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 19

System / cell line: presence ✕ Assay: protein-protein ✕ Clear

Human Protein Reference Database--2009 update.

PMID 18988627 · PMC2686490 · Nucleic acids research · 2009 · 8 claims · 8 setups

Full-text index only

HPRD is a curated database of experimentally derived human protein-protein interactions, post-translational modifications, and tissue expression data

mastl proteins phosphorylation yeast mass
Computational verification of protein-protein interactions by orthologous co-expression.

PMID 15740634 · PMC555590 · BMC bioinformatics · 2005 · 7 claims · 8 setups

Full-text index only

Co-expression of orthologous protein pairs across multiple species can verify/predict S. cerevisiae PPIs with better performance than S. cerevisiae co-expression alone.

cerevisiae orthologs cdc28 yeast co-expression ortholog orthologous
Predicting candidate genes for human deafness disorders: a bioinformatics approach.

PMID 16854223 · PMC1564145 · BMC genomics · 2006 · 8 claims · 4 setups

Full-text index only

A bioinformatic approach combining expression databases and protein interaction data narrows ~2400 candidate genes across deafness loci to a manageable set of candidates.

genomic developing proteins positional expression protein-protein
Evolutionary origins of human apoptosis and genome-stability gene networks.

PMID 18832373 · PMC2577361 · Nucleic acids research · 2008 · 8 claims · 8 setups

Full-text index only

The entanglement of DNA repair, chromosome stability and apoptosis gene networks appears with the caspase gene family and the antiapoptotic gene BCL2.

apoptosis fully same orthologous protein-protein comparative orthology
Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.

PMID 19779614 · PMC2745575 · PloS one · 2009 · 8 claims · 8 setups

Full-text index only

A protein-centric data integration approach (Master Protein Directory) enables integration and mining of heterogeneous pathogen-host omics data across multiple research centers

macrophage hela vaccinia bacillus gene protein-protein comparative
Protein co-evolution, co-adaptation and interactions.

PMID 18818697 · PMC2556093 · The EMBO journal · 2008 · 8 claims · 6 setups

Full-text index only

The mirrortree method predicts protein-protein interactions by detecting pairs of protein families with similar phylogenetic trees (quantified as Pearson correlation of sequence similarity matrices).

nuoe intra-protein coli interacting phylogenetic correlated domain-restricted
Towards the identification of essential genes using targeted genome sequencing and comparative analysis.

PMID 17052348 · PMC1624830 · BMC genomics · 2006 · 8 claims · 8 setups

Full-text index only

Phyletic retention (ortholog presence across organisms) is the single most predictive feature of gene essentiality in both E. coli and S. cerevisiae.

coli cerevisiae comparative machine single-gene
Filtering high-throughput protein-protein interaction data using a combination of genomic features.

PMID 15833142 · PMC1127019 · BMC bioinformatics · 2005 · 8 claims · 8 setups

Full-text index only

A combination of three genomic features (interacting Pfam domains, GO annotations, sequence homology) using naive Bayesian networks predicts true protein-protein interactions with high sensitivity and good specificity.

saccharomyces bank caenorhabditis homo yeast mass naive
Evolution of insect proteomes: insights into synapse organization and synaptic vesicle life cycle.

PMID 18257909 · PMC2374702 · Genome biology · 2008 · 8 claims · 3 setups

Full-text index only

Compiled a list of 120 core presynaptic gene prototypes (PS120) and catalogued their conservation across insect proteomes.

insect vamp2 ps120 comparative sequence protein-protein
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

Full-text index only

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
Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes.

PMID 19906700 · PMC2808873 · Nucleic acids research · 2010 · 7 claims · 4 setups

Full-text index only

NCG is a web database integrating duplicability, orthology, evolutionary appearance, and network topology data for 736 human cancer genes

cancer proteome pten genome orthology protein-protein
Helicobacter pylori: after the genomes, back to biology.

PMID 12668641 · PMC2193897 · The Journal of experimental medicine · 2003 · 8 claims · 5 setups

Full-text index only

STM screening of 960 H. pylori mutants in gerbils identifies genes required for in vivo colonization

helicobacter diffuse signature-tagged genome yeast
Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms.

