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 64

System / cell line: known ✕ Assay: score ✕ Clear

An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer.

PMID 19881495 · PMC3086882 · Nature biotechnology · 2009 · 8 claims · 8 setups

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A 'concept signature' (ConSig) score algorithm ranks genes by association with molecular concepts characteristic of fusion or mutation cancer genes, nominating biologically important fusions from large candidate sets.

lung known leukemia tumor paired-end computational snp
Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome.

PMID 15892868 · PMC1175952 · Genome biology · 2005 · 8 claims · 6 setups

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Two quantitative benchmarks (functional-annotation-based and physical-interaction-based log likelihood ratio scores) can measure relative accuracy of human PPI datasets

medline annotated interactions consolidated conditional co-citation bayesian
Speeding disease gene discovery by sequence based candidate prioritization.

PMID 15766383 · PMC1274252 · BMC bioinformatics · 2005 · 7 claims · 8 setups

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Disease genes (OMIM) differ significantly from non-disease genes in sequence-based features including gene/cDNA/protein size, exon number, homolog conservation, secretion signal, 3' UTR length, CpG islands, and distance to nearest gene.

ensembl training same hgmd comparative machine tenfold
Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach.

PMID 15693947 · PMC551538 · Genome biology · 2005 · 7 claims · 8 setups

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FastCompare, a non-alignment-based, linear-time algorithm, computes a genome-wide conservation score for all k-mers (7-9 nt) between two genomes to identify conserved regulatory elements

cerevisiae elegans randomized computational randomized microarray
The HIV positive selection mutation database.

PMID 17108357 · PMC1669717 · Nucleic acids research · 2007 · 8 claims · 5 setups

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The database provides codon-level Ka/Ks selection pressure maps for HIV protease and the first 381 codons of RT, built from a novel ~50,000-sample clinical dataset.

hiv-1 stanford codon-specific selection conditional
Promoting human promoters.

PMID 16760901 · PMC1681504 · Molecular systems biology · 2006 · 8 claims · 5 setups

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A computational protocol using MARS on known sequence motifs can quantify transcription factor effects on human gene expression despite noise and data size challenges

gene liver cycle genes computational expression time-course
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.

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

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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
Mutation survey of known LCA genes and loci in the Saudi Arabian population.

PMID 18936139 · PMC2695987 · Investigative ophthalmology & visual science · 2009 · 7 claims · 4 setups

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Mutations in the 13 known LCA genes were identified in only 24% (9/37) of Saudi Arabian LCA families, far lower than the ~65% mutation detection rate reported in European populations

leukocyte affected kkesh-060 direct str homozygosity
Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.

PMID 18366609 · PMC2386062 · BMC genomics · 2008 · 8 claims · 7 setups

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The mapping algorithm identified 5,647 candidate bidirectional promoter regions in the mouse genome, similar in number to those previously found in human.

genome seven genes computational cage comparative
Reconstruction of human protein interolog network using evolutionary conserved network.

PMID 17493278 · PMC1885812 · BMC bioinformatics · 2007 · 8 claims · 7 setups

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A relative conservation score derived from maximal quasi-cliques in protein interaction networks, combined with other interaction features, can score and rank predicted human interologs for confidence.

ppi sequences interaction predicted interolog orthology quasi-clique
Update of the G2D tool for prioritization of gene candidates to inherited diseases.

PMID 17478516 · PMC1933178 · Nucleic acids research · 2007 · 8 claims · 4 setups

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G2D is a web server that prioritizes candidate genes for inherited diseases using three distinct algorithms based on different input information.

genome genomic etrb computational literature go-similarity
ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs.

PMID 16845048 · PMC1538778 · Nucleic acids research · 2006 · 6 claims · 4 setups

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ProMiR II improves on the original ProMiR by integrating free energy, G/C ratio, conservation score and entropy for more controllable miRNA prediction

genome cytomegalovirus six probabilistic 5-fold directional
Prediction of candidate primary immunodeficiency disease genes using a support vector machine learning approach.

