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: prediction ✕ Assay: directed ✕ Clear

Prediction of specificity-determining residues for small-molecule kinase inhibitors.

PMID 19032760 · PMC2655090 · BMC bioinformatics · 2008 · 8 claims · 5 setups

Full-text index only

S-Filter is a novel method combining sequence and structural information (within PFAAT) to predict specificity-determining residues and selectivity profiles for small-molecule kinase inhibitors

panel kinase-inhibitor sequence erk2 caliper radiometric solvent
VIRGO: computational prediction of gene functions.

PMID 16845022 · PMC1538839 · Nucleic acids research · 2006 · 8 claims · 6 setups

Full-text index only

VIRGO constructs a functional linkage network (FLN) from gene expression and molecular interaction data, labels genes with GO annotations, and propagates these labels to predict functions of unlabelled genes

cerevisiae sapiens leave-one-out gene protein-protein
An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions.

PMID 18445289 · PMC2386494 · BMC bioinformatics · 2008 · 8 claims · 6 setups

Full-text index only

Using RNAsubopt suboptimal solutions computed once for the wild-type sequence, specific multiple-point mutations likely to cause conformational rearrangement can be selected without brute-force enumeration.

example hepatitis minimum suboptimal multiple-point
Exome sequencing identifies the cause of a mendelian disorder.

PMID 19915526 · PMC2847889 · Nature genetics · 2010 · 8 claims · 7 setups

Full-text index only

Exome sequencing of a small number of unrelated affected individuals, combined with filtering against public SNP databases and HapMap exomes, is sufficient to identify the causal gene for a monogenic disorder of unknown etiology.

patients chromosomes dhodh utero exome directed sanger
Evaluation of the OPTC gene in primary open angle glaucoma: functional significance of a silent change.

PMID 17359525 · PMC1838427 · BMC molecular biology · 2007 · 8 claims · 8 setups

Full-text index only

OPTC is a candidate gene involved in POAG pathogenesis

genomic pcr optc retinal pcr-sscp dhplc sequencing
A MANBA mutation resulting in residual beta-mannosidase activity associated with severe leukoencephalopathy: a possible pseudodeficiency variant.

PMID 19728872 · PMC2745377 · BMC medical genetics · 2009 · 8 claims · 7 setups

Full-text index only

A novel homozygous missense mutation, c.1922G>A (p.Arg641His), in MANBA was identified in a patient with severe neurological disease featuring pyramidal and cerebellar involvement, a phenotype not previously reported in β-mannosidosis.

family hek293t lymphoid pcr-amplified fluorometric site-directed western
The DNA sequence of the human X chromosome.

PMID 15772651 · PMC2665286 · Nature · 2005 · 8 claims · 8 setups

Full-text index only

The euchromatic sequence of the human X chromosome was determined to 99.3% completeness (~155 Mb total)

pac selected chromosome clone-based shotgun comparative
Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

PMID 19756158 · PMC2742196 · PLoS computational biology · 2009 · 8 claims · 4 setups

Full-text index only

MIP active learning is a novel active learning method that preferentially seeks informative Positive (functionally active) examples rather than only maximizing classifier accuracy.

engineered p53 computational yeast-based regional homology
Dynamic interaction of MYC enhancer RNA with YEATS2 protein regulates MYC gene transcription in pancreatic cancer.

PMID 40216980 · PMC12117045 · EMBO reports · 2025 · 8 claims · 11 setups

Has reproduction · 90

MYC eRNAs (notably MYC-490-kb) are transcribed from the MYC super-enhancer and are upregulated by chronic TNF-α stimulation specifically in pancreatic cancer cells, not normal pancreatic epithelial cells

pdac miapaca-2 chronic myc-490-kb survival chip-seq nascent
Common variants of the beta and gamma subunits of the epithelial sodium channel and their relation to plasma renin and aldosterone levels in essential hypertension.

PMID 15661075 · PMC547905 · BMC medical genetics · 2005 · 8 claims · 7 setups

Full-text index only

Heterozygous carriage of common βENaC/γENaC variants (G589S, i12-17CT, V546I) is significantly more prevalent in essential hypertension patients (9.2%) than in normotensive males (2.9%) or blood donors (3.0%)

hypertensive lymphocytes βenac xenopus targeted pcr-rflp plasma

Experiments

Prediction of specificity-determining residues for small-molecule kinase inhibitors.

VIRGO: computational prediction of gene functions.

An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions.

Exome sequencing identifies the cause of a mendelian disorder.

Evaluation of the OPTC gene in primary open angle glaucoma: functional significance of a silent change.

A MANBA mutation resulting in residual beta-mannosidase activity associated with severe leukoencephalopathy: a possible pseudodeficiency variant.

The DNA sequence of the human X chromosome.

Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

Dynamic interaction of MYC enhancer RNA with YEATS2 protein regulates MYC gene transcription in pancreatic cancer.

Common variants of the beta and gamma subunits of the epithelial sodium channel and their relation to plasma renin and aldosterone levels in essential hypertension.