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 190

System / cell line: fraction ✕ Clear

The RCSB PDB information portal for structural genomics.

PMID 16381872 · PMC1347482 · Nucleic acids research · 2006 · 7 claims · 5 setups

Full-text index only

The RCSB PDB Structural Genomics Information Portal integrates three resources: Structural Genomics Initiatives, Targets (TargetDB/PepcDB), and Structures (functional coverage analysis).

structural nih genome sequence target production
Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes.

PMID 18053250 · PMC2246260 · Genome biology · 2007 · 8 claims · 4 setups

Full-text index only

Loss-of-function phenotypes in yeast are predictable from a gene's connections in a functional gene network via guilt-by-association.

saccharomyces guilt-by-association comparison network-guided
Inconsistencies in Neanderthal genomic DNA sequences.

PMID 17937503 · PMC2014787 · PLoS genetics · 2007 · 8 claims · 6 setups

Full-text index only

The Noonan et al. and Green et al. Neanderthal nuclear DNA datasets yield mutually inconsistent estimates of population split time and Neanderthal admixture proportion when analyzed with the same method

neanderthal green neanderthal-specific population-genetic fragment-length-stratified hapmap
A novel COL1A1 nonsense mutation causing osteogenesis imperfecta in a Chinese family.

PMID 17392686 · PMC2642918 · Molecular vision · 2007 · 8 claims · 5 setups

Full-text index only

A novel COL1A1 nonsense mutation (Q644X, C2464T in exon 36) causes osteogenesis imperfecta type I in this Chinese family

patients family genomic clinical microsatellite two-point
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

Full-text index only

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
hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes.

PMID 17207965 · PMC4647941 · Genomics · 2007 · 8 claims · 7 setups

Full-text index only

hORFeome v3.1 is a resource of 12,212 cloned human ORFs representing 10,214 genes, a 51% expansion over hORFeome v1.1

mgc cloned orfs genome gateway orf blat
Duplication count distributions in DNA sequences.

PMID 19256873 · PMC3121164 · Physical review. E, Statistical, nonlinear, and soft matter physics · 2008 · 8 claims · 8 setups

Full-text index only

Duplication count distributions N(c) for complex 40-mers show power-law-like decay for c roughly 3 to 50 (or higher) across human, C. elegans, A. thaliana, and D. melanogaster genomes.

genome elegans thaliana melanogaster genome-wide transposable homogeneous
Screening of common CYP1B1 mutations in Iranian POAG patients using a microarray-based PrASE protocol.

PMID 19096718 · PMC2603445 · Molecular vision · 2008 · 7 claims · 5 setups

Full-text index only

CYP1B1 mutations are implicated in POAG among Iranians, notably in the juvenile-onset form

genomic cyp1b1 poag microarray-based dideoxy sanger
DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

PMID 18987736 · PMC2603574 · Nature · 2008 · 8 claims · 8 setups

Full-text index only

Whole genome sequencing can identify unbiased, novel somatic mutations in a cytogenetically normal AML genome that would not have been found by candidate-gene resequencing.

aml tumor novo additional genome snp comparative
Proteomics of the lysosome.

PMID 18977398 · PMC2684028 · Biochimica et biophysica acta · 2009 · 8 claims · 8 setups

Full-text index only

The mammalian lysosome has been shown to contain ~60 soluble luminal proteins and ~25 transmembrane proteins

liver placenta brain conditioned lc-ms n-terminal man6-p
Mercury immune toxicity in harbour seals: links to in vitro toxicity.

PMID 18959786 · PMC2600635 · Environmental health : a global access science source · 2008 · 8 claims · 6 setups

Full-text index only

In vitro MeHg exposure reduces seal lymphocyte number, viability, metabolic activity, and DNA/RNA synthesis

blood pha-stimulated cytoplasmic cold trypan mts
The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

PMID 18949050 · PMC2569417 · PloS one · 2008 · 6 claims · 5 setups

Full-text index only

Within individual hosts, proteasome and TAP escape mutations in HIV-1 occur frequently

hiv-1 hla-genotyped predicted bioinformatic longitudinal ancestral
Organization of physical interactomes as uncovered by network schemas.