PMID 17166053 · PMC1664705 · PLoS computational biology · 2006 · 8 claims · 8 setups

Full-text index only

Integrating interactome and transcriptome data reveals a pair of transcriptionally anticorrelated network modules (P and D) each comprising hundreds of genes, present across individuals and species.

postmortem genes gene proteins microarray protein-protein hierarchical
Discovery and hypothesis generation through bioinformatics.

PMID 16522224 · PMC1431734 · Genome biology · 2006 · 8 claims · 8 setups

Full-text index only

Bioinformatics should be used as a tool for discovery and hypothesis generation, not merely to manage biological data

genome chemokine gene-expression proteins genome-wide phylogenetic microarray
The cohesin complex: sequence homologies, interaction networks and shared motifs.

PMID 11276426 · PMC30708 · Genome biology · 2001 · 8 claims · 8 setups

Full-text index only

Mouse Mmip1 and Smc3 (SMCD) share 99% sequence identity and are products of the same gene

smc1 smc3 mmip1 smc psi-blast phylogenetic sequence
The Hellenic type of nondeletional hereditary persistence of fetal hemoglobin results from a novel mutation (g.-109G>T) in the HBG2 gene promoter.

PMID 19050890 · PMC2690858 · Annals of hematology · 2009 · 7 claims · 7 setups

Full-text index only

HBG2:g.-109G>T is a novel promoter mutation causing a distinct ('Hellenic type') nd-HPFH

peripheral genomic nuclear mel cation reverse-phase denaturing
Nucleosome formation with the testis-specific histone H3 variant, H3t, by human nucleosome assembly proteins in vitro.

PMID 18281699 · PMC2367731 · Nucleic acids research · 2008 · 8 claims · 7 setups

Full-text index only

H3t/H4 forms nucleosomes with H2A/H2B via the salt-dialysis method, similar to conventional H3.1/H4

recombinant reconstituted his6-tagged hnap1 salt-dialysis micrococcal chaperone-mediated
Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes.

PMID 17158152 · PMC1802574 · Nucleic acids research · 2007 · 8 claims · 8 setups

Full-text index only

GLR is a novel maximum-likelihood measure of gene loss rate that probabilistically weighs all possible ancestral phyletic patterns rather than relying on a single parsimonious reconstruction.

synthetic eukaryotic simulated 16-species analytical comparative simulation
An attenuated phenotype of Costello syndrome in three unrelated individuals with a HRAS c.179G>A (p.Gly60Asp) mutation correlates with uncommon functional consequences.

PMID 25914166 · PMC4830354 · American journal of medical genetics. Part A · 2015 · 7 claims · 8 setups

Has reproduction

HRAS c.179G>A (p.Gly60Asp) causes an attenuated Costello syndrome phenotype without severe failure-to-thrive, intellectual disability, or cancer predisposition

cos-7 transiently patients parental ras co-immunoprecipitation immunoblotting

Experiments

Human Protein Reference Database--2009 update.

Computational verification of protein-protein interactions by orthologous co-expression.

Predicting candidate genes for human deafness disorders: a bioinformatics approach.

Evolutionary origins of human apoptosis and genome-stability gene networks.

Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.

Protein co-evolution, co-adaptation and interactions.

Towards the identification of essential genes using targeted genome sequencing and comparative analysis.

Filtering high-throughput protein-protein interaction data using a combination of genomic features.

Evolution of insect proteomes: insights into synapse organization and synaptic vesicle life cycle.

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

Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes.

Helicobacter pylori: after the genomes, back to biology.

Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms.

Discovery and hypothesis generation through bioinformatics.

The cohesin complex: sequence homologies, interaction networks and shared motifs.

The Hellenic type of nondeletional hereditary persistence of fetal hemoglobin results from a novel mutation (g.-109G>T) in the HBG2 gene promoter.

Nucleosome formation with the testis-specific histone H3 variant, H3t, by human nucleosome assembly proteins in vitro.

Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes.

An attenuated phenotype of Costello syndrome in three unrelated individuals with a HRAS c.179G>A (p.Gly60Asp) mutation correlates with uncommon functional consequences.