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 18

System / cell line: specific ✕ Assay: literature ✕ Clear

Epidemiology of doublet/multiplet mutations in lung cancers: evidence that a subset arises by chronocoordinate events.

PMID 19005564 · PMC2579325 · PloS one · 2008 · 8 claims · 7 setups

Full-text index only

Doublet mutations are significantly more frequent in EGFR (6.0%) and TP53 (2.3%) in human lung cancer than spontaneous doublets in mouse lacI (0.7%), about 8-fold and 3-fold higher respectively.

egfr tp53 laci lung literature comparative statistical
An analysis of human microRNA and disease associations.

PMID 18923704 · PMC2559869 · PloS one · 2008 · 8 claims · 8 setups

Full-text index only

MicroRNAs tend to show similar dysfunctional evidence (both up- or both down-regulated) for diseases within the same disease cluster, and different dysfunctional evidence between different disease clusters.

literature-derived diseases mirnas mirna literature bipartite mirna
In silico promoters: modelling of cis-regulatory context facilitates target predictio.

PMID 18505473 · PMC3823354 · Journal of cellular and molecular medicine · 2009 · 8 claims · 8 setups

Full-text index only

An integrated 'profiling of transcriptional targets' (PTT) strategy by Freebern et al. identified IGF-1 as a co-modulator of immune cell function genes in mitogen/drug-activated T cells.

serca2 rantes genes podocyte-associated literature-based promoter cross-referenced
Gene losses during human origins.

PMID 16464126 · PMC1361800 · PLoS biology · 2006 · 7 claims · 7 setups

Full-text index only

A comparative genomic screen identified 67 new human-specific nonprocessed pseudogenes, bringing the total (with 13 from prior literature) to 80 human-specific pseudogenes.

pseudogene chimpanzee human-specific population comparative phylogenetic fisher's
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

PMID 17576681 · PMC1934990 · Nucleic acids research · 2007 · 8 claims · 4 setups

Full-text index only

Cryptic 5'ss are best predicted by computational algorithms that accommodate nucleotide dependencies (e.g., Markov model, maximum entropy, maximum dependence decomposition) rather than by weight-matrix models

disease mammalian compiled literature minigene computational
Is replication the gold standard for validating genome-wide association findings?

PMID 19112512 · PMC2605260 · PloS one · 2008 · 8 claims · 4 setups

Full-text index only

The probability of replicating a specific GWA-identified variant decreases as the number of independent GWA/replication studies increases, when individual study power is less than 100%.

simulated diallelic hypothetical four statistical marker bayesian
Quasimonomorphic mononucleotide repeats for high-level microsatellite instability analysis.

PMID 15528790 · PMC3888729 · Disease markers · 2004 · 8 claims · 8 setups

Full-text index only

Mononucleotide repeats are more sensitive, specific, and easier to use than dinucleotide repeats for detecting MSI-H tumors

msi-h colon hmsh6-mutated tumors pentaplex pcr dinucleotide
Mutations associated with HNPCC predisposition -- Update of ICG-HNPCC/INSiGHT mutation database.

PMID 15528792 · PMC3839397 · Disease markers · 2004 · 8 claims · 4 setups

Full-text index only

The ICG-HNPCC/INSiGHT mutation database has grown from 126 predisposing mutations (1997) to 448 mutations occurring in 748 families (2003 update)

hnpcc tumor yeast families germline microsatellite functional
Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.

PMID 18989394 · PMC2566816 · PLoS computational biology · 2008 · 7 claims · 4 setups

Full-text index only

A novel Bayesian method, RASER, can detect site-specific evolutionary rate shifts and the lineages in which they occurred without pre-specifying candidate lineages.

hiv-1 simulated bayesian simulation structural
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.

PMID 16381831 · PMC1347497 · Nucleic acids research · 2006 · 6 claims · 6 setups

Full-text index only

miRNAMap integrates known miRNA genes from miRBase, literature-curated validated targets, and computationally predicted miRNA genes and targets for human, mouse, rat and dog.

conserved putative mirna-target normal comparative machine mirna
Genotypic analysis of two hypervariable human cytomegalovirus genes.

