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 737

System / cell line: type ✕ Clear

Plasmodium vivax dhfr and dhps mutations in isolates from Madagascar and therapeutic response to sulphadoxine-pyrimethamine.

PMID 18302746 · PMC2268703 · Malaria journal · 2008 · 6 claims · 7 setups

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pvdhfr and pvdhps mutations are common in Malagasy P. vivax isolates, with pvdhfr mutants far more prevalent than pvdhps mutants

vivax vivax-infected paired patients gene real-time microsatellite
Identification of ERGIC-53 as an intracellular transport receptor of alpha1-antitrypsin.

PMID 18283111 · PMC2265576 · The Journal of cell biology · 2008 · 8 claims · 6 setups

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α1-antitrypsin is a novel ERGIC-53 cargo protein identified via a YFP protein-fragment complementation assay (PCA) cDNA library screen

cos-1 hela hepg2 ergic-53 yfp sirna [35s]methionine
Opportunities and challenges in synthetic oligosaccharide and glycoconjugate research.

PMID 20161474 · PMC2794050 · Nature chemistry · 2009 · 8 claims · 7 setups

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A parallel combinatorial one-pot multi-step protecting-group procedure (Lewis acid catalyzed, up to seven steps) can transform tetra-O-TMS glucopyranosides into differentially protected monosaccharide building blocks without intermittent work-up/purification

library database oligovalent b-cells glycan bioinformatics one-pot
Reduced transcription of TCOF1 in adult cells of Treacher Collins syndrome patients.

PMID 20003452 · PMC2801500 · BMC medical genetics · 2009 · 8 claims · 5 setups

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TCOF1 transcript levels are significantly reduced (~18%) in leucocytes of TCS patients compared to controls

leucocytes mesenchymal leucocyte real-time direct flow
Rapid detection of SMARCB1 sequence variation using high resolution melting.

PMID 20003390 · PMC2801682 · BMC cancer · 2009 · 8 claims · 6 setups

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HRM screening of SMARCB1 amplicons has a zero false negative rate compared to direct sequencing

genomic same tumor rhabdoid high direct hrm
A restricted spectrum of NRAS mutations causes Noonan syndrome.

PMID 19966803 · PMC3118669 · Nature genetics · 2010 · 8 claims · 6 setups

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Germline NRAS mutations (T50I, G60E) cause a subset of Noonan syndrome cases via enhanced MAPK activation

cohort cos-7 recombinant nras mutation western ras
New generic primer system targeting mucosal/genital and cutaneous human papillomaviruses leads to the characterization of HPV 115, a novel Beta-papillomavirus species 3.

PMID 19948351 · PMC2813930 · Virology · 2010 · 8 claims · 8 setups

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The new CUT primer system detects a broader range of HPV genera/species and novel putative types than the FAP primer system (p<0.01)

skin cloned mixed-type gene nested sequencing molecular
CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features.

PMID 19922652 · PMC3091324 · Genome biology · 2009 · 8 claims · 8 setups

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CTCF binding sites can be classified into three occupancy-based classes (LowOc, MedOc, HighOc) based on similarity to the CTCF PWM motif

cd4+ hela imr90 embryonic chip-seq computational gene
Tyrosine phosphorylation inhibits PKM2 to promote the Warburg effect and tumor growth.

PMID 19920251 · PMC2812789 · Science signaling · 2009 · 7 claims · 8 setups

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Oncogenic FGFR1 directly phosphorylates PKM2 at tyrosine 105 (Y105), inhibiting its enzymatic activity

293t kg-1a recombinant h1299 ms-based co-transfection enzymatic
Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies.

PMID 19915672 · PMC2772813 · PloS one · 2009 · 8 claims · 8 setups

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MLSA of 89 genes across 108 global MTBC strains yields a single, highly robust phylogeny with virtually no homoplasy, congruent across parsimony, NJ, ML, and Bayesian methods.

global mtbc miru-vntr multilocus spoligotyping 15-loci-miru-vntr
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
Increasing the number of thyroid lesions classes in microarray analysis improves the relevance of diagnostic markers.

PMID 19893615 · PMC2764086 · PloS one · 2009 · 8 claims · 8 setups

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Simultaneous analysis of 347 thyroid samples across 12 histological classes from six datasets improves definition of diagnostic markers compared to prior binary-class studies

thyroid microarray gene real-time
A homozygous CARD9 mutation in a family with susceptibility to fungal infections.

