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).
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The repertoire of G protein-coupled receptors in the sea squirt Ciona intestinalis.
PMID 18452600 · PMC2396169 · BMC evolutionary biology · 2008 · 8 claims · 5 setups
169 gene products in the Ciona genome were identified as putative GPCRs
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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.
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U7 snRNAs: a computational survey.
PMID 18267300 · PMC5054213 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 6 setups
A computational (BLAST-based) survey identified bona fide U7 snRNA genes with characteristic upstream promoter elements (PSE) across most vertebrate genomes examined, plus numerous pseudogenes.
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The global landscape of sequence diversity.
PMID 17996061 · PMC2258180 · Genome biology · 2007 · 7 claims · 5 setups
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.
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Comparative analysis of plant genomes allows the definition of the "Phytolongins": a novel non-SNARE longin domain protein family.
PMID 19889231 · PMC2779197 · BMC genomics · 2009 · 8 claims · 6 setups
A novel, plant-specific family of longin-related proteins, the 'Phytolongins', was identified in land plant genomes.
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The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.
PMID 17712414 · PMC1942082 · PloS one · 2007 · 8 claims · 5 setups
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.
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Identifying related L1 retrotransposons by analyzing 3' transduced sequences.
PMID 12734010 · PMC156586 · Genome biology · 2003 · 8 claims · 6 setups
L1 elements with transduction-derived 3' sequence (L1-TDs) can be computationally identified using RepeatMasker/TSDfinder and grouped into families sharing a common progenitor via BLAST comparison of downstream sequences.
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The 'permeome' of the malaria parasite: an overview of the membrane transport proteins of Plasmodium falciparum.
PMID 15774027 · PMC1088945 · Genome biology · 2005 · 7 claims · 4 setups
P. falciparum encodes substantially more membrane transport proteins than originally annotated
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Has reproduction · 87
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
A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.
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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
A comparative genomics approach using hamster testis cDNA sequencing can identify genes not previously annotated in the human, mouse, rat and Fugu genomes
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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.
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Genome annotation of a 1.5 Mb region of human chromosome 6q23 encompassing a quantitative trait locus for fetal hemoglobin expression in adults.
PMID 15169551 · PMC441375 · BMC genomics · 2004 · 8 claims · 8 setups
A very large, previously uncharacterized gene, AHI1, containing WD40 and SH3 domains was discovered in the candidate interval
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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
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SysZNF: the C2H2 zinc finger gene database.
PMID 18974185 · PMC2686507 · Nucleic acids research · 2009 · 7 claims · 6 setups
SysZNF is a database that systematically catalogs C2H2-ZNF genes in human and mouse with physical location, gene models, expression probes, protein domains, homologs, and literature links
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Evidence of recombination in Hepatitis C Virus populations infecting a hemophiliac patient.
PMID 19922637 · PMC2784780 · Virology journal · 2009 · 7 claims · 6 setups
A new intragenotypic recombinant HCV strain (1b/1a), named H23, was detected in 1 of 10 hemophiliac patients studied
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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.