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 635

Assay: size ✕ Clear

A pan-cancer single cell landscape reveals heterogeneity and functional diversity of double-negative T cells.

PMID 41484771 · PMC12882460 · Molecular cancer · 2026 · 7 claims · 5 setups

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Integration of pan-cancer scRNA-seq data yields a comprehensive single-cell atlas of 157,025 high-quality DNT cells across 23 cancer types.

tumor dnt ffpe mc38 scrna-seq tcr multiplex
Effector gene silencing coordinated by histone methylation and small RNAs enhances host adaptation in a plant pathogen.

PMID 41505097 · PMC12781887 · Nucleic acids research · 2026 · 8 claims · 8 setups

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CRISPR/Cas9 editing of PsSu(z)12 abolishes H3K27me3 deposition at Avr1b and Avr3a, causing transcriptional reactivation and loss of avirulence

sojae soybean crispr homology-directed virulence
Transcriptome- and phenotype-based epistasis analysis in Caenorhabditis elegans reveals daf-16/FoxO-dependent and independent effects of daf-2/InsR in L1 starvation and recovery.

PMID 41528819 · PMC12958807 · G3 (Bethesda, Md.) · 2026 · 7 claims · 8 setups

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Differential gene expression caused by disruption of daf-2/InsR during L1 starvation is daf-16-dependent.

elegans bulk principal hierarchical
Variant-resolved prediction of context-specific isoform variation with a graph-based attention model.

PMID 41547351 · PMC13069856 · Cell genomics · 2026 · 8 claims · 8 setups

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Otari, an attention-based graph neural network trained on long-read transcriptomes across 30 tissues/brain regions, predicts tissue-specific differential isoform abundance

tissues genomic gtex hgmd long-read variant splice
Efficient recovery and DNA extraction for algae-associated microbial communities.

PMID 41560914 · PMC12813104 · Frontiers in plant science · 2025 · 8 claims · 7 setups

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A universal trade-off exists between the quantity and quality of DNA extracted from algal biofilm microbial communities.

macroalgae extracted microbial biofilm confocal concentration spectrophotometry
Humoral IgG1 responses to tumor antigens underpin clinical outcomes in immune checkpoint blockade.

PMID 41593194 · PMC13004670 · Nature medicine · 2026 · 8 claims · 5 setups

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PD-1 blockade induces tumor-specific IgG1+ plasma cell responses that complement cellular immunity and contribute to clinical benefit

tumor paired single-cell bulk multiplex
POSTN(+) fibroblast‑secreted small extracellular vesicles drive macrophage M2 polarization through BMP4/BMPR2/Smad signaling.

PMID 41645751 · PMC12891935 · Oncology reports · 2026 · 8 claims · 8 setups

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Integration of two HNSCC scRNA-seq datasets reveals two distinct fibroblast subtypes: POSTN- and POSTN+ fibroblasts

hnscc tcga-hnscc oscc oscc-derived single-cell bulk immunohistochemistry
Bridging unpaired single-cell multimodal data for integrative analyses with SuperMap.

PMID 41650244 · PMC12890892 · Proceedings of the National Academy of Sciences of the United States of America · 2026 · 8 claims · 7 setups

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SuperMap learns cross-modal feature mappings directly from unpaired multimodal data without requiring paired training data

pbmc bone skin embryos scrna-seq scnmt-seq asap-seq
Detection of large deletions in the LDL receptor gene with quantitative PCR methods.

PMID 15842735 · PMC1087844 · BMC medical genetics · 2005 · 7 claims · 3 setups

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MLPA was cheaper, more accurate and more precise than Real-Time PCR for detecting LDL receptor gene deletions

genomic real-time multiplex long-range
Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.

PMID 35248155 · PMC8898458 · Environmental microbiome · 2022 · 7 claims · 7 setups

Has reproduction · 83

MAGISTA, a random forest model built on alignment-free intra-bin distance-distribution statistics, can estimate MAG completeness and purity without relying on reference marker genes.

pooled hc227 contig sets shotgun novo alignment-free
The use of neuroproteomics in drug abuse research.

