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 15

System / cell line: donor ✕ Assay: cdna ✕ Clear

Accurate splice site prediction using support vector machines.

PMID 18269701 · PMC2230508 · BMC bioinformatics · 2007 · 8 claims · 5 setups

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Weighted degree (WD) kernel SVMs outperform Markov Chains, GeneSplicer and SpliceMachine for genome-wide splice site recognition

nn269 dgsplicer caenorhabditis arabidopsis svm genome-wide
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
Lost in the world of functional genomics, systems biology, and translational research: is there life after the Milstein award?

PMID 17681845 · PMC1994668 · Cytokine & growth factor reviews · 2007 · 8 claims · 8 setups

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Genomic and proteomic approaches provide a comprehensive view of virus-host interactions and advance understanding of innate immunity and interferon/cytokine signaling

cd4+ hela influenza-infected liver cdna microarray mass
Genome-wide survey of allele-specific splicing in humans.

PMID 18518984 · PMC2427040 · BMC genomics · 2008 · 8 claims · 5 setups

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A genome-wide computational scan identified 30,977 SNPs located within predicted splicing regulatory sequences (donor sites, acceptor sites, branch points, and ESEs)

genome cdna hapmap computational est exon
Defective splicing, disease and therapy: searching for master checkpoints in exon definition.

PMID 16855287 · PMC1524908 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Splicing-affecting genomic variations can account for up to 50% of mutations leading to gene dysfunction in some genes

random trans-acting tpo fibronectin minigene selex cdna
Identification of a novel splice-site mutation in the Lebercilin (LCA5) gene causing Leber congenital amaurosis.

PMID 18334959 · PMC2268850 · Molecular vision · 2008 · 7 claims · 5 setups

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A homozygous c.955G>A mutation at the last base of exon 6 of LCA5 disrupts the normal splice donor site.

genomic lca5 lymphocyte affected snp sanger splice
Mice and more.

PMID 14519193 · PMC328447 · Genome biology · 2003 · 8 claims · 7 setups

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A multispecies weighted conservation score, which accounts for each species' divergence rate, can identify conserved non-coding sequences (multispecies conserved sequences, MCSs) likely to be biologically significant

cftr ciona embryonic chromosome comparative genome bac-based
Spectrum and characterisation of BRCA1 and BRCA2 deleterious mutations in high-risk Czech patients with breast and/or ovarian cancer.

PMID 18489799 · PMC2413254 · BMC cancer · 2008 · 8 claims · 6 setups

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Pathogenic BRCA1/BRCA2 mutations were identified in 294 of 1,010 (29.1%) unrelated high-risk Czech probands

genomic pcr-amplified brca1 pha-stimulated truncation heteroduplex direct
Bladder tumour-derived somatic TSC1 missense mutations cause loss of function via distinct mechanisms.

PMID 18397877 · PMC2427143 · Human molecular genetics · 2008 · 8 claims · 8 setups

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All six somatic TSC1 missense mutations found in bladder tumours cause loss of TSC1 function, but via distinct molecular mechanisms.

hcv29 lines tsc1 bladder immunoblotting real-time co-immunoprecipitation
Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).

PMID 26248502 · PMC4528194 · Scientific reports · 2015 · 8 claims · 8 setups

Has reproduction · 70

AS events, including differentially-expressed-transcript-containing genes (DETs), are ubiquitous in head-kidney and spleen transcriptomes of C. idella

head-kidney idella assembled il-12p40α rna-seq rt-qpcr pcr
Modification of the Creator recombination system for proteomics applications--improved expression by addition of splice sites.

PMID 16519801 · PMC1421398 · BMC biotechnology · 2006 · 8 claims · 8 setups

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The Creator Splice system (5' intron splicing) significantly increases protein expression levels compared to the standard Creator system

hek293t mammalian coli vector immunoblot fluorescence bacterial
The impact of new research technologies on our understanding of environmental causes of disease: the concept of clinical vulnerability.

PMID 19948053 · PMC2793242 · Environmental health : a global access science source · 2009 · 8 claims · 8 setups

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GWAS-identified genetic variants confer only modest relative risks (1.15-1.5), comparable in magnitude to weak/contested environmental exposures

polish cohort nonsmokers low genome-wide biomarker epidemiological
ECgene: an alternative splicing database update.

PMID 17132829 · PMC1716719 · Nucleic acids research · 2007 · 8 claims · 5 setups

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ECgene provides functional annotation (domain, GO, expression pattern) for alternatively spliced genes

nine genome sage cdna genome-based chi-squared sage
CD70 (TNFSF7) is expressed at high prevalence in renal cell carcinomas and is rapidly internalised on antibody binding.

PMID 16892042 · PMC2360640 · British journal of cancer · 2006 · 6 claims · 6 setups

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CD70 was identified by proteomic analysis of plasma membrane preparations as highly expressed in A498 and SW839 RCC-derived cell lines

a498 frozen normal proteomics flow immunohistochemistry
RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence.

PMID 24643046 · PMC3958415 · PloS one · 2014 · 8 claims · 8 setups

Has reproduction · 41

Infection of PAMs with either LV or Lena affects signaling pathways directly linked to the innate immune response, including IRF activation, RIG1-like receptors, TLRs and PKR pathways.

pulmonary prrsv-infected lena-infected 3-week-old rna-seq immunoperoxidase quantitative

Experiments

Accurate splice site prediction using support vector machines.

Computational analysis of splicing errors and mutations in human transcripts.

Lost in the world of functional genomics, systems biology, and translational research: is there life after the Milstein award?

Genome-wide survey of allele-specific splicing in humans.

Defective splicing, disease and therapy: searching for master checkpoints in exon definition.

Identification of a novel splice-site mutation in the Lebercilin (LCA5) gene causing Leber congenital amaurosis.

Mice and more.

Spectrum and characterisation of BRCA1 and BRCA2 deleterious mutations in high-risk Czech patients with breast and/or ovarian cancer.

Bladder tumour-derived somatic TSC1 missense mutations cause loss of function via distinct mechanisms.

Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).

Modification of the Creator recombination system for proteomics applications--improved expression by addition of splice sites.

The impact of new research technologies on our understanding of environmental causes of disease: the concept of clinical vulnerability.

ECgene: an alternative splicing database update.

CD70 (TNFSF7) is expressed at high prevalence in renal cell carcinomas and is rapidly internalised on antibody binding.

RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence.