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 336

System / cell line: paired ✕ Clear

Discovery of key regulators in classical monocyte phenotypes linked to COVID-19 severity using single-cell multi-omics sequencing.

PMID 41732268 · PMC12925236 · iScience · 2026 · 8 claims · 8 setups

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Two severity-associated classical monocyte (cMono) subtypes, IL7R+ and CD163+, exist with distinct transcriptional and epigenetic landscapes.

pbmcs pbmc classical cmono single-nucleus differential multimodal
Integrative CSF profiling identifies disease-specific immune responses in leptomeningeal disease.

PMID 41794040 · PMC13006398 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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CSF exhibits distinct, disease-specific immune landscapes across CNSL, BrMs, and GB-associated LMD

csf peripheral brain cell-free single-cell deep spatial
MIRit: an integrative R framework for the identification of impaired miRNA-mRNA regulatory networks in complex diseases.

PMID 41800385 · PMC12961272 · Bioinformatics advances · 2026 · 8 claims · 5 setups

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MIRit is a comprehensive, open-source R/Bioconductor framework for integrative miRNA–mRNA analysis that supports both paired and unpaired datasets using statistically appropriate methods.

myocardial ccrcc brodmann synthetic mirna-seq microarray small
Frequent and multiple mutations at minisatellite loci in sporadic human colorectal and gastric cancers--possible mechanistic differences from microsatellite instability in cancer cells.

PMID 11985787 · PMC5927018 · Japanese journal of cancer research : Gann · 2002 · 6 claims · 3 setups

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MN mutations occur significantly more frequently in sporadic colorectal cancer (56%) than in gastric cancer (25%)

sporadic same multilocus pcr-simple
Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index.

PMID 41252442 · PMC12758600 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 4 setups

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Cleanifier is a fast, memory-frugal alignment-free tool for detecting and removing human contamination using gapped k-mers (spaced seeds) and a human pangenome index.

genomes genome cami t2t host-contamination pangenome
A computational pipeline to visualize DNA-protein binding states using dSMF data.

PMID 35463472 · PMC9026571 · STAR protocols · 2022 · 8 claims · 2 setups

Has reproduction · 89

The pipeline maps states of protein-binding DNA in vivo using dSMF data and identifies binding states at an enhancer in Drosophila S2 cells

drosophila dual-enzyme starr-seq
A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference.

PMID 32019526 · PMC7001327 · BMC plant biology · 2020 · 8 claims · 6 setups

Has reproduction · 62

Inter-specific differences in vertical distribution/microhabitat preference are associated with distinct dynamics of gene expression during dehydration and rehydration phases

hymenophyllum caudiculatum annotated rna-seq chlorophyll relative
Evaluation of multiple displacement amplification in a 5 cM STR genome-wide scan.

PMID 16055919 · PMC1182175 · Nucleic acids research · 2005 · 7 claims · 5 setups

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MDA genotyping call rates and accuracy are only marginally lower than for genomic DNA

genomic same monozygotic subset genome-wide genome
Preponderance of the oncogenic V599E and V599K mutations in B-raf kinase domain is enhanced in melanoma cutaneous/subcutaneous metastases.

PMID 15935100 · PMC1164406 · BMC cancer · 2005 · 8 claims · 4 setups

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B-raf exon 15 somatic mutations occur in 24/60 (40%) of cutaneous/subcutaneous melanoma metastases, similar to the frequency in primary melanomas

paraffin-embedded cloned same predicted pcr cloning blastx
A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

PMID 25202605 · PMC4103609 · Applications in plant sciences · 2014 · 8 claims · 8 setups

Has reproduction · 87

A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.

compositae same species helianthus targeted genome genomic
Genomic and Immune Landscape of Recurrent and/or Metastatic Squamous Cell Carcinoma of the Head and Neck Progressing on Anti-PD-1 Treatment.

PMID 41666253 · PMC13044521 · Cancer immunology research · 2026 · 6 claims · 8 setups

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Tumor biopsies from anti-PD-1-resistant SCCHN show significantly more EGFR and MYCL amplifications and increased MYC pathway alterations compared with anti-PD-1-naive tumors

ffpe blood tumor whole-exome bulk multiplex
VHL synthetic lethality screens uncover CBF-β as a negative regulator of STING.

PMID 41820368 · PMC13121600 · Nature communications · 2026 · 8 claims · 8 setups

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CBFB (CBF-β) is a synthetic lethal interactor of VHL in ccRCC cell lines

786o ccrcc tcga genome-wide competitive immunoblot
Divergent clonal evolution and tumor microenvironment remodeling shape gastric cancer peritoneal metastasis.

PMID 41882239 · PMC13181027 · Communications biology · 2026 · 8 claims · 7 setups

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Substantial intra-patient heterogeneity exists between GCPM and primary tumors at both genetic and functional (transcriptomic) levels

gastric wgs paired genes whole-genome whole-transcriptome mutational
Hypoxia-driven remodeling of SELENOP(+) macrophages shapes T cell dynamics and promotes ovarian cancer metastasis.

