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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Genome-wide census and expression profiling of chicken neuropeptide and prohormone convertase genes.
PMID 20006904 · PMC2814002 · Neuropeptides · 2010 · 8 claims · 5 setups
Bioinformatic survey of chicken genome/EST/HTGS databases identifies previously unreported chicken neuropeptide genes
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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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AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond.
PMID 17135205 · PMC1781224 · Nucleic acids research · 2007 · 7 claims · 3 setups
AnimalQTLdb houses publicly available QTL data for multiple livestock species (pig, cattle, chicken) in one comparable database.
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Pseudofam: the pseudogene families database.
PMID 18957444 · PMC2686518 · Nucleic acids research · 2009 · 8 claims · 7 setups
Pseudofam is an online database of pseudogene families built by mapping pseudogenes to Pfam protein families, providing query tools, statistics, and sequence alignments
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Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.
PMID 18564434 · PMC2453528 · BMC genomics · 2008 · 8 claims · 6 setups
Jmjd6 has been misleadingly annotated as a transmembrane receptor for engulfment of apoptotic cells; recent evidence contradicts this transmembrane receptor function
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A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example.
PMID 16271148 · PMC1310624 · BMC genomics · 2005 · 8 claims · 5 setups
Integrating EST-based expression data with phylogenetic analysis is a valid new method for functionally annotating multigenic protein families
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Comparative genomics of vertebrate Fox cluster loci.
PMID 17062144 · PMC1634998 · BMC genomics · 2006 · 8 claims · 3 setups
Two additional human paralogous Fox cluster regions exist, on chromosomes 14 and 20, beyond the previously known chromosome 6 and 16 loci
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Comparative genomics of Lbx loci reveals conservation of identical Lbx ohnologs in bony vertebrates.
PMID 18541024 · PMC2446394 · BMC evolutionary biology · 2008 · 8 claims · 3 setups
Extant bony vertebrates (osteichthyans) retain only Lbx1- and Lbx2-type genes; no distinct Lbx3/Lbx4 proteins exist.
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Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties.
PMID 18673550 · PMC2533329 · BMC evolutionary biology · 2008 · 8 claims · 6 setups
The human TRIM family is split into two groups (group 1 and group 2) that differ in domain structure, genomic organization, and evolutionary properties.
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Has reproduction · 80
Structure of the intergenic spacers in chicken ribosomal DNA.
PMID 31655542 · PMC6815422 · Genetics, selection, evolution : GSE · 2019 · 7 claims · 6 setups
Long-read PacBio sequencing of a chicken NOR-containing BAC clone resolved three complete IGS sequences plus rRNA gene clusters that are otherwise missing from genome assemblies.
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Extreme conservation of noncoding DNA near HoxD complex of vertebrates.
PMID 15462684 · PMC524357 · BMC genomics · 2004 · 7 claims · 7 setups
Three blocks of extremely conserved non-coding DNA (CR1, CR2, CR3) exist within 7 kb upstream of the HoxD complex, 3' of Evx-2, conserved from fish to human.
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AgBase: a functional genomics resource for agriculture.
PMID 16961921 · PMC1618847 · BMC genomics · 2006 · 8 claims · 7 setups
AgBase is a curated, web-accessible database providing structural and functional (GO) annotation for agricultural genomes and their pathogens.
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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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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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Assessing the gene space in draft genomes.
PMID 19042974 · PMC2615622 · Nucleic acids research · 2009 · 6 claims · 7 setups
The proportion of mapped CEGs in a draft genome assembly is a useful metric for describing gene space completeness, complementing N50 and x-fold coverage.
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NEIBank: genomics and bioinformatics resources for vision research.
PMID 18648525 · PMC2480482 · Molecular vision · 2008 · 8 claims · 7 setups
NEIBank is an integrated genomics and bioinformatics resource for vision research, combining EST/cDNA clone data, SAGE expression data, and eye disease gene databases.