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 14

System / cell line: secondary ✕ Assay: signal ✕ Clear

Quality control of highly multiplexed proteomic immunostaining with quantum dots: correcting for crosstalk.

PMID 19963937 · PMC5859565 · Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference · 2009 · 8 claims · 5 setups

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Crosstalk between multiplexed QD-antibody reporters occurs and can be on the same order of magnitude as the intended signal, varying by tissue and reagent.

ffpe prostate renal pure multiplexed single-primary-antibody wavelength-resolved
Multiple functions of precursor BDNF to CNS neurons: negative regulation of neurite growth, spine formation and cell survival.

PMID 19674479 · PMC2743674 · Molecular brain · 2009 · 7 claims · 8 setups

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R125M, R127L, and R125M/R127L BDNF SNP variants are poorly cleaved, resulting in predominant secretion of proBDNF (CR-proBDNF)

bdnf hippocampal cortical cerebellar bioinformatic western immunoprecipitation
Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure.

PMID 35869080 · PMC9307511 · Nature communications · 2022 · 7 claims · 4 setups

Has reproduction · 80

DiffScan is a computational framework combining a Normalization module and a Scan module to identify SVRs at nucleotide resolution from SP data.

transcripts platforms bacillus multi-subcellular simulated negative benchmark
Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays.

PMID 15722479 · PMC549431 · Nucleic acids research · 2005 · 7 claims · 4 setups

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Two base deletion probes display the highest average hybridization specificity, followed by single base substitution, single base deletion, and single base insertion probes.

atm hybridized probe oligonucleotide transcription microarray
Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada.

PMID 17288567 · PMC1796603 · BMC evolutionary biology · 2007 · 8 claims · 8 setups

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Gene tree parsimony applied to EST data with widespread gene duplication can infer an organismal phylogeny in excellent agreement with the expected angiosperm phylogeny.

angiosperms animal oryza proteobacteria gene site-heterogeneous codon
Proteomic and genetic approaches identify Syk as an AML target.

PMID 19800574 · PMC2803063 · Cancer cell · 2009 · 8 claims · 8 setups

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EGFR inhibitors (e.g., gefitinib) induce AML differentiation through a non-EGFR, off-target mechanism

hl-60 aml molm-14 luciferase-labeled phospho-tyrosine kinome-wide secondary
In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology.

PMID 15871745 · PMC1156887 · BMC genomics · 2005 · 7 claims · 6 setups

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Only 14±2% of canine transcripts were detected by U133A probe sets versus 49±6% of human transcripts when hybridized to the same chip

canine tissues hg-u133a probes microarray sequence ortholog
Antibody protein array analysis of the tear film cytokines.

PMID 18677223 · PMC3786218 · Optometry and vision science : official publication of the American Academy of Optometry · 2008 · 7 claims · 4 setups

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Tear fluid contains factors with affinity for plastic, capture antibodies, and IgG that create matrix effects profoundly impacting dot ELISA/array reliability

tear normalized antibody 12-plex two-step
Getting started in computational immunology.

PMID 18769677 · PMC2518523 · PLoS computational biology · 2008 · 8 claims · 7 setups

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Affinity maturation is driven by cycles of somatic hypermutation and affinity-dependent selection acting on B cell Ig receptors.

splenic lymphocytes lymph secondary flow microdissection intravital
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
Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective.

PMID 18397526 · PMC2643940 · Genome biology · 2008 · 8 claims · 8 setups

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The SNP A/S ratio is a robust measure of selective constraint, correlating with interspecies Ka/Ks ratios and with protein sequence conservation.

sequence genes proteins sequences snp interspecies sequence
Adaptations to climate in candidate genes for common metabolic disorders.

PMID 18282109 · PMC2242814 · PLoS genetics · 2008 · 8 claims · 7 setups

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A network-based bioinformatics approach (Molecular Triangulation) was used to select 82 candidate genes belonging to the core subnetwork of metabolic syndrome phenotypes.

individuals population genic compiled snp spearman bayesian
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
SGCEdb: a flexible database and web interface integrating experimental results and analysis for structural genomics focusing on Caenorhabditis elegans.

PMID 16381914 · PMC1347399 · Nucleic acids research · 2006 · 8 claims · 8 setups

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SGCEdb is a flexible, reusable database and web interface for reporting and analyzing structural genomics experiment results, focused on C. elegans

elegans expressed soluble crystallized recombinant solubility purification

Experiments

Quality control of highly multiplexed proteomic immunostaining with quantum dots: correcting for crosstalk.

Multiple functions of precursor BDNF to CNS neurons: negative regulation of neurite growth, spine formation and cell survival.

Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure.

Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays.

Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada.

Proteomic and genetic approaches identify Syk as an AML target.

In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology.

Antibody protein array analysis of the tear film cytokines.

Getting started in computational immunology.

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

Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective.

Adaptations to climate in candidate genes for common metabolic disorders.

MEROPS: the peptidase database.

SGCEdb: a flexible database and web interface integrating experimental results and analysis for structural genomics focusing on Caenorhabditis elegans.