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 38

System / cell line: omim ✕ Clear

ChimerDB 2.0--a knowledgebase for fusion genes updated.

PMID 19906715 · PMC2808913 · Nucleic acids research · 2010 · 8 claims · 4 setups

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ChimerDB 2.0 is an updated knowledgebase integrating fusion transcripts from GenBank transcriptome analysis with Sanger CGP, OMIM, PubMed, and Mitelman's database data.

genbank sra pubmed transcript-to-genome ngs literature
Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network.

PMID 19728866 · PMC2768980 · Genome biology · 2009 · 6 claims · 6 setups

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Integrating 16 genomic features (32 sub-features) via a naïve Bayes classifier produces a genome-scale FLN of 21,657 human genes and 22,388,609 weighted links that outperforms any individual data source for inferring functional linkages.

genome gene omim known naïve linkage disease-centric
Atlas - a data warehouse for integrative bioinformatics.

PMID 15723693 · PMC554782 · BMC bioinformatics · 2005 · 8 claims · 3 setups

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Atlas is a biological data warehouse that locally stores and integrates sequences, molecular interactions, homology information, functional annotations, and ontologies

in-house gene omim genome molecular gene-disease
Functional coverage of the human genome by existing structures, structural genomics targets, and homology models.

PMID 16118666 · PMC1188274 · PLoS computational biology · 2005 · 8 claims · 5 setups

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Existing PDB structures provide single-domain coverage for 37% of functional classes in the human genome and complete (whole-protein) structure coverage for 25%.

genome functional registered omim comparative kendall's homology
Integration of text- and data-mining using ontologies successfully selects disease gene candidates.

PMID 15767279 · PMC1065256 · Nucleic acids research · 2005 · 7 claims · 6 setups

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Integrating eVOC anatomical ontology-based text-mining of PubMed abstracts with data-mining of gene expression annotation successfully selects and prioritizes candidate disease genes

biomedical refseq training independent text-mining data-mining candidate
Using random walks to identify cancer-associated modules in expression data.

PMID 24128261 · PMC4015830 · BioData mining · 2013 · 8 claims · 8 setups

Has reproduction

Walktrap-GM, a random-walk community detection algorithm adapted with stopping criteria (maximum modularity, maximum size, maximum module score), identifies modules significantly enriched with cancer genes in expression-weighted interaction networks.

hepatocellular breast sporadic geo gene differential interaction
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
Comparative analysis of cancer genes in the human and chimpanzee genomes.

PMID 16438707 · PMC1382208 · BMC genomics · 2006 · 7 claims · 6 setups

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All 333 examined human cancer genes have intact, highly conserved orthologs in the chimpanzee genome (99.38% protein identity).

chimpanzee non-human cancer comparative pcr targeted
The RCSB PDB information portal for structural genomics.

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

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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
InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale.

PMID 17868464 · PMC2375030 · Genome biology · 2007 · 8 claims · 8 setups

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InSite predicts protein-pair-specific binding motifs ('Motif M on protein A binds to protein B') by integrating heterogeneous PPI and motif-motif interaction evidence within a Bayesian network trained by EM

saccharomyces homo bank computational yeast tandem
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

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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
An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases.

PMID 19091018 · PMC2638159 · BMC bioinformatics · 2008 · 6 claims · 5 setups

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Existing SNP/disease databases are fragmented; no combined resource widely supports gene-, SNP-, and disease-related information together

private disease uniprot snps database controlled sequence
Genome-wide analysis of human disease alleles reveals that their locations are correlated in paralogous proteins.

PMID 18989397 · PMC2565504 · PLoS computational biology · 2008 · 7 claims · 5 setups

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The locations of sequence variants are correlated between paralogous human proteins more than expected by chance.

dbsnp best-hit omicia hgmd genome-wide correlation disease
Distribution and effects of nonsense polymorphisms in human genes.

PMID 18852891 · PMC2561068 · PloS one · 2008 · 8 claims · 8 setups

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Nonsense SNPs occur at a lower density than nonsynonymous SNPs, indicating stronger purifying selection against premature stop codons than amino acid changes.

genome genes nonsense snps genome-wide snp codon
Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies.

PMID 18263617 · PMC2275105 · Nucleic acids research · 2008 · 8 claims · 7 setups

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Genes correlated with a common complex trait are more likely to share GO functional annotations than genes not correlated with that trait

genes candidate simulated alzheimer's genome-wide term null-hypothesis
Correlation of microsynteny conservation and disease gene distribution in mammalian genomes.

PMID 19909546 · PMC2779822 · BMC genomics · 2009 · 7 claims · 8 setups

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Density of mouse orthologs of human disease genes correlates with regions of conserved microsynteny in the mouse genome

genes autosomes dog genome comparative blat sliding-window
MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease.

PMID 19758471 · PMC2745589 · BMC bioinformatics · 2009 · 8 claims · 5 setups

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MtSNPscore, a weighted scoring pipeline combining literature evidence, in silico predictions, and case/control frequency, can prioritize likely pathogenic mtDNA variations

sporadic mitochondrial reported ataxia mitochondrial functional compensatory
DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis.

PMID 17980028 · PMC2186358 · BMC bioinformatics · 2007 · 7 claims · 3 setups

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The DAVID Gene Concept, a single-linkage algorithm, merges gene clusters from Entrez Gene, UniRef100, and PIR-NREF100 that share protein IDs and species into unified DAVID gene clusters, improving cross-referencing between NCBI and UniProt systems

members entire usp8 sequence annotation

Experiments

ChimerDB 2.0--a knowledgebase for fusion genes updated.

Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network.

Atlas - a data warehouse for integrative bioinformatics.

Functional coverage of the human genome by existing structures, structural genomics targets, and homology models.

Integration of text- and data-mining using ontologies successfully selects disease gene candidates.

Using random walks to identify cancer-associated modules in expression data.

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

Comparative analysis of cancer genes in the human and chimpanzee genomes.

The RCSB PDB information portal for structural genomics.

InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale.

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

An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases.

Genome-wide analysis of human disease alleles reveals that their locations are correlated in paralogous proteins.

Distribution and effects of nonsense polymorphisms in human genes.

Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies.

Correlation of microsynteny conservation and disease gene distribution in mammalian genomes.

MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease.

DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis.