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).

• 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

• 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

• In silico and in vivo splicing analysis of MLH1 and MSH2 missense mutations shows exon- and tissue-specific effects.

  PMID 16995940 · PMC1590028 · BMC genomics · 2006 · 8 claims · 6 setups

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  In silico ESE-prediction algorithms (ESEfinder, RescueESE, PESX) do not reliably predict actual in vivo splicing behavior of missense mutations

  hmlh1 same cos-7 hela ese splice minigene

• ChimerDB--a knowledgebase for fusion sequences.

  PMID 16381848 · PMC1347382 · Nucleic acids research · 2006 · 8 claims · 6 setups

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  ChimerDB integrates bioinformatics analysis of mRNA/EST sequences, manually collected literature data, and OMIM translocation data into a single fusion sequence knowledgebase

  genome candidate pubmed omim blat splice-site ecgene

• Prediction and assessment of splicing alterations: implications for clinical testing.

  PMID 18951448 · PMC2832470 · Human mutation · 2008 · 8 claims · 5 setups

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  Bioinformatic prediction alone is insufficient; in vitro analysis is needed to confirm or establish splicing aberrations for clinical variant classification

  brca1 lymphocytes mammalian large bioinformatic cycloheximide mini-gene

• Comprehensive splice-site analysis using comparative genomics.

  PMID 16914448 · PMC1557818 · Nucleic acids research · 2006 · 8 claims · 6 setups

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  Over half a million splice sites were collected from five species (H. sapiens, M. musculus, D. melanogaster, C. elegans, A. thaliana) and classified into four main subtypes: U2-type GT-AG and GC-AG, and U12-type GT-AG and AT-AC.

  refseq u2-type genes comparative information phylogenetic

• 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

• 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

• 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

• 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

• 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

• Evaluation of SCN8A as a candidate gene for autosomal dominant essential tremor.

  PMID 18718804 · PMC2877193 · Parkinsonism & related disorders · 2009 · 7 claims · 6 setups

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  Mutations in the coding sequence and splice sites of human SCN8A do not appear to be a common cause of autosomal dominant essential tremor in Caucasian patients.

  genomic neurologically ethnically scn8a heteroduplex pcr snp

• 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

• Database resources of the National Center for Biotechnology Information.

  PMID 17170002 · PMC1781113 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  NCBI maintains an integrated suite of database resources (Entrez, PubMed, RefSeq, dbSNP, BLAST, etc.) for molecular biology data retrieval and analysis

  genbank genomic eukaryotic completely sequence rapid est

• Computational comparison of two mouse draft genomes and the human golden path.

  PMID 12537546 · PMC151282 · Genome biology · 2003 · 8 claims · 7 setups

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  The Celera and public mouse genome assemblies differ in about 10% of the mouse genome, with complementary strengths (Celera higher base-pair accuracy and overall coverage; public assembly higher quality in some finished BAC regions and freely accessible)

  newly genome chromosome genomic blat blastn repeat

• Pairagon+N-SCAN_EST: a model-based gene annotation pipeline.

  PMID 16925839 · PMC1810554 · Genome biology · 2006 · 7 claims · 5 setups

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  Pairagon+N-SCAN_EST, using only native alignments, was as accurate as ENSEMBL and ExoGean in the EGASP mRNA/EST evidence assessment

  encode genome cdna-to-genome novo comparative

• Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans.

  PMID 18842128 · PMC2572040 · Biology direct · 2008 · 8 claims · 6 setups

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  The Turmoil-1 transposable element in C. elegans incorporated two unrelated protein-coding sequences into its inverted terminal repeats (ITRs)

  turmoil-1 rrm elegans predicted pairwise maximum genome-wide

• 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

• A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

  PMID 25202605 · PMC4103609 · Applications in plant sciences · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.

  compositae same species helianthus targeted genome genomic

• 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