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 103

System / cell line: splice-site ✕ Clear

Computational analysis of splicing errors and mutations in human transcripts.

PMID 18194514 · PMC2234086 · BMC genomics · 2008 · 8 claims · 4 setups

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Retained introns are significantly shorter than constitutively spliced introns

refseq genes intron exon computational splice prediction
ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization.

PMID 16845044 · PMC1538898 · Nucleic acids research · 2006 · 8 claims · 2 setups

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The ASPIC algorithm, using an optimization procedure that minimizes splice site predictions and transcript isoforms from multiple EST-genome alignments, outperforms other similar AS-prediction tools in sensitivity and selectivity

hnrpr specified comparative algorithm
Deep transcriptomics reveals cell-specific isoforms of pan-neuronal genes.

PMID 40379625 · PMC12084633 · Nature communications · 2025 · 8 claims · 5 setups

Has reproduction · 84

Pan-neuronal genes (expressed in many/all neurons) harbor highly cell-specific splice variants/isoforms restricted to single or few neuron types.

elegans short-read whole-animal rt-pcr
GENCODE: producing a reference annotation for ENCODE.

PMID 16925838 · PMC1810553 · Genome biology · 2006 · 8 claims · 8 setups

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GENCODE annotation combines initial manual annotation by HAVANA, experimental validation, and refinement based on results to identify protein-coding genes in ENCODE regions

tissues encode rt-pcr comparative automated
Mutation analysis of SDHB and SDHC: novel germline mutations in sporadic head and neck paraganglioma and familial paraganglioma and/or pheochromocytoma.

PMID 16405730 · PMC1343542 · BMC medical genetics · 2006 · 8 claims · 4 setups

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Germline mutations of SDHB and SDHC play a minor role in sporadic head and neck paraganglioma

peripheral genomic ebv-transformed conformation pira-pcr rt-pcr
Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

PMID 17452356 · PMC1904267 · Nucleic acids research · 2007 · 8 claims · 7 setups

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PASE (Prediction of Alternative Signaling Exons) is a computational algorithm combining Markov splice-site models, a Bayesian classifier, species conservation, and Scansite motif scoring to identify novel alternative cassette exons involved in cell signaling.

elegans pooled pcr known semi-nested cloning initio
Designating eukaryotic orthology via processed transcription units.

PMID 18445630 · PMC2425467 · Nucleic acids research · 2008 · 8 claims · 5 setups

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Existing ortholog databases discard/ignore alternative splicing via all-against-all protein comparisons, causing ambiguous ortholog calls and misclassification of AS isoforms as in-paralogs

ortholog blat exon-intron blast-based
Mutation spectrum of homogentisic acid oxidase (HGD) in alkaptonuria.

PMID 19862842 · PMC2830005 · Human mutation · 2009 · 8 claims · 6 setups

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Mutations in HGD, which encodes homogentisate dioxygenase, cause AKU by blocking conversion of homogentisic acid to maleylacetoacetic acid in the tyrosine catabolic pathway

aku hgd recombinant hgd missense splice
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
The RYR2-encoded ryanodine receptor/calcium release channel in patients diagnosed previously with either catecholaminergic polymorphic ventricular tachycardia or genotype negative, exercise-induced long QT syndrome: a comprehensive open reading frame mutational analysis.

PMID 19926015 · PMC2880864 · Journal of the American College of Cardiology · 2009 · 8 claims · 6 setups

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Comprehensive open-reading-frame RYR2 mutational analysis reveals possible CPVT1 mutations located outside the three canonical hot-spot domains

genomic hair-root reference patients pcr screening multi-tissue
Mutational hot spot potential of a novel base pair mutation of the CSPG2 gene in a family with Wagner syndrome.

PMID 19901218 · PMC3514888 · Archives of ophthalmology (Chicago, Ill. : 1960) · 2009 · 8 claims · 4 setups

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No COL2A1 mutations were found, making ocular Stickler syndrome an unlikely diagnosis for this family

genomic family complete pcr clinical
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
Exome sequencing in 38 patients with intracranial aneurysms and subarachnoid hemorrhage.

