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 24

System / cell line: pseudogenes ✕ Assay: analysis ✕ Clear

Analysis of the glutathione S-transferase (GST) gene family.

PMID 15607001 · PMC3500200 · Human genomics · 2004 · 8 claims · 4 setups

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The complete human GST gene family comprises 16 genes in six subfamilies: alpha (GSTA), mu (GSTM), omega (GSTO), pi (GSTP), theta (GSTT) and zeta (GSTZ).

genome gst gst-related gstk1 gene sequence phylogenetic
Rapid bursts of androgen-binding protein (Abp) gene duplication occurred independently in diverse mammals.

PMID 18269759 · PMC2291036 · BMC evolutionary biology · 2008 · 8 claims · 5 setups

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The mouse Abp gene repertoire is twice as large as previously reported, comprising 30 Abpa and 34 Abpbg genes/pseudogenes

c57bl mus rodent genomic comparative pcr phylogenetic
The DNA sequence and analysis of human chromosome 13.

PMID 15057823 · PMC2665288 · Nature · 2004 · 8 claims · 8 setups

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95.5 Mb of finished sequence from chromosome 13 was completed, containing 633 genes and 296 pseudogenes.

chromosome rpci-11 genomic comparative fluorescence
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
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 genomic analysis of three Leishmania species that cause diverse human disease.

PMID 17572675 · PMC2592530 · Nature genetics · 2007 · 8 claims · 6 setups

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L. infantum and L. braziliensis genomes were sequenced and show marked conservation of synteny with L. major, with only ~200 genes differentially distributed among the three species

infantum major braziliensis leishmania whole-genome comparative pcr
Pseudofam: the pseudogene families database.

PMID 18957444 · PMC2686518 · Nucleic acids research · 2009 · 8 claims · 7 setups

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Pseudofam is an online database of pseudogene families built by mapping pseudogenes to Pfam protein families, providing query tools, statistics, and sequence alignments

eukaryotic over pseudogenes pseudogene blast family sequence
RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation.

PMID 19958502 · PMC2788391 · BMC genomics · 2009 · 7 claims · 4 setups

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RExPrimer integrates local SNP, indel, pseudogene, and CNV/structural variation databases with the Primer3 core algorithm to avoid mis-priming and SNP-in-Primer effects.

genomic cyp2d6 genome pcr penta-plex sequence
miRGen: a database for the study of animal microRNA genomic organization and function.

PMID 17108354 · PMC1669779 · Nucleic acids research · 2007 · 8 claims · 6 setups

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miRGen is an integrated database combining Genomics, Targets, and Clusters interfaces to study miRNA genomic organization and function across 11 animal genomes

animal genome mouse-human mirna genomic mirna cross-species
Systematic identification of pseudogenes through whole genome expression evidence profiling.

PMID 16945953 · PMC1636364 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Developed a novel bioinformatics method that identifies pseudogenes by profiling whole-genome transcript and protein expression evidence

genome ensembl vega celera spliced protein-to-genome pseudogene
Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

PMID 19754956 · PMC2753554 · BMC genomics · 2009 · 8 claims · 8 setups

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1750 transcribed pseudogene annotations (TPAs) were identified in the human genome, ~11.5% of all human pseudogene annotations.

genome rhesus vega-annotated tpas transcript-to-genome same synteny
The DNA sequence of the human X chromosome.

PMID 15772651 · PMC2665286 · Nature · 2005 · 8 claims · 8 setups

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The euchromatic sequence of the human X chromosome was determined to 99.3% completeness (~155 Mb total)

pac selected chromosome clone-based shotgun 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
Widespread ectopic expression of olfactory receptor genes.

PMID 16716209 · PMC1508154 · BMC genomics · 2006 · 8 claims · 6 setups

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OR genes show widespread, locus-dependent, heterogeneous ectopic expression across dozens of non-olfactory human and mouse tissues

tissues olfactory intact probesets microarray est custom
NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis.

PMID 19818133 · PMC2784325 · Genome biology · 2009 · 8 claims · 5 setups

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Determined and manually annotated the complete genome sequence of N. meningitidis clinical isolate strain 8013

meningitidis archived strain neisseria whole-genome transposon targeted
Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface.

PMID 27832824 · PMC5105290 · Genome biology · 2016 · 7 claims · 7 setups

Has reproduction · 84

The A. glabripennis genome encodes a uniquely diverse arsenal of enzymes that degrade the main plant cell wall polysaccharide networks (cellulose, hemicellulose, pectin) and detoxify plant allelochemicals.

anoplophora glabripennis insect whole-genome genome orthology
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
Fast-evolving noncoding sequences in the human genome.

PMID 17578567 · PMC2394770 · Genome biology · 2007 · 8 claims · 6 setups

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1,356 conserved noncoding sequences show human-specific accelerated substitution rates (ANC sequences) relative to chimpanzee

chimpanzee genome hapmap comparative genomic segmental
Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

PMID 17214878 · PMC1779775 · BMC genomics · 2007 · 8 claims · 7 setups

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The proportion of subjects lacking DEFA3 varies significantly by population, from 10% to 37%

genomic hapmap 150-kb alpha-defensin pcr-rflp snp linkage
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

Experiments

Analysis of the glutathione S-transferase (GST) gene family.

Rapid bursts of androgen-binding protein (Abp) gene duplication occurred independently in diverse mammals.

The DNA sequence and analysis of human chromosome 13.

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

Gene duplication: the genomic trade in spare parts.

Comparative genomic analysis of three Leishmania species that cause diverse human disease.

Pseudofam: the pseudogene families database.

RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation.

miRGen: a database for the study of animal microRNA genomic organization and function.

Systematic identification of pseudogenes through whole genome expression evidence profiling.

Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

The DNA sequence of the human X chromosome.

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

Widespread ectopic expression of olfactory receptor genes.

NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis.

Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface.

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

Fast-evolving noncoding sequences in the human genome.

Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

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