PMID 41526347 · PMC12852879 · Nature communications · 2026 · 8 claims · 8 setups

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SELENOP+ macrophages co-occur and spatially co-localize with precursor exhausted (GZMH+) CD8+ T cells and activate these T cells via selenoprotein P in vitro and in vivo.

hgsoc million pseudo-bulk hgsoc-derived scrna-seq sctcr-seq spatial
Multimodal-based analysis of single-cell ATAC-seq data enables highly accurate delineation of clinically relevant tumor cell subpopulations.

PMID 41530870 · PMC12888741 · Genome medicine · 2026 · 8 claims · 8 setups

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MAAS integrates chromatin accessibility, CNVs, and SNVs from scATAC-seq data to identify functional tumor cell subpopulations

tumor pediatric b-cell glioblastoma scatac-seq bulk gene
Mutational Signatures and Clonal Hematopoiesis in Intestinal Metaplasia across Countries with Varying Stomach Cancer Incidence.

PMID 41532847 · PMC13056296 · Cancer discovery · 2026 · 8 claims · 8 setups

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High-depth targeted sequencing of >1,500 IM samples from six countries identified 47 significantly mutated driver genes, including ARID1A, KRAS/MAPK pathway genes, and PIGR

subset matched saliva hek293t high-depth whole-genome genome-wide
Dysregulated expression of cell cycle regulators CDC20, PLK1, BUB1, CDC45, CDCA5 in pancreatic ductal adenocarcinoma.

PMID 41699006 · PMC13002898 · Scientific reports · 2026 · 8 claims · 8 setups

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CDC20, PLK1, BUB1, CDC45, and CDCA5 are concordantly identified as hub genes across seven NCBI-GEO datasets and the Pakistani RNA-seq dataset

pakistani pdac overlapping tcga-paad bulk functional protein-protein
Unique phenotypic and T cell receptor characteristics of CD8(+) T cells accumulated in the brains of Alzheimer's disease mice.

PMID 41794902 · PMC13087195 · Scientific reports · 2026 · 8 claims · 5 setups

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Brain CD8+ T cells segregate into two major, mutually exclusive Trm populations: a CXCR6-related immunosuppressive cluster (cd8_c0) present in both aged non-Tg and 5xFAD_WT mice, and an AD-associated stem-like cluster (cd8_c1) present only in 5xFAD mice.

brain-derived brain cd8+ clonally scrna-seq paired cellchat
Reconstructing single-cell resolution from spatial transcriptomics with CellRefiner.

PMID 41760664 · PMC13066420 · Nature communications · 2026 · 8 claims · 8 setups

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CellRefiner is a physical/particle-based model (subcellular element method) that integrates scRNA-seq and spatial transcriptomics data to reconstruct single-cell resolution spatial data

hypothalamic embryo hippocampus visual merfish seqfish slide-seqv2
Exposure to the widely used herbicide atrazine results in deregulation of global tissue-specific RNA transcription in the third generation and is associated with a global decrease of histone trimethylation in mice.

PMID 27655631 · PMC5175363 · Nucleic acids research · 2016 · 8 claims · 8 setups

Has reproduction · 10

Embryonic ATZ exposure affects meiosis, spermiogenesis and reduces spermatozoa number in F3 generation male mice

testis dissociated epididymis chip-seq strand-specific h&e

Experiments

Discovery of key regulators in classical monocyte phenotypes linked to COVID-19 severity using single-cell multi-omics sequencing.

Integrative CSF profiling identifies disease-specific immune responses in leptomeningeal disease.

MIRit: an integrative R framework for the identification of impaired miRNA-mRNA regulatory networks in complex diseases.

Frequent and multiple mutations at minisatellite loci in sporadic human colorectal and gastric cancers--possible mechanistic differences from microsatellite instability in cancer cells.

Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index.

A computational pipeline to visualize DNA-protein binding states using dSMF data.

A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference.

Evaluation of multiple displacement amplification in a 5 cM STR genome-wide scan.

Preponderance of the oncogenic V599E and V599K mutations in B-raf kinase domain is enhanced in melanoma cutaneous/subcutaneous metastases.

A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

Genomic and Immune Landscape of Recurrent and/or Metastatic Squamous Cell Carcinoma of the Head and Neck Progressing on Anti-PD-1 Treatment.

VHL synthetic lethality screens uncover CBF-β as a negative regulator of STING.

Divergent clonal evolution and tumor microenvironment remodeling shape gastric cancer peritoneal metastasis.

Hypoxia-driven remodeling of SELENOP(+) macrophages shapes T cell dynamics and promotes ovarian cancer metastasis.

Multimodal-based analysis of single-cell ATAC-seq data enables highly accurate delineation of clinically relevant tumor cell subpopulations.

Mutational Signatures and Clonal Hematopoiesis in Intestinal Metaplasia across Countries with Varying Stomach Cancer Incidence.

Dysregulated expression of cell cycle regulators CDC20, PLK1, BUB1, CDC45, CDCA5 in pancreatic ductal adenocarcinoma.

Unique phenotypic and T cell receptor characteristics of CD8(+) T cells accumulated in the brains of Alzheimer's disease mice.

Reconstructing single-cell resolution from spatial transcriptomics with CellRefiner.

Exposure to the widely used herbicide atrazine results in deregulation of global tissue-specific RNA transcription in the third generation and is associated with a global decrease of histone trimethylation in mice.