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 10

System / cell line: tree ✕ Assay: combined ✕ Clear

Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms.

PMID 15629046 · PMC5172449 · Genomics, proteomics & bioinformatics · 2004 · 8 claims · 7 setups

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Sequence-based molecular phylogenies widely support a sister relationship between animals and fungi, grouped as the Opisthokonta

nine animals completed fungal combined sequence biochemical
Integrated analysis of genetic and proteomic data identifies biomarkers associated with adverse events following smallpox vaccination.

PMID 18923431 · PMC2692715 · Genes and immunity · 2009 · 7 claims · 6 setups

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A two-stage strategy (Random Forest filtering followed by decision tree modeling) can integrate categorical genetic and continuous proteomic data to identify biomarkers of AE risk

ebv-transformed serum combined rf-filtered snp serum random
Genome comparison without alignment using shortest unique substrings.

PMID 15910684 · PMC1166540 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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A number of sequence comparison tasks, including detection of unique genomic regions, can be accomplished efficiently without an alignment step using shortest unique substrings.

caenorhabditis genome mycoplasma shuffled genome-wide upstream-region local
A computational screen for type I polyketide synthases in metagenomics shotgun data.

PMID 18953415 · PMC2568958 · PloS one · 2008 · 8 claims · 6 setups

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Combining HMM domain searches with maximum-likelihood phylogenetic trees can discriminate true PKS I sequences from evolutionarily related but functionally different enzymes (e.g., FAS I) in metagenomic data.

predicted hmm-identified reference hmm hmm maximum-likelihood robinson-foulds
Structural evolution of the protein kinase-like superfamily.

PMID 16244704 · PMC1261164 · PLoS computational biology · 2005 · 8 claims · 5 setups

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All kinases in the superfamily share a 'universal core' domain consisting only of the regions required for ATP binding and the phosphotransfer reaction.

bank representative same kinase comparative manual structure-annotated
A human genome-wide library of local phylogeny predictions for whole-genome inference problems.

PMID 18710563 · PMC2556685 · BMC genomics · 2008 · 7 claims · 5 setups

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A genome-wide library of nearly 16 million local maximum parsimony phylogenies was constructed from HapMap CEU and YRI SNP data across all human autosomes

hapmap 5-snp genome-wide first maximum mutual pearson
Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes.

PMID 16757574 · PMC1475747 · Nucleic acids research · 2006 · 6 claims · 8 setups

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Applying seven independent computational disease-gene prioritization methods in concert to 9556 positional candidate genes identifies a prioritized set of likely T2D and obesity candidate genes

pubmed genes same randomly geneseeker evoc disease
In silico analysis of missense substitutions using sequence-alignment based methods.

PMID 18951440 · PMC3431198 · Human mutation · 2008 · 8 claims · 7 setups

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Carefully validated PMSA-based computational algorithms can achieve predictive values of ~75-95% for classifying missense substitutions as pathogenic or neutral.

clinically sequence curated deep blosum62 sift align-gvgd
Human stool contains a previously unrecognized diversity of novel astroviruses.

PMID 19814825 · PMC2765957 · Virology journal · 2009 · 8 claims · 8 setups

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Human stool contains a previously unrecognized diversity of astroviruses beyond the classic 8 serotypes and AstV-MLB1/AstV-VA1

stool consensus-pcr-positive negative one consensus specific sanger
Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.

PMID 18778477 · PMC2553089 · BMC medicine · 2008 · 7 claims · 7 setups

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A custom BOAC SNP panel of 3404 SNPs in 983 genes was developed using the Affymetrix GeneChip Targeted Genotyping Platform, focused on non-synonymous coding SNPs and regulatory-region SNPs in candidate genes.

coriell myeloma duplicate snp targeted genotyping machine

Experiments

Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms.

Integrated analysis of genetic and proteomic data identifies biomarkers associated with adverse events following smallpox vaccination.

Genome comparison without alignment using shortest unique substrings.

A computational screen for type I polyketide synthases in metagenomics shotgun data.

Structural evolution of the protein kinase-like superfamily.

A human genome-wide library of local phylogeny predictions for whole-genome inference problems.

Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes.

In silico analysis of missense substitutions using sequence-alignment based methods.

Human stool contains a previously unrecognized diversity of novel astroviruses.

Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.