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 331

Assay: deletion ✕ Clear

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
Proteomic screen defines the hepatocyte nuclear factor 1alpha-binding partners and identifies HMGB1 as a new cofactor of HNF1alpha.

PMID 18160415 · PMC2275099 · Nucleic acids research · 2008 · 8 claims · 8 setups

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HMGB1 is a novel HNF1α-interacting protein identified via a co-IP-MS screening strategy

hepg2 recombinant co-immunoprecipitation immunofluorescence gst
Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes.

PMID 18053250 · PMC2246260 · Genome biology · 2007 · 8 claims · 4 setups

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Loss-of-function phenotypes in yeast are predictable from a gene's connections in a functional gene network via guilt-by-association.

saccharomyces guilt-by-association comparison network-guided
Single nucleotide polymorphisms in bone turnover-related genes in Koreans: ethnic differences in linkage disequilibrium and haplotype.

PMID 18036257 · PMC2222243 · BMC medical genetics · 2007 · 8 claims · 5 setups

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Resequencing 81 candidate osteoporosis genes in 24 Koreans identified 942 variants (888 SNPs, 43 indels, 11 microsatellites)

genomic sequenced korean common sanger sequence population
In silico screening of mutational effects on enzyme-proteic inhibitor affinity: a docking-based approach.

PMID 17559675 · PMC1913526 · BMC structural biology · 2007 · 8 claims · 4 setups

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A rigid-body docking-based approach can predict mutational effects on binding energetics for three structurally distinct enzyme-proteic inhibitor systems (hRI-Ang, Bn-Bs, BPTI-β-Trypsin)

ribonuclease barnase bovine hri-ang rigid-body cluster
QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data.

PMID 17341461 · PMC1874617 · Nucleic acids research · 2007 · 8 claims · 7 setups

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QuantiSNP (OB-HMM) provides probabilistic quantification of copy number states and significantly improves accuracy of segmental aneuploidy identification and breakpoint mapping relative to existing tools (BeadStudio/Illumina)

genomic same pseudo-normal artificially snp fish molecular
Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada.

PMID 17288567 · PMC1796603 · BMC evolutionary biology · 2007 · 8 claims · 8 setups

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Gene tree parsimony applied to EST data with widespread gene duplication can infer an organismal phylogeny in excellent agreement with the expected angiosperm phylogeny.

angiosperms animal oryza proteobacteria gene site-heterogeneous codon
Cruciform extrusion propensity of human translocation-mediating palindromic AT-rich repeats.

PMID 17264116 · PMC1851657 · Nucleic acids research · 2007 · 8 claims · 4 setups

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Cruciform extrusion propensity of PATRRs depends on both length and central symmetry of the repeat.

plasmids same single-stranded patrr-containing cruciform endonuclease secondary
Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia.

PMID 19039135 · PMC2746051 · Science (New York, N.Y.) · 2008 · 8 claims · 7 setups

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Diagnosis and relapse ALL samples show different patterns of CNAs, with relapse-acquired abnormalities preferentially affecting cell cycle regulation and B-cell development genes

matched bone leukemia diagnosis snp flow quantitative
The molecular landscape of ASPM mutations in primary microcephaly.

PMID 19028728 · PMC2658750 · Journal of medical genetics · 2009 · 8 claims · 7 setups

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ASPM mutations are the most common cause of MCPH

consanguineous genomic parents one polymorphic sanger family
Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1.

PMID 18992264 · PMC2682550 · Mutation research · 2009 · 8 claims · 8 setups

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A combined functional assay, bioinformatics prediction, and structural modeling approach can classify BRCA1 variants of uncertain significance

saccharomyces cerevisiae hek-293t yeast yeast β-galactosidase dual
Context dependent function of APPb enhancer identified using enhancer trap-containing BACs as transgenes in zebrafish.

PMID 18832376 · PMC2577333 · Nucleic acids research · 2008 · 8 claims · 6 setups

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A novel enhancer trap method retrofitting BACs with Tn10-based transposons enables nontargeted, functional mapping of noncontiguous cis-regulatory elements as zebrafish transgenes.

zebrafish bac genomic transgenic field bac
Cardiovascular genomics, personalized medicine, and the National Heart, Lung, and Blood Institute: part I: the beginning of an era.

