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).
-
Full-text index only
The DNA sequence and analysis of human chromosome 13.
PMID 15057823 · PMC2665288 · Nature · 2004 · 8 claims · 8 setups
95.5 Mb of finished sequence from chromosome 13 was completed, containing 633 genes and 296 pseudogenes.
-
Full-text index only
Improving the specificity of exon prediction using comparative genomics.
PMID 18831778 · PMC2559877 · BMC genomics · 2008 · 8 claims · 6 setups
A log-odds ratio scoring method based on codon conservation across human-mouse/human-dog alignments and adjacent-codon dependency can classify putative exons as coding vs non-coding.
-
Full-text index only
Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.
PMID 15774015 · PMC1084245 · BMC genomics · 2005 · 6 claims · 4 setups
Integrated phylogenetic foot printing and transcription factor binding site (TFBS) prediction identified a consensus putative STK11/LKB1 promoter region between nucleotides -1090 and -1472
-
Full-text index only
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.
PMID 16381831 · PMC1347497 · Nucleic acids research · 2006 · 6 claims · 6 setups
miRNAMap integrates known miRNA genes from miRBase, literature-curated validated targets, and computationally predicted miRNA genes and targets for human, mouse, rat and dog.
-
Full-text index only
DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes.
PMID 15608249 · PMC539965 · Nucleic acids research · 2005 · 5 claims · 8 setups
Comparative human-mouse genome analysis identifies conserved sequence tags (CSTs, >=70% identity over >=100bp) that frequently correspond to non-coding elements with putative regulatory or structural roles
-
Full-text index only
Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.
PMID 16646984 · PMC1557991 · Genome biology · 2006 · 8 claims · 4 setups
A six-frame genomic ORF translation used as an MS search database can detect novel peptides absent from standard protein databases, revealing incomplete genome annotation.
-
Full-text index only
miRGen 2.0: a database of microRNA genomic information and regulation.
PMID 19850714 · PMC2808909 · Nucleic acids research · 2010 · 7 claims · 6 setups
miRGen 2.0 is a database providing comprehensive information about the genomic position of human and mouse microRNA coding transcripts and their regulation by transcription factors
-
Full-text index only
Backseat drivers take the wheel.
PMID 18068625 · PMC2705833 · Cancer cell · 2007 · 8 claims · 8 setups
Systematic resequencing combined with functional validation can distinguish rare driver FLT3 mutations from passenger mutations in AML patients negative for known activating mutations
-
Full-text index only
Paired-end mapping reveals extensive structural variation in the human genome.
PMID 17901297 · PMC2674581 · Science (New York, N.Y.) · 2007 · 8 claims · 8 setups
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
-
Has reproduction · 84
Genome of the endangered Guatemalan Beaded Lizard, Heloderma charlesbogerti, reveals evolutionary relationships of squamates and declines in effective population sizes.
PMID 36226801 · PMC9713440 · G3 (Bethesda, Md.) · 2022 · 8 claims · 7 setups
The assembled draft genome of H. charlesbogerti totals 2.31 Gb, similar in size to related species
-
Full-text index only
Genome-wide diversity and selective pressure in the human rhinovirus.
PMID 17477878 · PMC1892812 · Virology journal · 2007 · 7 claims · 6 setups
Whole genome and subgenomic phylogenies of HRV are essentially identical at every locus, indicating consistent phylogenetic patterns across the genome.
-
Full-text index only
Genetic and biochemical studies in Argentinean patients with variegate porphyria.
PMID 18570668 · PMC2467414 · BMC medical genetics · 2008 · 8 claims · 6 setups
All 18 studied VP patients harbored PPOX gene mutations in heterozygous state
-
Has reproduction · 60
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
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.
-
Full-text index only
The vertebrate genome annotation (Vega) database.
PMID 18003653 · PMC2238886 · Nucleic acids research · 2008 · 8 claims · 8 setups
Vega is a database for viewing manual genome annotation of human, mouse and zebrafish genomic sequences produced at the Wellcome Trust Sanger Institute.
-
Has reproduction · 66
RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.
PMID 23145190 · PMC3493385 · PLoS neglected tropical diseases · 2012 · 8 claims · 8 setups
S. stercoralis possesses homologs of nearly all C. elegans dauer genes, but with significant differences in protein structure, developmental regulation, and gene family expansion.
-
Has reproduction · 69
A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly.
PMID 23496952 · PMC3655071 · BMC genomics · 2013 · 8 claims · 8 setups
Representative de novo transcriptome assemblies are generated with as few as ~20 million reads for single-tissue samples and ~30 million reads for whole animals at the mRNA-coverage level.