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).

• Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform.

  PMID 17000641 · PMC1636412 · Nucleic acids research · 2006 · 8 claims · 6 setups

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  An anonymous SHyP oligonucleotide microarray can capture genomic signatures of DNA sequence variation from any organism, including a previously unsequenced species

  genomic gonystylus subset restriction-digested custom self-self blast

• FeatureScan: revealing property-dependent similarity of nucleotide sequences.

  PMID 16845077 · PMC1538849 · Nucleic acids research · 2006 · 6 claims · 5 setups

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  FeatureScan transforms nucleotide sequences into numerical signals of physico-chemical/conformational properties and compares them via a convolution/correlation (Fourier transform) method rather than comparing letters

  randomly fully same chimpanzee signal-theoretic featurescan blast

• CorGen--measuring and generating long-range correlations for DNA sequence analysis.

  PMID 16845099 · PMC1538783 · Nucleic acids research · 2006 · 8 claims · 3 setups

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  CorGen is a web server that measures long-range correlations in DNA sequences and generates random sequences with the same (or user-specified) correlation and composition parameters

  chromosome query synthetic long-range sequence

• Aggregation propensity of the human proteome.

  PMID 18927604 · PMC2557143 · PLoS computational biology · 2008 · 8 claims · 7 setups

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  Long proteins have, on average, less intense/pronounced aggregation peaks than short proteins

  proteome non-membrane proteins membrane sequence-based correlation statistical

• 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

• Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes.

  PMID 18086709 · PMC2241899 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  Preferred nucleotide sequences around the initiation codon are diverse among eukaryote species, but differences roughly reflect evolutionary relationships between species

  eukaryote genes hexanucleotide saccharomyces comparative cluster hexanucleotide

• EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.

  PMID 17984073 · PMC2238967 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  EPGD is a gene-centered, internet-accessible database integrating paralog family and paralogon information for 26 eukaryotic genomes.

  sequences homologous proteins coding pairwise single sequence

• 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

• Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes.

  PMID 15809229 · PMC1074396 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  Comparative gene finding (SGP2) between human and chicken, followed by RT-PCR verification, adds at most ~0.2% new genes to the multi-exonic human gene catalog

  chicken predicted human-chicken cdna comparative blastp pairwise

• A high throughput method for genome-wide analysis of retroviral integration.

  PMID 17028098 · PMC1636494 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  VITA uses MmeI to cleave DNA at a fixed distance from its recognition site, generating 21-22 bp genomic tags that serve as signatures of lentiviral integration sites.

  hela ht3 genome chromosomes isf vita sanger

• Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.

  PMID 17305421 · PMC1797821 · PLoS computational biology · 2007 · 8 claims · 8 setups

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  The synonymous substitution rate (dS) of HIV env is strongly correlated with disease progression parameters (progression time, CD4+ decline rate, viral load increase rate), unlike the nonsynonymous rate (dN).

  longitudinal backbone env intra-patient relaxed-clock correlation site-to-site

• Sequence similarity network reveals common ancestry of multidomain proteins.

  PMID 18475320 · PMC2377100 · PLoS computational biology · 2008 · 8 claims · 6 setups

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  Traditional homology definitions do not capture multidomain evolution; the authors extend the definition to include domain insertion via a common ancestral locus model.

  curated complete well-studied sequence alignment domain

• Functional diversity of HIV-1 envelope proteins expressed by contemporaneous plasma viruses.

  PMID 18312646 · PMC2270869 · Retrovirology · 2008 · 8 claims · 7 setups

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  Infectivity of recombinant viruses carrying different Env proteins from the same patient varies over an approximately 10-fold range, even among viruses with similar tropism.

  env u373 mt4-r5 u373-r5 phylogenetic infectivity flow

• Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.

  PMID 19906729 · PMC2808989 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  Patrocles is a database compiling DSPs predicted to perturb miRNA-mediated gene regulation across seven vertebrate species, covering targets, miRNA precursors and silencing machinery.

  3'-utr mirbase hapmap comparative snp mirna

• Homogeneous point mutation detection by quantum dot-mediated two-color fluorescence coincidence analysis.

  PMID 16517937 · PMC1390686 · Nucleic acids research · 2006 · 8 claims · 6 setups

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  QD-mediated two-color fluorescence coincidence detection combined with oligonucleotide ligation assay (OLA) enables separation-free, homogeneous point mutation detection.

  synthetic same β-globin kras ola fluorescence photon

• Automatic discovery of cross-family sequence features associated with protein function.

  PMID 16409628 · PMC1395344 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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  A self-supervised data mining approach can find relationships between sequence features and functional annotations without preconceived functional categories.

  non-redundant same evolved eukaryotic self-supervised experiment self-organizing

• Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation.

  PMID 18653530 · PMC2528163 · Nucleic acids research · 2008 · 8 claims · 7 setups

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  A new computational pipeline identifies trans-SAs using ESTs (not just mRNAs) across 10 animal species, improving coverage over prior methods

  est unannotated trans-sa tus computational coding hybridization

• Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues.

  PMID 16188928 · PMC4631381 · Bioinformatics (Oxford, England) · 2005 · 7 claims · 4 setups

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  Genes upregulated in squamous cell lung cancer are highly connected (well-connected) nodes in the protein interactome

  squamous ophid degs oligonucleotide interaction connectivity

• How to find soluble proteins: a comprehensive analysis of alpha/beta hydrolases for recombinant expression in E. coli.

  PMID 15804363 · PMC1079826 · BMC genomics · 2005 · 7 claims · 7 setups

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  Predicted solubility in E. coli (via CV-CV') depends on hydrolase size, phylogenetic origin, homologous family, and superfamily

  lipase bacterial small genera cv-cv correlation grouped

• 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