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).

• Expression of full-length p53 and its isoform Deltap53 in breast carcinomas in relation to mutation status and clinical parameters.

  PMID 17054774 · PMC1636663 · Molecular cancer · 2006 · 7 claims · 7 setups

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  The alternative splice isoform Δp53 mRNA is co-expressed with full-length p53 mRNA in breast tumors and cell lines

  breast universal p53 subset qrt-pcr bioinformatic structure

• F-SNP: computationally predicted functional SNPs for disease association studies.

  PMID 17986460 · PMC2238878 · Nucleic acids research · 2008 · 6 claims · 8 setups

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  F-SNP is a database integrating functional effect predictions for SNPs from 16 bioinformatics tools/databases across four categories: splicing, transcription, translation, and post-translation

  genome protein-coding genomic genome-wide non-synonymous exonic nonsense

• Identification of common genetic variation that modulates alternative splicing.

  PMID 17571926 · PMC1904363 · PLoS genetics · 2007 · 7 claims · 8 setups

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  Common SNPs located close to intron-exon boundaries are associated with and causally modulate alternative splicing patterns in human genes

  ceph lcls skipped additional rt-pcr snp resequencing

• Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs.

  PMID 18838389 · PMC2582632 · Nucleic acids research · 2008 · 7 claims · 8 setups

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  Although 86% of individual human exons are conserved in the mouse genome, only a small fraction (431/20392, ~2%) of human AS variants are perfectly conserved AS variants in mice.

  genome full-length ~3x10^7 isoform whole-genome full-length polysome

• PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data.

  PMID 24747190 · PMC4411361 · Genomics, proteomics & bioinformatics · 2014 · 8 claims · 3 setups

  Has reproduction · 90

  PrimerSeq is a user-friendly stand-alone software with a GUI for systematic design and visualization of RT-PCR primers for alternative splicing analysis using user-provided RNA-seq data.

  heart genome rna-seq rt-pcr

• Advances in the study of SR protein family.

  PMID 15626328 · PMC5172405 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 8 setups

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  SR proteins promote assembly of the early splicesome via protein-protein interactions in their RS-domain that recruit components of the splicing machinery.

  nuclear bovine drosophila caenorhabditis selex rna-binding splicing

• Accelerating rare disease diagnostics by linking DNA and RNA through an explainable and interactive RNA-guided workflow.

  PMID 41685349 · PMC12891912 · NAR genomics and bioinformatics · 2026 · 8 claims · 6 setups

  Has reproduction

  A streamlined RNA-guided workflow combining OUTRIDER, FRASER, Borzoi, and MOLGENIS VIP was developed to identify gene-disease associations by linking outlier gene expression/splicing to prioritized patient-level variants

  udn blood clinvar wgs wgs bulk rna-seq

• Does distance matter? Variations in alternative 3' splicing regulation.

  PMID 17704130 · PMC2018619 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  Alternative 3' splice sites can be distinguished from constitutive splice sites by a combination of sequence/conservation properties that vary depending on the distance between the splice sites.

  intronic human-mouse same comparative polypyrimidine branch

• Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

  PMID 17576681 · PMC1934990 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  Cryptic 5'ss are best predicted by computational algorithms that accommodate nucleotide dependencies (e.g., Markov model, maximum entropy, maximum dependence decomposition) rather than by weight-matrix models

  disease mammalian compiled literature minigene computational

• Expression quantitative trait loci in sheep liver and muscle contribute to variations in meat traits.

  PMID 33461502 · PMC7812657 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 5 setups

  Has reproduction · 90

  Gene expression, exon expression, and intron excision ratio (splicing) molecular phenotypes are significantly heritable in sheep liver and muscle

  liver sheep sequencing snp heritability

• Melusin gene (ITGB1BP2) nucleotide variations study in hypertensive and cardiopathic patients.

  PMID 20017903 · PMC2803168 · BMC medical genetics · 2009 · 6 claims · 5 setups

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  Only three nucleotide variations in ITGB1BP2 were found among 928 screened subjects, indicating a high degree of conservation of the gene in the populations analyzed

  genomic hela itgb1bp2 melusin direct minigene in-silico

• Functional redundancy of exon 12 of BRCA2 revealed by a comprehensive analysis of the c.6853A>G (p.I2285V) variant.