PMID 32367296 · PMC7419486 · Journal of neurology · 2020 · 8 claims · 6 setups

Has reproduction · 78

Sequence variants in PCNT, RNF213 and THSD1 support a role as susceptibility factors for cerebrovascular disease (UIA/aSAH)

unrelated affected additional 75-patient exome sanger gene
p53 mutations, protein expression and cell proliferation in squamous cell carcinomas of the head and neck.

PMID 7710950 · PMC2033757 · British journal of cancer · 1995 · 6 claims · 4 setups

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There is a discrepancy between p53 immunoreactivity and p53 gene mutation status, with mutations found in similar proportions of immunopositive and immunonegative tumours.

formalin-fixed extracted p53-immunonegative scchn immunohistochemistry pcr-single sequencing
Loss or somatic mutations of hMSH2 occur in hereditary nonpolyposis colorectal cancers with hMSH2 germline mutations.

PMID 8613431 · PMC5921088 · Japanese journal of cancer research : Gann · 1996 · 5 claims · 4 setups

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hMSH2 germline mutations were detected in 5 of 36 Japanese HNPCC kindreds (14%)

peripheral tumor sscp somatic loss
The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

PMID 12361482 · PMC131051 · BMC genetics · 2002 · 8 claims · 7 setups

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The human TDH gene is located at chromosome 8p23-22, spans 10 kb, and has 8 exons that would be expected to encode a 369-residue ORF.

genomic predicted cdna tissues genomic sequence pcr
Pegasys: software for executing and integrating analyses of biological sequences.

PMID 15096276 · PMC406494 · BMC bioinformatics · 2004 · 8 claims · 7 setups

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Pegasys is a flexible, modular, customizable software system for executing and integrating heterogeneous biological sequence analysis tools

eukaryotic formatted genomic input initio sequence gene
Molecular analysis of X-linked chronic granulomatous disease in five unrelated Korean patients.

PMID 15082894 · PMC2822302 · Journal of Korean medical science · 2004 · 8 claims · 4 setups

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Five unrelated Korean X-linked CGD patients each carry a distinct CYBB gene mutation: c.1663insT, c.1111-1G>T, c.39_40insG, c.927delC, and c.434T>C

neutrophils genomic splice-site activated pcr-single sequencing
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
High frequency of the IVS2-2A>G DNA sequence variation in SLC26A5, encoding the cochlear motor protein prestin, precludes its involvement in hereditary hearing loss.

PMID 16086836 · PMC1190179 · BMC medical genetics · 2005 · 8 claims · 6 setups

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IVS2-2A>G allele frequency does not differ significantly between hearing-impaired cases and controls among Hispanics and Caucasians (p=0.45)

genomic mitochondrial slc26a5 pcr sequence splice

Experiments

Computational analysis of splicing errors and mutations in human transcripts.

ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization.

Deep transcriptomics reveals cell-specific isoforms of pan-neuronal genes.

GENCODE: producing a reference annotation for ENCODE.

Mutation analysis of SDHB and SDHC: novel germline mutations in sporadic head and neck paraganglioma and familial paraganglioma and/or pheochromocytoma.

Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

Designating eukaryotic orthology via processed transcription units.

Mutation spectrum of homogentisic acid oxidase (HGD) in alkaptonuria.

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

The RYR2-encoded ryanodine receptor/calcium release channel in patients diagnosed previously with either catecholaminergic polymorphic ventricular tachycardia or genotype negative, exercise-induced long QT syndrome: a comprehensive open reading frame mutational analysis.

Mutational hot spot potential of a novel base pair mutation of the CSPG2 gene in a family with Wagner syndrome.

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

Exome sequencing in 38 patients with intracranial aneurysms and subarachnoid hemorrhage.

p53 mutations, protein expression and cell proliferation in squamous cell carcinomas of the head and neck.

Loss or somatic mutations of hMSH2 occur in hereditary nonpolyposis colorectal cancers with hMSH2 germline mutations.

The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

Pegasys: software for executing and integrating analyses of biological sequences.

Molecular analysis of X-linked chronic granulomatous disease in five unrelated Korean patients.

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

High frequency of the IVS2-2A>G DNA sequence variation in SLC26A5, encoding the cochlear motor protein prestin, precludes its involvement in hereditary hearing loss.