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 8

System / cell line: pseudogene ✕ Assay: database ✕ 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
Genome-wide survey for biologically functional pseudogenes.

PMID 16680195 · PMC1456316 · PLoS computational biology · 2006 · 8 claims · 6 setups

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A subset of ancient, cross-species-conserved pseudogenes (30 of 1,453 candidate quartets) show evidence consistent with retained biological function

human-mouse chimpanzee cross-species maximum-likelihood synteny
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
In Silico screening for functional candidates amongst hypothetical proteins.

PMID 19754976 · PMC2758874 · BMC bioinformatics · 2009 · 7 claims · 6 setups

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An in silico selection strategy combining subcellular targeting-signal prediction with protein domain identification can enrich for true functional proteins among hypothetical proteins

hypothetical targetp-selected mitochondria-predicted subcellular domain database
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
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
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

Has reproduction · 100

44 venom peptide genes were identified, distributed across four of the eleven chromosomes and organized in tandem repeat clusters.

tetramorium bicarinatum vpg venom whole-genome blast gene
IgVH genes from different anatomical regions, with different histopathological patterns, of a rheumatoid arthritis patient suggest cyclic re-entry of mature synovial B-cells in the hypermutation process.

PMID 11056671 · PMC17813 · Arthritis research · 2000 · 8 claims · 5 setups

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Somatically mutated IgVH genes with amino acid deletions and mixed IgV molecules were found in all three anatomical regions, suggesting a novel pathway for generating (auto)antibody specificities

synovial same cryosections formalin-fixed cdna seminested double

Experiments

Gene losses during human origins.

Genome-wide survey for biologically functional pseudogenes.

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

In Silico screening for functional candidates amongst hypothetical proteins.

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

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

The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.

IgVH genes from different anatomical regions, with different histopathological patterns, of a rheumatoid arthritis patient suggest cyclic re-entry of mature synovial B-cells in the hypermutation process.