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).

Publications 1.3k Datasets 392.5k Experiments 783

Assay: tumor ✕ Clear

Spatiotemporal Transcriptomics Characterizes Immune Microenvironment During Mouse Liver Aging.

PMID 42010880 · PMC13096584 · Aging cell · 2026 · 8 claims · 8 setups

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T cells are the immune cell population with the most pronounced transcriptomic alterations during liver aging

liver nash cirrhotic hcc scrna-seq snrna-seq stereo-seq
Interpretable, flexible and spatially aware integration of multiple spatial transcriptomics datasets from diverse sources.

PMID 42045691 · PMC13175893 · Nature genetics · 2026 · 6 claims · 7 setups

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INSPIRE is a deep-learning method that unifies adversarial learning with a GNN-based encoder and integrated NMF to interpretably integrate multiple spatial transcriptomics datasets

synthetic dorsolateral brain cortex simulated visium spatial
Sensitive detection of somatic mutations in GC-rich cancer gene promoters.

PMID 42088607 · PMC13136893 · NAR cancer · 2026 · 8 claims · 8 setups

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Gene promoters, due to high GC content (CpG islands, ~70% of promoters), are systematically undersampled and have poor coverage in whole cancer genomes, causing missed somatic mutation calls

gm12878 cancer ffpe lines hybrid whole-genome dnase-seq
IMIREG: a lineage-resolved regulon signature unveiling immune engagement archetypes and predicting immunotherapy response across diverse cancers.

PMID 42092126 · PMC13234301 · NPJ precision oncology · 2026 · 8 claims · 8 setups

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IMIREG, a 14-regulon transcriptional signature, robustly predicts clinical benefit from ICB across 50 immunotherapy cohorts (52 treatment arms) spanning 16 cancer types with mean AUROC = 0.71

imvigor210 matched gtex healthy bulk scrna-seq pathway
pmid-42111187

PMID 42111187 · PMC13157187 · 8 claims · 8 setups

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cfDNAanalyzer integrates feature extraction, feature processing/selection, and machine learning model building into a single one-command-line toolkit for cfDNA genomic sequencing data

balanced breast healthy multi-cancer cfdna machine computational
pmid-42111394

PMID 42111394 · PMC13155427 · 8 claims · 8 setups

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KRT5+ cells represent bona fide cancer-propagating cells (CPCs) in HGSC

hgsc skov3 facs-sorted nod immunohistochemistry lentiviral organoid
pmid-42118153

PMID 42118153 · PMC13165028 · 8 claims · 8 setups

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PRECISE-seq is a contact-dependent proximity labeling sequencing platform using Sortase A (SrtA)-catalyzed ligation to simultaneously profile antigen specificity, TCR potency, and phenotypic landscape at single-cell resolution

hek293t k562-hla-a2 ot-i cd45.1+ flow
The AICL-KLRF1 axis supports CD4-CD8 T cell communication and cytokine competence in pre-exhausted CD8(+) T cells.

PMID 41851343 · PMC13121605 · EMBO reports · 2026 · 8 claims · 8 setups

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Progressive expression of KLRB1, KLRG1, GPR56, and KLRF1 tracks CD8+ T cell differentiation stages (TN, TCM, TEM, TEMRA), mirroring the pattern previously shown in CD4+ T cells

unstimulated cd3+-enriched enriched cd8+ flow sorting-based spatial
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
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
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
Partial domain adaptation enables cross domain cell type annotation between scRNA-seq and snRNA-seq.

PMID 42090457 · PMC13170964 · PLoS computational biology · 2026 · 7 claims · 5 setups

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ScNucAdapt is a partial domain adaptation framework that enables cross-domain cell type annotation between paired or unpaired scRNA-seq and snRNA-seq datasets.

bladder kidney cortex frozen scrna-seq snrna-seq
Comprehensive analyses of telomerase component DKC1 and its association with clinical, molecular and immune landscapes in uterine corpus endometrial carcinoma.

PMID 40458122 · PMC12127311 · Frontiers in cell and developmental biology · 2025 · 8 claims · 8 setups

Has reproduction · 71

DKC1 mRNA and protein expression are significantly upregulated in UCEC tumors compared with non-tumorous endometrial tissue

ucec ishikawa rna-seq proteomics immunohistochemistry

Experiments

Spatiotemporal Transcriptomics Characterizes Immune Microenvironment During Mouse Liver Aging.

Interpretable, flexible and spatially aware integration of multiple spatial transcriptomics datasets from diverse sources.

Sensitive detection of somatic mutations in GC-rich cancer gene promoters.

IMIREG: a lineage-resolved regulon signature unveiling immune engagement archetypes and predicting immunotherapy response across diverse cancers.

pmid-42111187

pmid-42111394

pmid-42118153

The AICL-KLRF1 axis supports CD4-CD8 T cell communication and cytokine competence in pre-exhausted CD8(+) T cells.

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

Introduction: the challenge of incidental findings.

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

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

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

HArmonized single-cell RNA-seq Cell type Assisted Deconvolution (HASCAD).

Putting proteins in one place.

Integrative functional genomics.

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

Mathematical models in mammalian cell biology.

Partial domain adaptation enables cross domain cell type annotation between scRNA-seq and snRNA-seq.

Comprehensive analyses of telomerase component DKC1 and its association with clinical, molecular and immune landscapes in uterine corpus endometrial carcinoma.