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).

• Exploring phenotype-related single-cells through attention-enhanced representation learning.

  PMID 41566378 · PMC12906058 · Genome medicine · 2026 · 6 claims · 5 setups

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  scPhase, an attention-based multiple instance learning (AMIL) framework with Mixture-of-Experts aggregation, predicts sample-level clinical phenotypes from raw scRNA-seq data and generalizes across patient cohorts

  pbmcs brain tumor scrna-seq

• The Ly6g(high) Neutrophil Subset Dictates Breast Cancer Lung Metastasis via CD8(+) T Cell Death.

  PMID 41625479 · PMC12857760 · Cancer communications (London, England) · 2026 · 8 claims · 8 setups

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  Neutrophils in the lung metastatic niche comprise two functionally distinct subsets, Ly6g^high and Ly6g^low, based on Ly6g expression level

  lung cramp cd8+ neutrophils single-cell flow genetic

• A multi-omics features-based approach integrating immunogenicity and inflammation enhances immunotherapy benefit in clear cell renal cell carcinoma.

  PMID 41640425 · PMC12864441 · Frontiers in cell and developmental biology · 2025 · 7 claims · 8 setups

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  The TIs-ML multi-omics model predicts ICB response/survival in ccRCC with superior accuracy (AUC > 0.997) compared to single biomarkers like PD-L1 and TMB

  autoimmune igan scrna-seq bulk bulk scrna-seq scissor-based

• CeLLTra: aligning cell names with gene expression via a pathway-informed transformer.

  PMID 41652996 · PMC12881829 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 4 setups

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  Grouping genes into pathway-defined gene sets as Transformer input tokens (instead of using individual genes or discretized bins) mitigates the long-sequence problem and improves representation learning of scRNA-Seq gene expression profiles.

  tabula tumor-infiltrating scrna-seq

• DANST enables cell-type deconvolution in spatial transcriptomics using deep domain adversarial neural networks.

  PMID 41663685 · PMC12996496 · Communications biology · 2026 · 7 claims · 6 setups

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  DANST, a deconvolution framework using deep domain adversarial neural networks, achieves superior cell-type deconvolution accuracy compared with existing methods on human and mouse benchmark datasets

  heart cortex visual brain spatial cell-type

• Integrative Multiomic Classification Reveals Distinct Origins and Evolutionary Trajectories of Thymic Epithelial Tumors.

  PMID 41671387 · PMC13012242 · Cancer research · 2026 · 8 claims · 8 setups

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  TETs stratify into three molecular subgroups with distinct origins: GTF2I-type thymomas, CN-type thymomas, and thymic carcinomas

  tet thymic hek293t whole-exome whole-genome bulk

• Increased IL4I1 expression predicts poor survival and modulates the immune microenvironment in acute myeloid leukemia.

  PMID 41680858 · PMC12910993 · Journal of translational medicine · 2026 · 8 claims · 8 setups

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  IL4I1 mRNA expression is significantly elevated in AML compared to normal controls

  tcga-laml bone thp-1-derived thp-1 bulk kaplan-meier deg

• Multi-cohort and single-cell profiling of aging genes reveals prognostic and therapeutic targets in breast cancer.

  PMID 41732271 · PMC12924738 · iScience · 2026 · 8 claims · 7 setups

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  The eight-gene MLAG signature outperforms 100 previously published prognostic models across 12 independent breast cancer cohorts

  tcga-brca senescent normal single-cell machine univariate gene

• HRCHY-CytoCommunity identifies hierarchical tissue organization in cell-type spatial maps.

  PMID 41764165 · PMC13065825 · Nature communications · 2026 · 8 claims · 5 setups

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  HRCHY-CytoCommunity is an end-to-end graph neural network framework that jointly identifies multi-level (coarse tissue compartment and fine cellular neighborhood) tissue structures from cell-type spatial maps using differentiable graph pooling, adaptive edge pruning, and consistency/balance regularization.

  healthy colorectal simulated breast codex visium merfish

• pmid-41778850

  PMID 41778850 · PMC7619144 · 7 claims · 8 setups

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  AT2 cells and surfactant lipids (e.g., PC, PE, PI, PG) are enriched in the vicinity of breast cancer lung metastases in both patients and mice

  postmortem lungs lung at2 immunohistochemistry maldi-msi longitudinal

• pmid-41786602

  PMID 41786602 · PMC13138013 · 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

• SMAGEXP: a galaxy tool suite for transcriptomics data meta-analysis.

  PMID 30698691 · PMC6354025 · GigaScience · 2019 · 8 claims · 5 setups

  Has reproduction · 82

  SMAGEXP integrates the metaMA and metaRNASeq R packages into the Galaxy platform to provide a unified gene expression meta-analysis tool suite

  oral lung microarray affymetrix rna-seq

• Introduction: the challenge of incidental findings.

  PMID 18547190 · PMC2587006 · The Journal of law, medicine & ethics : a journal of the American Society of Law, Medicine & Ethics · 2008 · 8 claims · 5 setups

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  No consensus exists on how to handle incidental findings in human subjects research

  publicly healthy asymptomatic families empirical functional colonography

• Lower incidence of K-ras codon 12 mutation in flat colorectal adenomas than in polypoid adenomas.

  PMID 8144396 · PMC5919417 · Japanese journal of cancer research : Gann · 1994 · 5 claims · 3 setups

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  Flat colorectal adenomas have a significantly lower K-ras codon 12 mutation frequency than polypoid adenomas and cancers.

  flat polypoid colorectal k-ras

• Frameshift mutations at mononucleotide repeats in RAD50 recombinational DNA repair gene in colorectal cancers with microsatellite instability.

  PMID 11429044 · PMC5926751 · Japanese journal of cancer research : Gann · 2001 · 6 claims · 3 setups

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  RAD50 (A)9 mononucleotide repeat is frequently frameshift-mutated in MSI-H colorectal cancer cell lines and primary tumors

  colorectal same pcr-based msi

• 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

• Putting proteins in one place.

  PMID 12790144 · PMC1316915 · Environmental health perspectives · 2003 · 8 claims · 7 setups

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  Rapamycin inhibits TOR, causing the silencing protein Sir3 to detach from chromatin at stress-response genes, triggering a coordinated multigene stress response that halts cancer cell proliferation

  saccharomyces yeast vascular skin chemical chromatin microarray

• Integrative functional genomics.

  PMID 15239826 · PMC463286 · Genome biology · 2004 · 8 claims · 8 setups

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  Ultra-conserved noncoding elements exist across human, mouse and rat genomes at very high sequence identity, often far from genes

  yeast tissue-cultured mammalian genomic comparative targeted chip-chip

• Highlights of international conference of immunogenomics and immunomics, October 8-12, 2006 Budapest, Hungary.

  PMID 17470366 · PMC7130317 · Cellular immunology · 2006 · 8 claims · 8 setups

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  An 'immunological constant of rejection' involving interferon-stimulated genes (ISGs) and innate immune effector functions (IEF) underlies diverse immune-mediated tissue destruction processes (allograft rejection, cancer rejection, autoimmunity, infection)

  hla-b44 plasma macrophages complement proteomics shotgun cap

• Mathematical models in mammalian cell biology.

  PMID 18638360 · PMC2530880 · Genome biology · 2008 · 8 claims · 8 setups

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  A point mutation in the circadian Per2 gene causes familial advanced sleep phase syndrome (FASPS) via a phosphorylation defect that alters PER2 stability and subcellular localization.

  culture skin hela mammalian live-cell confocal phosphoprotein