PMID 18949022 · PMC2561054 · PLoS computational biology · 2008 · 7 claims · 5 setups

Full-text index only

A computational procedure can systematically identify 'emergent' network schemas that are both recurrent and over-represented relative to randomized networks preserving lower-order subschema distributions

cerevisiae sapiens uncharacterized network cross-species functional
A novel procedure for genotyping of single nucleotide polymorphisms in trisomy with genomic DNA and the invader assay.

PMID 18940863 · PMC2602776 · Nucleic acids research · 2008 · 7 claims · 4 setups

Full-text index only

A novel Invader assay-based procedure can accurately determine SNP genotypes in trisomic genomic DNA samples in a simple, cost-effective manner

genomic same synthetic invader pyrosequencing hplc
Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

PMID 18793467 · PMC2537574 · BMC bioinformatics · 2008 · 8 claims · 7 setups

Full-text index only

Inter-species conservation is the strongest single predictor of disease-associated coding mutations among the factors tested.

hgmd refseq aligned svm svm reciprocal inter-species
Random amino acid mutations and protein misfolding lead to Shannon limit in sequence-structure communication.

PMID 18769673 · PMC2518838 · PloS one · 2008 · 8 claims · 6 setups

Full-text index only

The protein sequence-structure map behaves as a noisy digital communication channel whose capacity C exceeds the transmission rate R for native structures, satisfying Shannon's noisy channel theorem

chains pdbselect25 same single-domain statistical channel negative
A network model for the correlation between epistasis and genomic complexity.

PMID 18648534 · PMC2481279 · PloS one · 2008 · 8 claims · 5 setups

Full-text index only

In small networks with multifunctional nodes, lack of redundancy, and absence of alternative pathways, epistasis is antagonistic on average.

two-pathway network
Sequence similarity network reveals common ancestry of multidomain proteins.

PMID 18475320 · PMC2377100 · PLoS computational biology · 2008 · 8 claims · 6 setups

Full-text index only

Traditional homology definitions do not capture multidomain evolution; the authors extend the definition to include domain insertion via a common ancestral locus model.

curated complete well-studied sequence alignment domain
An original SERPINA3 gene cluster: elucidation of genomic organization and gene expression in the Bos taurus 21q24 region.

PMID 18384666 · PMC2373789 · BMC genomics · 2008 · 8 claims · 7 setups

Full-text index only

The bovine genome contains a cluster of eight SERPINA3 genes and one pseudogene (SERPINA3P) sharing high sequence identity and identical structural organization

bovine bac roslin deduced southern bac radiation
Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.

PMID 18267968 · PMC2367719 · Nucleic acids research · 2008 · 6 claims · 8 setups

Full-text index only

The seed arm (guide strand positions 2-8), its complementary passenger-strand sequence, the 5' end of the guide strand, and the 3' overhang of the passenger strand can be simultaneously replaced with DNA without substantial loss of gene-silencing activity.

cho-k1 e14tg2a recombinant hela dual-luciferase rt-pcr electrophoresis

Experiments

The RCSB PDB information portal for structural genomics.

Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes.

Inconsistencies in Neanderthal genomic DNA sequences.

A novel COL1A1 nonsense mutation causing osteogenesis imperfecta in a Chinese family.

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.

hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes.

Duplication count distributions in DNA sequences.

Screening of common CYP1B1 mutations in Iranian POAG patients using a microarray-based PrASE protocol.

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

Proteomics of the lysosome.

Mercury immune toxicity in harbour seals: links to in vitro toxicity.

The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

Organization of physical interactomes as uncovered by network schemas.

A novel procedure for genotyping of single nucleotide polymorphisms in trisomy with genomic DNA and the invader assay.

Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

Random amino acid mutations and protein misfolding lead to Shannon limit in sequence-structure communication.

A network model for the correlation between epistasis and genomic complexity.

Sequence similarity network reveals common ancestry of multidomain proteins.

An original SERPINA3 gene cluster: elucidation of genomic organization and gene expression in the Bos taurus 21q24 region.

Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.