PMID 19801557 · PMC2780952 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2009 · 6 claims · 3 setups

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An SVM trained on 69 binary features of known PID genes can accurately classify PID vs non-PID genes and predict novel candidate PID genes

genome training svm support leave-one-out sensitivity
BRCA1 and BRCA2 mutation predictions using the BOADICEA and BRCAPRO models and penetrance estimation in high-risk French-Canadian families.

PMID 16417652 · PMC1413985 · Breast cancer research : BCR · 2006 · 8 claims · 7 setups

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BOADICEA predicts accurately the number of BRCA1 and BRCA2 mutations across family groups and discriminates well between carriers and noncarriers

french-canadian families brca1-positive same targeted full-length multiplex
Analysis of protein sequence and interaction data for candidate disease gene prediction.

PMID 17020920 · PMC1636487 · Nucleic acids research · 2006 · 8 claims · 7 setups

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Combining CPS and CMP using known disease genes as input achieves sensitivity 0.52 and specificity 0.97, reducing candidate lists 13-fold

ophid biocarta kegg pfam-annotated common benchmarking multiple-interval
Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.

PMID 17316440 · PMC1852407 · Genome biology · 2007 · 8 claims · 6 setups

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CDK consensus motifs are frequently clustered (closely spaced) in known CDK substrate proteins rather than uniformly distributed

cerevisiae cycle reanalysis statistical optimal
Analysis of X chromosome inactivation in autism spectrum disorders.

PMID 18361425 · PMC4867005 · American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2008 · 6 claims · 5 setups

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No significant excess of skewed XCI was found in mothers of children with ASD or in affected girls compared to controls

genomic multiplex mecp2 four chromosome non-parametric mutation
The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.

PMID 15608292 · PMC540057 · Nucleic acids research · 2005 · 8 claims · 6 setups

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Built a library of 1134 HMM models (359 matrix-derived, 718 factor-derived, 57 JASPAR-derived), corresponding to 863 distinct TF names, from TRANSFAC and JASPAR binding site data

genome drosophila transfac b99 profile sequence case-study
Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: case study of primary immunodeficiencies.

PMID 19073697 · PMC2632920 · Nucleic acids research · 2009 · 8 claims · 5 setups

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Combining high protein-interaction network scores with significant PID-related GO terms identifies novel PID candidate genes

immunome known protein-interaction gene comparative
ATBF1 and NQO1 as candidate targets for allelic loss at chromosome arm 16q in breast cancer: absence of somatic ATBF1 mutations and no role for the C609T NQO1 polymorphism.

PMID 18416817 · PMC2377272 · BMC cancer · 2008 · 8 claims · 7 setups

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Five genes (NQO1, ATBF1, DBNDD1, HSBP1, CGI-38) at 16q show significantly lower mRNA expression in breast tumors with LOH at 16q compared to tumors without LOH

ductal same sporadic paired cdna quantitative genotyping

Experiments

An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer.

Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome.

Speeding disease gene discovery by sequence based candidate prioritization.

Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach.

The HIV positive selection mutation database.

Promoting human promoters.

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

Mutation survey of known LCA genes and loci in the Saudi Arabian population.

Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.

Reconstruction of human protein interolog network using evolutionary conserved network.

Update of the G2D tool for prioritization of gene candidates to inherited diseases.

ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs.

Prediction of candidate primary immunodeficiency disease genes using a support vector machine learning approach.

BRCA1 and BRCA2 mutation predictions using the BOADICEA and BRCAPRO models and penetrance estimation in high-risk French-Canadian families.

Analysis of protein sequence and interaction data for candidate disease gene prediction.

Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.

Analysis of X chromosome inactivation in autism spectrum disorders.

The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.

Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: case study of primary immunodeficiencies.

ATBF1 and NQO1 as candidate targets for allelic loss at chromosome arm 16q in breast cancer: absence of somatic ATBF1 mutations and no role for the C609T NQO1 polymorphism.