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).

• SVC: structured visualization of evolutionary sequence conservation.

  PMID 15991338 · PMC1160265 · Nucleic acids research · 2005 · 7 claims · 5 setups

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  SVC aligns protein-coding sequences of orthologous gene pairs and maps them back onto their encoding exons/introns to generate a scaffold of conserved gene structure.

  orthologous exonic tblastx blastn sliding-window

• 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

• 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

• ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.

  PMID 16381947 · PMC1347478 · Nucleic acids research · 2006 · 7 claims · 6 setups

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  ABS is a public database of experimentally identified TF binding sites conserved in orthologous vertebrate gene promoters, manually curated from the literature.

  orthologous literature sequence pairwise

• The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.

  PMID 15608292 · PMC540057 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  Built a library of 1134 HMM models (359 matrix-derived, 718 factor-derived, 57 JASPAR-derived), corresponding to 863 distinct TF names, from TRANSFAC and JASPAR binding site data

  genome drosophila transfac b99 profile sequence case-study

• A high throughput method for genome-wide analysis of retroviral integration.

  PMID 17028098 · PMC1636494 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  VITA uses MmeI to cleave DNA at a fixed distance from its recognition site, generating 21-22 bp genomic tags that serve as signatures of lentiviral integration sites.

  hela ht3 genome chromosomes isf vita sanger

• Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues.

  PMID 37995291 · PMC10697738 · Bioinformatics (Oxford, England) · 2023 · 7 claims · 6 setups

  Has reproduction · 79

  CLSM6A, a CNN-based model set, predicts single-nucleotide-resolution m6A RNA modification sites across eight cell lines and three tissues in H. sapiens

  clsm6a learned last-layer computational model-based propagation-based

• The HIV positive selection mutation database.

  PMID 17108357 · PMC1669717 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  The database provides codon-level Ka/Ks selection pressure maps for HIV protease and the first 381 codons of RT, built from a novel ~50,000-sample clinical dataset.

  hiv-1 stanford codon-specific selection conditional

• Distribution and effects of nonsense polymorphisms in human genes.

  PMID 18852891 · PMC2561068 · PloS one · 2008 · 8 claims · 8 setups

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  Nonsense SNPs occur at a lower density than nonsynonymous SNPs, indicating stronger purifying selection against premature stop codons than amino acid changes.

  genome genes nonsense snps genome-wide snp codon

• The relationship of potential G-quadruplex sequences in cis-upstream regions of the human genome to SP1-binding elements.

  PMID 18353860 · PMC2377421 · Nucleic acids research · 2008 · 7 claims · 1 setups

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  A large number of upstream PQSSs incorporate the SP1-binding element, establishing a clear link between PQSS occurrence and SP1 elements

  genome genome-wide

• 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

• Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes.

  PMID 17447839 · PMC1853124 · PLoS computational biology · 2007 · 8 claims · 8 setups

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  A new algorithm using spliced ESTs (cross-validated against Known Genes and GenBank mRNA) comprehensively maps bidirectional promoters in the human genome

  genome transcripts tissues proteins comparative taf250 cpg

• Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.

  PMID 19906729 · PMC2808989 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  Patrocles is a database compiling DSPs predicted to perturb miRNA-mediated gene regulation across seven vertebrate species, covering targets, miRNA precursors and silencing machinery.

  3'-utr mirbase hapmap comparative snp mirna

• Diet and DNA.

  PMID 15174456 · PMC1315985 · Environmental health perspectives · 2004 · 8 claims · 8 setups

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  The tombusvirus CIRV p19 protein selectively binds short (21-22 nt) silencing siRNAs, using tryptophan residues Trp39 and Trp42 as molecular 'calipers' that stack with the ends of the siRNA duplex

  cirv blood rice smokers x-ray site-directed mass

• 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

• Human SNPs resulting in premature stop codons and protein truncation.

  PMID 16595072 · PMC3500177 · Human genomics · 2006 · 8 claims · 6 setups

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  Genome-wide screening of dbSNP identified 28 validated X-SNPs from 28 genes with known minor allele frequencies.

  genome transcripts validated x-snp-encoded database blast exon-intron

• Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.

  PMID 18989394 · PMC2566816 · PLoS computational biology · 2008 · 7 claims · 4 setups

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  A novel Bayesian method, RASER, can detect site-specific evolutionary rate shifts and the lineages in which they occurred without pre-specifying candidate lineages.

  hiv-1 simulated bayesian simulation structural

• Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

  PMID 19906316 · PMC2784480 · BMC genomics · 2009 · 8 claims · 7 setups

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  Intronic single-block ESTs with poly(A/T) tails reveal previously unidentified novel transcript variants missed by existing databases.

  genome poly est cdna est blast cdna

• Genome-wide census and expression profiling of chicken neuropeptide and prohormone convertase genes.

  PMID 20006904 · PMC2814002 · Neuropeptides · 2010 · 8 claims · 5 setups

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  Bioinformatic survey of chicken genome/EST/HTGS databases identifies previously unreported chicken neuropeptide genes

  chicken blast microarray est