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 602

Assay: alignment ✕ Clear

Centromere-associated protein-E is essential for the mammalian mitotic checkpoint to prevent aneuploidy due to single chromosome loss.

PMID 12925705 · PMC2173788 · The Journal of cell biology · 2003 · 7 claims · 8 setups

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CENP-E-null cells cannot sustain a mitotic checkpoint arrest in response to one or a few unattached kinetochores, causing cells to enter anaphase with missegregating chromosomes and become aneuploid

embryonic mefs hepatocytes bubr1 real-time quantitative immunofluorescence
Molecular epidemiology of O139 Vibrio cholerae: mutation, lateral gene transfer, and founder flush.

PMID 12890320 · PMC3023423 · Emerging infectious diseases · 2003 · 8 claims · 4 setups

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Lateral gene transfer (LGT) produced roughly three times as many nucleotide changes as point mutation among the 96 O139 isolates.

vibrio same novel aligned multilocus pcr blast
RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.

PMID 23145190 · PMC3493385 · PLoS neglected tropical diseases · 2012 · 8 claims · 8 setups

Has reproduction · 66

S. stercoralis possesses homologs of nearly all C. elegans dauer genes, but with significant differences in protein structure, developmental regulation, and gene family expansion.

strongyloides stercoralis mongolian adapter-ligated polyadenylated novo comparative
Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G.

PMID 15269786 · PMC479043 · PLoS biology · 2004 · 7 claims · 6 setups

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APOBEC3G has been under strong, recurrent positive selection throughout primate evolution (~33 million years)

apobec3g pairwise human-chimpanzee apobec1 pcr phylogenetic sliding
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
High frequency of the IVS2-2A>G DNA sequence variation in SLC26A5, encoding the cochlear motor protein prestin, precludes its involvement in hereditary hearing loss.

PMID 16086836 · PMC1190179 · BMC medical genetics · 2005 · 8 claims · 6 setups

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IVS2-2A>G allele frequency does not differ significantly between hearing-impaired cases and controls among Hispanics and Caucasians (p=0.45)

genomic mitochondrial slc26a5 pcr sequence splice
Genome wide survey of G protein-coupled receptors in Tetraodon nigroviridis.

PMID 16022726 · PMC1187884 · BMC evolutionary biology · 2005 · 8 claims · 8 setups

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466 Tetraodon GPCRs (Tnig-GPCRs) were identified genome-wide, of which 457 had not been previously reported

tetraodon tnig-gpcr non-rhodopsin-like domain sequence transmembrane
In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology.

PMID 15871745 · PMC1156887 · BMC genomics · 2005 · 7 claims · 6 setups

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Only 14±2% of canine transcripts were detected by U133A probe sets versus 49±6% of human transcripts when hybridized to the same chip

canine tissues hg-u133a probes microarray sequence ortholog
Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.

PMID 15804358 · PMC1079825 · BMC genomics · 2005 · 8 claims · 8 setups

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Human, mouse, and rat SPAM1/Spam1 transcripts initiate within an ERV1 pol (internal coding) region rather than within an LTR

testis panel genome 5'-race non-quantitative
Glia maturation factor gamma (GMFG): a cytokine-responsive protein during hematopoietic lineage development and its functional genomics analysis.

PMID 17127212 · PMC5054077 · Genomics, proteomics & bioinformatics · 2006 · 8 claims · 6 setups

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GMFG is a cytokine-responsive protein in EPO-induced (erythroid) and G-CSF-induced (myeloid) hematopoietic lineage development

ac133+ excised e14 tissues 2-de lc-ms rt-pcr
Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs.

PMID 17029642 · PMC1635982 · BMC genomics · 2006 · 8 claims · 7 setups

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The number of index-species (IS) mismatches in a primer pair significantly reduces amplification success, with an estimated 6-8% decrease in success rate per additional mismatch.

dog hamster pcr primer pcr blast sequence
Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes.

PMID 16998185 · PMC1636426 · Nucleic acids research · 2006 · 8 claims · 6 setups

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Fungal Pop8 is evolutionarily related to the Rpp14/Pop5 protein family, suggesting Pop8 is the fungal orthologue of Rpp14

sequences sequence eukaryotic mrp psi-blast phylogenetic hmm
AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome.

PMID 16925833 · PMC1810548 · Genome biology · 2006 · 8 claims · 5 setups

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AUGUSTUS predicted significantly more genes correctly than any other ab initio program in EGASP

genome human-mouse genes initio comparative extrinsic
Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication.

PMID 16899447 · PMC1557810 · Nucleic acids research · 2006 · 8 claims · 8 setups

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The RE1 PSSM identifies functional RE1 binding sites with greater sensitivity and selectivity than the previously used RE1 consensus sequence

fibroblast hela hek293 set genome-wide electrophoretic rt-pcr
Mixed Cryptosporidium infections and HIV.

PMID 16707069 · PMC3373040 · Emerging infectious diseases · 2006 · 7 claims · 5 setups

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Mixed Cryptosporidium infections were detected in 7 of 21 patients originally diagnosed with only C. canis or C. felis

stool nested ssu sequencing
Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak.

PMID 16700631 · PMC1463904 · PLoS medicine · 2006 · 8 claims · 6 setups

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The Indian Ocean outbreak was initiated by a strain related to East African CHIKV isolates, which subsequently evolved via a traceable microevolution history

chikv partial pseudoscutellaris mosquito nucleotide phylogenetic focus
Heterotachy in mammalian promoter evolution.

PMID 16683025 · PMC1449885 · PLoS genetics · 2006 · 8 claims · 5 setups

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The rate of promoter evolution relative to control sequences is not consistent between or within mammalian lineages over time (heterotachy)

promoter ancient chimpanzee comparative ancient micro-indel
Reference based annotation with GeneMapper.

PMID 16600017 · PMC1557983 · Genome biology · 2006 · 7 claims · 6 setups

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GeneMapper transfers reference gene annotations to target genomes with higher accuracy than GeneWise and Projector

orthologous human-mouse chicken encode reference-based multi-species reciprocal
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
Microsatellite instability analysis in hereditary non-polyposis colon cancer using the Bethesda consensus panel of microsatellite markers in the absence of proband normal tissue.

PMID 16426447 · PMC1373649 · BMC medical genetics · 2006 · 7 claims · 4 setups

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MSI status can be determined in the absence of proband non-tumor tissue by comparing tumor alleles to alleles carried by the proband's progenitors

proband's peripheral hmsh2 microsatellite direct targeted

Experiments

Centromere-associated protein-E is essential for the mammalian mitotic checkpoint to prevent aneuploidy due to single chromosome loss.

Molecular epidemiology of O139 Vibrio cholerae: mutation, lateral gene transfer, and founder flush.

RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.

Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G.

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

High frequency of the IVS2-2A>G DNA sequence variation in SLC26A5, encoding the cochlear motor protein prestin, precludes its involvement in hereditary hearing loss.

Genome wide survey of G protein-coupled receptors in Tetraodon nigroviridis.

In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology.

Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.

Glia maturation factor gamma (GMFG): a cytokine-responsive protein during hematopoietic lineage development and its functional genomics analysis.

Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs.

Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes.

AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome.

Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication.

Mixed Cryptosporidium infections and HIV.

Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak.

Heterotachy in mammalian promoter evolution.

Reference based annotation with GeneMapper.

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

Microsatellite instability analysis in hereditary non-polyposis colon cancer using the Bethesda consensus panel of microsatellite markers in the absence of proband normal tissue.