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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Coffee, caffeine-related genes, and Parkinson's disease: a case-control study.
PMID 18759349 · PMC4554698 · Movement disorders : official journal of the Movement Disorder Society · 2008 · 8 claims · 5 setups
Coffee drinking (ever/never or by cups/day) was not associated with PD susceptibility
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Has reproduction · 79
Contribution of retrotransposition to developmental disorders.
PMID 31604926 · PMC6789007 · Nature communications · 2019 · 7 claims · 8 setups
De novo retrotransposition events, though rare, can be diagnostic causes of severe developmental disorders
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Coverage of whole proteome by structural genomics observed through protein homology modeling database.
PMID 17146617 · PMC1769342 · Journal of structural and functional genomics · 2006 · 8 claims · 7 setups
FAMSBASE, a homology-modeling database of whole-genome ORFs, currently covers about 50% of predicted ORFs (368,724 of 734,193) across 276 genomes with modeled 3D structures.
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Widespread ultraconservation divergence in primates.
PMID 18492662 · PMC2464743 · Molecular biology and evolution · 2008 · 8 claims · 4 setups
The number of UCEs has decreased throughout primate evolution, from ~1,000 in ancestral primates to 635 in modern humans.
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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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Sequences of complete human cytomegalovirus genomes from infected cell cultures and clinical specimens.
PMID 19906940 · PMC2885759 · The Journal of general virology · 2010 · 8 claims · 5 setups
Both PCR sequencing and IGA sequencing (via de novo assembly guiding reference-dependent assembly plus PCR finishing) can successfully generate complete HCMV genome sequences from infected cell cultures and clinical specimens
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Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.
PMID 17982176 · PMC2238928 · Nucleic acids research · 2008 · 6 claims · 7 setups
Evola combines genome synteny-based computational ortholog detection with manual curation of phylogenetic trees by experts to yield more reliable orthologs than automated pairwise methods
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Patterns and rates of intron divergence between humans and chimpanzees.
PMID 17309804 · PMC1852421 · Genome biology · 2007 · 8 claims · 6 setups
Intron divergence (Ki) is strongly positively correlated with intron length
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A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.
PMID 19043541 · PMC2580819 · PLoS computational biology · 2008 · 8 claims · 5 setups
A general model-free methodological framework is proposed for reconstructing Contiguous Ancestral Regions (CARs) from conserved syntenies, generalizing prior computational and cytogenetic approaches
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The HuRef Browser: a web resource for individual human genomics.
PMID 19036787 · PMC2686481 · Nucleic acids research · 2009 · 7 claims · 6 setups
The HuRef Browser is a unified web application integrating assembly, annotation, and assembly-to-assembly comparison (ATAC) views for the diploid HuRef individual human genome.
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Genome-wide identification of human functional DNA using a neutral indel model.
PMID 16410828 · PMC1326222 · PLoS computational biology · 2006 · 8 claims · 8 setups
A neutral indel model predicting a geometric distribution of intergap segment (IGS) lengths fits human-mouse ancestral repeat (AR) alignment data excellently
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Stable patterns of gene expression regulating carbohydrate metabolism determined by geographic ancestry.
PMID 20016837 · PMC2790609 · PloS one · 2009 · 8 claims · 6 setups
151 'geo-ancestral genes' were identified that are both differentially expressed between AA and CAU subjects and contain SNPs distinguishing YRI (African) from CEU (European) HapMap populations
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Bases and spaces: resources on the web for accessing the draft human genome.
PMID 11178254 · PMC138875 · Genome biology · 2000 · 8 claims · 8 setups
By combining currently available genomic databases and mapping resources (GenBank/Entrez, UniGene, RH maps, BAC fingerprint maps, Ensembl, NIX), it is possible to devise strategies that fully exploit the fragmentary draft human genome sequence.
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Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.
PMID 15588320 · PMC544879 · BMC genomics · 2004 · 8 claims · 8 setups
The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation
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Genomes of Helicobacter pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island.
PMID 16872520 · PMC1553449 · BMC genomics · 2006 · 8 claims · 7 setups
Native Peruvian H. pylori strains comprise two lineages: predominant hp-Europe and ~20% hsp-Amerind (Amerindian ancestry, closer to Alaska strains)
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Dcode.org anthology of comparative genomic tools.
PMID 15980535 · PMC1160116 · Nucleic acids research · 2005 · 8 claims · 7 setups
The dcode.org suite (zPicture, Mulan, eShadow, rVista 2.0, multiTF, Creme 2.0, ECR Browser) provides integrated tools for comparative genomic analysis and non-coding regulatory element discovery.