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: genomic ✕ Assay: trace ✕ Clear

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
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
Decoding of superimposed traces produced by direct sequencing of heterozygous indels.

PMID 18654614 · PMC2429969 · PLoS computational biology · 2008 · 7 claims · 3 setups

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A dynamic programming method (implemented as web app Indelligent) can decode superimposed allelic sequences from a single mixed trace, using only the observed string of ambiguous peak calls, without a reference sequence or reverse trace.

genomic artificial simulated direct computational comparative
A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells.

PMID 19911041 · PMC2766639 · PLoS genetics · 2009 · 8 claims · 7 setups

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Padlock probes combined with high-throughput sequencing enable accurate, quantitative, low-bias digital RNA allelotyping of allele-specific expression

genomic pgp1 skin fibroblasts padlock quantitative gene
Highly individual methylation patterns of alternative glucocorticoid receptor promoters suggest individualized epigenetic regulatory mechanisms.

PMID 19004867 · PMC2602793 · Nucleic acids research · 2008 · 7 claims · 4 setups

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Methylation patterns of the five GR promoters activated in PBMCs are highly variable between individuals.

chromosome genomic pbmc multi-species phylogenetic bisulphite
A new mutation in BFSP2 (G1091A) causes autosomal dominant congenital lamellar cataracts.

PMID 18958306 · PMC2573734 · Molecular vision · 2008 · 8 claims · 7 setups

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The disease locus maps to chromosome 3q21-25, linked to markers D3S2322 and D3S1541

four-generation bfsp2 wild-type microsatellite direct denaturing
Database resources of the National Center for Biotechnology Information.

PMID 17170002 · PMC1781113 · Nucleic acids research · 2007 · 8 claims · 8 setups

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NCBI maintains an integrated suite of database resources (Entrez, PubMed, RefSeq, dbSNP, BLAST, etc.) for molecular biology data retrieval and analysis

genbank genomic eukaryotic completely sequence rapid est
SNPdetector: a software tool for sensitive and accurate SNP detection.

PMID 16261194 · PMC1274293 · PLoS computational biology · 2005 · 7 claims · 7 setups

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SNPdetector, which models human visual inspection of sequencing traces, achieves low false positive and false negative rates in automated SNP and mutation detection

inbred unrelated zebra same pcr manual comparative
Human PAML browser: a database of positive selection on human genes using phylogenetic methods.

PMID 17962310 · PMC2238824 · Nucleic acids research · 2008 · 8 claims · 5 setups

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The Human PAML Browser is a web-accessible database of codeml-based positive selection test results for 13,721 human genes with orthologs in UCSC multispecies alignments.

same genes orangutan codeml gene sequence
A dispermic chimera with mixed field blood group B and mosaic 46,XY/47,XYY karyotype.

PMID 17596670 · PMC2693654 · Journal of Korean medical science · 2007 · 7 claims · 7 setups

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The propositus shows mixed-field agglutination with anti-B that mimics the B3 ABO subtype but is not caused by a B3 allele.

propositus relatives serologic allele-specific haplotype-specific
Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human.

PMID 17288572 · PMC1796608 · BMC evolutionary biology · 2007 · 8 claims · 6 setups

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Widespread transcription occurs across the human genome outside known gene annotations, and the bulk of TARs represent genuine transcripts rather than experimental artifacts

liver chimpanzee h-invitational tar genome blastn secondary
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
Mutation G61C in the CRYGD gene causing autosomal dominant congenital coralliform cataracts.

PMID 18334953 · PMC2268897 · Molecular vision · 2008 · 8 claims · 6 setups

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A G61C (P.G61C) missense mutation in CRYGD causes autosomal dominant congenital coralliform cataracts in this family

four-generation genomic crygd wild-type genotyping direct denaturing
iMapper: a web application for the automated analysis and mapping of insertional mutagenesis sequence data against Ensembl genomes.

PMID 18974167 · PMC2639305 · Bioinformatics (Oxford, England) · 2008 · 6 claims · 3 setups

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iMapper is a web application for automated analysis and mapping of insertional mutagenesis sequence data against vertebrate and invertebrate Ensembl genomes (human, mouse, rat, zebrafish, Drosophila, S. cerevisiae).

piggybac splinkerette-pcr-derived sequence splinkerette genome throughput
Limited copy number-high resolution melting (LCN-HRM) enables the detection and identification by sequencing of low level mutations in cancer biopsies.

PMID 19811662 · PMC2766370 · Molecular cancer · 2009 · 7 claims · 6 setups

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LCN-HRM enables detection and sequencing-based characterisation of low-level mutations that are undetectable by direct sequencing alone

hct116 ffpe genomic tx84 dideoxynucleotide high lcn-hrm

Experiments

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

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

Decoding of superimposed traces produced by direct sequencing of heterozygous indels.

A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells.

Highly individual methylation patterns of alternative glucocorticoid receptor promoters suggest individualized epigenetic regulatory mechanisms.

A new mutation in BFSP2 (G1091A) causes autosomal dominant congenital lamellar cataracts.

Database resources of the National Center for Biotechnology Information.

SNPdetector: a software tool for sensitive and accurate SNP detection.

Human PAML browser: a database of positive selection on human genes using phylogenetic methods.

A dispermic chimera with mixed field blood group B and mosaic 46,XY/47,XYY karyotype.

Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human.

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

Mutation G61C in the CRYGD gene causing autosomal dominant congenital coralliform cataracts.

iMapper: a web application for the automated analysis and mapping of insertional mutagenesis sequence data against Ensembl genomes.

Limited copy number-high resolution melting (LCN-HRM) enables the detection and identification by sequencing of low level mutations in cancer biopsies.