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).

• An SVM-based system for predicting protein subnuclear localizations.

  PMID 16336650 · PMC1325059 · BMC bioinformatics · 2005 · 7 claims · 3 setups

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  New kernels defined on k-peptide vectors mapped by BLOSUM62-based high-scored pair matrices (D1, D2, D3) improve SVM discrimination of protein subnuclear localization compared to conventional k-peptide encodings.

  single-localization multi-localization same svm sequence

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

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

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  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

• GPCR genes are preferentially retained after whole genome duplication.

  PMID 18382678 · PMC2270905 · PloS one · 2008 · 8 claims · 6 setups

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  WGD-derived nGPCR duplicates in Tetraodon nigroviridis are retained at a significantly higher rate (23.5%) than the genome-wide average (15%)

  vertebrate ngpcr nigroviridis syntenic phylogenetic chromosomal

• Comparative sequence analysis of leucine-rich repeats (LRRs) within vertebrate toll-like receptors.

  PMID 17517123 · PMC1899181 · BMC genomics · 2007 · 8 claims · 4 setups

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  A new method combining known LRR structures, multiple sequence alignment, and secondary structure prediction identifies and aligns LRRs in TLRs more accurately than PFAM/InterPro/SMART

  tlrs lrr-containing tlr2 mammalian comparative structural secondary

• In silico analysis of missense substitutions using sequence-alignment based methods.

  PMID 18951440 · PMC3431198 · Human mutation · 2008 · 8 claims · 7 setups

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  Carefully validated PMSA-based computational algorithms can achieve predictive values of ~75-95% for classifying missense substitutions as pathogenic or neutral.

  clinically sequence curated deep blosum62 sift align-gvgd

• In silico meets in vivo.

  PMID 18304380 · PMC2374716 · Genome biology · 2008 · 8 claims · 8 setups

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  About 10% of positions in multiple sequence alignments of the human genome with other vertebrate genomes are likely incorrect.

  genome lines prokaryotic genomes genome genome-wide gene

• The DNA sequence and analysis of human chromosome 13.

  PMID 15057823 · PMC2665288 · Nature · 2004 · 8 claims · 8 setups

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  95.5 Mb of finished sequence from chromosome 13 was completed, containing 633 genes and 296 pseudogenes.

  chromosome rpci-11 genomic comparative fluorescence

• Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

  PMID 17488840 · PMC1933192 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  A novel multiple whole-genome alignment algorithm treats all genomes symmetrically, avoiding dependence on a single base/reference genome

  genome vertebrate multi-species whole-genome conservation non-synonymous

• Variants in the ATM gene associated with a reduced risk of contralateral breast cancer.

  PMID 18701470 · PMC2562548 · Cancer research · 2008 · 7 claims · 4 setups

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  Carriers of common ATM variants (>=1% frequency) have a statistically significant reduction in risk of contralateral breast cancer (CBC)

  peripheral wecare atm mutation case-control variant

• 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

• Functional and clinical data of Best vitelliform macular dystrophy patients with mutations in the BEST1 gene.

  PMID 20057903 · PMC2802291 · Molecular vision · 2009 · 7 claims · 8 setups

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  BEST1 mutations are not correlated with the severity of functional and clinical data in Best VMD patients

  genomic unrelated best1 best1-4 direct chromosome pathogenicity

• 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

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  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