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 28

System / cell line: coding ✕ Assay: chromosomal ✕ Clear

On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees.

PMID 17971225 · PMC2246304 · Genome biology · 2007 · 8 claims · 4 setups

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Genes located in rearranged chromosomes show lower non-coding (KI), synonymous (KS), and non-synonymous (KA) divergence than genes in colinear chromosomes.

human-chimpanzee orthologous genome-wide pairwise lineage-specific permutation
Molecular genetics and structural genomics of the human protein kinase C gene module.

PMID 11897026 · PMC88812 · Genome biology · 2002 · 8 claims · 4 setups

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The nine human PKC genes are dispersed throughout the genome, with five isotypes (α, β, δ, ζ, ι) previously incorrectly assigned to chromosomes in the literature.

metaphase genome pkc genomic fluorescence bioinformatic snp
Defective DNA repair and increased genomic instability in Artemis-deficient murine cells.

PMID 12615897 · PMC2193825 · The Journal of experimental medicine · 2003 · 8 claims · 8 setups

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Artemis-deficient ES cells are severely impaired in VDJ coding joining but retain relatively normal RS (signal) joining

recombined southern rt-pcr colony
Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.

PMID 16680197 · PMC1456318 · PLoS genetics · 2006 · 7 claims · 7 setups

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SNPs in the Affymetrix 100K set are undersampled from coding regions (both synonymous and nonsynonymous) and oversampled from regions outside genes, relative to HapMap SNPs

genome autosomal hapmap chromosome snp chromosomal minor
Rubinstein-Taybi Syndrome: spectrum of CREBBP mutations in Italian patients.

PMID 17052327 · PMC1626071 · BMC medical genetics · 2006 · 8 claims · 8 setups

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RSTS is caused by chromosomal microdeletions and point mutations in one copy of CREBBP (16p13.3), consistent with haploinsufficiency of this dosage-sensitive gene

peripheral patient-parent genomic crebbp karyotyping bac microsatellite
A naturally occurring human RPA subunit homolog does not support DNA replication or cell-cycle progression.

PMID 19942684 · PMC2817474 · Nucleic acids research · 2010 · 8 claims · 7 setups

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Exogenous RPA4 expression does not support chromosomal DNA replication and causes cell-cycle arrest in G2/M

hela mammalian rpa4 western flow immunofluorescence
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
Previously described sequence variant in CDK5RAP2 gene in a Pakistani family with autosomal recessive primary microcephaly.

PMID 17764569 · PMC2072945 · BMC medical genetics · 2007 · 7 claims · 4 setups

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A nonsense mutation in CDK5RAP2 exon 4, correctly designated 246T>A (Y82X), was identified in all four affected individuals of a Pakistani family linked to MCPH3

pakistani affected unrelated one microsatellite sanger mutation
Identification of a novel splice-site mutation in the Lebercilin (LCA5) gene causing Leber congenital amaurosis.

PMID 18334959 · PMC2268850 · Molecular vision · 2008 · 7 claims · 5 setups

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A homozygous c.955G>A mutation at the last base of exon 6 of LCA5 disrupts the normal splice donor site.

genomic lca5 lymphocyte affected snp sanger splice
The jewels of our genome: the search for the genomic changes underlying the evolutionarily unique capacities of the human brain.

PMID 16733552 · PMC1464830 · PLoS genetics · 2006 · 8 claims · 7 setups

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Human and chimp genomes differ by ~35 million single nucleotide substitutions, corresponding to ~1.06% divergence after removing polymorphic sites

chimpanzee chimp population non-human genome snp high-density
EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.

PMID 17984073 · PMC2238967 · Nucleic acids research · 2008 · 8 claims · 8 setups

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EPGD is a gene-centered, internet-accessible database integrating paralog family and paralogon information for 26 eukaryotic genomes.

sequences homologous proteins coding pairwise single sequence
Oncogenic mutations in GNAQ occur early in uveal melanoma.

PMID 18719078 · PMC2634606 · Investigative ophthalmology & visual science · 2008 · 8 claims · 7 setups

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Activating GNAQ mutations at codon 209 occur in 33/67 (49%) of primary uveal melanomas, making it the most common known oncogenic mutation in UM

uveal peripheral normal well-characterized pcr sequencing array-based
Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration.

PMID 31492853 · PMC6731298 · Nature communications · 2019 · 8 claims · 7 setups

Has reproduction · 77

HIV-1 recurrently integrates into genes that are proximal to super-enhancer (SE) genomic elements in both patients and in vitro T cell cultures.

activated cd4+ cd3 uninfected hiv-1 chip-seq rna-seq
RummaGEO: Automatic mining of human and mouse gene sets from GEO.

PMID 39569206 · PMC11573963 · Patterns (New York, N.Y.) · 2024 · 8 claims · 7 setups

Has reproduction · 63

RummaGEO is a gene expression signature search engine built from automatically mined human and mouse RNA-seq perturbation studies in GEO

genes rummageo rummageo-derived leiden bulk gene leiden
Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences.

PMID 16759380 · PMC1525190 · BMC genomics · 2006 · 8 claims · 6 setups

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Overall pairwise genomic divergences among cattle, dog and human are relatively constant (0.32–0.37 change/site)

orthologous random cattle aligned three-way pairwise bac
MRX87 family with Aristaless X dup24bp mutation and implication for polyAlanine expansions.

PMID 17480217 · PMC1868705 · BMC medical genetics · 2007 · 8 claims · 7 setups

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The MRX87 disease locus maps to the Xp22-p21 interval, a known hot spot region for mental handicap

peripheral genomic pcr leukocytes two-point direct pcr
Genetic microheterogeneity and phenotypic variation of Helicobacter pylori arginase in clinical isolates.

PMID 17408487 · PMC1853099 · BMC microbiology · 2007 · 8 claims · 8 setups

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Arginase activity varies more than 100-fold among H. pylori clinical isolates and laboratory-adapted strains

minimally-passaged pylori coli arginase urease heterologous
Mutations in mRNA export mediator GLE1 result in a fetal motoneuron disease.

PMID 18204449 · PMC2684619 · Nature genetics · 2008 · 8 claims · 8 setups

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Mutations in GLE1, an mRNA export mediator, cause LCCS1

lccs1 laahd finnish healthy genomic microsatellite carrier
Evaluating genome sequencing strategies: trio, singleton, and standard testing in rare disease diagnosis.

PMID 40963120 · PMC12445032 · Genome medicine · 2025 · 7 claims · 4 setups

Has reproduction · 88

Trio genome sequencing (tGS) achieves higher prospective diagnostic yield than standard-of-care (SoC) and singleton genome sequencing (sGS) even when performed by a newly trained team.

individuals index blood short-read exome array
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

On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees.

Molecular genetics and structural genomics of the human protein kinase C gene module.

Defective DNA repair and increased genomic instability in Artemis-deficient murine cells.

Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.

Rubinstein-Taybi Syndrome: spectrum of CREBBP mutations in Italian patients.

A naturally occurring human RPA subunit homolog does not support DNA replication or cell-cycle progression.

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

Previously described sequence variant in CDK5RAP2 gene in a Pakistani family with autosomal recessive primary microcephaly.

Identification of a novel splice-site mutation in the Lebercilin (LCA5) gene causing Leber congenital amaurosis.

The jewels of our genome: the search for the genomic changes underlying the evolutionarily unique capacities of the human brain.

EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.

Oncogenic mutations in GNAQ occur early in uveal melanoma.

Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration.

RummaGEO: Automatic mining of human and mouse gene sets from GEO.

Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences.

MRX87 family with Aristaless X dup24bp mutation and implication for polyAlanine expansions.

Genetic microheterogeneity and phenotypic variation of Helicobacter pylori arginase in clinical isolates.

Mutations in mRNA export mediator GLE1 result in a fetal motoneuron disease.

Evaluating genome sequencing strategies: trio, singleton, and standard testing in rare disease diagnosis.

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