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 196

System / cell line: coli ✕ Clear

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
High incidence of human bocavirus infection in children in Spain.

PMID 17904416 · PMC7108365 · Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2007 · 8 claims · 6 setups

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HBoV is a significant contributor to acute lower respiratory tract infection in young children in Spain

nasopharyngeal cloned hbov-positive urine nested multiplex sanger
High-precision mapping of protein protein interfaces: an integrated genetic strategy combining en masse mutagenesis and DNA-level parallel analysis on a yeast two-hybrid platform.

PMID 17702760 · PMC2018616 · Nucleic acids research · 2007 · 7 claims · 4 setups

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An integrated strategy combining en masse pentapeptide insertion mutagenesis, yeast two-hybrid screening, and parallel genetic footprinting can map protein-protein interfaces at amino acid precision and is generally applicable to any interacting protein pair.

saccharomyces plasmid pooled individual yeast pcr-based restriction
Polymorphism and epitope sharing between the alleles of merozoite surface protein-1 of Plasmodium falciparum among Indian isolates.

PMID 17659072 · PMC1950510 · Malaria journal · 2007 · 7 claims · 6 setups

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PfMAD20 is the predominant PfMSP-1 allelic type among Indian field isolates

falciparum escherichia coli-expressed recombinant pcr recombinant sds-page
Common genomic features of Campylobacter jejuni subsp. doylei strains distinguish them from C. jejuni subsp. jejuni.

PMID 17535437 · PMC1892558 · BMC microbiology · 2007 · 8 claims · 6 setups

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Cjd strains are phylogenetically distinct from Cjj strains based on MLST and CGI analysis

geographically cjd novel jejuni multilocus comparative phenotypic
SNAP: predict effect of non-synonymous polymorphisms on function.

PMID 17526529 · PMC1920242 · Nucleic acids research · 2007 · 7 claims · 8 setups

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SNAP, a neural network-based method using sequence-derived information, predicts whether a non-synonymous SNP is neutral or non-neutral for protein function

combined escherichia bacteriophage hiv-1 neural benchmark comparative
Genetic distance and heterogenecity between quasispecies is a critical predictor to IFN response in Egyptian patients with HCV genotype-4.

PMID 17300723 · PMC1805740 · Virology journal · 2007 · 7 claims · 7 setups

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Genetic distance and heterogeneity between HCV quasispecies is a critical predictor of IFN response in Egyptian genotype-4 patients

serum pcr cloned 5'utr rt-pcr molecular sequencing
Cryptic loxP sites in mammalian genomes: genome-wide distribution and relevance for the efficiency of BAC/PAC recombineering techniques.

PMID 17284462 · PMC1865043 · Nucleic acids research · 2007 · 6 claims · 6 setups

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Cryptic lox P sites occur frequently and are homogeneously distributed across the mouse genome (1.2 primary sites per megabase).

genome bac coli el350 genome-wide sequence bacterial
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
Profiling humoral immune responses to P. falciparum infection with protein microarrays.

PMID 18937256 · PMC3021802 · Proteomics · 2008 · 7 claims · 5 setups

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A protein microarray platform of 250 Pf proteins, individually expressed cell-free and printed unpurified, can profile serum antibody responses across donor groups of differing immune status

sera coli genomic microarray immuno-dot elisa
A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus.

PMID 18631455 · PMC2727981 · Immunity · 2008 · 7 claims · 8 setups

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Transcriptional modules constructed from coordinately expressed genes across 8 diseases form stable, biologically coherent functional units

pbmc genes monocytes original microarray literature stimulation
Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth.

PMID 18505588 · PMC2430713 · BMC genomics · 2008 · 8 claims · 8 setups

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Comparative genomics of B. longum DJO10A (minimally cultured) and NCC2705 (culture collection strain) reveals 17 unique DNA regions in DJO10A and 6 in NCC2705 despite otherwise high genome collinearity and identity

bifidobacterium longum xbai-digested whole-genome base codon
High-resolution array comparative genomic hybridization of single micrometastatic tumor cells.

PMID 18344524 · PMC2367728 · Nucleic acids research · 2008 · 7 claims · 8 setups

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A protocol combining PCR-based whole genome amplification with arrays of highly purified BAC clones enables detection of DNA copy number changes in single cells

single bac amplified pi-scei array quantitative dot
The use of multiple displacement amplification to amplify complex DNA libraries.

PMID 18285362 · PMC2275127 · Nucleic acids research · 2008 · 7 claims · 8 setups

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MDA alone cannot select against/remove plasmid ligation multimers, unlike bacterial propagation

hes3 hes3-derived coli plasmids isolation flcdna gis-pet
Nucleosome formation with the testis-specific histone H3 variant, H3t, by human nucleosome assembly proteins in vitro.

PMID 18281699 · PMC2367731 · Nucleic acids research · 2008 · 8 claims · 7 setups

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H3t/H4 forms nucleosomes with H2A/H2B via the salt-dialysis method, similar to conventional H3.1/H4

recombinant reconstituted his6-tagged hnap1 salt-dialysis micrococcal chaperone-mediated
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
A biomedically enriched collection of 7000 human ORF clones.

PMID 18231609 · PMC2211400 · PloS one · 2008 · 8 claims · 4 setups

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Produced and made available over 7000 fully sequence-verified plasmid ORF clones representing over 3400 unique human genes, in both closed (stop codon) and fusion (no stop codon) formats.

genes mgc plasmid literature pcr sequence
High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.

PMID 20037647 · PMC2793016 · PloS one · 2009 · 7 claims · 7 setups

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A dirty genome approach using unfinished, unclosed genome sequences combined with proteomics can rapidly identify immunogenic proteins useful for diagnostic tool development

parachlamydia spots coli recombinant pyrosequencing solexa gel
'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
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

Experiments

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

High incidence of human bocavirus infection in children in Spain.

High-precision mapping of protein protein interfaces: an integrated genetic strategy combining en masse mutagenesis and DNA-level parallel analysis on a yeast two-hybrid platform.

Polymorphism and epitope sharing between the alleles of merozoite surface protein-1 of Plasmodium falciparum among Indian isolates.

Common genomic features of Campylobacter jejuni subsp. doylei strains distinguish them from C. jejuni subsp. jejuni.

SNAP: predict effect of non-synonymous polymorphisms on function.

Genetic distance and heterogenecity between quasispecies is a critical predictor to IFN response in Egyptian patients with HCV genotype-4.

Cryptic loxP sites in mammalian genomes: genome-wide distribution and relevance for the efficiency of BAC/PAC recombineering techniques.

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

Profiling humoral immune responses to P. falciparum infection with protein microarrays.

A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus.

Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth.

High-resolution array comparative genomic hybridization of single micrometastatic tumor cells.

The use of multiple displacement amplification to amplify complex DNA libraries.

Nucleosome formation with the testis-specific histone H3 variant, H3t, by human nucleosome assembly proteins in vitro.

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.

A biomedically enriched collection of 7000 human ORF clones.

High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.

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

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