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 27

System / cell line: chromosomes ✕ Assay: in-silico ✕ Clear

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
A high throughput method for genome-wide analysis of retroviral integration.

PMID 17028098 · PMC1636494 · Nucleic acids research · 2006 · 8 claims · 8 setups

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VITA uses MmeI to cleave DNA at a fixed distance from its recognition site, generating 21-22 bp genomic tags that serve as signatures of lentiviral integration sites.

hela ht3 genome chromosomes isf vita sanger
In silico discovery of gene-coding variants in murine quantitative trait loci using strain-specific genome sequence databases.

PMID 12537567 · PMC151180 · Genome biology · 2002 · 6 claims · 4 setups

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Strain-specific mouse genome sequence databases can be used in a high-throughput in silico pipeline to discover gene-coding variants within murine QTLs, without de novo sequencing.

strains genomic celera blast-based targeted phred
A novel WFS1 mutation in a family with dominant low frequency sensorineural hearing loss with normal VEMP and EcochG findings.

PMID 18518985 · PMC2435521 · BMC medical genetics · 2008 · 7 claims · 6 setups

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A novel heterozygous WFS1 mutation c.2054G>C (p.R685P) segregates faithfully with dominant LFSNHL in an American family

family wolframin pure-tone vestibular electrocochleography
Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution.

PMID 18410676 · PMC2375447 · BMC genomics · 2008 · 8 claims · 7 setups

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Chicken and turkey genomes differ by only two inter-chromosomal rearrangements (GGA2 orthologous to MGA3+6; GGA4 orthologous to MGA4+9), both involving centromeres.

chicken turkey broiler chromosome single fish
Mutations in JARID1C are associated with X-linked mental retardation, short stature and hyperreflexia.

PMID 18697827 · PMC3711528 · Journal of medical genetics · 2008 · 8 claims · 8 setups

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Four novel JARID1C mutations (p.A77T, p.V504M, p.E468GfsX2, p.R1481GfsX9) were identified in males with mental retardation across three screened cohorts.

genomic family carrier jarid1c dhplc allele-specific restriction
Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication.

PMID 18257913 · PMC2374708 · Genome biology · 2008 · 8 claims · 7 setups

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The macaque marker order on chromosome 17 represents the ancestral hominoid/mammalian organization

great felis mus rhesus comparative fish duplicon
Novel mutations in BBS5 highlight the importance of this gene in non-Caucasian Bardet-Biedl syndrome patients.

PMID 18203199 · PMC2578871 · American journal of medical genetics. Part A · 2008 · 6 claims · 8 setups

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Two novel homozygous missense mutations in BBS5 (p.Gly72Ser and p.Thr183Ala) were identified in non-Caucasian BBS patients (Somali and Sri Lankan)

genomic somali sri ethnically dhplc snp sanger
Implication of BRCA2 -26G>A 5' untranslated region polymorphism in susceptibility to sporadic breast cancer and its modulation by p53 codon 72 Arg>Pro polymorphism.

PMID 17945002 · PMC2242669 · Breast cancer research : BCR · 2007 · 8 claims · 7 setups

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-26G>A polymorphism in the BRCA2 5' UTR is functional: the A allele drives roughly twice the reporter gene expression of the G allele in MCF-7 and HeLa cells

mcf-7 hela brca2 peripheral luciferase transcription genotyping
The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements.

PMID 18699995 · PMC2542386 · BMC genomics · 2008 · 8 claims · 5 setups

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Some relatively recent (young) SDs accumulate in regions homologous to chromosomal inversions that occurred in the sister lineage

genome sds chimpanzee colinear comparative interspecific genomic
Functional and clinical data of Best vitelliform macular dystrophy patients with mutations in the BEST1 gene.

PMID 20057903 · PMC2802291 · Molecular vision · 2009 · 7 claims · 8 setups

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BEST1 mutations are not correlated with the severity of functional and clinical data in Best VMD patients

genomic unrelated best1 best1-4 direct chromosome pathogenicity
Genome comparison without alignment using shortest unique substrings.

PMID 15910684 · PMC1166540 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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A number of sequence comparison tasks, including detection of unique genomic regions, can be accomplished efficiently without an alignment step using shortest unique substrings.

caenorhabditis genome mycoplasma shuffled genome-wide upstream-region local
Detecting transcriptionally active regions using genomic tiling arrays.

PMID 16859498 · PMC1779562 · Genome biology · 2006 · 8 claims · 4 setups

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A non-parametric method (TranscriptionDetector) integrates single-channel p-values from multiple replicate arrays into a multi-channel p-value (MCPV) to identify transcribed probed loci without assumptions about intensity distributions.

anopheles chromosomes simulated genomic high-density sequence-based
Large-scale molecular analysis of a 34 Mb interval on chromosome 6q: major refinement of the RP25 interval.

PMID 18510646 · PMC2689154 · Annals of human genetics · 2008 · 7 claims · 5 setups

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Direct sequencing of 43 candidate genes in 7 Spanish arRP families identified 244 sequence variants (76 novel), none pathogenic, excluding these genes as disease-causing.

spanish rp5 population candidate direct comparative pcr
Insulin mutation screening in 1,044 patients with diabetes: mutations in the INS gene are a common cause of neonatal diabetes but a rare cause of diabetes diagnosed in childhood or adulthood.

PMID 18162506 · PMC7611804 · Diabetes · 2008 · 8 claims · 8 setups

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Heterozygous INS mutations are a common cause of permanent neonatal diabetes (PNDM) diagnosed before 6 months of age

peripheral patients mody young-onset pcr microsatellite variant
Large-scale copy number variants (CNVs): distribution in normal subjects and FISH/real-time qPCR analysis.

PMID 17565693 · PMC1920519 · BMC genomics · 2007 · 8 claims · 4 setups

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42 different CNVs were detected in 27 phenotypically normal individuals using 1 Mb resolution BAC array-CGH

genomic metaphase computational array-cgh fish real-time
Population history and natural selection shape patterns of genetic variation in 132 genes.

PMID 15361935 · PMC515367 · PLoS biology · 2004 · 7 claims · 5 setups

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Developed a rigorous computational approach that corrects for multiple hypothesis testing and models population demographic history to test for natural selection

genomic empirical snps chromosome comprehensive coalescent fst
Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments.

PMID 15860768 · PMC1087789 · Nucleic acids research · 2005 · 8 claims · 4 setups

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Selector oligonucleotides can circularize many distinct genomic restriction fragments in one reaction, enabling parallel amplification with a single universal primer pair instead of multiple target-specific primer pairs

genomic 7776-clone selector-based cdna restriction
Functional nsSNPs from carcinogenesis-related genes expressed in breast tissue: potential breast cancer risk alleles and their distribution across human populations.

PMID 16595073 · PMC3500178 · Human genomics · 2006 · 7 claims · 5 setups

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A bioinformatics strategy cross-referencing carcinogenesis-related gene lists with breast-tissue expression data can identify candidate breast cancer risk nsSNPs.

breast carcinogenesis-related nssnp-containing african gene snp functional
Genome-wide identification of human functional DNA using a neutral indel model.

PMID 16410828 · PMC1326222 · PLoS computational biology · 2006 · 8 claims · 8 setups

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A neutral indel model predicting a geometric distribution of intergap segment (IGS) lengths fits human-mouse ancestral repeat (AR) alignment data excellently

chromosome human-mouse genome individual whole-genome probabilistic comparative

Experiments

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

A high throughput method for genome-wide analysis of retroviral integration.

In silico discovery of gene-coding variants in murine quantitative trait loci using strain-specific genome sequence databases.

A novel WFS1 mutation in a family with dominant low frequency sensorineural hearing loss with normal VEMP and EcochG findings.

Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution.

Mutations in JARID1C are associated with X-linked mental retardation, short stature and hyperreflexia.

Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication.

Novel mutations in BBS5 highlight the importance of this gene in non-Caucasian Bardet-Biedl syndrome patients.

Implication of BRCA2 -26G>A 5' untranslated region polymorphism in susceptibility to sporadic breast cancer and its modulation by p53 codon 72 Arg>Pro polymorphism.

The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements.

Functional and clinical data of Best vitelliform macular dystrophy patients with mutations in the BEST1 gene.

Genome comparison without alignment using shortest unique substrings.

Detecting transcriptionally active regions using genomic tiling arrays.

Large-scale molecular analysis of a 34 Mb interval on chromosome 6q: major refinement of the RP25 interval.

Insulin mutation screening in 1,044 patients with diabetes: mutations in the INS gene are a common cause of neonatal diabetes but a rare cause of diabetes diagnosed in childhood or adulthood.

Large-scale copy number variants (CNVs): distribution in normal subjects and FISH/real-time qPCR analysis.

Population history and natural selection shape patterns of genetic variation in 132 genes.

Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments.

Functional nsSNPs from carcinogenesis-related genes expressed in breast tissue: potential breast cancer risk alleles and their distribution across human populations.

Genome-wide identification of human functional DNA using a neutral indel model.