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).

• Regulation Ratio: A Singular Multi-Omic Measurement of Gene Regulatory Mechanisms.

  PMID 42028238 · PMC13100350 · Computational and structural biotechnology journal · 2026 · 8 claims · 5 setups

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  A Regulation Ratio (RR), calculated as the ratio of gene-length-normalized POP-seq peak density to ATAC-seq peak density, quantifies the relative balance of post-transcriptional versus transcriptional regulation for individual genes

  hek293 computational atac-seq pop-seq rna-seq

• A spatially coordinated keratinocyte-fibroblast circuit recruits MMP9(+) myeloid cells to drive type I interferon-driven inflammation in photosensitive autoimmunity.

  PMID 42032302 · PMC13226071 · Nature immunology · 2026 · 8 claims · 8 setups

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  MMP9+CD14+ myeloid cells are critical mediators of photosensitivity, expanding in lesional skin, producing IFNβ, and colocalizing with cytotoxic CD4+ T cells at the dermal-epidermal junction

  skin blister punch donor scrna-seq 250-plex seqfish

• Single-cell profiling reveals distinct populations of tumor-associated macrophages and metastatic tumor cells in breast cancer brain metastasis.

  PMID 42034645 · PMC13247122 · Cell death & disease · 2026 · 8 claims · 8 setups

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  Single-cell profiling of BCBM identifies 12 tumor-associated macrophage (TAM) subtypes and 5 metastatic tumor cell (MTC) subtypes with distinct transcriptional profiles

  brain breast scrna-seq tams scrna-seq bulk copy

• Multi-Transcriptomic Analysis Reveals That EREG-Driven TME Crosstalk Defines Anti-EGFR Response in Colorectal Cancer.

  PMID 42043480 · PMC13115984 · Cancer medicine · 2026 · 8 claims · 8 setups

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  EGFRI eligibility (defined by left-sidedness, RAS/BRAF wild-type, MSS) stratifies cancer cell transcriptomic characteristics more strongly than sidedness alone.

  crc epcam+ aggregated cancer scrna-seq copy pseudobulk

• Semi-parametric empirical bayes method for multiplet detection in snATAC-seq with probabilistic multi-omic integration.

  PMID 42054434 · PMC13148828 · PLoS computational biology · 2026 · 8 claims · 5 setups

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  SEBULA models the singlet background directly from observed HCLC (high-coverage locus count) statistics using fragment-level snATAC-seq information, avoiding reliance on synthetic/artificial doublets.

  dogma-seq dogma-seq-derived seven snatac-seq q-q density

• CaHoT-GRN: context-aware high-order topology learning for robust single-cell gene regulatory network inference.

  PMID 42059479 · PMC13130071 · Briefings in bioinformatics · 2026 · 7 claims · 5 setups

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  CaHoT-GRN integrates pretrained biological language model embeddings (DNABERT for DNA, ESM for protein) with scRNA-seq expression data to improve GRN inference

  embryonic gene dataset-specific same scrna-seq-based sequence protein-protein

• Comprehensive multi-omics reveals dynamic chromatin changes and gene regulatory networks during duck folliculogenesis.

  PMID 42063177 · PMC13134274 · Journal of animal science and biotechnology · 2026 · 8 claims · 6 setups

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  H3K27ac dynamics, rather than chromatin accessibility alone, are strongly associated with stage-specific transcriptional increases during follicle selection and maturation

  granulosa gcs chicken rna-seq atac-seq cut&tag

• Helicobacter pylori-induced PPFIA4 orchestrates immune network-promoting gastritis and gastric bacterial colonization.

  PMID 42065246 · PMC13132368 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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  PPFIA4 is increased in GECs from gastric mucosa of H. pylori-infected patients and mice

  ags gastric il33 slam-seq scrna-seq western

• Pervasive enhanced transcription in inflammatory breast cancer tumors and PBMCs impacts RNA splicing and intronic RNAs in plasma.

  PMID 42066072 · PMC13134590 · Science advances · 2026 · 8 claims · 7 setups

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  TGIRT-seq of tumors, PBMCs, and plasma reveals widespread differences that distinguish IBC patients from non-IBC patients and healthy donors across breast cancer subtypes.

  ffpe pbmcs plasma frozen tgirt-seq differential principal

• pmid-42067854

  PMID 42067854 · PMC13135260 · 7 claims · 8 setups

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  Loss of ERG initiates a progressive EndMT program in which endothelial identity is lost rapidly (by 24 h) before mesenchymal identity, barrier dysfunction, and enhanced migration emerge later (by 72 h)

  telohaec huvec atac-seq rna-seq western

• pmid-42074497

  PMID 42074497 · PMC13116960 · 8 claims · 6 setups

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  Ionizing radiation induces extensive transcriptome reprogramming in mouse bone marrow HSCs 3 days after whole-body irradiation.

  bone deg transcriptome deg-encoded rna-seq gene kegg

• pmid-42074555

  PMID 42074555 · PMC13115875 · 8 claims · 8 setups

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  A cross-species single-cell/single-nucleus RNA-seq atlas of human fetal and mouse postnatal cochlea identifies 19 conserved major cell types

  cochlea fetal top scrna-seq snrna-seq cell-cell

• pmid-42074600

  PMID 42074600 · PMC13115820 · 7 claims · 8 setups

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  NuRepress is a computational framework that predicts candidate transcriptional repressors by integrating repressive chromatin architecture, functional (accessibility) signatures, and transcriptional outcomes

  pancreatic patski well-phased chip-seq atac-seq rna-seq

• pmid-42079667

  PMID 42079667 · PMC13128579 · 8 claims · 5 setups

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  TRACE, a clonotype-level CD8+ TRT classifier trained on an aggregated multi-study dataset, achieves robust holdout performance (mean MCC 0.84, F1 0.85)

  cd8+ expanded aggregated combined scrna-seq co-culture gene

• pmid-42081487

  PMID 42081487 · PMC13262731 · 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

• pmid-42086590

  PMID 42086590 · PMC13144409 · 8 claims · 5 setups

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  SLAM-seq (4sU metabolic labeling with T-to-C conversion detection) can be established and quantified in the adult zebrafish heart at the bulk level

  zebrafish macrophage-like bulk scslam-seq pathway

• pmid-42088639

  PMID 42088639 · PMC13137179 · 8 claims · 8 setups

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  Enhancer and polycomb chromatin regions progressively increase in genomic coverage during MASLD progression

  liver aml12 chip-seq bulk histological

• pmid-42093817

  PMID 42093817 · PMC13139726 · 7 claims · 5 setups

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  TDAGENE combines TDA features with a multilayer GAT via gate-controlled fusion to improve GRN inference accuracy

  scrna-seq gene string chip-seq grn persistent prior

• 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

• Segzoo: a turnkey system that summarizes genome annotations.

  PMID 42087325 · PMC13189851 · Bioinformatics (Oxford, England) · 2026 · 7 claims · 4 setups

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  Segzoo is a turnkey system that automates downloading of reference data and running of analyses to summarize SAGA genome annotations, requiring only a BED-format annotation file as input

  embryonic segway chip-seq segway segtools