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).

Publications 1.3k Datasets 392.5k Experiments 15

System / cell line: comparative ✕ Assay: pseudogene ✕ Clear

Gene losses during human origins.

PMID 16464126 · PMC1361800 · PLoS biology · 2006 · 7 claims · 7 setups

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A comparative genomic screen identified 67 new human-specific nonprocessed pseudogenes, bringing the total (with 13 from prior literature) to 80 human-specific pseudogenes.

pseudogene chimpanzee human-specific population comparative phylogenetic fisher's
Better smelling through genetics: mammalian odor perception.

PMID 18938244 · PMC2590501 · Current opinion in neurobiology · 2008 · 8 claims · 8 setups

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Odorant receptor (OR) gene repertoire size and pseudogene fraction vary dramatically across mammalian species

mammals subjects v1r trpc2 comparative genetic targeted
Gene duplication: the genomic trade in spare parts.

PMID 15252449 · PMC449868 · PLoS biology · 2004 · 8 claims · 7 setups

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Gene duplication relaxes selective constraint on one copy, allowing exploration of evolutionary space that is otherwise forbidden in single-copy genes, making duplication the major opportunity for new gene function evolution.

great genome recently yeast genome-wide molecular comparative
Comparative genomics search for losses of long-established genes on the human lineage.

PMID 18085818 · PMC2134963 · PLoS computational biology · 2007 · 8 claims · 6 setups

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A novel comparative genomics method (TransMap-based syntenic mapping of gene structures between human, mouse, and dog) can detect losses of well-established single-copy genes without relying on sequence homology to a parental gene, distinguishing them from typical duplication- or retrotransposition-derived pseudogenes.

dog genome chimp gorilla comparative overlap visual
Evolution of the NANOG pseudogene family in the human and chimpanzee genomes.

PMID 16469101 · PMC1457002 · BMC evolutionary biology · 2006 · 7 claims · 5 setups

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The NANOG gene and all pseudogenes except NANOGP8 occupy orthologous chromosomal positions in the chimpanzee genome, indicating they originated before the human-chimpanzee divergence.

chimpanzee megablast pcr flanking-sequence
Automatic annotation of eukaryotic genes, pseudogenes and promoters.

PMID 16925832 · PMC1810547 · Genome biology · 2006 · 8 claims · 6 setups

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Fgenesh++ gene prediction pipeline identifies 91% of coding nucleotides with 90% specificity

encode regions genes chromosome computational pseudogene promoter
DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.

PMID 16625196 · PMC2610434 · Nature · 2006 · 8 claims · 7 setups

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A finished sequence of human chromosome 17 (78,839,971 bases, ~2.8% of the euchromatic genome) was generated.

chromosome dog macaque genomic comparative segmental
Retropseudogenes derived from the human Ro/SS-A autoantigen-associated hY RNAs.

PMID 15817567 · PMC1074747 · Nucleic acids research · 2005 · 8 claims · 8 setups

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966 pseudogenes derived from the four human Y (hY) RNAs were characterized in the human genome

genome chimpanzee pseudogenes genomic megablast blat sequence
Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history.

PMID 16440057 · PMC1331980 · PLoS genetics · 2006 · 7 claims · 6 setups

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Complete 4.25-Mb sequence of the QBL haplotype was determined by BAC shotgun sequencing and compared with PGF (reference) and COX haplotypes

qbl pgf classical ceph bac comparative gene
Molecular correlates of host specialization in Staphylococcus aureus.

PMID 17971880 · PMC2040198 · PloS one · 2007 · 8 claims · 6 setups

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Genome sequencing of ET3-1 revealed genomic elements not previously identified in S. aureus, including homologs of virulence factors from other Gram-positive pathogens

aureus sequenced et3-1 bovine whole-genome comparative substitution
Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

PMID 20003482 · PMC2807441 · BMC genomics · 2009 · 8 claims · 6 setups

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Manual annotation of the mouse Chromosome 8 defensin region identifies 98 gene loci: 54 in the alpha-defensin cluster and 44 in the beta-defensin cluster

c57bl orthologous alpha-defensin defensin manual comparative sequence
Positive selection for the male functionality of a co-retroposed gene in the hominoids.

PMID 19832993 · PMC2773790 · BMC evolutionary biology · 2009 · 8 claims · 8 setups

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PIPSL is an extraordinary co-retroposed protein-coding gene that may participate in male-specific functions of humans and close relatives

african chimpanzee orangutan reconstructed population hka comparative
Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.

PMID 19779614 · PMC2745575 · PloS one · 2009 · 8 claims · 8 setups

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A protein-centric data integration approach (Master Protein Directory) enables integration and mining of heterogeneous pathogen-host omics data across multiple research centers

macrophage hela vaccinia bacillus gene protein-protein comparative
DNA sequence and analysis of human chromosome 9.

PMID 15164053 · PMC2734081 · Nature · 2004 · 8 claims · 8 setups

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The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs, representing >99.6% of the region.

bac chromosome fibres chimpanzee clone-based restriction computational
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

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The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation

bac genome metaphase overlapping manual repeat fluorescence

Experiments

Gene losses during human origins.

Better smelling through genetics: mammalian odor perception.

Gene duplication: the genomic trade in spare parts.

Comparative genomics search for losses of long-established genes on the human lineage.

Evolution of the NANOG pseudogene family in the human and chimpanzee genomes.

Automatic annotation of eukaryotic genes, pseudogenes and promoters.

DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.

Retropseudogenes derived from the human Ro/SS-A autoantigen-associated hY RNAs.

Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history.

Molecular correlates of host specialization in Staphylococcus aureus.

Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

Positive selection for the male functionality of a co-retroposed gene in the hominoids.

Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.

DNA sequence and analysis of human chromosome 9.

Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.