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 43

System / cell line: recombinant ✕ Assay: activity ✕ Clear

'Unknown' proteins and 'orphan' enzymes: the missing half of the engineering parts list--and how to find it.

PMID 20001958 · PMC3022307 · The Biochemical journal · 2009 · 8 claims · 8 setups

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Comparative genomics is the single most effective strategy for predicting functions of unknown proteins and finding genes for orphan enzymes

lactococcus lactis arabidopsis coli gene recombinant enzyme
Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

PMID 16351747 · PMC1866387 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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Systematic in silico search identified 5 novel human kinase genes (on chromosomes 1, 11, 13, 15, 16) and 1 pseudogene (chromosome X) absent from KinBase

genome genomic kinase psi-blast comparative genscan
Engineered apoptotic nucleases for chromatin research.

PMID 17626049 · PMC1935020 · Nucleic acids research · 2007 · 8 claims · 6 setups

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Inserting TEVP cleavage sites immediately downstream of the two caspase-3 sites in DFF45 (I1I2 mutant) makes DFF40 nuclease activity exclusively dependent on TEVP cleavage (DFF-T)

recombinant cerevisiae coli western plasmid serial
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
Sequence-non-specific effects of RNA interference triggers and microRNA regulators.

PMID 19843612 · PMC2800214 · Nucleic acids research · 2010 · 8 claims · 7 setups

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Reagents of RNAi and miRNA technologies often trigger unintended sequence-non-specific immune responses in addition to intended sequence-specific silencing

recombinant t98g hek293 hela kinase pkr microarray
Structural insights into the inhibited states of the Mer receptor tyrosine kinase.

PMID 19028587 · PMC2686088 · Journal of structural biology · 2009 · 8 claims · 8 setups

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Nucleotide-bound (ADP and ANP/AMP-PNP) Mer kinase domain adopts an autoinhibited DFG-Asp-in/αC-Glu-out conformation with an activation-loop residue inserted into the active site

recombinant phosphorylated mer x-ray positional differential
A feed-forward pathway drives LRRK2 kinase membrane recruitment and activation.

PMID 36149401 · PMC9576273 · eLife · 2022 · 8 claims · 8 setups

Has reproduction · 50

A C-terminal patch of the LRRK2 Armadillo domain (residues ~350–550, 'site #1') binds non-phosphorylated Rab29, Rab8A, and Rab10 with low-micromolar affinity

recombinant lrrk2 hela hek293t microscale confocal immunoblotting
Nonclassic congenital lipoid adrenal hyperplasia: a new disorder of the steroidogenic acute regulatory protein with very late presentation and normal male genitalia.

PMID 16968793 · PMC1865081 · The Journal of clinical endocrinology and metabolism · 2006 · 8 claims · 7 setups

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Homozygous StAR missense mutations Val187Met and Arg188Cys cause a novel, milder form of lipoid CAH ('non-classic lipoid CAH') presenting at 2-4 years of age rather than in infancy

blood cos-1 bacteria mitochondria sequencing cell-based recombinant
Protein isoaspartate methyltransferase prevents apoptosis induced by oxidative stress in endothelial cells: role of Bcl-Xl deamidation and methylation.

PMID 18806875 · PMC2532751 · PloS one · 2008 · 8 claims · 8 setups

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PCMT overexpression protects porcine aortic endothelial cells (PAEC) from H2O2-induced apoptosis, raising the threshold H2O2 concentration required to trigger cell death.

porcine paec umbilical huvec methyltransferase sds-page fragmentation
Functional diversity of HIV-1 envelope proteins expressed by contemporaneous plasma viruses.

PMID 18312646 · PMC2270869 · Retrovirology · 2008 · 8 claims · 7 setups

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Infectivity of recombinant viruses carrying different Env proteins from the same patient varies over an approximately 10-fold range, even among viruses with similar tropism.

env u373 mt4-r5 u373-r5 phylogenetic infectivity flow
Congenital bovine spinal dysmyelination is caused by a missense mutation in the SPAST gene.

PMID 19714378 · PMC2854348 · Neurogenetics · 2010 · 8 claims · 5 setups

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A missense mutation (R560Q) in the SPAST gene's ATPase domain causes bovine spinal dysmyelination

cattle bovine coli affinity-purified snp reverse cdna
C-terminal mutants of apolipoprotein L-I efficiently kill both Trypanosoma brucei brucei and Trypanosoma brucei rhodesiense.

PMID 19997494 · PMC2778949 · PLoS pathogens · 2009 · 8 claims · 8 setups

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The C-terminal helix of apoL1 is entirely responsible for its interaction with SRA

coli brucei computational papio bacterial trypanolytic nickel-bead
Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization.

PMID 16209721 · PMC1262696 · BMC biology · 2005 · 8 claims · 9 setups

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hLsg1 is the human orthologue of yeast Lsg1p and defines a family of circularly permuted GTPases named YRG (YlqF Related GTPases)

multi-species recombinant immunoprecipitated hela phylogenetic gtp gtpase
Functional analysis of human mutations in homeodomain transcription factor PITX3.

PMID 17888164 · PMC2093940 · BMC molecular biology · 2007 · 7 claims · 5 setups

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Both S13N and G219fs mutants show partial loss-of-function in DNA-binding and/or transactivation activity, with G219fs more severely affected than S13N

lens western immunocytochemistry electrophoretic
The key role of genomics in modern vaccine and drug design for emerging infectious diseases.

PMID 19855822 · PMC2752168 · PLoS genetics · 2009 · 8 claims · 8 setups

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Reverse vaccinology (in silico genome screening for surface/secreted proteins) can identify vaccine candidates far faster than conventional approaches, as demonstrated by the MenB project.

neisseria streptococcus coli vibrio reverse pan-genomic comparative
Raf-1 activation disrupts its binding to keratins during cell stress.

PMID 15314064 · PMC2172217 · The Journal of cell biology · 2004 · 8 claims · 8 setups

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Raf-1 kinase associates directly with keratin K8 (not K18), independent of Raf kinase activity and independent of Ras-Raf interaction

ht29 transgenic bhk-21 bhk co-immunoprecipitation co-transfection oxidative
Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics.

PMID 15230980 · PMC459218 · BMC molecular biology · 2004 · 8 claims · 8 setups

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P. falciparum produces full-length PfCnA/PfCnB (calcineurin) and PP7 as well as proteolytically processed catalytic cores in vivo, likely as intermediates of a degradation pathway

falciparum coli native falciparum-infected rt-pcr recombinant peptide
Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

PMID 17927842 · PMC2174947 · BMC molecular biology · 2007 · 7 claims · 8 setups

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A 34-nt sequence motif (-81 to -48) is present in all primate edn promoters and in macaque ecp promoter but is deleted in other primate ecp promoters

primate hepg2 32p-labeled sequence rt-pcr luciferase
Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass.

PMID 18443592 · PMC2742198 · Nature genetics · 2008 · 8 claims · 8 setups

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Osteoglycin (Ogn) is a major candidate regulator of rat LVM, with increased Ogn protein expression associated with elevated LVM

heart ogn cos-1 neonatal eqtl quantitative genome-wide
Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.

PMID 18267968 · PMC2367719 · Nucleic acids research · 2008 · 6 claims · 8 setups

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The seed arm (guide strand positions 2-8), its complementary passenger-strand sequence, the 5' end of the guide strand, and the 3' overhang of the passenger strand can be simultaneously replaced with DNA without substantial loss of gene-silencing activity.

cho-k1 e14tg2a recombinant hela dual-luciferase rt-pcr electrophoresis

Experiments

'Unknown' proteins and 'orphan' enzymes: the missing half of the engineering parts list--and how to find it.

Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

Engineered apoptotic nucleases for chromatin research.

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

Sequence-non-specific effects of RNA interference triggers and microRNA regulators.

Structural insights into the inhibited states of the Mer receptor tyrosine kinase.

A feed-forward pathway drives LRRK2 kinase membrane recruitment and activation.

Nonclassic congenital lipoid adrenal hyperplasia: a new disorder of the steroidogenic acute regulatory protein with very late presentation and normal male genitalia.

Protein isoaspartate methyltransferase prevents apoptosis induced by oxidative stress in endothelial cells: role of Bcl-Xl deamidation and methylation.

Functional diversity of HIV-1 envelope proteins expressed by contemporaneous plasma viruses.

Congenital bovine spinal dysmyelination is caused by a missense mutation in the SPAST gene.

C-terminal mutants of apolipoprotein L-I efficiently kill both Trypanosoma brucei brucei and Trypanosoma brucei rhodesiense.

Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization.

Functional analysis of human mutations in homeodomain transcription factor PITX3.

The key role of genomics in modern vaccine and drug design for emerging infectious diseases.

Raf-1 activation disrupts its binding to keratins during cell stress.

Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics.

Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass.

Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.