PMID 19926406 · PMC3947580 · Drug and alcohol dependence · 2010 · 8 claims · 8 setups

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Neuroproteomic technologies (2D-DIGE, iTRAQ, ICAT, etc.) enable identification of protein-level changes underlying effects of drugs of abuse such as amphetamine, morphine, cocaine, and alcohol.

rodent brain postmortem sectioned 2d-dige itraq heat
Preparation of mouse pancreatic tumor for single-cell RNA sequencing and analysis of the data.

PMID 34927097 · PMC8649395 · STAR protocols · 2021 · 6 claims · 7 setups

Has reproduction · 50

A combined mechanical and enzymatic dissociation protocol using the gentleMACS Dissociator yields a single-cell suspension from mouse pancreatic tumor tissue suitable for scRNA-seq while preserving cell characteristics

pancreatic dissociated single-cell scrna-seq tumor dead red
Variation resources at UC Santa Cruz.

PMID 17151077 · PMC1781230 · Nucleic acids research · 2007 · 8 claims · 8 setups

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The UCSC Genome Browser variation resources integrate polymorphism data from public collections (dbSNP, HapMap, Affymetrix, Perlegen, SeattleSNPs) into a common format with additional annotations and genomic context.

chimpanzee affymetrix hapmap perlegen snp fixed linkage
6th annual meeting of the Complex Trait Consortium.

PMID 17906895 · PMC2042027 · Mammalian genome : official journal of the International Mammalian Genome Society · 2007 · 8 claims · 7 setups

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The NIEHS Perlegen/resequencing project has generated over 8.5 million SNPs from 15 inbred mouse strains but shows a high false-negative discovery rate, with an estimated 45 million SNPs actually present.

inbred recombinant yeast gallstone genome affymetrix microarray
The chromosomal genome sequence of the sponge, Rhopaloeides odorabile Thompson, Murphy, Bergquist & Evans, 1987 (Dictyoceratida: Spongiidae) and its associated microbial metagenome sequences.

PMID 42232316 · PMC13224822 · Wellcome open research · 2026 · 8 claims · 8 setups

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A chromosome-level genome assembly was produced for the sponge Rhopaloeides odorabile using the Tree of Life pipeline

rhopaloeides odorabile-associated odorabile recovered pacbio hi-c sequencing

Experiments

A pan-cancer single cell landscape reveals heterogeneity and functional diversity of double-negative T cells.

Effector gene silencing coordinated by histone methylation and small RNAs enhances host adaptation in a plant pathogen.

Transcriptome- and phenotype-based epistasis analysis in Caenorhabditis elegans reveals daf-16/FoxO-dependent and independent effects of daf-2/InsR in L1 starvation and recovery.

Variant-resolved prediction of context-specific isoform variation with a graph-based attention model.

Efficient recovery and DNA extraction for algae-associated microbial communities.

Humoral IgG1 responses to tumor antigens underpin clinical outcomes in immune checkpoint blockade.

POSTN(+) fibroblast‑secreted small extracellular vesicles drive macrophage M2 polarization through BMP4/BMPR2/Smad signaling.

Bridging unpaired single-cell multimodal data for integrative analyses with SuperMap.

Detection of large deletions in the LDL receptor gene with quantitative PCR methods.

Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.

The use of neuroproteomics in drug abuse research.

Preparation of mouse pancreatic tumor for single-cell RNA sequencing and analysis of the data.

Variation resources at UC Santa Cruz.

6th annual meeting of the Complex Trait Consortium.

The chromosomal genome sequence of the sponge, Rhopaloeides odorabile Thompson, Murphy, Bergquist & Evans, 1987 (Dictyoceratida: Spongiidae) and its associated microbial metagenome sequences.