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 19

System / cell line: genomics ✕ Assay: cancer ✕ Clear

Review of state Comprehensive Cancer Control plans for genomics content.

PMID 15888219 · PMC1327702 · Preventing chronic disease · 2005 · 8 claims · 2 setups

Full-text index only

18 of 30 state CCC plans analyzed contained genomics-related components, with wide variability in content

written ccc content semistructured
iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type-Specific Markers of Immune-Cell Infiltration.

PMID 37023414 · PMC10236149 · Cancer immunology research · 2023 · 8 claims · 8 setups

Has reproduction · 94

Malignant cells cluster by patient in scRNA-seq data while immune and stromal cells cluster by cell type, making malignant cells uniquely suited to carry patient-level inflamed/cold signal

nsclc coad brca tcga scrna-seq bulk rna-seq
CanCellCap: robust cancer cell capture across tissue types on single-cell RNA-seq data by multi-domain learning.

PMID 40739511 · PMC12312500 · BMC biology · 2025 · 8 claims · 7 setups

Has reproduction · 42

CanCellCap identifies cancer cells in scRNA-seq data across 13 tissue types, 23 cancer types, and 7 sequencing platforms with 0.977 average accuracy

cancer testing sequencing unseen scrna-seq spatial
Determination of complete chromosomal haplotypes by bulk DNA sequencing.

PMID 33957932 · PMC8101039 · Genome biology · 2021 · 8 claims · 8 setups

Has reproduction · 97

A hierarchical computational strategy that first builds high-confidence local haplotype blocks from long-range/linked-read linkage and then concatenates them into whole-chromosome haplotypes using Hi-C contacts

rpe-1 na12878 aneuploid linked-read hi-c bulk
Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.

PMID 18704501 · PMC2525844 · Human genetics · 2008 · 6 claims · 5 setups

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Next-generation (Roche/454) resequencing of 136 kb at 8q24 in 39 prostate cancer cases and 40 controls generated a comprehensive catalog of common SNPs (MAF>1%), including 442 novel SNPs

genomic commercial plco unrelated targeted long-range genotyping
Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line.

PMID 18535014 · PMC2464741 · Molecular biology and evolution · 2008 · 8 claims · 7 setups

Full-text index only

Repair genes are numerically less common than apoptosis genes in the genomes of multicellular organisms

yeast familial human-mouse comparative gene mutation
Human synthetic lethal inference as potential anti-cancer target gene detection.

PMID 20015360 · PMC2804737 · BMC systems biology · 2009 · 7 claims · 8 setups

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Targeting the synthetic lethal partner of a gene mutated in cancer selectively damages tumor cells while sparing healthy cells, offering a rationale for anti-cancer drug design

saccharomyces sapiens ihsln genes database phylogenetic gene
H-DBAS: human-transcriptome database for alternative splicing: update 2010.

PMID 19969536 · PMC2808982 · Nucleic acids research · 2010 · 8 claims · 4 setups

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RNA-Seq tags from the polysome fraction identify AS exons that are very likely used for protein synthesis

dld-1 rna-seq western real-time
Splicing bioinformatics to biology.

PMID 16732900 · PMC1779529 · Genome biology · 2006 · 8 claims · 8 setups

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Mutually exclusive selection of Dscam exon 6 variants is governed by base pairing between a conserved intronic docking site and selector sequences adjacent to each alternative exon.

dscam alternative heterologous expressing comparative dicodon reporter
Proteomics and genomics: perspectives on drug and target discovery.

PMID 18302945 · PMC2386992 · Current opinion in chemical biology · 2008 · 8 claims · 8 setups

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Protein kinases account for approximately 25% of research and development projects in biotechnology and pharma

proteins blood carbohydrate medicinal x-ray microarrays glycan
Orthogonal cytokine engineering enables novel synthetic effector states escaping canonical exhaustion in tumor-rejecting CD8(+) T cells.

PMID 37081150 · PMC10154250 · Nature immunology · 2023 · 8 claims · 7 setups

Has reproduction · 37

Orthogonal engineering with PD1d/IL-2v/IL-33 reprograms adoptively transferred CD8+ T cells into a novel synthetic effector state (C5/TSE) that deviates from canonical TOX+ exhaustion

cd8+ b16-ova ot1 mice scrna-seq flow secretion
Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing.

PMID 36681937 · PMC10025442 · Briefings in bioinformatics · 2023 · 8 claims · 8 setups

Has reproduction · 94

HiCAT is a hierarchical, marker-based cell-type identifier that uses gene set analysis (GSA) scoring with markers structured in a three-level taxonomy tree (major-type, minor-type, subset)

pbmc cord melanoma lung scrna-seq computational
The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.

PMID 17108355 · PMC1669709 · Nucleic acids research · 2007 · 8 claims · 4 setups

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ASAP II expands human alternative splicing data ~3-fold over the previous ASAP database, to ~89,078 distinct alternative splicing relationships in 11,717 genes

genome animal aligned est genome-wide comparative est
Evolutionary origins of human apoptosis and genome-stability gene networks.

PMID 18832373 · PMC2577361 · Nucleic acids research · 2008 · 8 claims · 8 setups

Full-text index only

The entanglement of DNA repair, chromosome stability and apoptosis gene networks appears with the caspase gene family and the antiapoptotic gene BCL2.

apoptosis fully same orthologous protein-protein comparative orthology
Gene Dosage Analysis on the Single-Cell Transcriptomes Linking Cotranslational Protein Targeting to Metastatic Triple-Negative Breast Cancer.

PMID 34577617 · PMC8472593 · Pharmaceuticals (Basel, Switzerland) · 2021 · 7 claims · 5 setups

Has reproduction · 53

A computational framework integrating independently measured CNV (DNA sequencing) and single-cell RNA-seq from the same patients identifies recurrent concordant copy number gain and gene upregulation (CNG-UP) events and functional modules at the single-cell level.

metastatic top breast tnbc single-cell functional mutational
DBTSS provides a tissue specific dynamic view of Transcription Start Sites.

PMID 19910371 · PMC2808897 · Nucleic acids research · 2010 · 8 claims · 8 setups

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DBTSS update adds ~330 million new TSS Seq tags from 31 different human/mouse cell types or culture conditions.

normal dld1 beas2b ramos tss comparative
TRED: a transcriptional regulatory element database, new entries and other development.

PMID 17202159 · PMC1899102 · Nucleic acids research · 2007 · 8 claims · 3 setups

Full-text index only

TRED collects mammalian cis- and trans-regulatory elements together with experimental evidence, mapped onto assembled genomes

cancer-related computational literature database
Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.

PMID 37124622 · PMC10131083 · Frontiers in genetics · 2023 · 8 claims · 8 setups

Has reproduction · 71

Two distinct RNA modification patterns exist among BCa samples with radically varying clinical outcomes and biological characteristics

meta-geo tcga-blca bca genomics unsupervised lasso weighted
Charting the map of life.

PMID 11171541 · PMC1242061 · Environmental health perspectives · 2001 · 8 claims · 8 setups

Full-text index only

Only 3-5% of the human genome, corresponding to 30,000-100,000 genes, is thought to be biologically functional

drosophila genome haemophilus domestic genetic map-based whole-genome

Experiments

Review of state Comprehensive Cancer Control plans for genomics content.

iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type-Specific Markers of Immune-Cell Infiltration.

CanCellCap: robust cancer cell capture across tissue types on single-cell RNA-seq data by multi-domain learning.

Determination of complete chromosomal haplotypes by bulk DNA sequencing.

Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.

Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line.

Human synthetic lethal inference as potential anti-cancer target gene detection.

H-DBAS: human-transcriptome database for alternative splicing: update 2010.

Splicing bioinformatics to biology.

Proteomics and genomics: perspectives on drug and target discovery.

Orthogonal cytokine engineering enables novel synthetic effector states escaping canonical exhaustion in tumor-rejecting CD8(+) T cells.

Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing.

The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.

Evolutionary origins of human apoptosis and genome-stability gene networks.

Gene Dosage Analysis on the Single-Cell Transcriptomes Linking Cotranslational Protein Targeting to Metastatic Triple-Negative Breast Cancer.

DBTSS provides a tissue specific dynamic view of Transcription Start Sites.

TRED: a transcriptional regulatory element database, new entries and other development.

Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.

Charting the map of life.