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 21

System / cell line: sequence ✕ Assay: substrate ✕ Clear

RiboSubstrates: a web application addressing the cleavage specificities of ribozymes in designated genomes.

PMID 17076887 · PMC1634876 · BMC bioinformatics · 2006 · 7 claims · 4 setups

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RiboSubstrates is a web-based Perl application that scans a cDNA database for all potential substrates of a given ribozyme, including perfect matches, Wobble base-pair matches, and mismatch-containing matches.

homo hcv substrate ribozyme
NetworKIN: a resource for exploring cellular phosphorylation networks.

PMID 17981841 · PMC2238868 · Nucleic acids research · 2008 · 8 claims · 4 setups

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NetworKIN integrates consensus substrate motifs with probabilistic network context modelling to predict cellular kinase-substrate relations.

phosphoproteome kinome interactome 53bp1 consensus blastp probabilistic
Prediction of specificity-determining residues for small-molecule kinase inhibitors.

PMID 19032760 · PMC2655090 · BMC bioinformatics · 2008 · 8 claims · 5 setups

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S-Filter is a novel method combining sequence and structural information (within PFAAT) to predict specificity-determining residues and selectivity profiles for small-molecule kinase inhibitors

panel kinase-inhibitor sequence erk2 caliper radiometric solvent
The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

PMID 12361482 · PMC131051 · BMC genetics · 2002 · 8 claims · 7 setups

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The human TDH gene is located at chromosome 8p23-22, spans 10 kb, and has 8 exons that would be expected to encode a 369-residue ORF.

genomic predicted cdna tissues genomic sequence pcr
Protein kinases of the human malaria parasite Plasmodium falciparum: the kinome of a divergent eukaryote.

PMID 15479470 · PMC526369 · BMC genomics · 2004 · 8 claims · 4 setups

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65 ePK sequences were identified in the P. falciparum genome and classified via phylogenetic analysis relative to the seven established ePK groups

falciparum individual recombinant cmgc-group genome-wide blastp kinase
The pharmacogenomics of membrane transporters project: research at the interface of genomics and transporter pharmacology.

PMID 19940846 · PMC2923224 · Clinical pharmacology and therapeutics · 2010 · 8 claims · 8 setups

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PMT identified sequence variants in 129 membrane transporter genes in the SLC and ABC superfamilies, discovering over 3100 SNPs

sophie mammalian xenopus lymphoblastoid resequencing cellular heterologous
Comparative genomics and understanding of microbial biology.

PMID 10998382 · PMC2627966 · Emerging infectious diseases · 2000 · 8 claims · 7 setups

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GC content varies widely among prokaryotic genomes (29% in B. burgdorferi to 68% in M. tuberculosis) and shapes codon usage and amino acid composition.

completed same sequenced mycobacterium whole-genome comparative phylogenomic
Evolution of variants of yeast site-specific recombinase Flp that utilize native genomic sequences as recombination target sites.

PMID 17003057 · PMC1635253 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Stepwise directed evolution using chimeric FLRT (FRT/genomic hybrid) intermediate sites can generate Flp variants capable of recombining native genomic FRT-like sequences from the human IL10 gene (FL-IL10A, FL-IL10B).

coli flp il10 flp-holliday recombination site-specific computational
Multiplex SNP typing by bioluminometric assay coupled with terminator incorporation (BATI).

PMID 16141191 · PMC1197137 · Nucleic acids research · 2005 · 8 claims · 6 setups

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A novel 'bioluminometric assay coupled with terminator (ddNTP) incorporation' (BATI) platform was developed for multiplex SNP typing in a single reaction chamber.

pcr-amplified same sequence luciferase bioluminometric bati comparison
The 'permeome' of the malaria parasite: an overview of the membrane transport proteins of Plasmodium falciparum.

PMID 15774027 · PMC1088945 · Genome biology · 2005 · 7 claims · 4 setups

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P. falciparum encodes substantially more membrane transport proteins than originally annotated

falciparum genome-wide bioinformatic quantification
Identification and characterisation of the angiotensin converting enzyme-3 (ACE3) gene: a novel mammalian homologue of ACE.

PMID 17597519 · PMC1925091 · BMC genomics · 2007 · 7 claims · 7 setups

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A novel single-domain ACE-like gene, ACE3, exists in mouse, rat, cow, dog and human genomes, located on the same chromosome downstream of ACE.

dog predicted ace3 panel blast sequence homology
MEROPS: the peptidase database.