PMID 20031542 · PMC3097376 · Circulation. Cardiovascular genetics · 2008 · 7 claims · 8 setups

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Rare Mendelian mutations (e.g., in sarcomere genes, ion channels, FBN1, LMNA) cause specific rare cardiovascular conditions (hypertrophic/dilated cardiomyopathy, long-QT syndrome, thoracic aortic aneurysm, progeria) but explain little of common CVD risk.

community-based subjects dallas mice exon community-based gene
Characterization of large rearrangements in autosomal dominant polycystic kidney disease and the PKD1/TSC2 contiguous gene syndrome.

PMID 18818683 · PMC2756756 · Kidney international · 2008 · 8 claims · 8 setups

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Developed an MLPA assay with PKD1 exon 1-33 probes designed at single base-pair mismatches with the six PKD1 pseudogenes to achieve locus specificity

blood-derived blood crisp father mlpa long-range field
KCNQ4 mutations associated with nonsyndromic progressive sensorineural hearing loss.

PMID 18797286 · PMC2743278 · Current opinion in otolaryngology & head and neck surgery · 2008 · 8 claims · 8 setups

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KCNQ4 mutations at the DFNA2 locus on chromosome 1p34 cause autosomal dominant nonsyndromic progressive sensorineural hearing loss

seven-generation dfna2 xenopus kcnq4 linkage mutation heterologous
Additional EFNB1 mutations in craniofrontonasal syndrome.

PMID 18627045 · PMC2774847 · American journal of medical genetics. Part A · 2008 · 8 claims · 4 setups

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Loss-of-function mutations in EFNB1 (Xq13.1) are the cause of CFNS in the majority of patients

lymphoblastoid cfns patients additional pcr multiplex molecular
The malaria secretome: from algorithms to essential function in blood stage infection.

PMID 18551176 · PMC2408878 · PLoS pathogens · 2008 · 8 claims · 5 setups

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An expanded secretome (van Ooij secretome) built from a revised SignalP MaxS cutoff (0.571) plus HMMER-expanded HT-motif search yields 422 proteins (224 excluding RIFIN/STEVOR families).

falciparum berghei plasmodium signal comparative piggybac
Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line.

PMID 18535014 · PMC2464741 · Molecular biology and evolution · 2008 · 8 claims · 7 setups

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Repair genes are numerically less common than apoptosis genes in the genomes of multicellular organisms

yeast familial human-mouse comparative gene mutation
High resolution melting analysis for rapid and sensitive EGFR and KRAS mutation detection in formalin fixed paraffin embedded biopsies.

PMID 18495026 · PMC2408599 · BMC cancer · 2008 · 8 claims · 4 setups

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HRM correctly identified all 73 EGFR-mutation-positive FFPE samples previously found by sequencing, giving 100% sensitivity and 90% specificity

ffpe single high direct hrm
Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.

PMID 24885615 · PMC4070566 · BMC genomics · 2014 · 8 claims · 8 setups

Has reproduction · 50

A total of 40 candidate Hfq-dependent sRNAs were identified genome-wide in E. amylovora by combining RNA-seq with a Rho-independent terminator search.

erwinia intergenic candidate wounded small northern race

Experiments

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

Proteomic screen defines the hepatocyte nuclear factor 1alpha-binding partners and identifies HMGB1 as a new cofactor of HNF1alpha.

Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes.

Single nucleotide polymorphisms in bone turnover-related genes in Koreans: ethnic differences in linkage disequilibrium and haplotype.

In silico screening of mutational effects on enzyme-proteic inhibitor affinity: a docking-based approach.

QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data.

Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada.

Cruciform extrusion propensity of human translocation-mediating palindromic AT-rich repeats.

Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia.

The molecular landscape of ASPM mutations in primary microcephaly.

Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1.

Context dependent function of APPb enhancer identified using enhancer trap-containing BACs as transgenes in zebrafish.

Cardiovascular genomics, personalized medicine, and the National Heart, Lung, and Blood Institute: part I: the beginning of an era.

Characterization of large rearrangements in autosomal dominant polycystic kidney disease and the PKD1/TSC2 contiguous gene syndrome.

KCNQ4 mutations associated with nonsyndromic progressive sensorineural hearing loss.

Additional EFNB1 mutations in craniofrontonasal syndrome.

The malaria secretome: from algorithms to essential function in blood stage infection.

Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line.

High resolution melting analysis for rapid and sensitive EGFR and KRAS mutation detection in formalin fixed paraffin embedded biopsies.

Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.