PMID 18649324 · PMC2658010 · Journal of medical virology · 2008 · 8 claims · 8 setups

Full-text index only

UL146 sequences from 184 samples fall into the same 14 genotypes (G1-G14) previously defined, with no new genotypes found.

hcmv clinical pcr ul146 pcr nested molecular
Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers.

PMID 16034025 · PMC1179732 · Nucleic acids research · 2005 · 7 claims · 4 setups

Full-text index only

Partial EC numbers are semantically ambiguous, and databases that assign a gene to all reactions sharing the same partial EC number make a faulty inference, causing systematic misannotation.

e.coli biocyc vimss specific database comparative manual
Network-assisted protein identification and data interpretation in shotgun proteomics.

PMID 19690572 · PMC2736651 · Molecular systems biology · 2009 · 7 claims · 7 setups

Full-text index only

Confidently identified proteins in a sample form tightly connected sub-networks in the protein interaction network, with significantly higher clustering coefficients than random or topology-matched random sub-networks.

yeast organs mammary organ shotgun clique-enrichment microarray
Heterogeneous genomic molecular clocks in primates.

PMID 17029560 · PMC1592237 · PLoS genetics · 2006 · 7 claims · 7 setups

Full-text index only

Non-CpG site substitutions show clear generation-time dependency, consistent with a replication-error origin

baboon chimpanzee same human-chimpanzee relative phylogenetic four-species
GLIDA: GPCR--ligand database for chemical genomics drug discovery--database and tools update.

PMID 17986454 · PMC2238933 · Nucleic acids research · 2008 · 7 claims · 5 setups

Full-text index only

GLIDA is a public relational database integrating biological information on GPCRs with chemical information on their ligands and their binding interactions.

ligand gpcr glida principal sequence gene
When does a protein become an allergen? Searching for a dynamic definition based on most advanced technology tools.

PMID 18477011 · PMC2607534 · Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology · 2008 · 7 claims · 8 setups

Full-text index only

IgE-binding is not an intrinsic property of a protein but the result of an interaction between two molecules (antigen and IgE), so a molecule can only be classified relative to demonstrated IgE binding.

subjects allergic serum allergenic double-blind skin serum
Mutation spectrum of homogentisic acid oxidase (HGD) in alkaptonuria.

PMID 19862842 · PMC2830005 · Human mutation · 2009 · 8 claims · 6 setups

Full-text index only

Mutations in HGD, which encodes homogentisate dioxygenase, cause AKU by blocking conversion of homogentisic acid to maleylacetoacetic acid in the tyrosine catabolic pathway

aku hgd recombinant hgd missense splice
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

PMID 17478504 · PMC1933151 · Nucleic acids research · 2007 · 8 claims · 8 setups

Full-text index only

FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data

user-supplied gene predicted interactome gene kegg transcription

Experiments

Epidemiology of doublet/multiplet mutations in lung cancers: evidence that a subset arises by chronocoordinate events.

An analysis of human microRNA and disease associations.

In silico promoters: modelling of cis-regulatory context facilitates target predictio.

Gene losses during human origins.

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Is replication the gold standard for validating genome-wide association findings?

Quasimonomorphic mononucleotide repeats for high-level microsatellite instability analysis.

Mutations associated with HNPCC predisposition -- Update of ICG-HNPCC/INSiGHT mutation database.

Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.

miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.

Genotypic analysis of two hypervariable human cytomegalovirus genes.

Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers.

Network-assisted protein identification and data interpretation in shotgun proteomics.

Heterogeneous genomic molecular clocks in primates.

GLIDA: GPCR--ligand database for chemical genomics drug discovery--database and tools update.

When does a protein become an allergen? Searching for a dynamic definition based on most advanced technology tools.

Mutation spectrum of homogentisic acid oxidase (HGD) in alkaptonuria.

FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.