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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Insights into the coupling of duplication events and macroevolution from an age profile of animal transmembrane gene families.
PMID 16895434 · PMC1534073 · PLoS computational biology · 2006 · 8 claims · 7 setups
The density of transmembrane gene duplicates positively correlates with the estimated maximum number of cell types of common ancestors
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GPCR genes are preferentially retained after whole genome duplication.
PMID 18382678 · PMC2270905 · PloS one · 2008 · 8 claims · 6 setups
WGD-derived nGPCR duplicates in Tetraodon nigroviridis are retained at a significantly higher rate (23.5%) than the genome-wide average (15%)
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Web-based resources for comparative genomics.
PMID 16197736 · PMC3525128 · Human genomics · 2005 · 8 claims · 8 setups
Comparative genomics is an indispensable tool for identifying functional genome elements and exploring evolutionary genome dynamics
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Evaluation of models to predict BRCA germline mutations.
PMID 17016486 · PMC2360540 · British journal of cancer · 2006 · 7 claims · 7 setups
Four commonly used BRCA risk prediction models (BRCAPRO, Manchester, Penn, Myriad-Frank) have only modest ability to rule in or rule out BRCA1/2 germline mutation carrier status at a 10% probability threshold.
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Analysis of recent segmental duplications in the bovine genome.
PMID 19951423 · PMC2796684 · BMC genomics · 2009 · 8 claims · 6 setups
Recently duplicated sequence (≥1 kb, ≥90% identity) comprises 3.11% (94.4 Mb) of the bovine genome assembly (Btau_4.0)
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TreeFam: a curated database of phylogenetic trees of animal gene families.
PMID 16381935 · PMC1347480 · Nucleic acids research · 2006 · 7 claims · 6 setups
Tree-based inference of orthologs and paralogs is more robust than BLAST-based methods because evolutionary rates (and thus pairwise BLAST scores) vary across gene family members
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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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Insights into vertebrate evolution from the chicken genome sequence.
PMID 15693954 · PMC551526 · Genome biology · 2005 · 8 claims · 6 setups
Chicken has expanded gene families involved in egg production (e.g., avidin) and feather/scale/claw formation (avian-specific keratins) not present or lost in mammals
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Enlarged parietal foramina caused by mutations in the homeobox genes ALX4 and MSX2: from genotype to phenotype.
PMID 16319823 · PMC1477589 · European journal of human genetics : EJHG · 2006 · 7 claims · 8 setups
ALX4 and MSX2 mutations contribute approximately equally to PFM/CB and cause skull defects that are usually clinically indistinguishable
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Current status and the future for the genetics of type I diabetes.
PMID 19956094 · PMC2805458 · Genes and immunity · 2009 · 8 claims · 7 setups
A T1DGC genome-wide association meta-analysis of >7500 cases and >9000 controls identified 42 distinct genomic locations associated with T1D at P<10^-6.
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The meso-genomic era.
PMID 11516332 · PMC139414 · Genome biology · 2001 · 8 claims · 8 setups
Linkage disequilibrium (LD) between SNPs extends much further in Northern European populations (~120 kb) than in a Nigerian population (<10 kb), reflecting differing population histories (bottlenecks vs. constant expansion).
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The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.
PMID 38245722 · PMC10800049 · BMC genomics · 2024 · 8 claims · 8 setups
44 venom peptide genes were identified, distributed across four of the eleven chromosomes and organized in tandem repeat clusters.
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Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss).
PMID 15836796 · PMC1090573 · BMC genomics · 2005 · 8 claims · 7 setups
89 polymorphic microsatellite markers were developed from rainbow trout EST-derived cDNA clones
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Evolution and functional divergence of NLRP genes in mammalian reproductive systems.
PMID 19682372 · PMC2735741 · BMC evolutionary biology · 2009 · 7 claims · 7 setups
Major NLRP genes duplicated before the divergence of mammals, with lineage-specific duplications in primates (NLRP7, NLRP11) and rodents (Nlrp1, Nlrp4, Nlrp9)
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Comparative genomics and understanding of microbial biology.
PMID 10998382 · PMC2627966 · Emerging infectious diseases · 2000 · 8 claims · 7 setups
GC content varies widely among prokaryotic genomes (29% in B. burgdorferi to 68% in M. tuberculosis) and shapes codon usage and amino acid composition.