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).

• Genomic regions and candidate genes selected during the breeding of rice in Vietnam.

  PMID 35899250 · PMC9309459 · Evolutionary applications · 2022 · 8 claims · 7 setups

  Has reproduction · 75

  XP-CLR and FST scans identify genomic regions with distorted allele frequency/differentiation patterns resulting from differential selective pressures between Vietnamese rice subpopulations

  vietnamese indica subpopulation whole-genome whole-genome xp-clr fst

• In silico comparative genomic analysis of GABAA receptor transcriptional regulation.

  PMID 17603907 · PMC1934366 · BMC genomics · 2007 · 8 claims · 8 setups

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  Previously unreported putative promoters were identified for the β2, γ1, γ3, ε, θ and π GABA A receptor subunit genes

  subunit mammalian α1-β2-γ2-α6 cross-species promoter transcription

• Backseat drivers take the wheel.

  PMID 18068625 · PMC2705833 · Cancer cell · 2007 · 8 claims · 8 setups

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  Systematic resequencing combined with functional validation can distinguish rare driver FLT3 mutations from passenger mutations in AML patients negative for known activating mutations

  pretreatment baf3 additional normal targeted baf3 immunoprecipitation

• The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site.

  PMID 18367472 · PMC2377430 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  1226 eight-letter DNA words show statistically significant positional preferences relative to the TSS across 7914 human promoter regions

  putative nonredundant homo genes computational pssm semantic

• SNP@Promoter: a database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions.

  PMID 18315851 · PMC2259403 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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  SNP@Promoter is a database of human SNPs within putative promoter regions and predicted transcription factor binding sites

  genome predicted target computational snp evolutionary

• Dissecting microregulation of a master regulatory network.

  PMID 18294391 · PMC2289817 · BMC genomics · 2008 · 8 claims · 6 setups

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  143 human miRNAs (termed p53-miRs) each contain at least one putative p53 binding site within 10 kb flanking sequence and are predicted to target at least one known gene

  genome mirnas mirna-target predicted p53 mirna cross-referencing

• TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes.

  PMID 34197621 · PMC8464036 · Nucleic acids research · 2021 · 8 claims · 8 setups

  Has reproduction · 60

  TRAPID 2.0 is a web application performing global characterization of de novo transcriptomes via structural, functional, and taxonomic annotation in an initial processing phase, followed by an exploratory phase of downstream analyses.

  mmetsp query putative ciliate taxonomic similarity non-coding

• Paired-end mapping reveals extensive structural variation in the human genome.

  PMID 17901297 · PMC2674581 · Science (New York, N.Y.) · 2007 · 8 claims · 8 setups

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  Paired-end mapping (PEM) combining 3-kb fragment paired-end capture, massive 454 sequencing, and computational mapping detects SVs ~3 kb or larger with an average breakpoint resolution of 644 bp

  genomic na15510 stretched reference paired-end pcr array

• Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs.

  PMID 12783626 · PMC161800 · BMC genomics · 2003 · 8 claims · 5 setups

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  A comparative genomics approach using hamster testis cDNA sequencing can identify genes not previously annotated in the human, mouse, rat and Fugu genomes

  hamster testis predicted cdna northern comparative

• The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.

  PMID 17712414 · PMC1942082 · PloS one · 2007 · 8 claims · 5 setups

  Full-text index only

  P-POD is the first comparative genomics database to combine results from multiple computational ortholog/homolog prediction methods with manually curated literature-derived experimental evidence of functional conservation.

  sequences orthomcl yeast orthomcl jaccard phylogenetic

• Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications.

  PMID 24982883 · PMC4055022 · BioMed research international · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  Illumina RNA-Seq with Trinity de novo assembly produced a C. sinicus transcriptome of 69,751 contigs (average 928.8 bp, N50 1,127 bp) from 58.9 million reads.

  calanus sinicus genomic rna-seq novo sequence

• The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.

  PMID 15608288 · PMC540018 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  The TIGR Gene Indices (TGI) are a collection of 77 species-specific databases that cluster and assemble EST and known gene sequences into tentative consensus (TC) sequences to identify and characterize expressed transcripts.

  est clustered sequences sequence est sequence orf

• The vertebrate genome annotation (Vega) database.

  PMID 18003653 · PMC2238886 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  Vega is a database for viewing manual genome annotation of human, mouse and zebrafish genomic sequences produced at the Wellcome Trust Sanger Institute.

  genome zebrafish pig nod manual comparative transcript

• Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing.

  PMID 23979935 · PMC3789805 · G3 (Bethesda, Md.) · 2013 · 8 claims · 8 setups

  Has reproduction · 91

  An index of 23,859,893 (~24 million) homoeo-SNPs distinguishing A-genome from D-genome cotton was constructed at a density of one SNP per 32.3 bases of the D5 reference.

  gossypium longicalyx nine diploids whole-genome wgs read

• ARED 3.0: the large and diverse AU-rich transcriptome.

  PMID 16381826 · PMC1347415 · Nucleic acids research · 2006 · 7 claims · 6 setups

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  ARED 3.0 computationally mapped more than 4000 ARE-mRNAs to the human genome, representing 5-8% of human genes.

  records est est-derived combined computational est sequence

• The global landscape of sequence diversity.

  PMID 17996061 · PMC2258180 · Genome biology · 2007 · 7 claims · 5 setups

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  Eukaryotic sequence datasets show substantially greater genetic diversity (higher sequence/gene family discovery rates) than bacterial datasets, likely related to differences in modes of genetic inheritance.

  fully eukaryotic complete gene blast-based est gene

• Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation.

  PMID 17608949 · PMC1934372 · BMC genomics · 2007 · 7 claims · 5 setups

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  Developed a statistical model-fitting method to infer generalized (multi-allelic, copy-number-aware) genotypes from raw SNP microarray data

  individuals mother-father-child transcribed snp quantitative multiplex

• Starvation-induced transgenerational inheritance of small RNAs in C. elegans.

  PMID 25018105 · PMC4377509 · Cell · 2014 · 8 claims · 7 setups

  Has reproduction · 64

  L1 starvation induces changes in endogenous 22G small RNAs (STGs) that are inherited for at least three generations in fed descendants.

  elegans small small sequencing lifespan