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).

• 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

• 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

• Rbfox2 controls autoregulation in RNA-binding protein networks.

  PMID 24637117 · PMC3967051 · Genes & development · 2014 · 8 claims · 8 setups

  Has reproduction · 48

  Rbfox2 cross-regulates AS-NMD events within RNA-binding protein genes to alter their expression, tuning autoregulatory splicing networks and placing Rbfox2 at a critical node of a multilayer regulatory network.

  v6.5 fhfox2 top introns iclip sequencing rt-pcr

• 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

• Automatic annotation of eukaryotic genes, pseudogenes and promoters.

  PMID 16925832 · PMC1810547 · Genome biology · 2006 · 8 claims · 6 setups

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  Fgenesh++ gene prediction pipeline identifies 91% of coding nucleotides with 90% specificity

  encode regions genes chromosome computational pseudogene promoter

• 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

• TassDB: a database of alternative tandem splice sites.

  PMID 17142241 · PMC1669710 · Nucleic acids research · 2007 · 7 claims · 3 setups

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  TassDB is a relational database storing GYNGYN donor and NAGNAG acceptor tandem splice sites across eight species

  homo computational nagnag est maximum snp

• Mutational analysis of steroidogenic factor 1 (NR5a1) in 24 boys with bilateral anorchia: a French collaborative study.

  PMID 17940071 · PMC2990861 · Human reproduction (Oxford, England) · 2007 · 8 claims · 7 setups

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  A novel heterozygous V355M missense mutation in SF1 was identified in one boy with micropenis and testicular regression syndrome (bilateral anorchia)

  peripheral tsa201 tm3 cho sanger transient mammalian

• 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

• 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

• Alternative splicing and bioinformatic analysis of human U12-type introns.

  PMID 17332017 · PMC1874599 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  The long, evolutionarily conserved polypyrimidine (Py) tract of the JNK2 U2-U12 hybrid intron provides the signal for default inclusion of the downstream alternative exon 6b in non-neuronal cells

  hela hek293 genome jnk2 rt-pcr minigene bioinformatic

• Mutations in JARID1C are associated with X-linked mental retardation, short stature and hyperreflexia.

  PMID 18697827 · PMC3711528 · Journal of medical genetics · 2008 · 8 claims · 8 setups

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  Four novel JARID1C mutations (p.A77T, p.V504M, p.E468GfsX2, p.R1481GfsX9) were identified in males with mental retardation across three screened cohorts.

  genomic family carrier jarid1c dhplc allele-specific restriction

• RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

  PMID 24324815 · PMC3855774 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 38

  A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed field-grown upland cotton root tissues (913 up-regulated, 617 down-regulated).

  gossypium uppermost root reads bulk leaf rt-qpcr

• Mutation analysis in primary immunodeficiency diseases: case studies.

  PMID 19841577 · PMC2774237 · Current opinion in allergy and clinical immunology · 2009 · 8 claims · 8 setups

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  Genomic DNA Sanger sequencing is the standard first-line approach for identifying PIDD-causing mutations but has limitations that can yield false-negative or false-positive results

  mother parents ebv-transformed nemo genomic flow northern