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 34

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

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
A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.

PMID 16670430 · PMC1456330 · Nucleic acids research · 2006 · 8 claims · 7 setups

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Highly-degenerate RE1 sites are significantly enriched in promoters of validated and putative REST target genes compared to control promoters

orthologous randomized high-score promoters pssm-based comparative motif
Empirical Bayes analysis of quantitative proteomics experiments.

PMID 19829701 · PMC2759080 · PloS one · 2009 · 8 claims · 4 setups

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Developed a new empirical Bayes framework that models log2 SILAC protein ratios and is robust to non-Gaussian tails and data sparsity, unlike Gaussian mixture models or Efron's original spline-based approach

hela predicted computational silac utr gaussian
Heart disease, clinical proteomics and mass spectrometry.

PMID 15502250 · PMC3839266 · Disease markers · 2004 · 8 claims · 4 setups

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Proteins bound to serum albumin (the albuminome) will be altered in patients with heart failure compared to controls

swine animal general affinity maldi-tof tandem
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
Molecular analysis of a leprosy immunotherapeutic bacillus provides insights into Mycobacterium evolution.

PMID 17912347 · PMC1989137 · PloS one · 2007 · 8 claims · 8 setups

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MIP is the evolutionary predecessor/ancestor of the pathogenic Mycobacterium avium intracellulare complex (MAIC), having retained a free-living lifestyle rather than undergoing parasitic reductive genome evolution

mip diagnostic is900-specific pgg
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
Novel point mutation in the extracellular domain of the granulocyte colony-stimulating factor (G-CSF) receptor in a case of severe congenital neutropenia hyporesponsive to G-CSF treatment.

PMID 10449521 · PMC2195597 · The Journal of experimental medicine · 1999 · 7 claims · 8 setups

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A novel C→A point mutation at nucleotide 850 of GCSFR cDNA causes a Pro→His substitution at position 206 (P206H) in the proline-rich hinge of the CRH domain of the G-CSF receptor extracellular domain in an SCN patient hyporesponsive to G-CSF.

bone fibroblast 32d.cl8.6 32d rt-pcr genomic flow
A catalog of human cDNA expression clones and its application to structural genomics.

PMID 15345055 · PMC522878 · Genome biology · 2004 · 8 claims · 7 setups

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A high-throughput screening approach can identify human cDNA clones from the hEx1 library that express soluble protein in E. coli

hex1 ensembl coli recombinant small-scale tag-sequencing blastp
In silico meets in vivo.

PMID 18304380 · PMC2374716 · Genome biology · 2008 · 8 claims · 8 setups

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About 10% of positions in multiple sequence alignments of the human genome with other vertebrate genomes are likely incorrect.

genome lines prokaryotic genomes genome genome-wide gene
Plasma proteomics of pancreatic cancer patients by multi-dimensional liquid chromatography and two-dimensional difference gel electrophoresis (2D-DIGE): up-regulation of leucine-rich alpha-2-glycoprotein in pancreatic cancer.

PMID 17303479 · PMC7105233 · Journal of chromatography. B, Analytical technologies in the biomedical and life sciences · 2007 · 5 claims · 5 setups

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Pre-fractionation of plasma with immuno-affinity depletion and anion-exchange chromatography prior to 2D-DIGE substantially increases the number of detectable protein spots compared with unfractionated plasma.

plasma excised fractionated 2d-dige multi-dimensional lc-ms
BioDrugScreen: a computational drug design resource for ranking molecules docked to the human proteome.

PMID 19923229 · PMC2808957 · Nucleic acids research · 2010 · 6 claims · 5 setups

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BioDrugScreen is a web resource providing pre-docked and pre-scored receptor-ligand complexes for ranking molecules against human proteome targets

docked targets molecular binding continuum
DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues.

PMID 38600112 · PMC11006913 · Nature communications · 2024 · 8 claims · 5 setups

Has reproduction · 93

Many of the 92 assayed HD missense variants alter DNA binding affinity and/or specificity compared to their corresponding reference alleles

homeodomain hoxd13 cerevisiae amino universal chip-seq electrophoretic
A surrogate-based approach for post-genomic partner identification.

PMID 11602024 · PMC57814 · BMC biotechnology · 2001 · 8 claims · 5 setups

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Peptide surrogates derived from random phage display libraries contain amino acid sequence information that identifies the natural biological partner of the panned target via database searching.

biotinylated tnf-β analysis secondary phage sequence secondary
Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1.

PMID 17478514 · PMC1904287 · Nucleic acids research · 2007 · 8 claims · 5 setups

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62 YY1-related sequences were identified across genomes ranging from flying insects to humans, with high zinc finger domain conservation

genome insect yy1-related zinc blast sequence synonymous
From genomes to systems.

PMID 15535877 · PMC545775 · Genome biology · 2004 · 8 claims · 8 setups

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Biological networks (protein-gene interactions in the genome, protein-protein interactions in the proteome, biochemical reactions in the metabolome) are scale-free rather than random

serum trypanosoma alzheimer's complexes gel maldi-ms ft-icr
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
Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry.

PMID 15642101 · PMC549070 · Genome biology · 2005 · 8 claims · 4 setups

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PeptideAtlas, a public database integrating MS/MS-derived peptide identifications with the human genome, was built as an expandable resource for proteomic data.

subset drosophila ensembl lc-ms icat peptide-to-genome
Antibody binding loop insertions as diversity elements.

PMID 17023486 · PMC1635297 · Nucleic acids research · 2006 · 7 claims · 8 setups

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A lysozyme-binding VHH CDR3 loop can be grafted into two surface-exposed loops of superfolder GFP, conferring lysozyme-binding activity while the protein remains fluorescent.

gfp-anti-lysozyme coli full-length gfp-hcdr3 elisa flow surface
Genomes of Helicobacter pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island.

PMID 16872520 · PMC1553449 · BMC genomics · 2006 · 8 claims · 7 setups

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Native Peruvian H. pylori strains comprise two lineages: predominant hp-Europe and ~20% hsp-Amerind (Amerindian ancestry, closer to Alaska strains)

pylori peruvian spanish fluorescent multilocus oipa

Experiments

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

A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.

Empirical Bayes analysis of quantitative proteomics experiments.

Heart disease, clinical proteomics and mass spectrometry.

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

Molecular analysis of a leprosy immunotherapeutic bacillus provides insights into Mycobacterium evolution.

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

Novel point mutation in the extracellular domain of the granulocyte colony-stimulating factor (G-CSF) receptor in a case of severe congenital neutropenia hyporesponsive to G-CSF treatment.

A catalog of human cDNA expression clones and its application to structural genomics.

In silico meets in vivo.

Plasma proteomics of pancreatic cancer patients by multi-dimensional liquid chromatography and two-dimensional difference gel electrophoresis (2D-DIGE): up-regulation of leucine-rich alpha-2-glycoprotein in pancreatic cancer.

BioDrugScreen: a computational drug design resource for ranking molecules docked to the human proteome.

DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues.

A surrogate-based approach for post-genomic partner identification.

Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1.

From genomes to systems.

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

Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry.

Antibody binding loop insertions as diversity elements.

Genomes of Helicobacter pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island.