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 17

System / cell line: database ✕ Assay: fragment ✕ Clear

Frameshift mutations in coding repeats of protein tyrosine phosphatase genes in colorectal tumors with microsatellite instability.

PMID 19000305 · PMC2586028 · BMC cancer · 2008 · 7 claims · 6 setups

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16 PTP candidate genes containing coding mononucleotide repeats (cMNR) of at least 7 units were identified via bioinformatic analysis and screened in MSI-H cell lines, cancers, and adenomas

msi-h genome colorectal fragment bioinformatic sequencing
Genomic organization and single-nucleotide polymorphism map of desmuslin, a novel intermediate filament protein on chromosome 15q26.3.

PMID 11454237 · PMC34549 · BMC genetics · 2001 · 6 claims · 4 setups

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The desmuslin (DMN) gene was localized to chromosome 15q26.3 via electronic screening of the human genome database, and its 5-exon genomic organization was determined.

genomic electronic pcr pcr-restriction
Genomes of Helicobacter pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island.

PMID 16872520 · PMC1553449 · BMC genomics · 2006 · 8 claims · 7 setups

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Native Peruvian H. pylori strains comprise two lineages: predominant hp-Europe and ~20% hsp-Amerind (Amerindian ancestry, closer to Alaska strains)

pylori peruvian spanish fluorescent multilocus oipa
Sequence determinants of human microsatellite variability.

PMID 20015383 · PMC2806349 · BMC genomics · 2009 · 6 claims · 4 setups

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Mean and maximum number of repeats across individuals are positively correlated with heterozygosity

hgdp-ceph genome calibrated microsatellite blastn sequence
Bases and spaces: resources on the web for accessing the draft human genome.

PMID 11178254 · PMC138875 · Genome biology · 2000 · 8 claims · 8 setups

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By combining currently available genomic databases and mapping resources (GenBank/Entrez, UniGene, RH maps, BAC fingerprint maps, Ensembl, NIX), it is possible to devise strategies that fully exploit the fragmentary draft human genome sequence.

bac whole-genome draft submitted bac radiation initio
Automated recognition of retroviral sequences in genomic data--RetroTector.

PMID 17636050 · PMC1976444 · Nucleic acids research · 2007 · 8 claims · 8 setups

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RetroTector uses 'fragment threading' (detection of chains of conserved retroviral motifs satisfying distance constraints) combined with LTR detection and protein reconstruction to identify ERVs in genomic sequences

reference genome chimpanzee red motif whole-genome simulated
Toward proteome-scale identification and quantification of isoaspartyl residues in biological samples.

PMID 19663459 · PMC2756321 · Journal of proteome research · 2009 · 8 claims · 4 setups

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In ECD MS/MS, isoaspartyl (but not aspartyl) residues produce specific fragments c_n•+58.0054 (C2H2O2) and z_(l-n)-56.9976 (C2HO2), which serve as markers for Asp isomerization

a431 brain ecd cad label-free
Breakpoint Associated with a novel 2.3 Mb deletion in the VCFS region of 22q11 and the role of Alu (SINE) in recurring microdeletions.

PMID 16512914 · PMC1413517 · BMC medical genetics · 2006 · 8 claims · 5 setups

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Patient carries a novel 2.3 Mb deletion in 22q11.2 with proximal breakpoint between RH48663/RH48348 and distal breakpoint between D22S1138/SHGC-145314

genomic maternal 22qtdr chromosome semi-quantitative pcr fish
Polymorphism discovery and association analyses of the interferon genes in type 1 diabetes.

PMID 16504056 · PMC1402321 · BMC genetics · 2006 · 7 claims · 8 setups

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No statistical evidence of a major association between T1D and any of the interferon or interferon-related genes tested (IFNA cluster, IFNB1, IFNW1, IFNG, ICSBP1)

t1d european warren resequencing database tag
The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event?

PMID 19094205 · PMC2637867 · BMC evolutionary biology · 2008 · 8 claims · 4 setups

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AR was duplicated into two paralogs, AR-A and AR-B, during a teleost-specific whole genome duplication (WGD), after the split of Acipenseriformes but before the divergence of Osteoglossiformes.

fish full-length tetraodon rt-pcr database molecular
Oncogene mutations, copy number gains and mutant allele specific imbalance (MASI) frequently occur together in tumor cells.

PMID 19826477 · PMC2757721 · PloS one · 2009 · 8 claims · 8 setups

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Homozygous mutations of oncogenes are frequent (20%) across 833 cancer cell lines of 12 tumor types in the Sanger database

tumors cancer tumor lung direct database quantitative
Recombinant vaccine-derived poliovirus in Madagascar.

PMID 12899139 · PMC3023450 · Emerging infectious diseases · 2003 · 7 claims · 4 setups

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Five acute flaccid paralysis cases in southern Madagascar were associated with vaccine-derived poliovirus (VDPV) type 2 isolates

poliovirus genbank rflp partial sequence
Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.

PMID 15045028 · PMC374243 · PLoS biology · 2004 · 8 claims · 6 setups

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The ASPM gene shows accelerated (positively selected) evolution in the African hominoid clade, and this acceleration precedes hominid brain expansion by several million years.

chimpanzee retrofitted primate aspm tar restriction genomic
New approaches to the analysis of palindromic sequences from the human genome: evolution and polymorphism of an intronic site at the NF1 locus.

PMID 16340004 · PMC1310899 · Nucleic acids research · 2005 · 7 claims · 8 setups

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Long pure palindromes (>~200 bp) cannot be stably cloned in E.coli due to cruciform-driven instability, and no E.coli mutant fully overcomes this cloning block.

individuals e.coli cerevisiae yeast pcr plasmid phi-29
In vitro and in silico analysis reveals an efficient algorithm to predict the splicing consequences of mutations at the 5' splice sites.

PMID 17726045 · PMC2094079 · Nucleic acids research · 2007 · 8 claims · 6 setups

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Two exonic mutations, PINK1 E417G and PARK7 E64D, disrupt binding to U1 snRNA and cause skipping of the mutation-harboring exon

hek293 genome lymphocytes minigene artificial genome-wide
HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis.

PMID 24475057 · PMC3903476 · PloS one · 2014 · 8 claims · 5 setups

Has reproduction · 66

HTSstation is a web application suite coupling simple web forms to modular analysis pipelines for ChIP-seq, RNA-seq, 4C-seq and re-sequencing HTS applications, accessible at http://htsstation.epfl.ch.

embryonic mycobacterium forebrain rna-seq re-sequencing 4c-seq
A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla.

PMID 18925953 · PMC2580767 · BMC genetics · 2008 · 8 claims · 6 setups

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A 460–465 bp insertion is present in intron 4 of the Amel-Y locus in most Cetartiodactyla lineages (cetaceans and ruminants) but absent in pig

cetacea amel-y amel-x cetartiodactyla pcr sanger molecular

Experiments

Frameshift mutations in coding repeats of protein tyrosine phosphatase genes in colorectal tumors with microsatellite instability.

Genomic organization and single-nucleotide polymorphism map of desmuslin, a novel intermediate filament protein on chromosome 15q26.3.

Genomes of Helicobacter pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island.

Sequence determinants of human microsatellite variability.

Bases and spaces: resources on the web for accessing the draft human genome.

Automated recognition of retroviral sequences in genomic data--RetroTector.

Toward proteome-scale identification and quantification of isoaspartyl residues in biological samples.

Breakpoint Associated with a novel 2.3 Mb deletion in the VCFS region of 22q11 and the role of Alu (SINE) in recurring microdeletions.

Polymorphism discovery and association analyses of the interferon genes in type 1 diabetes.

The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event?

Oncogene mutations, copy number gains and mutant allele specific imbalance (MASI) frequently occur together in tumor cells.

Recombinant vaccine-derived poliovirus in Madagascar.

Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.

New approaches to the analysis of palindromic sequences from the human genome: evolution and polymorphism of an intronic site at the NF1 locus.

In vitro and in silico analysis reveals an efficient algorithm to predict the splicing consequences of mutations at the 5' splice sites.

HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis.

A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla.