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).

• TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences.

  PMID 17199898 · PMC1774580 · BMC bioinformatics · 2007 · 7 claims · 8 setups

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  TPRpred detects divergent/remote-homolog TPR repeat units that existing resources (Pfam, SMART, REP) fail to detect

  scop-derived malt nr-70 scop profile-based dali remote

• Positive natural selection in the evolution of human metapneumovirus attachment glycoprotein.

  PMID 17931731 · PMC7114232 · Virus research · 2008 · 7 claims · 5 setups

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  8 amino acid sites in the extracellular domain of hMPV lineage 1a show a higher rate of nonsynonymous than synonymous substitutions (posterior probability >0.95), indicating positive selection.

  unique hmpv sequence neighbor-joining codon

• Prioritization of candidate cancer genes--an aid to oncogenomic studies.

  PMID 18710882 · PMC2566894 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  Computational classifiers using combinations of protein conservation, gene structure, protein domains, protein interactions, and regulatory data can distinguish known cancer genes (CD/CR) from unlabelled human genes

  genes cancer interpro interactome averaged cross-validation domain

• Analysis of human sarcospan as a candidate gene for CFEOM1.

  PMID 11180757 · PMC29083 · BMC genetics · 2001 · 7 claims · 5 setups

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  Sarcospan sequence is unmutated in all six CFEOM1 families studied

  yac genomic extraocular genome pcr direct immunofluorescence

• 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

• Evaluation of SCN8A as a candidate gene for autosomal dominant essential tremor.

  PMID 18718804 · PMC2877193 · Parkinsonism & related disorders · 2009 · 7 claims · 6 setups

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  Mutations in the coding sequence and splice sites of human SCN8A do not appear to be a common cause of autosomal dominant essential tremor in Caucasian patients.

  genomic neurologically ethnically scn8a heteroduplex pcr snp

• nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms.

  PMID 15980516 · PMC1160133 · Nucleic acids research · 2005 · 6 claims · 4 setups

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  nsSNPAnalyzer is a web server that predicts whether a query nsSNP is disease-associated or functionally neutral using a Random Forest classifier combining structural and evolutionary information

  curated homologous structure random structural secondary

• Genetic variation of SARS coronavirus in Beijing Hospital.

  PMID 15200810 · PMC3323231 · Emerging infectious diseases · 2004 · 8 claims · 4 setups

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  113 sequence variations at 9 recurrent variant sites were identified in 29 full-length S-gene sequences compared to the BJ01 reference strain

  clinical extracted rna-derived cloned nested screening direct

• Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.

  PMID 16672049 · PMC1464126 · BMC genomics · 2006 · 8 claims · 7 setups

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  Seven genomic islands (VPaI-1 to VPaI-7, 10-81 kb) were identified in V. parahaemolyticus RIMD2210633 by aberrant GC content, presence of integrases/transposases, flanking direct repeats, and absence from related Vibrionaceae genomes.

  parahaemolyticus vulnificus clinical ecori-digested bioinformatic comparative pcr

• Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

  PMID 18846217 · PMC2557123 · PloS one · 2008 · 7 claims · 4 setups

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  A combinatorial mutation analysis identified 154 candidate recessive cancer genes (pRecessiveCancer<1.5x10-7, FDR=0.39)

  refseq tp53 tumor 154-gene est paired array

• Improving the specificity of exon prediction using comparative genomics.

  PMID 18831778 · PMC2559877 · BMC genomics · 2008 · 8 claims · 6 setups

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  A log-odds ratio scoring method based on codon conservation across human-mouse/human-dog alignments and adjacent-codon dependency can classify putative exons as coding vs non-coding.

  human-mouse human-dog genome simulated comparative single-genome simulated

• Comparative genomics comes of age.

  PMID 12186641 · PMC139393 · Genome biology · 2002 · 8 claims · 8 setups

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  Only about 50% of conserved sequence elements (exons+introns) in orthologous human-mouse genes correspond to exons, implying substantial non-exonic conservation

  orthologous chromosome chimpanzee somatic-cell comparative targeted tiled

• Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G.

  PMID 15269786 · PMC479043 · PLoS biology · 2004 · 7 claims · 6 setups

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  APOBEC3G has been under strong, recurrent positive selection throughout primate evolution (~33 million years)

  apobec3g pairwise human-chimpanzee apobec1 pcr phylogenetic sliding

• A genomics-based approach to biodefence preparedness.

  PMID 14708013 · PMC7097618 · Nature reviews. Genetics · 2004 · 7 claims · 8 setups

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  Genome sequence data are now available for essentially all 25-30 principal human bacterial pathogens, including most CDC category A-C bioterror agents

  bacillus brucella neisseria gastric comparative transcriptome two-dimensional

• SNPdetector: a software tool for sensitive and accurate SNP detection.

  PMID 16261194 · PMC1274293 · PLoS computational biology · 2005 · 7 claims · 7 setups

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  SNPdetector, which models human visual inspection of sequencing traces, achieves low false positive and false negative rates in automated SNP and mutation detection

  inbred unrelated zebra same pcr manual comparative

• 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

• Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools.

  PMID 16912992 · PMC1538848 · Nucleic acids research · 2006 · 7 claims · 8 setups

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  PANTHER HMMs built from family/subfamily multiple sequence alignments can classify novel protein sequences into functional groups based on statistically significant HMM match scores

  input gene genome-wide genes sequence gene numerical

• MACSIMS: multiple alignment of complete sequences information management system.

  PMID 16792820 · PMC1539025 · BMC bioinformatics · 2006 · 8 claims · 5 setups

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  MACSIMS is a multiple alignment-based information management system combining knowledge-based database mining with ab initio sequence predictions

  balibase-derived sequences same query automatic database initio

• Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space.

  PMID 16481312 · PMC1373602 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  The number of protein families continues to expand steadily as more genomes are sequenced, showing no sign of saturation.

  non-identical gene3d cath whole-gene domain transmembrane

• In silico and in vitro comparative analysis to select, validate and test SNPs for human identification.

  PMID 18076761 · PMC2222643 · BMC genomics · 2007 · 8 claims · 7 setups

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  A panel of 24 SNPs was selected and validated for human identification using 1,040 unrelated samples from three populations (Italian, Benin Gulf, Mongolian)

  genomic genome pan blood snp sequence cross-species