  PMID 19795481 · PMC3501199 · Human mutation · 2009 · 7 claims · 8 setups

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  BRCA2 c.6853A>G (p.I2285V) co-occurs in trans with the deleterious founder mutation c.5946delT, supporting classification as a neutral variant

  lymphocytes brca2 brca2-null ashkenazi rt-pcr splicing allelic

• Fully haplotyped genome assemblies of healthy individuals reveal variability in 5'ss strength and support by splicing regulatory proteins.

  PMID 40191587 · PMC11970367 · NAR genomics and bioinformatics · 2025 · 8 claims · 5 setups

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  44 individuals' fully haplotyped diploid genome assemblies (88 haplotypes) from the 1000 Genomes Project were used to comprehensively assess homozygous and heterozygous sequence variations around and within 5'ss

  healthy reconstructed same 5'ss long-read computational statistical

• CRESCENT, a comprehensive RNA-Seq expression, splicing, and coding/non-coding element network tool.

  PMID 41566196 · PMC12895761 · BMC bioinformatics · 2026 · 6 claims · 6 setups

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  CRESCENT is a Snakemake workflow performing fully automated, comprehensive RNA-Seq analysis integrating differential expression, differential alternative splicing (DAS), differential transcript usage (DTU), and GO enrichment

  arabidopsis bulk rna-seq-based rna-seq

• Prediction of Alzheimer's disease-specific phospholipase c gamma-1 SNV by deep learning-based approach for high-throughput screening.

  PMID 33397809 · PMC7826347 · Proceedings of the National Academy of Sciences of the United States of America · 2021 · 7 claims · 7 setups

  Has reproduction · 48

  An AD-specific frameshift insertion SNV in exon 27 of mouse PLCγ1 causes abnormal exon skipping (exons 26-30) during mRNA maturation in 5xFAD cortex

  cortex forebrain plcγ1 bulk rna-seq-based western

• Bioinformatics Analysis of the Characteristics and Correlation of m6A Methylation in Breast Cancer Progression.

  PMID 35655723 · PMC9148239 · Contrast media & molecular imaging · 2022 · 8 claims · 8 setups

  Has reproduction · 48

  Breast cancer samples can be classified into 4 m6A subtypes (quiescent, m6A methylation, protein-binding, mixed) based on Z-score median of Set1 (writer+reader) and Set2 (eraser) gene expression

  breast tcga-brca gse25066 bioinformatics survival alternative

• NET-prism enables RNA polymerase-dedicated transcriptional interrogation at nucleotide resolution.

  PMID 31156037 · PMC6693550 · RNA biology · 2019 · 8 claims · 7 setups

  Has reproduction · 67

  NET-prism, an adapted NET-seq protocol using immunoprecipitation of Pol II-associated factors, enables strand-specific, nucleotide-resolution interrogation of transcription dynamics for any Pol II-interacting protein.

  e14 mass western net-prism

• SMRT and Illumina RNA sequencing reveal novel insights into the heat stress response and crosstalk with leaf senescence in tall fescue.

  PMID 32746857 · PMC7397585 · BMC plant biology · 2020 · 8 claims · 7 setups

  Has reproduction · 30

  Combined PacBio SMRT and Illumina RNA sequencing generated a full-length reference transcriptome for tall fescue in the absence of a genome sequence.

  tall pooled nicotiana physiological illumina smrt

• APC mutation analysis by chemical cleavage of mismatch and a protein truncation assay in familial adenomatous polyposis.

  PMID 7524601 · PMC2033526 · British journal of cancer · 1994 · 7 claims · 8 setups

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  Chemical cleavage of mismatch (HOT) analysis combined with sequencing identified inactivating constitutional APC mutations in 9 of 10 (90%) linkage-confirmed FAP patients, far exceeding the ~30% detection rate reported in the literature.

  blood pcr pcr-amplified cdna chemical sequencing single-strand

• Genome informatics: taming the avalanche of genomic data.

  PMID 15642109 · PMC549058 · Genome biology · 2005 · 8 claims · 7 setups

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  Ultraconserved regions (>100 bp, 100% conserved among mammals) exist in the genome and their function remains unknown

  genes arabidopsis genome vertebrate comparative conservation whole-genome