PMID 19864672 · PMC2793117 · The New England journal of medicine · 2009 · 7 claims · 7 setups

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A homozygous CARD9 point mutation (Q295X, premature termination codon) is associated with autosomal recessive susceptibility to chronic mucocutaneous candidiasis.

family patients peripheral-blood peripheral snp microsatellite sanger
Neuroscience in the era of functional genomics and systems biology.

PMID 19829370 · PMC3645852 · Nature · 2009 · 8 claims · 7 setups

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Omics/discovery-based approaches do not eschew hypotheses but elevate hypothesis testing to high-throughput hypothesis generation and prioritization.

developing hippocampus bac-transgenic fetal situ gene bac-transgenic
Alzheimer's disease biomarker discovery in symptomatic and asymptomatic patients: experimental approaches and future clinical applications.

PMID 19796674 · PMC2840994 · Experimental gerontology · 2010 · 8 claims · 4 setups

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cDNA microarray screening of 6794 genes identified 32 genes aberrantly expressed (>1.8-fold) in the superior temporal gyrus of moderate dementia cases versus cognitively normal controls

post-mortem cortico-hippocampal cdna western culture
Genetic differences between avian and human isolates of Candida dubliniensis.

PMID 19788816 · PMC2819872 · Emerging infectious diseases · 2009 · 7 claims · 6 setups

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13 of 14 avian-associated C. dubliniensis isolates form a genetically distinct subgroup within MLST clade C1, separate from human isolates

candida fecal avian-associated multilocus pcr multiplex
Transcription dynamics.

PMID 19782025 · PMC6326382 · Molecular cell · 2009 · 8 claims · 8 setups

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Transcription factors locate their sparse specific binding sites via a 3D scanning mechanism combining rapid nuclear diffusion with frequent, very transient (seconds-scale) nonspecific chromatin interactions.

living linker lac glucocorticoid frap single-molecule nucleosome
A role of SCN9A in human epilepsies, as a cause of febrile seizures and as a potential modifier of Dravet syndrome.

PMID 19763161 · PMC2730533 · PLoS genetics · 2009 · 7 claims · 8 setups

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A heterozygous SCN9A missense mutation (p.N641Y) cosegregates with febrile seizures in the large K4425 family and is absent from ethnically matched population controls

family k4425 embryonic scn9a-n641y linkage copy deletion
mtDNA G10398A variant in African-American women with breast cancer provides resistance to apoptosis and promotes metastasis in mice.

PMID 19763141 · PMC2909846 · Journal of human genetics · 2009 · 8 claims · 8 setups

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The G10398A cybrid shows slower proliferation and delayed cell cycle progression (G1 accumulation, decreased G2/M) compared to wild-type G10398 cybrid

blood mitochondria g10398a cybrid pcr cybrid spectrophotometric
Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma.

PMID 19760750 · PMC2784016 · Human mutation · 2009 · 8 claims · 6 setups

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Two-round fast COLD-PCR followed by Sanger sequencing detects TP53 mutations at abundances as low as ~1%, below the sensitivity of conventional Sanger sequencing (~20-25%)

lung wild-type matched paired two-round real-time airs-rflp

Experiments

Plasmodium vivax dhfr and dhps mutations in isolates from Madagascar and therapeutic response to sulphadoxine-pyrimethamine.

Identification of ERGIC-53 as an intracellular transport receptor of alpha1-antitrypsin.

Opportunities and challenges in synthetic oligosaccharide and glycoconjugate research.

Reduced transcription of TCOF1 in adult cells of Treacher Collins syndrome patients.

Rapid detection of SMARCB1 sequence variation using high resolution melting.

A restricted spectrum of NRAS mutations causes Noonan syndrome.

New generic primer system targeting mucosal/genital and cutaneous human papillomaviruses leads to the characterization of HPV 115, a novel Beta-papillomavirus species 3.

CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features.

Tyrosine phosphorylation inhibits PKM2 to promote the Warburg effect and tumor growth.

Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies.

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

Increasing the number of thyroid lesions classes in microarray analysis improves the relevance of diagnostic markers.

A homozygous CARD9 mutation in a family with susceptibility to fungal infections.

Neuroscience in the era of functional genomics and systems biology.

Alzheimer's disease biomarker discovery in symptomatic and asymptomatic patients: experimental approaches and future clinical applications.

Genetic differences between avian and human isolates of Candida dubliniensis.

Transcription dynamics.

A role of SCN9A in human epilepsies, as a cause of febrile seizures and as a potential modifier of Dravet syndrome.

mtDNA G10398A variant in African-American women with breast cancer provides resistance to apoptosis and promotes metastasis in mice.

Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma.