HCC Based on a scRNA-Seq Study With CIBERSORTx.

  PMID 33043022 · PMC7527443 · Frontiers in medicine · 2020 · 6 claims · 8 setups

  Has reproduction · 78

  CIBERSORTx can combine scRNA-seq-derived signature matrices with bulk RNA-seq data to estimate proportions of 11 TIL subsets in HCC tumor and normal tissue

  tcga degs cd4-gzma prognostic scrna-seq cibersortx differential

• huSA: a comprehensive database for multi-dimensional resolution of bulk, single cell and spatial transcription profiles in skin diseases.

  PMID 41719583 · PMC12923168 · Database : the journal of biological databases and curation · 2026 · 7 claims · 8 setups

  Has reproduction · 50

  huSA is a comprehensive, publicly accessible database integrating bulk RNA-seq, scRNA-seq, and spatial transcriptomics data across 17 skin diseases and 63 independent datasets

  skin scrna-seq scrna-seq transcription cell-cell

• Single-Cell Multi-Tissue T Cell Clonal Dynamics Reveal Distinct Immune Coercion Landscapes in MSI and MSS Colorectal Cancer.

  PMID 41898550 · PMC13027115 · International journal of molecular sciences · 2026 · 8 claims · 5 setups

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  Immunotherapy response in CRC is better explained by TCR clonal dynamics (expansion, migration, functional transitions) than by MSI status alone

  crc single high-quality cd4+ scrna-seq tcr pseudotime

• Single-cell epigenetic and transcriptomic states across the continuum of monoclonal B cell lymphocytosis to chronic lymphocytic leukemia.

  PMID 41987205 · PMC13192028 · Genome biology · 2026 · 8 claims · 6 setups

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  The HC-MBL to CLL transition shows subclonal, epigenetic and transcriptomic stability, consistent with a continuous disease spectrum rather than distinct evolutionary phases.

  cd19+ lc-mbl single scrna-seq mtscatac-seq asap-seq

• Monocytes serve as Shiga toxin carriers during the development of hemolytic uremic syndrome.

  PMID 39871175 · PMC11773931 · Cellular & molecular biology letters · 2025 · 8 claims · 8 setups

  Has reproduction · 84

  Monocytes are the primary carriers that transport Stx2 from the periphery to the kidney during STEC-induced HUS

  peripheral thp-1 cfse-labeled evs single-cell flow toxin-cell

• Tumour-intrinsic features shape T cell differentiation through precursor to symptomatic multiple myeloma.

  PMID 41644568 · PMC12982522 · Nature communications · 2026 · 8 claims · 6 setups

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  MM is not characterized by T cell exhaustion but by antigen-driven terminal memory differentiation, unlike solid cancers

  bone cd69+ cd8+ smm single-cell cite-seq gene

• Antigen specificity of clonally enriched CD8(+) T cells in multiple sclerosis.

  PMID 41644766 · PMC12956596 · Nature immunology · 2026 · 8 claims · 7 setups

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  A subset of 23 highly expanded, CSF-enriched CD8+ T cell clonotypes exists predominantly in the CSF of the MS/CIS cohort.

  paired cd8+ cd4+ csf single-cell differential pseudotime

• 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

• Single-cell and spatial profiling of peripheral blood and synovium unveils pro-arthritis CNBP(+) myeloid cells.

  PMID 41928282 · PMC13169754 · Journal of translational medicine · 2026 · 8 claims · 8 setups

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  Peripheral CNBP+ monocytes are expanded and show elevated 'inflammatory response' pathway scores in arthritis patients

  peripheral blood synovial arthritis single-cell bulk immunofluorescence

• omnideconv: a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data.

  PMID 41582216 · PMC12837286 · Genome biology · 2026 · 8 claims · 6 setups

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  omnideconv is an R package providing a unified interface to twelve second-generation deconvolution methods (AutoGeneS, BayesPrism, Bseq-SC, Bisque, CDseq, CIBERSORTx, CPM, DWLS, MOMF, MuSiC, SCDC, Scaden)

  blood-derived pbmc blood spleen bulk scrna-seq pseudo-bulk

• Regulatory-like FOXP3+Helios+CD4+ T conventional cells correlate with T-cell activation after Orca-T immunotherapy.

  PMID 41758930 · PMC13197979 · Blood · 2026 · 8 claims · 6 setups

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  Orca-T immunotherapy leads to increased phenotypic T-cell activation compared with unmanipulated PBSC grafts, persisting for months after treatment.

  peripheral sorted fresh cryopreserved flow single-cell tcr

• Alternative polyadenylation links RNA processing to iron metabolism in human erythropoiesis.

  PMID 41805127 · PMC12972907 · Nucleic acids research · 2026 · 8 claims · 8 setups

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  CPSF6 facilitates erythropoiesis; its depletion impairs heme synthesis and causes intracellular iron deficiency

  cd34+ cd34+-derived bone erythroid scrna-seq bulk long-read

• 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

• Divergent macrophage-regulated T cell states determine response to Bacillus Calmette-Guérin vaccine in high-risk bladder cancer.

  PMID 42081487 · PMC13262731 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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  BCG responders show an increase in Th17-like Th1 CD4+ T cells with greater proinflammatory cytokine expression

  bladder pbmcs cd4+ separate scrna-seq trajectory flow

• To Explore the Key Subgroup and Their Immune Microenvironment During the Formation of Coronary Plaque With scRNA-seq.

  PMID 40454289 · PMC12126265 · Cardiology research and practice · 2025 · 6 claims · 8 setups

  Has reproduction · 33

  C1 RACK1+ NK cells are a crucial subgroup for understanding coronary plaque formation, exhibiting the highest cell stemness/differentiation potential and positioned at the start of the pseudotime trajectory

  coronary scrna-seq five type single-cell doublet copy

• Single-Cell Analysis Reveals Characterization of Infiltrating T Cells in Moderately Differentiated Colorectal Cancer.

  PMID 33584715 · PMC7873865 · Frontiers in immunology · 2020 · 8 claims · 8 setups

  Has reproduction · 45

  Eight distinct T cell populations can be identified from CRC tumor tissue by unsupervised clustering of scRNA-seq data

  tumor-infiltrating peripheral cd4+ tumor single-cell unsupervised pearson

• Single-cell analysis reveals multi-faceted features of B cell development, together with age-associated B cell subpopulations.

  PMID 41520091 · PMC12905261 · Communications biology · 2026 · 8 claims · 8 setups

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  18 B cell subpopulations were identified spanning the full developmental continuum from early progenitors to plasma cells, including 4 previously unappreciated minor subpopulations (FTLhi, S100A8hi immature; FOShi, HSPA1Ahi naïve).

  in-house enriched tonsil peripheral scrna-seq scvdj-seq velocity

• 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