PMID 19892822 · PMC2808883 · Nucleic acids research · 2010 · 8 claims · 5 setups

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MEROPS is a manually curated hierarchical classification of peptidases and protein inhibitors organized into protein species, families, and clans based on sequence and structural homology.

archaean holotype c-x-c proteins comparative domain substrate
Characterization of a natural mutator variant of human DNA polymerase lambda which promotes chromosomal instability by compromising NHEJ.

PMID 19806195 · PMC2751832 · PloS one · 2009 · 8 claims · 8 setups

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The W438 hPolλ variant has reduced base substitution fidelity in vitro compared to wild-type R438

normal recombinant hpolλ short pcr-sscp ber m13mp2
Back to basics.

PMID 12186643 · PMC139395 · Genome biology · 2002 · 8 claims · 8 setups

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Human PDS (Pendrin) gene mutations damage ear structures and are linked to hereditary deafness and goiter

chromosome pendrin yeast carbonic genome gene mudpit
Mutation in mitochondrial complex I ND6 subunit is associated with defective response to hypoxia in human glioma cells.

PMID 15248896 · PMC481082 · Molecular cancer · 2004 · 8 claims · 8 setups

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An unreported T14634C mutation in the mtDNA-encoded ND6 subunit of Complex I is present in the hypoxia-sensitive glioma cell line M010b but not in hypoxia-tolerant lines.

gbm m010b m006x mtdna quantitative mitochondrial
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
Single nucleotide polymorphism discovery and functional assessment of variation in the UDP-glucuronosyltransferase 2B7 gene.

PMID 18622261 · PMC2680356 · Pharmacogenetics and genomics · 2008 · 7 claims · 7 setups

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UGT2B7 haplotype 4 is associated with increased enzyme activity (M3G and M6G formation)

liver caucasian ugt2b7 gene snp enzymatic
SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions.

PMID 19934256 · PMC2808967 · Nucleic acids research · 2010 · 8 claims · 6 setups

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SuperCYP is a comprehensive relational database aggregating CYP enzyme, drug metabolism, SNP/mutation, and structural information from literature and web resources.

scientific pubmed cyp-drug cyp text mutation manual
Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells.

PMID 16251401 · PMC1270952 · Nucleic acids research · 2005 · 8 claims · 8 setups

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ZFNs combining the FokI nuclease domain with custom zinc finger proteins can deliver site-specific double-strand breaks to plant and mammalian genomes.

foki zif268-derived coli zfns limited foot-printing x-ray
CHEK2 mutations affecting kinase activity together with mutations in TP53 indicate a functional pathway associated with resistance to epirubicin in primary breast cancer.

PMID 18725978 · PMC2518116 · PloS one · 2008 · 7 claims · 6 setups

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TP53 mutations, especially those affecting the L2/L3 DNA-binding domains, are associated with resistance (progressive disease) to epirubicin therapy

snap-frozen tumor u-2-os patients pcr bisulphite loss

Experiments

RiboSubstrates: a web application addressing the cleavage specificities of ribozymes in designated genomes.

NetworKIN: a resource for exploring cellular phosphorylation networks.

Prediction of specificity-determining residues for small-molecule kinase inhibitors.

The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

Protein kinases of the human malaria parasite Plasmodium falciparum: the kinome of a divergent eukaryote.

The pharmacogenomics of membrane transporters project: research at the interface of genomics and transporter pharmacology.

Comparative genomics and understanding of microbial biology.

Evolution of variants of yeast site-specific recombinase Flp that utilize native genomic sequences as recombination target sites.

Multiplex SNP typing by bioluminometric assay coupled with terminator incorporation (BATI).

The 'permeome' of the malaria parasite: an overview of the membrane transport proteins of Plasmodium falciparum.

Identification and characterisation of the angiotensin converting enzyme-3 (ACE3) gene: a novel mammalian homologue of ACE.

MEROPS: the peptidase database.

Characterization of a natural mutator variant of human DNA polymerase lambda which promotes chromosomal instability by compromising NHEJ.

Back to basics.

Mutation in mitochondrial complex I ND6 subunit is associated with defective response to hypoxia in human glioma cells.

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

Single nucleotide polymorphism discovery and functional assessment of variation in the UDP-glucuronosyltransferase 2B7 gene.

SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions.

Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells.

CHEK2 mutations affecting kinase activity together with mutations in TP53 indicate a functional pathway associated with resistance to epirubicin in primary breast cancer.