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 21

System / cell line: lines ✕ Assay: effect ✕ Clear

Early feature extraction drives model performance in high-resolution chromatin accessibility prediction.

PMID 41526189 · PMC12951969 · Genome research · 2026 · 8 claims · 6 setups

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Early feature extraction (via ConvNeXt V2 blocks), rather than downstream architecture type, is the primary determinant of prediction accuracy in high-resolution chromatin accessibility prediction.

lines cancer sets gm12878 atac-seq peak input-shift
ROR1-PI3K/AKT signaling drives adaptive resistance to cell cycle blockade in TP53 mutated ovarian cancer.

PMID 41748546 · PMC13004963 · Cell death & disease · 2026 · 7 claims · 8 setups

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A shared PI3K/AKT-regulated signaling node governs drug adaptation across all long-term resistant (lt-res) ADA and PTX models

hgsoc kuramochi jhos2 parental long-term inducible overexpression
Differential recruitment of pre-mRNA splicing factors to alternatively spliced transcripts in vivo.

PMID 16231974 · PMC1262628 · PLoS biology · 2005 · 8 claims · 8 setups

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Distinct combinations of pre-mRNA splicing factors are recruited to sites of alternatively spliced transcripts in intact cells, providing the first in vivo evidence for differential splicing factor association.

cos-1 cos-7 tau10-1 rt-pcr quantitative rna-fish
CDKN2A and CDK4 mutation analysis in Italian melanoma-prone families: functional characterization of a novel CDKN2A germ line mutation.

PMID 11556834 · PMC2375081 · British journal of cancer · 2001 · 7 claims · 6 setups

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Germ line CDKN2A mutations were found in 5 of 15 (33.3%) Italian melanoma-prone families, including one novel mutation (P48T) and three known pathogenic mutations (R24P, G101W, N71S)

genomic radiolabelled tig-er u2os sscp protein-protein retroviral
Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.

PMID 33514540 · PMC7846174 · Science advances · 2021 · 8 claims · 8 setups

Has reproduction · 63

>700 tissue-specific transcriptomes generated from w1118 and 141 DGRP Drosophila lines, forming a circadian gene expression atlas

w1118 dgrp drosophila dgrp-796 bulk high uas-rnai
Expanding the vision of environmental health at UNC-CH.

PMID 15248304 · PMC1247395 · Environmental health perspectives · 2004 · 8 claims · 8 setups

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Human breast tumors arise from at least two distinct cell types, basal and luminal epithelial, with different clinical behavior

breast chinese carolina rodent microarray functional genetic
Accurate prediction of the functional significance of single nucleotide polymorphisms and mutations in the ABCA1 gene.

PMID 16429166 · PMC1342637 · PLoS genetics · 2005 · 8 claims · 5 setups

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PANTHER subPSEC scores correctly predicted the functional impact of >94% (16/17) of tested naturally occurring ABCA1 variants

abca1 stably subpsec cholesterol rt-pcr
Translation affects mRNA stability in a codon-dependent manner in human cells.

PMID 31012849 · PMC6529216 · eLife · 2019 · 8 claims · 6 setups

Has reproduction · 87

Translation affects mRNA stability in a codon-dependent manner in human cells

293t time-course orfome slam-seq
Parameter-efficient fine-tuning enables scalable transfer of regulatory sequence models to novel contexts.

PMID 41618434 · PMC12930932 · Genome biology · 2026 · 8 claims · 7 setups

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PEFT enables accurate transfer of Borzoi to new datasets while significantly reducing GPU memory and runtime compared to joint training or full fine-tuning

gtex encode wi-38 thp-1 bulk eqtl variant-flowfish
Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes.

PMID 37190091 · PMC10137100 · Cells · 2023 · 8 claims · 8 setups

Has reproduction · 54

Single-cell transcriptomic analysis of EPCAM+Lin- epithelial cells identified unique gene signatures/markers that distinguish ER+, HER2+, ER+HER2+, and TNBC molecular subtypes

breast epcam+cd45-cd8a-cd4-cd19-cd3e cancer identified single-cell differential crispr-cas9
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

PMID 15592405 · PMC2263125 · Nature · 2004 · 8 claims · 8 setups

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A genetic variation map of 2.8 million SNPs was constructed for chicken by comparing 3 domestic breeds to Red Jungle Fowl

domestic red same white partial comparative pcr
Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

PMID 25122667 · PMC4232532 · G3 (Bethesda, Md.) · 2014 · 8 claims · 8 setups

Has reproduction · 50

330,995 SNPs were identified in transcribed regions between B. rapa genotypes R500 and IMB211, at an average frequency of one SNP per 200 bases.

brassica r500 rapa genomic bulk reference-based snp
DHODH links mitochondrial bioenergetics, one-carbon metabolism, and DNA repair to sustain aggressive prostate adenocarcinoma.

PMID 41612476 · PMC12930642 · Cell communication and signaling : CCS · 2026 · 8 claims · 8 setups

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DHODH is markedly overexpressed in malignant prostate epithelial cells and abundant in tumors

tcga-prad gse141445 22rv1 bulk single-cell lentiviral
KLF5 controls subtype-independent highly interactive enhancers in pancreatic cancer to regulate cell survival.

PMID 41849608 · PMC12998525 · Science advances · 2026 · 8 claims · 8 setups

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KLF5 binds subtype-independent highly interactive enhancers in PDAC that interact with essential genes

classical aspc1 panel l3.6pl atac-seq h3k27ac h3k4me3-anchored
Identification of Cell Subpopulation-Specific Driver Genes Reveals Ideal Candidates for Renal Cell Carcinoma Immunotherapy.

PMID 42074110 · PMC13115843 · International journal of molecular sciences · 2026 · 8 claims · 8 setups

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25 immune-related candidate driver genes were identified from tumor, myeloid, and lymphoid cell gene regulatory networks (GRNs) using SCENIC and topological Q statistics.

kidney lymphoid rcc tcga-kirc single-cell scenic genome-wide
Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.

PMID 35012625 · PMC8743438 · Genome biology · 2022 · 8 claims · 9 setups

Has reproduction · 68

GENEVA (Gene Expression Variance Analysis) is a semi-automated framework that mines large-scale public RNA-seq datasets to identify conditions associated with a gene's expression variance

gtex genetic lncap heart rna-seq meta-analysis electronic
Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 In Vitro Infection.

PMID 35464437 · PMC9019466 · Frontiers in immunology · 2022 · 8 claims · 8 setups

Has reproduction · 90

Differential polyadenylation occurs in infected Calu-3 and Vero cells at a late time point (48 hpi)

vero calu-3 genes direct pcr poly
Cross-ancestry genome-wide association studies of liver function biomarkers uncover pleiotropic variants, systemic disease links and therapeutic targets.

PMID 41689074 · PMC13005531 · Genome medicine · 2026 · 8 claims · 8 setups

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5,507 lead signals (P<5x10^-9) were identified for seven LFQBs across ancestries, including 210 novel loci

hope biobank combined cross-ancestry gwas cross-ancestry functional-informed
Ensembl 2013.

PMID 23203987 · PMC3531136 · Nucleic acids research · 2013 · 8 claims · 8 setups

Has reproduction · 85

Ensembl (http://www.ensembl.org) provides genome information for sequenced chordate genomes, currently supporting 70 species with a focus on human, mouse, zebrafish and rat.

genome species supported variants evidence-based rna-seq chip-seq
Novel STAT1 alleles in otherwise healthy patients with mycobacterial disease.

PMID 16934001 · PMC1550284 · PLoS genetics · 2006 · 7 claims · 6 setups

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The E320Q, Q463H, and L706S STAT1 alleles are intrinsically deleterious for both IFNG/GAF-mediated and IFNA/ISGF3-mediated immunity when tested in STAT1-deficient transfected cells

ebv-transformed sv40-transformed nuclear stat1-deficient cdna western immunofluorescence

Experiments

Early feature extraction drives model performance in high-resolution chromatin accessibility prediction.

ROR1-PI3K/AKT signaling drives adaptive resistance to cell cycle blockade in TP53 mutated ovarian cancer.

Differential recruitment of pre-mRNA splicing factors to alternatively spliced transcripts in vivo.

CDKN2A and CDK4 mutation analysis in Italian melanoma-prone families: functional characterization of a novel CDKN2A germ line mutation.

Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.

Expanding the vision of environmental health at UNC-CH.

Accurate prediction of the functional significance of single nucleotide polymorphisms and mutations in the ABCA1 gene.

Translation affects mRNA stability in a codon-dependent manner in human cells.

Parameter-efficient fine-tuning enables scalable transfer of regulatory sequence models to novel contexts.

Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes.

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

DHODH links mitochondrial bioenergetics, one-carbon metabolism, and DNA repair to sustain aggressive prostate adenocarcinoma.

KLF5 controls subtype-independent highly interactive enhancers in pancreatic cancer to regulate cell survival.

Identification of Cell Subpopulation-Specific Driver Genes Reveals Ideal Candidates for Renal Cell Carcinoma Immunotherapy.

Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.

Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 In Vitro Infection.

Cross-ancestry genome-wide association studies of liver function biomarkers uncover pleiotropic variants, systemic disease links and therapeutic targets.

Ensembl 2013.

Novel STAT1 alleles in otherwise healthy patients with mycobacterial disease.